From 80ac6dcfdfb3840134f78974ccfdf2e7273c54e3 Mon Sep 17 00:00:00 2001 From: Steven Hamilton Date: Wed, 28 Feb 2018 16:34:20 -0500 Subject: [PATCH] Updating directory structure. --- .../c5g7_3d_flux_ref.h5 | Bin .../c5g7_3d_output_ref.h5 | Bin .../Source/Inputs => Inputs}/c5g7_252g.xml | 0 .../c5g7_3d_cpu_1024node.xml | 0 .../Inputs => Inputs}/c5g7_3d_cpu_128node.xml | 0 .../Inputs => Inputs}/c5g7_3d_cpu_1node.xml | 0 .../c5g7_3d_cpu_1node_long.xml | 0 .../Inputs => Inputs}/c5g7_3d_cpu_256node.xml | 0 .../Inputs => Inputs}/c5g7_3d_cpu_32node.xml | 0 .../Inputs => Inputs}/c5g7_3d_cpu_512node.xml | 0 .../Inputs => Inputs}/c5g7_3d_cpu_8node.xml | 0 .../Inputs => Inputs}/c5g7_3d_cpu_short.xml | 0 .../c5g7_3d_gpu_1024node.xml | 0 .../Inputs => Inputs}/c5g7_3d_gpu_128node.xml | 0 .../Inputs => Inputs}/c5g7_3d_gpu_1node.xml | 0 .../c5g7_3d_gpu_1node_long.xml | 0 .../Inputs => Inputs}/c5g7_3d_gpu_256node.xml | 0 .../Inputs => Inputs}/c5g7_3d_gpu_32node.xml | 0 .../Inputs => 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a/Profugus/Source/Correct_Results/c5g7_3d_flux_ref.h5 b/Correct_Results/c5g7_3d_flux_ref.h5 similarity index 100% rename from Profugus/Source/Correct_Results/c5g7_3d_flux_ref.h5 rename to Correct_Results/c5g7_3d_flux_ref.h5 diff --git a/Profugus/Source/Correct_Results/c5g7_3d_output_ref.h5 b/Correct_Results/c5g7_3d_output_ref.h5 similarity index 100% rename from Profugus/Source/Correct_Results/c5g7_3d_output_ref.h5 rename to Correct_Results/c5g7_3d_output_ref.h5 diff --git a/Profugus/Source/Inputs/c5g7_252g.xml b/Inputs/c5g7_252g.xml similarity index 100% rename from Profugus/Source/Inputs/c5g7_252g.xml rename to Inputs/c5g7_252g.xml diff --git a/Profugus/Source/Inputs/c5g7_3d_cpu_1024node.xml b/Inputs/c5g7_3d_cpu_1024node.xml similarity index 100% rename from Profugus/Source/Inputs/c5g7_3d_cpu_1024node.xml rename to Inputs/c5g7_3d_cpu_1024node.xml diff --git a/Profugus/Source/Inputs/c5g7_3d_cpu_128node.xml b/Inputs/c5g7_3d_cpu_128node.xml similarity index 100% rename from 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a/Profugus/Source/Inputs/c5g7_3d_cpu_512node.xml b/Inputs/c5g7_3d_cpu_512node.xml similarity index 100% rename from Profugus/Source/Inputs/c5g7_3d_cpu_512node.xml rename to Inputs/c5g7_3d_cpu_512node.xml diff --git a/Profugus/Source/Inputs/c5g7_3d_cpu_8node.xml b/Inputs/c5g7_3d_cpu_8node.xml similarity index 100% rename from Profugus/Source/Inputs/c5g7_3d_cpu_8node.xml rename to Inputs/c5g7_3d_cpu_8node.xml diff --git a/Profugus/Source/Inputs/c5g7_3d_cpu_short.xml b/Inputs/c5g7_3d_cpu_short.xml similarity index 100% rename from Profugus/Source/Inputs/c5g7_3d_cpu_short.xml rename to Inputs/c5g7_3d_cpu_short.xml diff --git a/Profugus/Source/Inputs/c5g7_3d_gpu_1024node.xml b/Inputs/c5g7_3d_gpu_1024node.xml similarity index 100% rename from Profugus/Source/Inputs/c5g7_3d_gpu_1024node.xml rename to Inputs/c5g7_3d_gpu_1024node.xml diff --git a/Profugus/Source/Inputs/c5g7_3d_gpu_128node.xml b/Inputs/c5g7_3d_gpu_128node.xml similarity index 100% rename from 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a/Profugus/Source/Inputs/c5g7_3d_gpu_512node.xml b/Inputs/c5g7_3d_gpu_512node.xml similarity index 100% rename from Profugus/Source/Inputs/c5g7_3d_gpu_512node.xml rename to Inputs/c5g7_3d_gpu_512node.xml diff --git a/Profugus/Source/Inputs/c5g7_3d_gpu_8node.xml b/Inputs/c5g7_3d_gpu_8node.xml similarity index 100% rename from Profugus/Source/Inputs/c5g7_3d_gpu_8node.xml rename to Inputs/c5g7_3d_gpu_8node.xml diff --git a/Profugus/CPU_1024node/Correct_Results b/Profugus/CPU_1024node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/CPU_1024node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/CPU_1024node/Inputs b/Profugus/CPU_1024node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/CPU_1024node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/CPU_1024node/Scripts/build_executable.x b/Profugus/CPU_1024node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/CPU_1024node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_1024node/Scripts/build_helper.sh b/Profugus/CPU_1024node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/CPU_1024node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_1024node/Scripts/check_executable.x b/Profugus/CPU_1024node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/CPU_1024node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/CPU_1024node/Scripts/check_helper.sh b/Profugus/CPU_1024node/Scripts/check_helper.sh deleted file mode 100755 index 815e3f8..0000000 --- a/Profugus/CPU_1024node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/CPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/CPU_1024node/Scripts/check_profugus.py b/Profugus/CPU_1024node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/CPU_1024node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/CPU_1024node/Scripts/lsf.template.x b/Profugus/CPU_1024node/Scripts/lsf.template.x deleted file mode 100755 index c38f9dc..0000000 --- a/Profugus/CPU_1024node/Scripts/lsf.template.x +++ /dev/null @@ -1,142 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_cpu_1024node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/CPU_1024node/Scripts/submit_executable.x b/Profugus/CPU_1024node/Scripts/submit_executable.x deleted file mode 100755 index 45a2a8a..0000000 --- a/Profugus/CPU_1024node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_cpu_1024node" - nodes = "1024" - ppn = "20" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUM_NODES} --cpu_per_rs 20 --tasks_per_rs 160 --rs_per_host 1 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_cpu_1024node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_1024node/Scripts/submit_helper.sh b/Profugus/CPU_1024node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/CPU_1024node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_128node/Correct_Results b/Profugus/CPU_128node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/CPU_128node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/CPU_128node/Inputs b/Profugus/CPU_128node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/CPU_128node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/CPU_128node/Scripts/build_executable.x b/Profugus/CPU_128node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/CPU_128node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_128node/Scripts/build_helper.sh b/Profugus/CPU_128node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/CPU_128node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_128node/Scripts/check_executable.x b/Profugus/CPU_128node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/CPU_128node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/CPU_128node/Scripts/check_helper.sh b/Profugus/CPU_128node/Scripts/check_helper.sh deleted file mode 100755 index 815e3f8..0000000 --- a/Profugus/CPU_128node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/CPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/CPU_128node/Scripts/check_profugus.py b/Profugus/CPU_128node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/CPU_128node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/CPU_128node/Scripts/lsf.template.x b/Profugus/CPU_128node/Scripts/lsf.template.x deleted file mode 100755 index 56568a7..0000000 --- a/Profugus/CPU_128node/Scripts/lsf.template.x +++ /dev/null @@ -1,142 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_cpu_128node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/CPU_128node/Scripts/submit_executable.x b/Profugus/CPU_128node/Scripts/submit_executable.x deleted file mode 100755 index 53e9944..0000000 --- a/Profugus/CPU_128node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_cpu_128node" - nodes = "128" - ppn = "20" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUM_NODES} --cpu_per_rs 20 --tasks_per_rs 160 --rs_per_host 1 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_cpu_128node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_128node/Scripts/submit_helper.sh b/Profugus/CPU_128node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/CPU_128node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_1node/Correct_Results b/Profugus/CPU_1node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/CPU_1node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/CPU_1node/Inputs b/Profugus/CPU_1node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/CPU_1node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/CPU_1node/Scripts/build_executable.x b/Profugus/CPU_1node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/CPU_1node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_1node/Scripts/build_helper.sh b/Profugus/CPU_1node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/CPU_1node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_1node/Scripts/check_executable.x b/Profugus/CPU_1node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/CPU_1node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/CPU_1node/Scripts/check_helper.sh b/Profugus/CPU_1node/Scripts/check_helper.sh deleted file mode 100755 index 2ee3327..0000000 --- a/Profugus/CPU_1node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/CPU_1node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/CPU_1node/Scripts/check_profugus.py b/Profugus/CPU_1node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/CPU_1node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/CPU_1node/Scripts/lsf.template.x b/Profugus/CPU_1node/Scripts/lsf.template.x deleted file mode 100755 index d61eb12..0000000 --- a/Profugus/CPU_1node/Scripts/lsf.template.x +++ /dev/null @@ -1,142 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_cpu_1node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/CPU_1node/Scripts/submit_executable.x b/Profugus/CPU_1node/Scripts/submit_executable.x deleted file mode 100755 index 88904f7..0000000 --- a/Profugus/CPU_1node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_cpu_1node" - nodes = "1" - ppn = "160" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUM_NODES} --cpu_per_rs 20 --tasks_per_rs 160 --rs_per_host 1 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_cpu_1node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_1node/Scripts/submit_helper.sh b/Profugus/CPU_1node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/CPU_1node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_1node_long/Correct_Results b/Profugus/CPU_1node_long/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/CPU_1node_long/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/CPU_1node_long/Inputs b/Profugus/CPU_1node_long/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/CPU_1node_long/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/CPU_1node_long/Scripts/build_executable.x b/Profugus/CPU_1node_long/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/CPU_1node_long/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_1node_long/Scripts/build_helper.sh b/Profugus/CPU_1node_long/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/CPU_1node_long/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_1node_long/Scripts/check_executable.x b/Profugus/CPU_1node_long/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/CPU_1node_long/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/CPU_1node_long/Scripts/check_helper.sh b/Profugus/CPU_1node_long/Scripts/check_helper.sh deleted file mode 100755 index 2ee3327..0000000 --- a/Profugus/CPU_1node_long/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/CPU_1node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/CPU_1node_long/Scripts/check_profugus.py b/Profugus/CPU_1node_long/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/CPU_1node_long/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/CPU_1node_long/Scripts/lsf.template.x b/Profugus/CPU_1node_long/Scripts/lsf.template.x deleted file mode 100755 index 83a6536..0000000 --- a/Profugus/CPU_1node_long/Scripts/lsf.template.x +++ /dev/null @@ -1,142 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_cpu_1node_long.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/CPU_1node_long/Scripts/submit_executable.x b/Profugus/CPU_1node_long/Scripts/submit_executable.x deleted file mode 100755 index 1c41450..0000000 --- a/Profugus/CPU_1node_long/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_cpu_1node" - nodes = "1" - ppn = "160" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "04:00" - joblaunchcommand = "jsrun --nrs ${NUM_NODES} --cpu_per_rs 20 --tasks_per_rs 160 --rs_per_host 1 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_cpu_1node_long.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_1node_long/Scripts/submit_helper.sh b/Profugus/CPU_1node_long/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/CPU_1node_long/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_256node/Correct_Results b/Profugus/CPU_256node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/CPU_256node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/CPU_256node/Inputs b/Profugus/CPU_256node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/CPU_256node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/CPU_256node/Scripts/build_executable.x b/Profugus/CPU_256node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/CPU_256node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_256node/Scripts/build_helper.sh b/Profugus/CPU_256node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/CPU_256node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_256node/Scripts/check_executable.x b/Profugus/CPU_256node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/CPU_256node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/CPU_256node/Scripts/check_helper.sh b/Profugus/CPU_256node/Scripts/check_helper.sh deleted file mode 100755 index 815e3f8..0000000 --- a/Profugus/CPU_256node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/CPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/CPU_256node/Scripts/check_profugus.py b/Profugus/CPU_256node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/CPU_256node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/CPU_256node/Scripts/lsf.template.x b/Profugus/CPU_256node/Scripts/lsf.template.x deleted file mode 100755 index f4b8ab6..0000000 --- a/Profugus/CPU_256node/Scripts/lsf.template.x +++ /dev/null @@ -1,142 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_cpu_256node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/CPU_256node/Scripts/submit_executable.x b/Profugus/CPU_256node/Scripts/submit_executable.x deleted file mode 100755 index 462c3fe..0000000 --- a/Profugus/CPU_256node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_cpu_256node" - nodes = "256" - ppn = "20" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUM_NODES} --cpu_per_rs 20 --tasks_per_rs 160 --rs_per_host 1 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_cpu_256node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_256node/Scripts/submit_helper.sh b/Profugus/CPU_256node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/CPU_256node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_32node/Correct_Results b/Profugus/CPU_32node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/CPU_32node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/CPU_32node/Inputs b/Profugus/CPU_32node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/CPU_32node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/CPU_32node/Scripts/build_executable.x b/Profugus/CPU_32node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/CPU_32node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_32node/Scripts/build_helper.sh b/Profugus/CPU_32node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/CPU_32node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_32node/Scripts/check_executable.x b/Profugus/CPU_32node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/CPU_32node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/CPU_32node/Scripts/check_helper.sh b/Profugus/CPU_32node/Scripts/check_helper.sh deleted file mode 100755 index 815e3f8..0000000 --- a/Profugus/CPU_32node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/CPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/CPU_32node/Scripts/check_profugus.py b/Profugus/CPU_32node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/CPU_32node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/CPU_32node/Scripts/lsf.template.x b/Profugus/CPU_32node/Scripts/lsf.template.x deleted file mode 100755 index 4e558f2..0000000 --- a/Profugus/CPU_32node/Scripts/lsf.template.x +++ /dev/null @@ -1,142 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_cpu_32node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/CPU_32node/Scripts/submit_executable.x b/Profugus/CPU_32node/Scripts/submit_executable.x deleted file mode 100755 index f3ed269..0000000 --- a/Profugus/CPU_32node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_cpu_32node" - nodes = "32" - ppn = "20" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUM_NODES} --cpu_per_rs 20 --tasks_per_rs 160 --rs_per_host 1 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_cpu_32node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_32node/Scripts/submit_helper.sh b/Profugus/CPU_32node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/CPU_32node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_512node/Correct_Results b/Profugus/CPU_512node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/CPU_512node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/CPU_512node/Inputs b/Profugus/CPU_512node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/CPU_512node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/CPU_512node/Scripts/build_executable.x b/Profugus/CPU_512node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/CPU_512node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_512node/Scripts/build_helper.sh b/Profugus/CPU_512node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/CPU_512node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_512node/Scripts/check_executable.x b/Profugus/CPU_512node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/CPU_512node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/CPU_512node/Scripts/check_helper.sh b/Profugus/CPU_512node/Scripts/check_helper.sh deleted file mode 100755 index 815e3f8..0000000 --- a/Profugus/CPU_512node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/CPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/CPU_512node/Scripts/check_profugus.py b/Profugus/CPU_512node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/CPU_512node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/CPU_512node/Scripts/lsf.template.x b/Profugus/CPU_512node/Scripts/lsf.template.x deleted file mode 100755 index 594a893..0000000 --- a/Profugus/CPU_512node/Scripts/lsf.template.x +++ /dev/null @@ -1,142 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_cpu_512node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/CPU_512node/Scripts/submit_executable.x b/Profugus/CPU_512node/Scripts/submit_executable.x deleted file mode 100755 index 2015f07..0000000 --- a/Profugus/CPU_512node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_cpu_512node" - nodes = "512" - ppn = "20" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUM_NODES} --cpu_per_rs 20 --tasks_per_rs 160 --rs_per_host 1 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_cpu_512node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_512node/Scripts/submit_helper.sh b/Profugus/CPU_512node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/CPU_512node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_8node/Correct_Results b/Profugus/CPU_8node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/CPU_8node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/CPU_8node/Inputs b/Profugus/CPU_8node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/CPU_8node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/CPU_8node/Scripts/build_executable.x b/Profugus/CPU_8node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/CPU_8node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_8node/Scripts/build_helper.sh b/Profugus/CPU_8node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/CPU_8node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_8node/Scripts/check_executable.x b/Profugus/CPU_8node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/CPU_8node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/CPU_8node/Scripts/check_helper.sh b/Profugus/CPU_8node/Scripts/check_helper.sh deleted file mode 100755 index 815e3f8..0000000 --- a/Profugus/CPU_8node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/CPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/CPU_8node/Scripts/check_profugus.py b/Profugus/CPU_8node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/CPU_8node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/CPU_8node/Scripts/lsf.template.x b/Profugus/CPU_8node/Scripts/lsf.template.x deleted file mode 100755 index 68c7304..0000000 --- a/Profugus/CPU_8node/Scripts/lsf.template.x +++ /dev/null @@ -1,142 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_cpu_8node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/CPU_8node/Scripts/submit_executable.x b/Profugus/CPU_8node/Scripts/submit_executable.x deleted file mode 100755 index d0a3bdf..0000000 --- a/Profugus/CPU_8node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_cpu_8node" - nodes = "8" - ppn = "20" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUM_NODES} --cpu_per_rs 20 --tasks_per_rs 160 --rs_per_host 1 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_cpu_8node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_8node/Scripts/submit_helper.sh b/Profugus/CPU_8node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/CPU_8node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_short/Correct_Results b/Profugus/CPU_short/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/CPU_short/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/CPU_short/Inputs b/Profugus/CPU_short/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/CPU_short/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/CPU_short/Scripts/build_executable.x b/Profugus/CPU_short/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/CPU_short/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_short/Scripts/build_helper.sh b/Profugus/CPU_short/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/CPU_short/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/CPU_short/Scripts/check_executable.x b/Profugus/CPU_short/Scripts/check_executable.x deleted file mode 100755 index 8a8b57e..0000000 --- a/Profugus/CPU_short/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = False - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/CPU_short/Scripts/check_helper.sh b/Profugus/CPU_short/Scripts/check_helper.sh deleted file mode 100755 index f450bc9..0000000 --- a/Profugus/CPU_short/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/CPU_short/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/CPU_short/Scripts/lsf.template.x b/Profugus/CPU_short/Scripts/lsf.template.x deleted file mode 100755 index 1e34f9b..0000000 --- a/Profugus/CPU_short/Scripts/lsf.template.x +++ /dev/null @@ -1,142 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_cpu_short.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/CPU_short/Scripts/submit_executable.x b/Profugus/CPU_short/Scripts/submit_executable.x deleted file mode 100755 index a571646..0000000 --- a/Profugus/CPU_short/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_cpu_short" - nodes = "1" - ppn = "20" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUM_NODES} --cpu_per_rs 20 --tasks_per_rs 160 --rs_per_host 1 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_cpu_short.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numbernodes__"),nodes), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/CPU_short/Scripts/submit_helper.sh b/Profugus/CPU_short/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/CPU_short/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_1024node/Correct_Results b/Profugus/GPU_1024node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/GPU_1024node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/GPU_1024node/Inputs b/Profugus/GPU_1024node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/GPU_1024node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/GPU_1024node/Scripts/build_executable.x b/Profugus/GPU_1024node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/GPU_1024node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_1024node/Scripts/build_helper.sh b/Profugus/GPU_1024node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/GPU_1024node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_1024node/Scripts/check_executable.x b/Profugus/GPU_1024node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/GPU_1024node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/GPU_1024node/Scripts/check_helper.sh b/Profugus/GPU_1024node/Scripts/check_helper.sh deleted file mode 100755 index 95ff59a..0000000 --- a/Profugus/GPU_1024node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/GPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/GPU_1024node/Scripts/check_profugus.py b/Profugus/GPU_1024node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/GPU_1024node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/GPU_1024node/Scripts/lsf.template.x b/Profugus/GPU_1024node/Scripts/lsf.template.x deleted file mode 100755 index 2b1f0dd..0000000 --- a/Profugus/GPU_1024node/Scripts/lsf.template.x +++ /dev/null @@ -1,141 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_gpu_1024node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/GPU_1024node/Scripts/submit_executable.x b/Profugus/GPU_1024node/Scripts/submit_executable.x deleted file mode 100755 index 633f551..0000000 --- a/Profugus/GPU_1024node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_gpu_1024node" - nodes = "1024" - ppn = "4" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUMPROCS} --cpu_per_rs 1 --gpu_per_rs 1 --tasks_per_rs 1 --rs_per_host 4 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_gpu_1024node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_1024node/Scripts/submit_helper.sh b/Profugus/GPU_1024node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/GPU_1024node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_128node/Correct_Results b/Profugus/GPU_128node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/GPU_128node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/GPU_128node/Inputs b/Profugus/GPU_128node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/GPU_128node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/GPU_128node/Scripts/build_executable.x b/Profugus/GPU_128node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/GPU_128node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_128node/Scripts/build_helper.sh b/Profugus/GPU_128node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/GPU_128node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_128node/Scripts/check_executable.x b/Profugus/GPU_128node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/GPU_128node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/GPU_128node/Scripts/check_helper.sh b/Profugus/GPU_128node/Scripts/check_helper.sh deleted file mode 100755 index 95ff59a..0000000 --- a/Profugus/GPU_128node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/GPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/GPU_128node/Scripts/check_profugus.py b/Profugus/GPU_128node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/GPU_128node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/GPU_128node/Scripts/lsf.template.x b/Profugus/GPU_128node/Scripts/lsf.template.x deleted file mode 100755 index 71c1761..0000000 --- a/Profugus/GPU_128node/Scripts/lsf.template.x +++ /dev/null @@ -1,141 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_gpu_128node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/GPU_128node/Scripts/submit_executable.x b/Profugus/GPU_128node/Scripts/submit_executable.x deleted file mode 100755 index 570ba0e..0000000 --- a/Profugus/GPU_128node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_gpu_128node" - nodes = "128" - ppn = "4" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUMPROCS} --cpu_per_rs 1 --gpu_per_rs 1 --tasks_per_rs 1 --rs_per_host 4 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_gpu_128node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_128node/Scripts/submit_helper.sh b/Profugus/GPU_128node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/GPU_128node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_1node/Correct_Results b/Profugus/GPU_1node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/GPU_1node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/GPU_1node/Inputs b/Profugus/GPU_1node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/GPU_1node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/GPU_1node/Scripts/build_executable.x b/Profugus/GPU_1node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/GPU_1node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_1node/Scripts/build_helper.sh b/Profugus/GPU_1node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/GPU_1node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_1node/Scripts/check_executable.x b/Profugus/GPU_1node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/GPU_1node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/GPU_1node/Scripts/check_helper.sh b/Profugus/GPU_1node/Scripts/check_helper.sh deleted file mode 100755 index 77c100f..0000000 --- a/Profugus/GPU_1node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/GPU_1node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/GPU_1node/Scripts/check_profugus.py b/Profugus/GPU_1node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/GPU_1node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/GPU_1node/Scripts/lsf.template.x b/Profugus/GPU_1node/Scripts/lsf.template.x deleted file mode 100755 index b421f85..0000000 --- a/Profugus/GPU_1node/Scripts/lsf.template.x +++ /dev/null @@ -1,142 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_gpu_1node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/GPU_1node/Scripts/submit_executable.x b/Profugus/GPU_1node/Scripts/submit_executable.x deleted file mode 100755 index 9ba063d..0000000 --- a/Profugus/GPU_1node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_gpu_1node" - nodes = "1" - ppn = "160" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUM_NODES} --cpu_per_rs 20 --gpu_per_rs 4 --tasks_per_rs 4 --rs_per_host 1 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_gpu_1node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_1node/Scripts/submit_helper.sh b/Profugus/GPU_1node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/GPU_1node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_1node_long/Correct_Results b/Profugus/GPU_1node_long/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/GPU_1node_long/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/GPU_1node_long/Inputs b/Profugus/GPU_1node_long/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/GPU_1node_long/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/GPU_1node_long/Scripts/build_executable.x b/Profugus/GPU_1node_long/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/GPU_1node_long/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_1node_long/Scripts/build_helper.sh b/Profugus/GPU_1node_long/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/GPU_1node_long/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_1node_long/Scripts/check_executable.x b/Profugus/GPU_1node_long/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/GPU_1node_long/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/GPU_1node_long/Scripts/check_helper.sh b/Profugus/GPU_1node_long/Scripts/check_helper.sh deleted file mode 100755 index 77c100f..0000000 --- a/Profugus/GPU_1node_long/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/GPU_1node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/GPU_1node_long/Scripts/check_profugus.py b/Profugus/GPU_1node_long/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/GPU_1node_long/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/GPU_1node_long/Scripts/lsf.template.x b/Profugus/GPU_1node_long/Scripts/lsf.template.x deleted file mode 100755 index 71aa50e..0000000 --- a/Profugus/GPU_1node_long/Scripts/lsf.template.x +++ /dev/null @@ -1,142 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_gpu_1node_long.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/GPU_1node_long/Scripts/submit_executable.x b/Profugus/GPU_1node_long/Scripts/submit_executable.x deleted file mode 100755 index 300690f..0000000 --- a/Profugus/GPU_1node_long/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_gpu_1node" - nodes = "1" - ppn = "160" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "04:00" - joblaunchcommand = "jsrun --nrs ${NUM_NODES} --cpu_per_rs 20 --gpu_per_rs 4 --tasks_per_rs 4 --rs_per_host 1 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_gpu_1node_long.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_1node_long/Scripts/submit_helper.sh b/Profugus/GPU_1node_long/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/GPU_1node_long/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_256node/Correct_Results b/Profugus/GPU_256node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/GPU_256node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/GPU_256node/Inputs b/Profugus/GPU_256node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/GPU_256node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/GPU_256node/Scripts/build_executable.x b/Profugus/GPU_256node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/GPU_256node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_256node/Scripts/build_helper.sh b/Profugus/GPU_256node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/GPU_256node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_256node/Scripts/check_executable.x b/Profugus/GPU_256node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/GPU_256node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/GPU_256node/Scripts/check_helper.sh b/Profugus/GPU_256node/Scripts/check_helper.sh deleted file mode 100755 index 95ff59a..0000000 --- a/Profugus/GPU_256node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/GPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/GPU_256node/Scripts/check_profugus.py b/Profugus/GPU_256node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/GPU_256node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/GPU_256node/Scripts/lsf.template.x b/Profugus/GPU_256node/Scripts/lsf.template.x deleted file mode 100755 index 6a52e07..0000000 --- a/Profugus/GPU_256node/Scripts/lsf.template.x +++ /dev/null @@ -1,141 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_gpu_256node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/GPU_256node/Scripts/submit_executable.x b/Profugus/GPU_256node/Scripts/submit_executable.x deleted file mode 100755 index 525ea07..0000000 --- a/Profugus/GPU_256node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_gpu_256node" - nodes = "256" - ppn = "4" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUMPROCS} --cpu_per_rs 1 --gpu_per_rs 1 --tasks_per_rs 1 --rs_per_host 4 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_gpu_256node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_256node/Scripts/submit_helper.sh b/Profugus/GPU_256node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/GPU_256node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_32node/Correct_Results b/Profugus/GPU_32node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/GPU_32node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/GPU_32node/Inputs b/Profugus/GPU_32node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/GPU_32node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/GPU_32node/Scripts/build_executable.x b/Profugus/GPU_32node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/GPU_32node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_32node/Scripts/build_helper.sh b/Profugus/GPU_32node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/GPU_32node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_32node/Scripts/check_executable.x b/Profugus/GPU_32node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/GPU_32node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/GPU_32node/Scripts/check_helper.sh b/Profugus/GPU_32node/Scripts/check_helper.sh deleted file mode 100755 index 95ff59a..0000000 --- a/Profugus/GPU_32node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/GPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/GPU_32node/Scripts/check_profugus.py b/Profugus/GPU_32node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/GPU_32node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/GPU_32node/Scripts/lsf.template.x b/Profugus/GPU_32node/Scripts/lsf.template.x deleted file mode 100755 index ca800eb..0000000 --- a/Profugus/GPU_32node/Scripts/lsf.template.x +++ /dev/null @@ -1,141 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_gpu_32node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/GPU_32node/Scripts/submit_executable.x b/Profugus/GPU_32node/Scripts/submit_executable.x deleted file mode 100755 index 101b2a3..0000000 --- a/Profugus/GPU_32node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_gpu_32node" - nodes = "32" - ppn = "4" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUMPROCS} --cpu_per_rs 1 --gpu_per_rs 1 --tasks_per_rs 1 --rs_per_host 4 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_gpu_32node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_32node/Scripts/submit_helper.sh b/Profugus/GPU_32node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/GPU_32node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_512node/Correct_Results b/Profugus/GPU_512node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/GPU_512node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/GPU_512node/Inputs b/Profugus/GPU_512node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/GPU_512node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/GPU_512node/Scripts/build_executable.x b/Profugus/GPU_512node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/GPU_512node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_512node/Scripts/build_helper.sh b/Profugus/GPU_512node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/GPU_512node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_512node/Scripts/check_executable.x b/Profugus/GPU_512node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/GPU_512node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/GPU_512node/Scripts/check_helper.sh b/Profugus/GPU_512node/Scripts/check_helper.sh deleted file mode 100755 index 95ff59a..0000000 --- a/Profugus/GPU_512node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/GPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/GPU_512node/Scripts/check_profugus.py b/Profugus/GPU_512node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/GPU_512node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/GPU_512node/Scripts/lsf.template.x b/Profugus/GPU_512node/Scripts/lsf.template.x deleted file mode 100755 index 397da42..0000000 --- a/Profugus/GPU_512node/Scripts/lsf.template.x +++ /dev/null @@ -1,141 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_gpu_512node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/GPU_512node/Scripts/submit_executable.x b/Profugus/GPU_512node/Scripts/submit_executable.x deleted file mode 100755 index 7512f2e..0000000 --- a/Profugus/GPU_512node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_gpu_512node" - nodes = "512" - ppn = "4" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUMPROCS} --cpu_per_rs 1 --gpu_per_rs 1 --tasks_per_rs 1 --rs_per_host 4 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_gpu_512node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_512node/Scripts/submit_helper.sh b/Profugus/GPU_512node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/GPU_512node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_8node/Correct_Results b/Profugus/GPU_8node/Correct_Results deleted file mode 120000 index 03fd1fb..0000000 --- a/Profugus/GPU_8node/Correct_Results +++ /dev/null @@ -1 +0,0 @@ -../Source/Correct_Results \ No newline at end of file diff --git a/Profugus/GPU_8node/Inputs b/Profugus/GPU_8node/Inputs deleted file mode 120000 index 7d63e10..0000000 --- a/Profugus/GPU_8node/Inputs +++ /dev/null @@ -1 +0,0 @@ -../Source/Inputs \ No newline at end of file diff --git a/Profugus/GPU_8node/Scripts/build_executable.x b/Profugus/GPU_8node/Scripts/build_executable.x deleted file mode 100755 index 7c1e461..0000000 --- a/Profugus/GPU_8node/Scripts/build_executable.x +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python3 - -import getopt -import sys -import os -import shutil -#import popen2 -import subprocess -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center of Computational Science, Scientifc Computing Group. -# - -# -# This build the simple fortran program. -# - -def main(): - - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - - # - # Create the temporary workspace. - # Save the tempoary workspace for the submit executable. - # - create_tmp_workspace(path_to_workspace) - - # - #--Making the binary. - # - make_exit_status = make_binary(path_to_workspace) - if make_exit_status == 0: - make_exit_value = 0 - else: - make_exit_value = 1 - - return make_exit_value - -def make_binary(path_to_workspace): - - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 2 tail paths in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - # - # Get the path to the Source directory for the application. - # - path_to_source = os.path.join(dir_head2,"Source") - - print(path_to_source) - - # - # Now make the path to the build directory. - # - path_to_build_directory = os.path.join(path_to_workspace,"build_directory") - - # - #Copy Source to build directory. - # - cmd1 = "cp -rf " + path_to_source + " " + path_to_build_directory - print(cmd1) - os.system(cmd1) - # - # Change back to build directory. - # - os.chdir(path_to_build_directory) - - # Make executable. - cwd = os.getcwd() - print(cwd) - make_command = "./build_profugus.sh" - make_exit_status = os.system(make_command) - - return make_exit_status - - -def usage(): - print("Usage: build_executable.x [-h|--help] -p -i ") - print("A driver program that the build the binary for the test.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - - - - -def create_tmp_workspace(path1): - # - # Fisrt check to see if the path1 does not already exist. - # - os.makedirs(path1) - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_8node/Scripts/build_helper.sh b/Profugus/GPU_8node/Scripts/build_helper.sh deleted file mode 100755 index 83632e8..0000000 --- a/Profugus/GPU_8node/Scripts/build_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./build_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/GPU_8node/Scripts/check_executable.x b/Profugus/GPU_8node/Scripts/check_executable.x deleted file mode 100755 index 02a938c..0000000 --- a/Profugus/GPU_8node/Scripts/check_executable.x +++ /dev/null @@ -1,158 +0,0 @@ -#! /usr/bin/env python3 - -import sys -import os -import getopt -import filecmp -import re - -def check_executable_driver(path_to_results, - test_id_string): - - - # - # Compare the results. - # - jstatus = check_results(path_to_results) - - # - # Write the statis of the results to job data file. - # - write_to_job_data(path_to_results,jstatus) - -def get_path_to_correct_results(): - cwd = os.getcwd() - - # - # Get the head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # This is the path to the correct results. - # - crslts = os.path.join(dir_head1,"Correct_Results") - - return crslts - -def check_results(path_to_results): - #----------------------------------------------------- - #Define good and bad results. - # - - #----------------------------------------------------- - GOOD_RESULTS=1 - BAD_RESULTS=0 - - re_exp = re.compile("Total execution time") - - # - # Make the file name paths to numbers squared. - # - file1 = os.path.join(path_to_results,"stdout.txt") - file_obj = open(file1,"r") - tlines = file_obj.readlines() - file_obj.close() - - ip = 0 - for record1 in tlines: - if re_exp.match(record1): - ip = ip+1; - - expected_passes = 1 - check_h5 = True - if check_h5: - expected_passes += 1 - # - # Get path to the correct results. - # - path_to_correct_results = get_path_to_correct_results() - ref_outfile = "c5g7_3d_output_ref.h5" - ref_fluxfile = "c5g7_3d_flux_ref.h5" - outfile = "c5g7_3d_output.h5" - fluxfile = "c5g7_3d_flux.h5" - - # Link reference files into results directory - if (not os.path.islink(os.path.join(path_to_results,ref_outfile))): - os.symlink(os.path.join(path_to_correct_results,ref_outfile), - os.path.join(path_to_results,ref_outfile)) - - if (not os.path.islink(os.path.join(path_to_results,ref_fluxfile))): - os.symlink(os.path.join(path_to_correct_results,ref_fluxfile), - os.path.join(path_to_results,ref_fluxfile)) - - import check_profugus - - h5_result = check_profugus.check_solution(path_to_results) - if h5_result == 0: - ip += 1 - - if ip == expected_passes: - ival = GOOD_RESULTS - print("Passed") - else: - ival = BAD_RESULTS - print("Failed") - - return ival - -def write_to_job_data(path_to_results,jstatus): - - (dir_head1, dir_tail1) = os.path.split(path_to_results) - (dir_head2, dir_tail2) = os.path.split(dir_head1) - - file1 = os.path.join(dir_head2,"Status",dir_tail1,"job_status.txt") - file1_obj = open(file1,"w") - - # Set the string to write to the job_status.txt file. - if jstatus == 0: - pf = "1" - elif jstatus == 1: - pf = "0" - elif jstatus >= 2: - pf = "2" - string1 = "%s\n" % (pf) - - file1_obj.write(string1) - file1_obj.close() - - - -def usage(): - print("Usage: check_executable.x [-h|--help] [-i ] [-p ]") - print("A program that checks the results located at ") - print("The check executable must write the status of the results to the file") - print("Status//job_status.txt'.") - print("") - print("-h, --help Prints usage information.") - print("-p The absoulte path to the results of a test.") - print("-i The test string unique id.") - - - -if __name__ == "__main__": - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:") - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - for o, a in opts: - if o == "-p": - path_to_results = a - elif o == "-i": - test_id_string = a - elif o == ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - check_executable_driver(path_to_results, - test_id_string) diff --git a/Profugus/GPU_8node/Scripts/check_helper.sh b/Profugus/GPU_8node/Scripts/check_helper.sh deleted file mode 100755 index 95ff59a..0000000 --- a/Profugus/GPU_8node/Scripts/check_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_results="/lustre/atlas/scratch/sphamil/csc244/olcf4-acceptance-tests/summitdev/Profugus/GPU_32node/Run_Archive/${id}" - -./check_executable.x -p ${path_to_results} -i ${id} diff --git a/Profugus/GPU_8node/Scripts/check_profugus.py b/Profugus/GPU_8node/Scripts/check_profugus.py deleted file mode 120000 index b63f408..0000000 --- a/Profugus/GPU_8node/Scripts/check_profugus.py +++ /dev/null @@ -1 +0,0 @@ -../../Source/Scripts/check_profugus.py \ No newline at end of file diff --git a/Profugus/GPU_8node/Scripts/lsf.template.x b/Profugus/GPU_8node/Scripts/lsf.template.x deleted file mode 100755 index 8edf5ce..0000000 --- a/Profugus/GPU_8node/Scripts/lsf.template.x +++ /dev/null @@ -1,141 +0,0 @@ -#! /bin/bash -l -#BSUB -q __batchqueue__ -#BSUB -J __jobname__ -#BSUB -o __resultsdir__/__jobname__.o%J -#BSUB -e __resultsdir__/__jobname__.e%J -#BSUB -nnodes __numbernodes__ -#BSUB -W __walltime__ -#BSUB -P __projectid__ - -#----------------------------------------------------- -# Set up the environment for use of the harness. - -# - -#----------------------------------------------------- -source __rgtenvironmentalfile__ -module load __nccstestharnessmodule__ -module load gcc/4.8.5 -module load python/3.5.2 -module load py-h5py/2.6.0-py3 -module load spectrum-mpi -module list - -#----------------------------------------------------- -# Define some variables. - -# - -#----------------------------------------------------- -EXECUTABLE="__pathtoexecutable__" -STARTINGDIRECTORY="__startingdirectory__" -WORKDIR="__workdir__" -RESULTSDIR="__resultsdir__" -UNIQUE_ID_STRING="__unique_id_string__" -INPUTDIR=${STARTINGDIRECTORY}/../Inputs -NUMPROCS="__numberprocessors__" -NUM_NODES="__numbernodes__" - -echo "EXECUTABLE" -echo ${EXECUTABLE} -echo "WORKDIR" -echo ${WORKDIR} -echo "RESULTSDIR" -echo ${RESULTSDIR} -echo "INPUTDIR" -echo ${INPUTDIR} -echo "STARTINGDIRECTORY" -echo ${STARTINGDIRECTORY} -echo "NUMPROCS" -echo ${NUMPROCS} -echo "NUM_NODES" -echo ${NUM_NODES} - -#----------------------------------------------------- -# Ensure that we are in the correct starting - -# directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Make the working scratch space directory. - -# - -#----------------------------------------------------- -if [ ! -e $WORKDIR ] -then - mkdir -p $WORKDIR -fi - -#----------------------------------------------------- -# Make the results directory. - -# - -#----------------------------------------------------- -if [ ! -e $RESULTSDIR ] -then - mkdir -p $RESULTSDIR -fi - -#----------------------------------------------------- -# Change directory to the working directory. - -# - -#----------------------------------------------------- -cd $WORKDIR - -echo "Changed to working directory" -pwd -ls -l - -#----------------------------------------------------- -# Link input files into current directory -# - -#----------------------------------------------------- -echo "Contents of input directory:" -ls -l ${INPUTDIR}/ - -ln -s ${INPUTDIR}/c5g7_3d_gpu_8node.xml . -ln -s ${INPUTDIR}/c5g7_252g.xml . - -#----------------------------------------------------- -# Run the executable. - -# - -#----------------------------------------------------- -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode start - -__joblaunchcommand__ - -log_binary_execution_time.py --scriptsdir $STARTINGDIRECTORY --uniqueid $UNIQUE_ID_STRING --mode final - -sleep 30 -#----------------------------------------------------- -# Enusre that we return to the starting directory. - -# - -#----------------------------------------------------- -cd $STARTINGDIRECTORY - -#----------------------------------------------------- -# Copy the results back to the $RESULTSDIR - -# - -#----------------------------------------------------- -cp -rf $WORKDIR/* $RESULTSDIR && rm -rf $WORKDIR - -#----------------------------------------------------- -# Move the batch file name to $RESULTSDIR - -# - -#----------------------------------------------------- -mv __batchfilename__ $RESULTSDIR - -#----------------------------------------------------- -# Check the final results. - -# - -#----------------------------------------------------- -check_executable_driver.py -p $RESULTSDIR -i $UNIQUE_ID_STRING - -#----------------------------------------------------- -# The script now determines if we are to resubmit - -# itself. - -# - -#----------------------------------------------------- -case __resubmitme__ in - 0) - test_harness_driver.py -r;; - - 1) - echo "No resubmit";; -esac diff --git a/Profugus/GPU_8node/Scripts/submit_executable.x b/Profugus/GPU_8node/Scripts/submit_executable.x deleted file mode 100755 index 3101033..0000000 --- a/Profugus/GPU_8node/Scripts/submit_executable.x +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python - -import os -import getopt -import sys -import re -import time -import subprocess -import shlex - -# -# Author: Arnold Tharrington -# Email: arnoldt@ornl.gov -# National Center for Computational Sciences, Scientific Computing Group. -# -# Modified by: Veronica G. Vergara Larrea -# National Center for Computational Sciences, User Assistance Group. - - -def main(): - # - # Get the command line arguments. - # - try: - opts,args = getopt.getopt(sys.argv[1:],"hi:p:r") - - except getopt.GetoptError: - usage() - sys.exit(2) - - # - # Parse the command line arguments. - # - if opts == []: - usage() - sys.exit() - - # - # Initialize some variables. - # - batch_recursive_mode = "1" - - for o, a in opts: - if o == "-p": - path_to_workspace = a - elif o == "-i": - test_id_string = a - elif o == "-r": - batch_recursive_mode = "0" - elif o in ("-h", "--help"): - usage() - sys.exit() - else: - usage() - sys.exit() - - # - # Make the batch script. - # - scheduler = "lsf" - batchfilename = make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler) - - # - # Submit the batch file to the scheduler. - # - sched_job_id = send_to_scheduler(batchfilename,scheduler) - print("Job id =" + str(sched_job_id)) - - - # - #Write pbs job id to job_id.txt in the Status dir. - # - write_job_id_to_status(sched_job_id,test_id_string) - - -def make_batch_script(batch_recursive_mode,path_to_workspace,test_id_string,scheduler): - # - # Define the batch file names. - # - if scheduler == "pbs": - print("Using PBS scheduler syntax") - batchtemplatefilename = "pbs.template.x" - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax") - batchtemplatefilename = "lsf.template.x" - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - batchfilename = "run_profugus.sh" - - # - # Define the parse definitons and the regular expressions. - # - - nccstestharnessmodule = os.environ["RGT_NCCS_TEST_HARNESS_MODULE"] - rgtenvironmentalfile = os.environ["RGT_ENVIRONMENTAL_FILE"] - jobname = "profugus_gpu_8node" - nodes = "8" - ppn = "4" - ranks = str(int(nodes) * int(ppn)) - batchqueue = "batch" - pbsaccountid = os.environ["RGT_PBS_JOB_ACCNT_ID"] - pathtoexecutable = os.path.join(path_to_workspace,"build_directory","bin/xmc") - startingdirectory = os.getcwd() - resultsdir = get_path_to_results_dir(test_id_string) - workdir = os.path.join(path_to_workspace,"workdir") - resubmitme = batch_recursive_mode - walltime = "01:00" - joblaunchcommand = "jsrun --nrs ${NUMPROCS} --cpu_per_rs 1 --gpu_per_rs 1 --tasks_per_rs 1 --rs_per_host 4 -E LD_LIBRARY_PATH ${EXECUTABLE} -i c5g7_3d_gpu_8node.xml | tee stdout.txt" - - rg_array = [ - (re.compile("__jobname__"),jobname), - (re.compile("__walltime__"),walltime), - (re.compile("__numberprocessors__"),ranks), - (re.compile("__numbernodes__"),nodes), - (re.compile("__nccstestharnessmodule__"),nccstestharnessmodule), - (re.compile("__rgtenvironmentalfile__"),rgtenvironmentalfile), - (re.compile("__batchqueue__"),batchqueue), - (re.compile("__projectid__"),pbsaccountid), - (re.compile("__pathtoexecutable__"),pathtoexecutable), - (re.compile("__startingdirectory__"),startingdirectory), - (re.compile("__resultsdir__"),resultsdir), - (re.compile("__workdir__"),workdir), - (re.compile("__joblaunchcommand__"),joblaunchcommand), - (re.compile("__resubmitme__"),resubmitme), - (re.compile("__unique_id_string__"),test_id_string), - (re.compile("__batchfilename__"),batchfilename), - ] - - # - # Read the lines of the batch template file. - # - templatefileobject = open(batchtemplatefilename,"r") - tlines = templatefileobject.readlines() - templatefileobject.close() - - # - # Here is where we actually make the pbs batch file from pbs.template.x. - # - fileobject = open(batchfilename,"w") - for record1 in tlines: - for (regexp,text1) in rg_array: - record1 = regexp.sub(text1,record1) - fileobject.write(record1) - fileobject.close() - - return batchfilename - - -def get_path_to_results_dir(test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # - # Now join dir_head1 to make the path. This path should be unique. - # - path1 = os.path.join(dir_head1,"Run_Archive",test_id_string) - - return path1 - -def write_job_id_to_status(sched_job_id,test_id_string): - # - # Get the current working directory. - # - cwd = os.getcwd() - - # - # Get the 1 head path in the cwd. - # - (dir_head1, dir_tail1) = os.path.split(cwd) - - # Make sure "Status" directory exists - dir1 = os.path.join(dir_head1,"Status",test_id_string) - if not os.path.exists(dir1): - os.makedirs(dir1) - - # - # Now join again to make the path. This path should be unique. - # - path1 = os.path.join(dir1,"job_id.txt") - - # - # Write the pbs job id to the file. - # - fileobj = open(path1,"w") - string1 = "%20s\n" % (sched_job_id) - fileobj.write(string1) - fileobj.close() - - return path1 - - -def send_to_scheduler(batchfilename,scheduler): - - t1="t1.out" - t2="t1.err" - - if scheduler == "pbs": - print("Using PBS scheduler syntax to submit job") - sched_id = 0 - elif scheduler == "lsf": - print("Using LSF scheduler syntax to submit job") - sched_id = 1 - else: - print("Scheduler " + scheduler + " is not supported") - sched_id = -1 - - # Set the appropriate qcommand for each scheduler - data = "" - with open(batchfilename,'r') as fobj: - data = fobj.read() - - if sched_id == 0: - submit_command = "qsub " - qcommand = submit_command + batchfilename - elif sched_id == 1: - submit_command = "bsub " - qcommand = submit_command + batchfilename - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - # Split the arguments for the command - - # Execute the command as a subprocess - args = shlex.split(qcommand) - my_stdout = None - my_stderr = None - if sched_id == 0: - p = subprocess.Popen(args,stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - elif sched_id == 1: - p = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - (my_stdout, my_stderr) = p.communicate() - else: - print("Unsupported scheduler (sched_id = " + str(sched_id) + ")") - - jobid = extract_jobid(my_stdout,sched_id) - - return jobid - - -def extract_jobid(records,sched_id): - - if sched_id == 0: - print("Extracting PBS jobID") - jobid = records[0].strip() - print(jobid) - elif sched_id == 1: - print("Extracting LSF jobID") - words = records.split() - job_id = words[1].replace("<","") - job_id = job_id.replace(">","") - - else: - print("Non-supported scheduler requested") - - return job_id - -def usage(): - print("Usage: submit_executable.x [-h|--help] -p -i ") - print("") - print("A driver program that the submits the binary thru batch for the testing.") - print("The submit program also writes the job id of the submitted batch job to the file") - print("'Status//job_id.txt'. The only line in job_id.txt is the job id.") - print() - print("-h, --help Prints usage information.") - print("-p The absolute path to the workspace. This path ") - print(" must have the appropiate permissions to permit ") - print(" the user of the test to r,w, and x. ") - print("-i The test id string. The build program ") - print(" uses this string to make a unique directory ") - print(" within path_to_workspace. We don't want ") - print(" concurrent builds to clobber each other. ") - print(" The submit program uses this string to write the") - print(" job schedule id to 'Status//job_id.txt.") - print("-r The batch script will resubmit itself, otherwise") - print(" only 1 instance will be submitted ") - - -if __name__ == "__main__" : - main() diff --git a/Profugus/GPU_8node/Scripts/submit_helper.sh b/Profugus/GPU_8node/Scripts/submit_helper.sh deleted file mode 100755 index 60d228c..0000000 --- a/Profugus/GPU_8node/Scripts/submit_helper.sh +++ /dev/null @@ -1,4 +0,0 @@ -id="1" -path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}" - -./submit_executable.x -p ${path_to_workspace} -i ${id} diff --git a/Profugus/Source/Scripts/check_profugus.py b/Scripts/check_profugus.py similarity index 100% rename from Profugus/Source/Scripts/check_profugus.py rename to Scripts/check_profugus.py diff --git a/Profugus/Source/build_profugus.sh b/build_profugus.sh similarity index 100% rename from Profugus/Source/build_profugus.sh rename to build_profugus.sh diff --git a/Profugus/Source/src/CMakeLists.txt b/src/CMakeLists.txt similarity index 100% rename from Profugus/Source/src/CMakeLists.txt rename to src/CMakeLists.txt diff --git a/Profugus/Source/src/LICENSE b/src/LICENSE similarity index 100% rename from Profugus/Source/src/LICENSE rename to src/LICENSE diff --git a/Profugus/Source/src/PackagesList.cmake b/src/PackagesList.cmake similarity index 100% rename from Profugus/Source/src/PackagesList.cmake rename to src/PackagesList.cmake diff --git a/Profugus/Source/src/ProjectName.cmake b/src/ProjectName.cmake similarity index 100% rename from Profugus/Source/src/ProjectName.cmake rename to src/ProjectName.cmake diff --git a/Profugus/Source/src/README.rst b/src/README.rst similarity index 100% rename from Profugus/Source/src/README.rst rename to src/README.rst diff --git a/Profugus/Source/src/TPLsList.cmake b/src/TPLsList.cmake similarity index 100% rename from Profugus/Source/src/TPLsList.cmake rename to src/TPLsList.cmake diff --git 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a/Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_FunctionObjectXMLConverter.cpp b/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_FunctionObjectXMLConverter.cpp similarity index 100% rename from Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_FunctionObjectXMLConverter.cpp rename to src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_FunctionObjectXMLConverter.cpp diff --git a/Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_FunctionObjectXMLConverter.hpp b/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_FunctionObjectXMLConverter.hpp similarity index 100% rename from Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_FunctionObjectXMLConverter.hpp rename to src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_FunctionObjectXMLConverter.hpp diff --git a/Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_FunctionObjectXMLConverterDB.cpp 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a/Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLInputSource.hpp b/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLInputSource.hpp similarity index 100% rename from Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLInputSource.hpp rename to src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLInputSource.hpp diff --git a/Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLInputStream.cpp b/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLInputStream.cpp similarity index 100% rename from Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLInputStream.cpp rename to src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLInputStream.cpp diff --git a/Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLInputStream.hpp b/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLInputStream.hpp similarity index 100% rename from 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a/Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLObjectImplem.cpp b/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLObjectImplem.cpp similarity index 100% rename from Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLObjectImplem.cpp rename to src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLObjectImplem.cpp diff --git a/Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLObjectImplem.hpp b/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLObjectImplem.hpp similarity index 100% rename from Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLObjectImplem.hpp rename to src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLObjectImplem.hpp diff --git a/Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLParameterListCoreHelpers.cpp b/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLParameterListCoreHelpers.cpp similarity 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a/Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLParser.cpp b/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLParser.cpp similarity index 100% rename from Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLParser.cpp rename to src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLParser.cpp diff --git a/Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLParser.hpp b/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLParser.hpp similarity index 100% rename from Profugus/Source/src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLParser.hpp rename to src/Trilinos/packages/teuchos/parameterlist/src/Teuchos_XMLParser.h