Adding longer running tests.

Profugus/CPU_1node_long/Correct_Results

+../Source/Correct_Results
\ No newline at end of file

Profugus/CPU_1node_long/Inputs

+../Source/Inputs
\ No newline at end of file

Profugus/CPU_1node_long/Scripts/build_executable.x

+#!/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 <path_to_worspace> -i <test_id_string>")
+    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()

Profugus/CPU_1node_long/Scripts/build_helper.sh

+id="1"
+path_to_workspace="/ccs/home/sphamil/Codes/Profugus/build/acceptance/${id}"
+
+./build_executable.x -p ${path_to_workspace} -i ${id}

Profugus/CPU_1node_long/Scripts/check_executable.x

+#! /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 <test_id_string>] [-p <path_to_results>]")
+    print("A program that checks the results located at <path_to_results>")
+    print("The check executable must write the status of the results to the file")
+    print("Status/<test_id_string>/job_status.txt'.")
+    print("")
+    print("-h, --help            Prints usage information.")                              
+    print("-p <path_to_results>  The absoulte path to the results of a test.")
+    print("-i <test_id_string>   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)

Profugus/CPU_1node_long/Scripts/check_helper.sh

+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}

Profugus/CPU_1node_long/Scripts/check_profugus.py

+../../Source/Scripts/check_profugus.py
\ No newline at end of file

Profugus/CPU_1node_long/Scripts/lsf.template.x

+#! /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 

Profugus/CPU_1node_long/Scripts/submit_executable.x

+#!/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)