Commit 3999abf3 authored by delcmo's avatar delcmo
Browse files

renamed some of the file with prefix to make them available in the navigation... 

renamed some of the file with prefix to make them available in the navigation tab in Workbench, removed commented blocks in input file and added REANME file with contain.
parent 8f5255f3

README.md

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File names and descriptions:

* pipe_3840.drive: contains logic to generated driver script used by Dakota to run Nek4nuc

  application.

* pipe_3840.in: Dakota input file.

* pipe_3840.re2: Nek5000 mesh file containing the spectral element mesh of the pipe.

* pipe_3840.tmpl: Nek4nuc templated input file that will be used by the Dakota driver to

  generate a Nek4nuc input file.

* pipe_3840.txt: text file containing coordinates of probes for collecting instanteneous 

  velocity fields and compute the FFT.

* pipe_3840_pipe_exp_data.txt: text file containing coordinates of probes for line plots 

  sub-block.

* pipe_3840_exp_xyz_coord.txt: contains experimental data of the time-averaged velocity

   field.

* pipe_3840_tabular_output.dat: data file with results from the Dakota-Nek4nuc study.

dakota_driver.py

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#!/usr/bin/env python



# Dakota will execute this script as

#   generic_driver.py params.in results.out

# The command line arguments will be extracted by dakota.interfacing automatically.

# necessary python modules

import os

import sys

import json



sys.path.insert(0, "/home/lpswile/Workbench-Linux/wasppy")

sys.path.insert(0, "/projects/dakota/install/cts/intel/dakota-6.11.0.Linux.x86_64/share/dakota/Python/dakota") # dakota_install/share/dakota/Python/dakota

import waspdrive # Workbench Analysis Sequence Processor driver module

from interfacing import interfacing as di # Dakota's interface module



# ----------------------------

# Parse Dakota parameters file

# ----------------------------



params, results = di.read_parameters_file()



#dump params to external params.json file for future use by the template engine

params_for_template_engine_file_path = "params.json"

with open(params_for_template_engine_file_path, 'w') as outfile:

    f=json.dump(params._variables,  outfile, default=lambda o: o.__dict__)

#note that in object params, _variables is an OrderedDict

#params.descriptors will output this ordered _variables

# -------------------------------

# Pre-processing

# Convert and send to application

# Or copy parameters into template to generate input file

# -------------------------------



# Set up the data structures

continuous_vars = [params[k] for k in params.descriptors]

#continuous_vars are defined in dakota .in file as cdv_descriptor



active_set_vector = 0



# Alternatively, the ASV can be accessed by index in

# function, gradient, hessian order

#for i, bit in enumerate(results["obj_fn"].asv):

#    if bit:

#        active_set_vector += 1 << i



# Obtain the drive module's input

# This file contains the application information and extraction logic

import glob

driver_inputs = glob.glob("*.drive")

if len(driver_inputs) == 0:

    raise ValueError("Unable to find drive file in "+os.getcwd()+"; did you forget to copy or link the file?")



driver_document = waspdrive.process_drive_input(driver_inputs[0])

rtncode=waspdrive.run_external_app(driver_document, params_for_template_engine_file_path)



#follow the logic in ddi file to extract required responses

res_output=waspdrive.extract_results(driver_document)



retval = dict([])

retval['fns']=res_output





# ----------------------------

# Return the results to Dakota

# ----------------------------



# Insert extracted values into results

# Results iterator provides an index, response name, and response

try:

  for i, n, r in results:

    if r.asv.function:

        try:

            r.function = retval['fns'][i]

        except:

            pass

# Catch Dakota 6.9 exception where results interface has changed

# ValueError: too many values to unpack            

except ValueError: 

  i = 0

  for n, r in results.items():

      r.function = retval['fns'][i]

      i+=1

results.write()



#dump to external results.json file

with open('results.json', 'w') as outfile:

    rst=json.dump(results,  outfile, default=lambda o: o.__dict__)

multidim_parameter_study.in

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# DAKOTA INPUT FILE: multidimensional parameter study



environment

	tabular_graphics_data

	  tabular_graphics_file = 'multidim_param_study_tabular_output'



method

        multidim_parameter_study

	partition 2 5 2 



variables

	active all



        discrete_uncertain_set

	  integer 2

	    num_set_values 3 6 

	    set_values 5 10 15 4 6 8 10 12 14

	  descriptor 'filterWeight' 'lx1'

          real 1

            num_set_values 3 

            set_values   0.1 0.5 0.9

	  descriptor       'filterCutoffRatio'



interface

   analysis_drivers = 'python dakota_driver.py'

   fork

   work_directory

     named 'pipe_workdir'

   directory_tag

   directory_save

   copy_files = "pipe_3840.re2"

                "pipe_3840.tmpl"

                "pipe_3840_31000.fld"

                "dakota_driver.py"

                "pipe_3840.drive"

                "pipe_3840.txt"

                "test.py"

                "expPoints.txt"

                "longPipeRe31k.txt"

                "script-postprocess.py"

   replace

   parameters_file = 'params.in'

   results_file = 'results.out'

   file_save file_tag

   asynchronous evaluation_concurrency = 4 



responses

	response_functions = 2 

        descriptors = 'L2_error_norm' 'Friction_velocity'

	no_gradients

	no_hessians

pipe_3840.drive

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## Apollo

#application "/home/mxd/NEAMS+VisIt-rev67bd6a14e-Linux/rte/entry.sh /home/mxd/NEAMS+VisIt-rev67bd6a14e-Linux/rte/nek4nuc.py -i pipe_3840.parn -e /opt/openmpi-3.1.1-gcc-4.8.5/bin/mpirun -v 0 -nek '/home/mxd/Nek5000-v17'"

### Application block ###

application "/ascldap/users/lpswile/Workbench-Linux/rte/entry.sh /ascldap/users/lpswile/Workbench-Linux/rte/nek4nuc.py -i pipe_3840.parn -e srun -v 0 -nek '/ascldap/users/lpswile/Nek5000'"

## Panacea

#application "/home/mxd/NEAMS+VisIt-rev67bd6a14e-Linux/rte/entry.sh /home/mxd/NEAMS+VisIt-rev67bd6a14e-Linux/rte/nek4nuc.py -i pipe_3840.parn -e /software/tools/apps/openmpi/gcc4/1.10.2/bin/mpirun -v 0 -nek '/home/mxd/Nek5000-v17'"

## Local

#application "/Users/mxd/ORNL-Research/Workbench/Workbench-Darwin/rte/entry.sh /Users/mxd/ORNL-Research/Workbench/Workbench-Darwin/rte/nek4nuc.py -i rectangle.parn -e /usr/local/bin/mpirun -v 0 -nek '/Users/mxd/ORNL-Research/Nek5000-project/Nek5000'"

            input_file 'pipe_3840.parn'

            input_tmpl 'pipe_3840.tmpl'



#extract_from 'pipe_3840.dragLogic/pipe_3840.frctVel.txt'  find last_line # add optional integer N to grab the last N lines 

#column 1 delimiter ' '



extract_from 'pipe_3840.linePlots/pipe_3840.avg.txt' using "/ascldap/users/lpswile/Workbench-Linux/rte/entry.sh script-postprocess.py"

### Extract block ###

# Extract friction velocity

extract_from 'pipe_3840.dragLogic/pipe_3840.frctVel.txt' find last_line 

column 1 delimiter ' '

# Compute L2 error norm between Nek5000 data and experimental data

extract_from 'pipe_3840.linePlots/pipe_3840.avg.txt' using "/ascldap/users/lpswile/Workbench-Linux/rte/entry.sh pipe_3840_postprocess.py"



### Scheduler block ###

scheduler

    header = "#!/bin/bash"

             "#SBATCH --nodes=2"
@@ -23,27 +19,3 @@ scheduler 
             "module purge"

             "module load sparc-dev/intel"

    submit_path = '/usr/bin/sbatch'
 


## Apollo

##scheduler

##    scheduler_header = "#!/bin/bash"

##                       "#PBS -m bea"

##                       "#PBS -M mxd@ornl.gov"

##                       "#PBS -l nodes=1:ppn=12"

##                       "#PBS -N DakNek"

##                       "#PBS -l walltime=00:30:00"

##    submit_path = "/opt/torque-6.1.3/bin/qsub"



## Panacea

#scheduler

#    scheduler_header = "#!/bin/bash"

#                       "#PBS -W group_list=cades-nsed"

#                       "#PBS -A nsed"

#                       "#PBS -l qos=std"

#                       "#PBS -m bea"

#                       "#PBS -M mxd@ornl.gov"

#                       "#PBS -l nodes=1:ppn=1"

#                       "#PBS -l walltime=00:10:00"

#                       "#PBS -N DakNek"

#                       "module load mpi/openmpi/gcc4/1.10.2"

#    submit_path = "/opt/torque/bin/qsub"

pipe_3840.in

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# DAKOTA INPUT FILE: multidimensional parameter study



environment

  tabular_graphics_data

    tabular_graphics_file = 'pipe_3840_tabular_output.dat'



method

  multidim_parameter_study

    partition 2 5 2



variables

  active all

  discrete_uncertain_set

    integer 2

      num_set_values 3 6 

      set_values 5 10 15 4 6 8 10 12 14

	  descriptor 'filterWeight' 'lx1'

    real 1

      num_set_values 3 

      set_values 0.1 0.5 0.9

	  descriptor 'filterCutoffRatio'



interface

  analysis_drivers = 'python dakota_driver.py'

  fork

  work_directory

    named 'pipe_3841_workdir'

    directory_tag

    directory_save

  copy_files = "pipe_3840.re2"

              "pipe_3840.tmpl"

              "pipe_3840_31000.fld"

              "dakota_driver.py"

              "pipe_3840.drive"

              "pipe_3840.txt"

              "pipe_3840_exp_xyz_coord.txt"

              "pipe_3840_pipe_exp_data.txt"

              "pipe_3840_postprocess.py"

   replace

   parameters_file = 'params.in'

   results_file = 'results.out'

   file_save file_tag

   asynchronous evaluation_concurrency = 4



responses

	response_functions = 2 

        descriptors = 'L2_error_norm' 'Friction_velocity'

	no_gradients

	no_hessians