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update submit.py for archer #65

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update submit.py for archer #65

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a804279
Merge pull request #2 from seismology/master
harriet-godwin Sep 11, 2018
f74f11c
Update submit.py
harriet-godwin Sep 11, 2018
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31 changes: 29 additions & 2 deletions submit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -213,7 +213,7 @@ def define_arguments():
"with MPIRUN"
parser.add_argument('-q', '--queue',
choices=['SuperMUC', 'background', 'foreground',
'monch'],
'monch', 'torque'],
default='background',
help=helptext)

Expand Down Expand Up @@ -792,7 +792,34 @@ def define_arguments():
run_cmd = cmd_string % (mpirun_cmd, args.nslaves + 1)
print('Starting local job in %s' % run_dir)
subprocess.check_call(run_cmd, shell=True)


if args.queue == 'torque':
# Create a .pbs submission script for archer
job_script = os.path.join(run_dir, 'submit_job.pbs')
if not args.tasks_per_node:
tasks_per_node = 24
else:
tasks_per_node = args.tasks_per_node
nodes = math.ceil((args.nslaves)/tasks_per_node)
with open(job_script, 'w') as f:
text_out = "#! /bin/bash --login \n"
text_out += "#PBS -l select=%s \n" % str(int(nodes))
text_out += "#PBS -l walltime=%s:00:00 \n" % str(args.wall_time)
text_out += "#PBS -A n03-ox2 \n"
text_out += "cd %s \n" % run_dir
text_out += "module unload PrgEnv-cray/5.2.82 \n"
text_out += "module load PrgEnv-gnu \n"
text_out += "module load fftw \n"
text_out += "module load cray-netcdf-hdf5parallel/4.4.1.1 \n"
text_out += "module load atp \n"
text_out += "module load doxygen/1.8.4 \n"
text_out += "export ATP_ENABLED=1 \n"
text_out += "ulimit -s unlimited \n"
text_out += "aprun -n %s %s/mc_kernel inparam \n" % (str(args.nslaves), run_dir)
f.write(text_out)
os.chdir(run_dir)
subprocess.call(['qsub', job_script])

elif args.queue == 'SuperMUC':
# Create a LoadLeveler job script for SuperMUC

Expand Down