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qorca
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qorca
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#!/usr/bin/env python
from __future__ import print_function
import os
import argparse
def get_args():
parser = argparse.ArgumentParser()
parser.add_argument("filenames", action='store', help='.inp file(s) sumbit to the queue', nargs='+')
parser.add_argument("-ca", action='store_true', default=False,
help='Copy all of the files in the current dir')
parser.add_argument("-cs", action='store_true', default=False,
help="Copy all files from the scratch directory")
parser.add_argument("-notrashtmp", action='store_true', default=False,
help="Don't trash the temporary files that may be generated")
return parser.parse_args()
def print_bash_script(inp_filename, ca, cs, notrashtmp):
sh_filename = str(inp_filename.replace('.inp', '.sh'))
with open(sh_filename, 'w') as bash_script:
print('#!/bin/bash', file=bash_script)
#print('#SBATCH --reservation=training', file=bash_script)
#print('#SBATCH --partition=medium', file=bash_script)
print('#SBATCH --ntasks-per-node=16', file=bash_script)
print('#SBATCH --time=14:00:00', file=bash_script)
print('#SBATCH --job-name=' + inp_filename.replace('.inp', ''), file=bash_script)
print('module load ORCA/5.0.1-gompi-2019b-dba', file=bash_script)
print('export ORIG=$PWD', file=bash_script)
print('export SCR=/scratch/$USER/$SLURM_JOB_ID', file=bash_script)
print('mkdir -p $SCR', file=bash_script)
print('dos2unix ' + inp_filename + ' > /dev/null 2>&1', file=bash_script)
if ca:
print('cp * $SCR', file=bash_script)
else:
print('cp ' + inp_filename + ' $SCR', file=bash_script)
print('#', file=bash_script)
print('cd $SCR', file=bash_script)
print('/apps/system/easybuild/software/ORCA/5.0.1-gompi-2019b-dba/orca $SCR/' + inp_filename + ' > $ORIG/' + inp_filename.replace('.inp', '.out'), file=bash_script)
if notrashtmp:
pass
else:
print('rm -f *.tmp', file=bash_script)
if cs:
print('cp * $ORIG', file=bash_script)
else:
print('cp *.xyz *.hess *.out $ORIG > /dev/null 2>&1', file=bash_script)
print('cd / ', file=bash_script)
print('rm -Rf $SCR', file=bash_script)
print('cd $ORIG', file=bash_script)
print('rm "$ORIG"/*.sh.*', file=bash_script)
print('rm "$ORIG"/slurm*.out', file=bash_script)
return sh_filename
def run_sbatch(script_filename):
os.system('sbatch ' + script_filename)
return 0
if __name__ == '__main__':
args = get_args()
for filename in args.filenames:
if filename.endswith(".inp"):
sh_filename = print_bash_script(filename, args.ca, args.cs, args.notrashtmp)
run_sbatch(sh_filename)
else:
print("file (): not submitted: does not have .inp extension".format(filename))