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qorcaDirac.py
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qorcaDirac.py
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#!/usr/bin/env python3
import os
import argparse
def get_args():
"""Get the command line arguments passed to this script using argparse"""
parser = argparse.ArgumentParser()
parser.add_argument("filenames",
action='store',
help='.inp file(s) submit to the queue',
nargs='+')
parser.add_argument("-ca", "--copy_all",
action='store_true',
default=False,
help='Copy all of the files in the current directory '
'to the compute node.')
parser.add_argument("-cs", "--copy_scratch",
action='store_true',
default=False,
help="Copy all files from the scratch directory back "
"to this directory when the calculation is "
"finished.")
parser.add_argument('-v', '--version',
action='store',
type=str,
choices=['4_1', '4_2'],
default='4_2',
help="Which version of ORCA should be used for the "
"calculation? Default: 4.2.1")
parser.add_argument("-np", "--num_processors",
type=int,
default=0,
help="Override the number of cores specified in the "
"input file. Useful for running calculations "
"with >4 GB memory per core.")
return parser.parse_args()
def num_cores(inp_filename, args):
"""Get the number of cores that this input file will need
Returns:
(int): Number of cores
Raises:
(ValueError, IndexError): If the input file is malformatted
"""
_num_cores = 1 # Default value
try:
keyword_line = next(line for line in open(inp_filename, 'r')
if line.startswith('!'))
# Number of cores can be defined with PALX in the keyword line
for item in keyword_line.split():
if item.lower().startswith("pal"):
_num_cores = int(item[3:])
except StopIteration:
exit(f'{inp_filename} was not a correctly formatted. Must have a '
f'line starting with a !')
# Could also have a %pal directive in the input file...
for line in open(inp_filename, 'r'):
if 'nprocs' in line:
# expecting a ... nprocs X ... format to the line
idx = next(i for i, item in enumerate(line.split())
if 'nprocs' == item.lower())
_num_cores = int(line.split()[idx+1])
# Command line argument overrides whatever is found
if args.num_processors != 0:
_num_cores = args.num_processors
return _num_cores
def print_sub_script(sh_filename, inp_filename, args):
"""
Print the submission script appropriate for an ORCA input file
-------------------------------------------------------------
Arguments:
sh_filename (str): Submission script filename
inp_filename (str): Input filename
args (Namespace): Command line arguments
"""
if args.version == '4_1':
orca_path = '/usr/local/orca_4_1_1_linux_x86-64/orca'
elif args.version == '4_2':
orca_path = '/usr/local/orca_4_2_1_linux_x86-64/orca'
else:
exit(f"{args.version} is not a recognised ORCA version")
with open(sh_filename, 'w') as sub_script:
print('#!/bin/csh',
'#$ -cwd',
f'#$ -pe smp {num_cores(inp_filename, args)}',
'#$ -l s_rt=360:00:00',
'#',
'setenv ORIG $PWD',
'setenv SCR $TMPDIR',
'module load mpi/openmpi3-x86_64',
f'cp {"*" if args.copy_all else inp_filename} $SCR',
f'cd $SCR',
f'{orca_path} {inp_filename} > {inp_filename.replace(".inp", ".out")}',
'rm -f *.tmp',
sep='\n', file=sub_script)
if args.copy_scratch:
print('cp -R * $ORIG', file=sub_script)
else:
print('cp *.xyz *.hess *.out $ORIG', file=sub_script)
print('rm *.sh.*', file=sub_script)
return None
if __name__ == '__main__':
arguments = get_args()
for filename in arguments.filenames:
if not filename.endswith('.inp'):
exit(f'Filename must end with .inp. Found: {filename}')
script_filename = filename.replace('.inp', '.sh')
# The queuing system cannot work with scripts starting with a digit...
if script_filename[0].isdigit():
script_filename = f'_{script_filename}'
print_sub_script(script_filename,
inp_filename=filename,
args=arguments)
os.system(f'qsub {script_filename}')