if parallel:
prog_str = "%s pmemd.MPI -O " % mpi_cmd
else:
prog_str = "pmemd -O "
if opt.pbs:
# Make the PBS_Script instance
pbs_job = PBS_Script(template=opt.pbs_template)
# Change the queue if desired
if opt.pbs_queue:
pbs_job.queue = opt.pbs_queue
# Set the PBS job name
pbs_job.set_name(opt.job_name)
# Determine processor count
nproc = opt.nproc.split(",")
nproc = [int(i) for i in nproc]
if not opt.pbs_nproc:
pbs_nproc = nproc[:]
else:
pbs_nproc = opt.pbs_nproc.split(",")
pbs_nproc = [int(i) for i in pbs_nproc]
pbs_job.set_proc_count(pbs_nproc)
# Set walltime
pbs_job.set_walltime(opt.walltime)
else: prog_str = '%s sander.MPI -O ' % mpi_cmd
else:
if len(args) == 2:
if opt.cuda: 'pmemd.cuda -O'
else: prog_str = 'pmemd -O '
else: prog_str = 'sander -O'
if opt.pbs:
# Make the PBS_Script instance
pbs_job = PBS_Script(template=opt.pbs_template)
# Change the queue if desired
if opt.pbs_queue: pbs_job.queue = opt.pbs_queue
# Set the PBS job name
pbs_job.set_name(opt.job_name)
# Determine processor count
nproc = opt.nproc.split(',')
nproc = [int(i) for i in nproc]
if not opt.pbs_nproc: pbs_nproc = nproc[:]
else:
pbs_nproc = opt.pbs_nproc.split(',')
pbs_nproc = [int(i) for i in pbs_nproc]
pbs_job.set_proc_count(pbs_nproc)
# Set walltime
pbs_job.set_walltime(opt.walltime)
opt.path = path.join(getenv('%sroot' % opt.version))
if not path.exists(args[0]):
print >> sys.stderr, "Error: Gaussian input file %s doesn't exist!" % args[
1]
sys.exit()
# Create the gaussian PBSjob instance
gaussjob = PBS_Script(name=opt.name, template=opt.template)
gaussjob.set_proc_count([1])
# Source the resource file
if not path.exists(path.join(opt.path, 'bsd', '%s.profile' % opt.version)):
print >> sys.stderr, 'Error: Missing %sprofile script! Looked in %s' % (
opt.version, path.join(opt.path, 'bsd'))
sys.exit(1)
gaussjob.add_command('source %s' %
(path.join(opt.path, 'bsd', '%s.profile' % opt.version)))
gaussjob.add_command(opt.version + ' ' + args[0])
# Set a random name if no name had been set
if not opt.name: gaussjob.set_name()
# Do we ask permission before submitting the job or just submit it?
if opt.jobfile: gaussjob.print_submit(opt.jobfile)
elif not opt.force: gaussjob.submit_ask()
else:
gaussjob.submit()
if not opt.path:
opt.path = path.join(getenv('%sroot' % opt.version))
if not path.exists(args[0]):
print >> sys.stderr, "Error: Gaussian input file %s doesn't exist!" % args[1]
sys.exit()
# Create the gaussian PBSjob instance
gaussjob = PBS_Script(name=opt.name, template=opt.template)
gaussjob.set_proc_count([1])
# Source the resource file
if not path.exists(path.join(opt.path, 'bsd', '%s.profile' % opt.version)):
print >> sys.stderr, 'Error: Missing %sprofile script! Looked in %s' % (
opt.version, path.join(opt.path, 'bsd'))
sys.exit(1)
gaussjob.add_command('source %s' % (path.join(opt.path, 'bsd', '%s.profile' %
opt.version)))
gaussjob.add_command(opt.version + ' ' + args[0])
# Set a random name if no name had been set
if not opt.name: gaussjob.set_name()
# Do we ask permission before submitting the job or just submit it?
if opt.jobfile: gaussjob.print_submit(opt.jobfile)
elif not opt.force: gaussjob.submit_ask()
else: gaussjob.submit()
