parallel = True
# Set up the command string
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)
if len(args) == 2:
if opt.cuda: prog_str = '%s pmemd.cuda.MPI -O' % mpi_cmd
else: prog_str = '%s pmemd.MPI -O ' % mpi_cmd
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)
