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)
cmd_str = ("%s -i %s.min.mdin -p %s -c %s -r %s.min.rst7 -o %s.min.mdout " + "-inf %s.min.mdinfo -suffix %s") % (
prog_str,
prefix,
args[0],
args[1],
prefix,
prefix,
prefix,
prefix,
)
if opt.rst_wt:
cmd_str += " -ref %s" % args[1]
# 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)
cmd_str = ("%s -i %s.%s.mdin -p %s -c %s -r %s.%s.rst7 -o %s.%s." +
"mdout -inf %s.%s.mdinfo -x %s.%s.nc -suffix %s") % (prog_str,
prefix, opt.label, args[0], args[1], prefix, opt.label, prefix,
opt.label, prefix, opt.label, prefix, opt.label, prefix)
if opt.rst_wt:
cmd_str += " -ref %s" % args[1]
if len(args) == 3:
cmd_str += " -cpin %s -cpout %s.%s.cpout -cprestrt %s.%s.cpin" % (args[2],
prefix, opt.label, prefix, opt.label)
pbs_job.add_command(cmd_str)
# If we just want to print the jobfile
