nproc = [int(i) for i in nproc] parallel = False for n in nproc: if n > 1: 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:
# Set up the command string if parallel: 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]
sys.exit(1) if not opt.version in ('g09', 'g03'): print >> sys.stderr, 'Error: Gaussian version must be g03 or g09!' sys.exit(1) 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()
parser.print_help() sys.exit(1) if not opt.version in ('g09', 'g03'): print >> sys.stderr, 'Error: Gaussian version must be g03 or g09!' sys.exit(1) 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()