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Job_Restore.py
executable file
·164 lines (114 loc) · 6.85 KB
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Job_Restore.py
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#!/usr/bin/env python
__author__ = "Chen Zheng"
__maintainer__ = "Chen Zheng"
__email__ = "chz022@ucsd.edu"
__status__ = "Personal use"
__version__ = "2.0"
__date__ = "Jan 18, 2015"
import argparse
import os,glob
import subprocess
from monty.os import cd
import logging
def submit_command(args,entry):
var_dic = vars(args)
logging.debug(var_dic)
logging.debug('Wall time is none is: {}'.format(var_dic['walltime']==None))
subcommand = 'qsend_multi {} -q {} -v {} -c {} -n {} -nod {} -ib {} -w {}'.format(entry,var_dic['queue'],
var_dic['verbosity'], var_dic['command'],
var_dic['name'], var_dic['nnodes'],
var_dic['ibswitch'],var_dic['walltime'])
logging.debug('Resub command is: \n {}'.format(subcommand))
return subcommand
#This is a funciton we used for check, restore and resub job using PBS system
#Integrate with check_CONTCARRElax command
def check_resub_relax2(args):
if args.debug:
logging.basicConfig(level=logging.DEBUG)
dir_entry = parse_entry(args)
for ele in dir_entry:
with cd(ele):
logging.debug('Current dir path is: {}'.format(os.getcwd()))
if not os.path.exists('Complete'):
os.makedirs('Complete')
exclude = set(['Complete'])
result_dir_entry = [f for f in os.listdir('.') if f not in exclude]
for subdir in result_dir_entry:
check_command = 'check_CONTCARRELAX2 {} -st Yes -stdic Complete/'.format(subdir)
subprocess.call(check_command,shell=True)
no_relax2_file = [f for f in os.listdir('.') if f not in exclude]
for dir_ele in no_relax2_file:
resub_command = submit_command(args,dir_ele)
restore_command = 'restoretoinital {}'.format(dir_ele)
subprocess.call(restore_command,shell=True)
subprocess.call(resub_command,shell=True)
logging.debug('Folder with no_relax2_file is: {}'.format(no_relax2_file))
#Function for parsing directories and return with target directories entry to be analysis
def parse_entry(args):
rootpath = args.directories[0].rstrip('/')
pathdepth = glob.glob(rootpath+'/*'*int(args.depth))
subdir_list = filter(lambda f: os.path.isdir(f),pathdepth)
logging.debug('The directory contained in the path directory is: {}'.format(subdir_list))
# logging.debug('The type of subdir_list parameter is:{}'.format(type(subdir_list)))
return subdir_list
def main():
parser = argparse.ArgumentParser(description="""
pmg is a convenient script that uses pymatgen to perform many
analyses, plotting and format conversions. This script works based on
several sub-commands with their own options. To see the options for the
sub-commands, type "pmg sub-command -h".""",
epilog="""
Author: Chen Zheng
Version: {}
Last updated: {}""".format(__version__, __date__))
subparsers = parser.add_subparsers()
parser_resub = subparsers.add_parser("relaxresub", help="Resub job based on existing of relax2 file.")
parser_resub.add_argument("directories", metavar="dir", default=".",
type=str, nargs="*",
help="directory to process (default to .)")
parser_resub.add_argument("-dep", "--depth", dest='depth', default="1",
type=str, nargs="?",
help="Depth level of children directory that will be group together")
parser_resub.add_argument("-db", "--debug", dest="debug", action="store_true",
help="Debug mode, provides information used for debug")
parser_resub.add_argument("-stdic", "--storedirectory",metavar="dir",type=str,
help="directory to move folder that does contain CONTCAR.relax2 file to")
parser_resub.add_argument("-st", "--store",type=str,choices=["No", "Yes"],
default='No',help="Option to move folder that does contain CONTCAR.Relax2.gz to \
other directory specified in argument storedirectory")
parser_resub.add_argument("-q", "--queue", dest="queue", type=str,
nargs="?", default="glean",
choices=["home", "condo", "glean",'hotel'],
help="Queue to send jobs to. Defaults to 'glean'. "
"Other option is 'condo' or 'home' or 'hotel'.")
parser_resub.add_argument("-v", "--verbosity", dest="verbosity", type=str,
nargs="?", default="bae", choices=["ae", "bae"],
help="Verbosity of the run. Standard PBS "
"notification settings. Options are a (abort "
"only - the default), ae (abort and end) and bae ("
"begin, abort and end).")
parser_resub.add_argument("-c", "--command", dest="command", type=str,
nargs="?", default="run_vasp",
choices=["run_vasp", "run_vasp_md","run_vasp_glean",'run_vasp_single'],
help="Command to run. Defaults to 'vasp'.")
parser_resub.add_argument("-n", "--name", dest="name", type=str,
nargs="?", default="jobs",
help="Name for your jobs. Makes it easier to "
"identify which series of jobs they "
"belong to. Keep it short and crytic.")
parser_resub.add_argument('-nod','--numnodes',dest='nnodes',type=int,
nargs="?",default='1',help='Command to setup number of nodes.')
parser_resub.add_argument("-ib", "--ibswitch", dest="ibswitch", type=str,
choices=['ib','ib:ibswitch3','ib:ibswitch4','ib:rack1','ib:rack2','sandy'],
nargs="?", default="ib",
help="Command to setup ibswitch. Defaults to 'ib'")
parser_resub.add_argument("-w", "--walltime", dest="walltime", type=int,
nargs="?", default=None,
help="Provide a walltime for the job in hours. "
"Defaults are specified for each queue. But for "
"the hotel queue, you must specify a walltime.")
parser_resub.set_defaults(func=check_resub_relax2)
args = parser.parse_args()
args.func(args)
if __name__ == "__main__":
main()