parser.add_argument("--resubmit",
help="wether to submit missing jobs",
action="store_true")
parser.add_argument("--resubmit_log_only",
help="wether to submit missing jobs",
action="store_true")
parser.add_argument(
"--name_subfield",
help="Specify multiple key-value pairs to specify format conversion",
nargs=2,
action="append",
default=[])
parser.add_argument(
"--name_subfield_regexp",
help="Specify multiple key-value pairs to specify format conversion")
parser.add_argument("--clean_target",
help="pattern of stuff to be removed."
" Note this is not a Regex. "
"It uses the Linux path expansions like *",
action="append",
default=[])
#parser.add_argument("--serialize_local", help="If resubmitting job, just run locally", action="store_true", default=False)
#parser.add_argument("--log_file", help="On top of everything else, save to a file")
args = parser.parse_args()
helpers.configure_logging(int(args.parsimony))
run(args)
if s:
values = helpers.name_parse(file, subfield_regexp, subfield_position)
mem = int(s.group(4))/1024
vmem = int(s.group(2))/1024
walltime= _to_sec(s.group(3))
cputime = _to_sec(s.group(1))
name_ = names_re_.search(file).group(1) if names_re_ else file
r_ = (name_, mem, vmem, walltime,cputime)
if values:
r_ += values
r.append(r_)
r = pandas.DataFrame(r, columns=["name", "memory", "v_memory", "walltime", "cputime"] + subfield_names)
r.to_csv(args.output, sep="\t", index=False)
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser("Compare jobs to expected result")
parser.add_argument("-logs_folder", help="Where the submission jobs will be saved", default="jobs")
parser.add_argument("-logs_pattern", help="Log name pattern")
parser.add_argument("-output", help="Path where the output will be saved", default="job_log.txt")
parser.add_argument("-verbosity", help="Log verbosity level. 1 is everything being logged. 10 is only high level messages, above 10 will hardly log anything", default = 10, type=int)
parser.add_argument("-name_subfield", help="Specify multiple key-value pairs to specify format conversion", nargs=2, action="append", default =[])
parser.add_argument("-name_subfield_regexp", help="Specify multiple key-value pairs to specify format conversion")
args = parser.parse_args()
helpers.configure_logging(int(args.verbosity))
run(args)