Run a job to extract and convert all the surface variables

#!/usr/bin/env python

# Extract surface variables from a month's V3 output
#  and convert to netCDF

import tempfile
import argparse
import subprocess
import os

parser = argparse.ArgumentParser()
parser.add_argument("--startyear", help="Year run started", type=int, required=True)
parser.add_argument("--year", help="Year to extract", type=int, required=True)
parser.add_argument("--month", help="Month to extract", type=int, required=True)
parser.add_argument("--version", help="Version to extract", type=int, default=451)
args = parser.parse_args()

tfile = tempfile.NamedTemporaryFile(delete=False, mode="w")
tfile.write("#!/bin/bash\n")
tfile.write("#SBATCH --output=v3_conversion-%d-%d-%%j.out\n" % (args.year, args.month))
tfile.write("#SBATCH -q regular\n")
tfile.write("#SBATCH --time-min=4:00:00\n")
tfile.write("#SBATCH -C knl\n")
tfile.write("#SBATCH -N 1\n")
tfile.write("#SBATCH -t 6:00:00\n")
tfile.write("#SBATCH -J V3co%04d%02d\n" % (args.year, args.month))
tfile.write("#SBATCH -L SCRATCH\n\n")
tfile.write("module load ncl\n")
tfile.write("module load nco\n")
tfile.write("module load python\n\n")
tfile.write(
    "mkdir -p %s/20CRv3.final/version_%d.%d.%d/%02d/%02d\n"
    % (
        os.getenv("SCRATCH"),
        int(args.version / 100),
        int((args.version % 100) / 10),
        int(args.version % 10),
        args.year,
        args.month,
    )
)
tfile.write("export OMP_NUM_THREADS=5\n\n")
ldir = os.path.abspath(os.path.dirname(__file__))
tfile.write(
    "%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=prmsl &\n"
    % (ldir, args.startyear, args.year, args.month, args.version)
)
tfile.write(
    "%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=air.2m &\n"
    % (ldir, args.startyear, args.year, args.month, args.version)
)
tfile.write(
    "%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=uwnd.10m &\n"
    % (ldir, args.startyear, args.year, args.month, args.version)
)
tfile.write(
    "%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=vwnd.10m &\n"
    % (ldir, args.startyear, args.year, args.month, args.version)
)
tfile.write(
    "%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=air.sfc &\n"
    % (ldir, args.startyear, args.year, args.month, args.version)
)
tfile.write(
    "%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=icec &\n"
    % (ldir, args.startyear, args.year, args.month, args.version)
)
# tfile.write('%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=hgt --level=850 &\n' %
#                                                         (ldir,args.startyear,args.year,args.month,args.version))
# tfile.write('%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=tmp --level=850 &\n' %
#                                                         (ldir,args.startyear,args.year,args.month,args.version))
# tfile.write('%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=tmp --level=925 &\n' %
#                                                         (ldir,args.startyear,args.year,args.month,args.version))
# tfile.write('%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=spfh --level=850 &\n' %
#                                                         (ldir,args.startyear,args.year,args.month,args.version))
# tfile.write('%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=uwnd --level=850 &\n' %
#                                                         (ldir,args.startyear,args.year,args.month,args.version))
# tfile.write('%s/extract_anl_var.py --startyear=%d --year=%d --month=%d --version=%d --var=vwnd --level=850 &\n' %
#                                                         (ldir,args.startyear,args.year,args.month,args.version))
tfile.write(
    "%s/extract_fg_var.py --startyear=%d --year=%d --month=%d --version=%d --var=prate &\n"
    % (ldir, args.startyear, args.year, args.month, args.version)
)
tfile.write(
    "%s/extract_obs.py --startyear=%d --year=%d --month=%d --version=%d &\n"
    % (ldir, args.startyear, args.year, args.month, args.version)
)
tfile.write("wait\n")
# tfile.write('%s/cleanup.py --startyear=%d --year=%d --month=%d --version=%d\n' %
#                                                         (ldir,args.startyear,args.year,args.month,args.version))
tfile.close()

proc = subprocess.Popen("sbatch %s" % tfile.name, shell=True)
(out, err) = proc.communicate()
if out is not None or err is not None:
    raise Exception("Failed to submit %s" % tfile.name)
os.remove(tfile.name)