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zaihuajizaihuaji
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Merge pull request #8 from NCAR/hua-work-miscs
rda => gdex bash/tcshqsub
2 parents e866de4 + 7482aab commit 94b1805

5 files changed

Lines changed: 41 additions & 41 deletions

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‎pyproject.toml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
66

77
[project]
88
name = "rda_python_miscs"
9-
version = "1.0.6"
9+
version = "1.0.7"
1010
authors = [
1111
{ name="Zaihua Ji", email="zji@ucar.edu" },
1212
]

‎src/rda_python_miscs/bashqsub.py‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@
3939
'o' : None, # will set to default if not provided
4040
'e' : None,
4141
'A' : "P43713000",
42-
'q' : "rda@casper-pbs",
42+
'q' : "gdex@casper-pbs",
4343
# 'm' : 'a',
4444
'm' : 'n',
4545
}
@@ -50,9 +50,9 @@
5050
def main():
5151

5252
aname = 'bashqsub'
53-
pname = 'rdaqsub'
53+
pname = 'gdexqsub'
5454
PgLOG.set_help_path(__file__)
55-
rdasub = PgLOG.BCHCMDS['PBS']
55+
gdexsub = PgLOG.BCHCMDS['PBS']
5656
coptions = {'cmd' : None, 'cwd' : None, 'env' : None, 'mod' : None, 'res' : 'default'} # customized options
5757
copts = '|'.join(coptions)
5858
option = None
@@ -61,7 +61,7 @@ def main():
6161
if not argv: PgLOG.show_usage(aname)
6262
PgLOG.PGLOG['LOGFILE'] = pname + ".log"
6363
PgLOG.cmdlog("{} {}".format(aname, ' '.join(argv)))
64-
if not PgLOG.valid_command(rdasub): PgLOG.pglog("{}: miss {} command to submit batch job".format(rdasub, PgLOG.PGLOG['PBSNAME']), PgLOG.LGWNEX)
64+
if not PgLOG.valid_command(gdexsub): PgLOG.pglog("{}: miss {} command to submit batch job".format(gdexsub, PgLOG.PGLOG['PBSNAME']), PgLOG.LGWNEX)
6565

6666
while argv:
6767
arg = argv.pop(0)
@@ -80,7 +80,7 @@ def main():
8080
if option == "env": option = 'v'
8181
continue
8282

83-
if not option: PgLOG.pglog("{}: Value passed in without leading option for {}".format(arg, rdasub), PgLOG.LGEREX)
83+
if not option: PgLOG.pglog("{}: Value passed in without leading option for {}".format(arg, gdexsub), PgLOG.LGEREX)
8484
if arg.find(' ') > -1 and not re.match(r'^[\'\"].*[\'\"]$', arg): # quote string with space but not quoted yet
8585
if arg.find("'") > -1:
8686
arg = '"{}"'.format(arg)
@@ -111,18 +111,18 @@ def main():
111111
if not cmd: PgLOG.pglog(coptions['cmd'] + ": Cannot find given command to run", PgLOG.LGWNEX)
112112
if args: cmd += " " + args
113113

114-
sbuf = build_bash_script(cmd, coptions, rdasub)
114+
sbuf = build_bash_script(cmd, coptions, gdexsub)
115115
PgLOG.pglog(sbuf, PgLOG.MSGLOG)
116116
PgLOG.PGLOG['ERR2STD'] = ['bind mouting']
117-
PgLOG.pgsystem(rdasub, PgLOG.LOGWRN, 6, sbuf)
117+
PgLOG.pgsystem(gdexsub, PgLOG.LOGWRN, 6, sbuf)
118118
PgLOG.PGLOG['ERR2STD'] = []
119119

120120
sys.exit(0)
121121

122122
#
123123
# build bash script to submit a PBS batch job
124124
#
125-
def build_bash_script(cmd, coptions, rdasub):
125+
def build_bash_script(cmd, coptions, gdexsub):
126126

127127
buf = "#!/usr/bin/bash\n\n" # qsub starting bash script
128128

‎src/rda_python_miscs/bashqsub.usg‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,17 @@
11

22
To submit a job execution as a batch job in bash script on a PBS node via 'qsub'.
33

4-
Usage: rdaqsub [qsub-options] [-cwd WorkDir] [-env EnvironmentPairs] \
5-
[-mod Modules] [-res Reservation] -cmd Command [cmd-options]
4+
Usage: bashqsub [qsub-options] [-cwd WorkDir] [-env EnvironmentPairs] \
5+
[-mod Modules] [-res Reservation] -cmd Command [cmd-options]
66

77
- qsub-options, accepts options that can be passed to 'qsub' in a bash script.
88
Check qsub man page for help on the PBS batch options. Here is the list of
99
qsub options that are included at default:
10-
-o LOGPATH/rdaqsub/
11-
-e LOGPATH/rdaqsub/
10+
-o LOGPATH/gdexqsub/
11+
-e LOGPATH/gdexqsub/
1212
-A P43713000
1313
-m a
14-
-q regular
14+
-q gdex
1515
-l walltime=6:00:00,select=1:node=1:mem=1gb
1616

1717
- Option -cwd, set the working directory for the Command to be executed. If
@@ -33,10 +33,10 @@
3333
A bash script example:
3434
#!/usr/bin/bash
3535

36-
#PBS -o /gpfs/u/home/rdadata/dssdb/log/rdaqsub/
37-
#PBS -e /gpfs/u/home/rdadata/dssdb/log/rdaqsub/
36+
#PBS -o /gpfs/u/home/gdexdata/dssdb/log/gdexqsub/
37+
#PBS -e /gpfs/u/home/gdexdata/dssdb/log/gdexqsub/
3838
#PBS -A P43713000
39-
#PBS -q rda@casper-pbs
39+
#PBS -q gdex@casper-pbs
4040
#PBS -m n
4141
#PBS -N dsrqst
4242
#PBS -l walltime=1:00:00
@@ -56,9 +56,9 @@ module load conda
5656
module load grib-util
5757
module load wgrib2
5858

59-
conda activate /glade/work/rdadata/conda-envs/pg-casper
59+
conda activate /glade/work/gdexdata/conda-envs/pg-casper
6060

61-
echo /gpfs/u/home/rdadata/bin/dsrqst d277000 PR -RI 750748 -b -d
62-
/gpfs/u/home/rdadata/bin/dsrqst d277000 PR -RI 750748 -b -d
61+
echo /glade/work/gdexdata/conda-envs/pg-casper/bin/dsrqst d277000 PR -RI 750748 -b -d
62+
/glade/work/gdexdata/conda-envs/pg-casper/bin/dsrqst d277000 PR -RI 750748 -b -d
6363

6464
date

‎src/rda_python_miscs/tcshqsub.py‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@
3939
'o' : None, # will set to default if not provided
4040
'e' : None,
4141
'A' : "P43713000",
42-
'q' : "rda@casper-pbs",
42+
'q' : "gdex@casper-pbs",
4343
# 'm' : 'a',
4444
'm' : 'n',
4545
}
@@ -50,9 +50,9 @@
5050
def main():
5151

5252
aname = 'tcshqsub'
53-
pname = 'rdaqsub'
53+
pname = 'gdexqsub'
5454
PgLOG.set_help_path(__file__)
55-
rdasub = PgLOG.BCHCMDS['PBS']
55+
gdexsub = PgLOG.BCHCMDS['PBS']
5656
coptions = {'cmd' : None, 'cwd' : None, 'env' : None, 'mod' : None, 'res' : 'default'} # customized options
5757
copts = '|'.join(coptions)
5858
option = None
@@ -61,7 +61,7 @@ def main():
6161
if not argv: PgLOG.show_usage(aname)
6262
PgLOG.PGLOG['LOGFILE'] = pname + ".log"
6363
PgLOG.cmdlog("{} {}".format(aname, ' '.join(argv)))
64-
if not PgLOG.valid_command(rdasub): PgLOG.pglog("{}: miss {} command to submit batch job".format(rdasub, PgLOG.PGLOG['PBSNAME']), PgLOG.LGWNEX)
64+
if not PgLOG.valid_command(gdexsub): PgLOG.pglog("{}: miss {} command to submit batch job".format(gdexsub, PgLOG.PGLOG['PBSNAME']), PgLOG.LGWNEX)
6565

6666
while argv:
6767
arg = argv.pop(0)
@@ -80,7 +80,7 @@ def main():
8080
if option == "env": option = 'v'
8181
continue
8282

83-
if not option: PgLOG.pglog("{}: Value passed in without leading option for {}".format(arg, rdasub), PgLOG.LGEREX)
83+
if not option: PgLOG.pglog("{}: Value passed in without leading option for {}".format(arg, gdexsub), PgLOG.LGEREX)
8484
if arg.find(' ') > -1 and not re.match(r'^[\'\"].*[\'\"]$', arg): # quote string with space but not quoted yet
8585
if arg.find("'") > -1:
8686
arg = '"{}"'.format(arg)
@@ -111,18 +111,18 @@ def main():
111111
if not cmd: PgLOG.pglog(coptions['cmd'] + ": Cannot find given command to run", PgLOG.LGWNEX)
112112
if args: cmd += " " + args
113113

114-
sbuf = build_tcsh_script(cmd, coptions, rdasub)
114+
sbuf = build_tcsh_script(cmd, coptions, gdexsub)
115115
PgLOG.pglog(sbuf, PgLOG.MSGLOG)
116116
PgLOG.PGLOG['ERR2STD'] = ['bind mouting']
117-
PgLOG.pgsystem(rdasub, PgLOG.LOGWRN, 6, sbuf)
117+
PgLOG.pgsystem(gdexsub, PgLOG.LOGWRN, 6, sbuf)
118118
PgLOG.PGLOG['ERR2STD'] = []
119119

120120
sys.exit(0)
121121

122122
#
123123
# build tcsh script to submit a PBS batch job
124124
#
125-
def build_tcsh_script(cmd, coptions, rdasub):
125+
def build_tcsh_script(cmd, coptions, gdexsub):
126126

127127
buf = "#!/bin/tcsh\n\n" # sbatch starting tcsh script
128128

‎src/rda_python_miscs/tcshqsub.usg‎

Lines changed: 13 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,17 @@
11

22
To submit a job execution as a batch job in tcsh script on a PBS node via 'qsub'.
33

4-
Usage: rdaqsub [qsub-options] [-cwd WorkDir] [-env EnvironmentPairs] \
5-
[-mod Modules] [-res Reservation] -cmd Command [cmd-options]
4+
Usage: tcshqsub [qsub-options] [-cwd WorkDir] [-env EnvironmentPairs] \
5+
[-mod Modules] [-res Reservation] -cmd Command [cmd-options]
66

77
- qsub-options, accepts options that can be passed to 'qsub' in a tcsh script.
88
Check qsub man page for help on the PBS batch options. Here is the list of
99
qsub options that are included at default:
10-
-o LOGPATH/rdaqsub/
11-
-e LOGPATH/rdaqsub/
10+
-o LOGPATH/gdexqsub/
11+
-e LOGPATH/gdexqsub/
1212
-A P43713000
1313
-m a
14-
-q regular
14+
-q gdex
1515
-l walltime=6:00:00,select=1:node=1:mem=1gb
1616

1717
- Option -cwd, set the working directory for the Command to be executed. If
@@ -33,17 +33,17 @@
3333
A tash script example:
3434
#!/bin/tcsh
3535

36-
#PBS -o /gpfs/u/home/rdadata/dssdb/log/rdaqsub/
37-
#PBS -e /gpfs/u/home/rdadata/dssdb/log/rdaqsub/
36+
#PBS -o /gpfs/u/home/gdexdata/dssdb/log/gdexqsub/
37+
#PBS -e /gpfs/u/home/gdexdata/dssdb/log/gdexqsub/
3838
#PBS -A P43713000
39-
#PBS -q rda@casper-pbs
39+
#PBS -q gdex@casper-pbs
4040
#PBS -m a
4141
#PBS -N dsrqst
4242
#PBS -l walltime=12:00:00
4343
#PBS -l select=1:mem=20gb
4444
setenv HOME /gpfs/u/home/davestep
45-
source /etc/profile.d/z00_modules.tsh
46-
source /glade/u/apps/opt/conda/etc/profile.d/conda.tsh
45+
source /etc/profile.d/z00_modules.csh
46+
source /glade/u/apps/opt/conda/etc/profile.d/conda.csh
4747
source /gpfs/u/home/davestep/.tcshrc
4848
pwd; hostname; date
4949

@@ -56,7 +56,7 @@ module load conda
5656
module load grib-util
5757
module load wgrib2
5858

59-
conda activate /glade/work/rdadata/conda-envs/pg-casper
59+
conda activate /glade/work/gdexdata/conda-envs/pg-casper
6060

61-
echo /gpfs/u/home/rdadata/bin/dsrqst d628000 SP -RI 729708 -NP -b -d
62-
/gpfs/u/home/rdadata/bin/dsrqst d628000 SP -RI 729708 -NP -b -d
61+
echo /glade/work/gdexdata/conda-envs/pg-casper/bin/dsrqst d628000 SP -RI 729708 -NP -b -d
62+
/glade/work/gdexdata/conda-envs/pg-casper/bin/dsrqst d628000 SP -RI 729708 -NP -b -d

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