diff --git a/pyproject.toml b/pyproject.toml index ea2c15f..dcd1ebd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta" [project] name = "rda_python_miscs" -version = "1.0.6" +version = "1.0.7" authors = [ { name="Zaihua Ji", email="zji@ucar.edu" }, ] diff --git a/src/rda_python_miscs/bashqsub.py b/src/rda_python_miscs/bashqsub.py index 59fdf07..2b8e769 100644 --- a/src/rda_python_miscs/bashqsub.py +++ b/src/rda_python_miscs/bashqsub.py @@ -39,7 +39,7 @@ 'o' : None, # will set to default if not provided 'e' : None, 'A' : "P43713000", - 'q' : "rda@casper-pbs", + 'q' : "gdex@casper-pbs", # 'm' : 'a', 'm' : 'n', } @@ -50,9 +50,9 @@ def main(): aname = 'bashqsub' - pname = 'rdaqsub' + pname = 'gdexqsub' PgLOG.set_help_path(__file__) - rdasub = PgLOG.BCHCMDS['PBS'] + gdexsub = PgLOG.BCHCMDS['PBS'] coptions = {'cmd' : None, 'cwd' : None, 'env' : None, 'mod' : None, 'res' : 'default'} # customized options copts = '|'.join(coptions) option = None @@ -61,7 +61,7 @@ def main(): if not argv: PgLOG.show_usage(aname) PgLOG.PGLOG['LOGFILE'] = pname + ".log" PgLOG.cmdlog("{} {}".format(aname, ' '.join(argv))) - if not PgLOG.valid_command(rdasub): PgLOG.pglog("{}: miss {} command to submit batch job".format(rdasub, PgLOG.PGLOG['PBSNAME']), PgLOG.LGWNEX) + if not PgLOG.valid_command(gdexsub): PgLOG.pglog("{}: miss {} command to submit batch job".format(gdexsub, PgLOG.PGLOG['PBSNAME']), PgLOG.LGWNEX) while argv: arg = argv.pop(0) @@ -80,7 +80,7 @@ def main(): if option == "env": option = 'v' continue - if not option: PgLOG.pglog("{}: Value passed in without leading option for {}".format(arg, rdasub), PgLOG.LGEREX) + if not option: PgLOG.pglog("{}: Value passed in without leading option for {}".format(arg, gdexsub), PgLOG.LGEREX) if arg.find(' ') > -1 and not re.match(r'^[\'\"].*[\'\"]$', arg): # quote string with space but not quoted yet if arg.find("'") > -1: arg = '"{}"'.format(arg) @@ -111,10 +111,10 @@ def main(): if not cmd: PgLOG.pglog(coptions['cmd'] + ": Cannot find given command to run", PgLOG.LGWNEX) if args: cmd += " " + args - sbuf = build_bash_script(cmd, coptions, rdasub) + sbuf = build_bash_script(cmd, coptions, gdexsub) PgLOG.pglog(sbuf, PgLOG.MSGLOG) PgLOG.PGLOG['ERR2STD'] = ['bind mouting'] - PgLOG.pgsystem(rdasub, PgLOG.LOGWRN, 6, sbuf) + PgLOG.pgsystem(gdexsub, PgLOG.LOGWRN, 6, sbuf) PgLOG.PGLOG['ERR2STD'] = [] sys.exit(0) @@ -122,7 +122,7 @@ def main(): # # build bash script to submit a PBS batch job # -def build_bash_script(cmd, coptions, rdasub): +def build_bash_script(cmd, coptions, gdexsub): buf = "#!/usr/bin/bash\n\n" # qsub starting bash script diff --git a/src/rda_python_miscs/bashqsub.usg b/src/rda_python_miscs/bashqsub.usg index 1102695..bffd895 100644 --- a/src/rda_python_miscs/bashqsub.usg +++ b/src/rda_python_miscs/bashqsub.usg @@ -1,17 +1,17 @@ To submit a job execution as a batch job in bash script on a PBS node via 'qsub'. - Usage: rdaqsub [qsub-options] [-cwd WorkDir] [-env EnvironmentPairs] \ - [-mod Modules] [-res Reservation] -cmd Command [cmd-options] + Usage: bashqsub [qsub-options] [-cwd WorkDir] [-env EnvironmentPairs] \ + [-mod Modules] [-res Reservation] -cmd Command [cmd-options] - qsub-options, accepts options that can be passed to 'qsub' in a bash script. Check qsub man page for help on the PBS batch options. Here is the list of qsub options that are included at default: - -o LOGPATH/rdaqsub/ - -e LOGPATH/rdaqsub/ + -o LOGPATH/gdexqsub/ + -e LOGPATH/gdexqsub/ -A P43713000 -m a - -q regular + -q gdex -l walltime=6:00:00,select=1:node=1:mem=1gb - Option -cwd, set the working directory for the Command to be executed. If @@ -33,10 +33,10 @@ A bash script example: #!/usr/bin/bash -#PBS -o /gpfs/u/home/rdadata/dssdb/log/rdaqsub/ -#PBS -e /gpfs/u/home/rdadata/dssdb/log/rdaqsub/ +#PBS -o /gpfs/u/home/gdexdata/dssdb/log/gdexqsub/ +#PBS -e /gpfs/u/home/gdexdata/dssdb/log/gdexqsub/ #PBS -A P43713000 -#PBS -q rda@casper-pbs +#PBS -q gdex@casper-pbs #PBS -m n #PBS -N dsrqst #PBS -l walltime=1:00:00 @@ -56,9 +56,9 @@ module load conda module load grib-util module load wgrib2 -conda activate /glade/work/rdadata/conda-envs/pg-casper +conda activate /glade/work/gdexdata/conda-envs/pg-casper -echo /gpfs/u/home/rdadata/bin/dsrqst d277000 PR -RI 750748 -b -d -/gpfs/u/home/rdadata/bin/dsrqst d277000 PR -RI 750748 -b -d +echo /glade/work/gdexdata/conda-envs/pg-casper/bin/dsrqst d277000 PR -RI 750748 -b -d +/glade/work/gdexdata/conda-envs/pg-casper/bin/dsrqst d277000 PR -RI 750748 -b -d date diff --git a/src/rda_python_miscs/tcshqsub.py b/src/rda_python_miscs/tcshqsub.py index 2776aef..eb9af66 100644 --- a/src/rda_python_miscs/tcshqsub.py +++ b/src/rda_python_miscs/tcshqsub.py @@ -39,7 +39,7 @@ 'o' : None, # will set to default if not provided 'e' : None, 'A' : "P43713000", - 'q' : "rda@casper-pbs", + 'q' : "gdex@casper-pbs", # 'm' : 'a', 'm' : 'n', } @@ -50,9 +50,9 @@ def main(): aname = 'tcshqsub' - pname = 'rdaqsub' + pname = 'gdexqsub' PgLOG.set_help_path(__file__) - rdasub = PgLOG.BCHCMDS['PBS'] + gdexsub = PgLOG.BCHCMDS['PBS'] coptions = {'cmd' : None, 'cwd' : None, 'env' : None, 'mod' : None, 'res' : 'default'} # customized options copts = '|'.join(coptions) option = None @@ -61,7 +61,7 @@ def main(): if not argv: PgLOG.show_usage(aname) PgLOG.PGLOG['LOGFILE'] = pname + ".log" PgLOG.cmdlog("{} {}".format(aname, ' '.join(argv))) - if not PgLOG.valid_command(rdasub): PgLOG.pglog("{}: miss {} command to submit batch job".format(rdasub, PgLOG.PGLOG['PBSNAME']), PgLOG.LGWNEX) + if not PgLOG.valid_command(gdexsub): PgLOG.pglog("{}: miss {} command to submit batch job".format(gdexsub, PgLOG.PGLOG['PBSNAME']), PgLOG.LGWNEX) while argv: arg = argv.pop(0) @@ -80,7 +80,7 @@ def main(): if option == "env": option = 'v' continue - if not option: PgLOG.pglog("{}: Value passed in without leading option for {}".format(arg, rdasub), PgLOG.LGEREX) + if not option: PgLOG.pglog("{}: Value passed in without leading option for {}".format(arg, gdexsub), PgLOG.LGEREX) if arg.find(' ') > -1 and not re.match(r'^[\'\"].*[\'\"]$', arg): # quote string with space but not quoted yet if arg.find("'") > -1: arg = '"{}"'.format(arg) @@ -111,10 +111,10 @@ def main(): if not cmd: PgLOG.pglog(coptions['cmd'] + ": Cannot find given command to run", PgLOG.LGWNEX) if args: cmd += " " + args - sbuf = build_tcsh_script(cmd, coptions, rdasub) + sbuf = build_tcsh_script(cmd, coptions, gdexsub) PgLOG.pglog(sbuf, PgLOG.MSGLOG) PgLOG.PGLOG['ERR2STD'] = ['bind mouting'] - PgLOG.pgsystem(rdasub, PgLOG.LOGWRN, 6, sbuf) + PgLOG.pgsystem(gdexsub, PgLOG.LOGWRN, 6, sbuf) PgLOG.PGLOG['ERR2STD'] = [] sys.exit(0) @@ -122,7 +122,7 @@ def main(): # # build tcsh script to submit a PBS batch job # -def build_tcsh_script(cmd, coptions, rdasub): +def build_tcsh_script(cmd, coptions, gdexsub): buf = "#!/bin/tcsh\n\n" # sbatch starting tcsh script diff --git a/src/rda_python_miscs/tcshqsub.usg b/src/rda_python_miscs/tcshqsub.usg index 082c586..e675ae8 100644 --- a/src/rda_python_miscs/tcshqsub.usg +++ b/src/rda_python_miscs/tcshqsub.usg @@ -1,17 +1,17 @@ To submit a job execution as a batch job in tcsh script on a PBS node via 'qsub'. - Usage: rdaqsub [qsub-options] [-cwd WorkDir] [-env EnvironmentPairs] \ - [-mod Modules] [-res Reservation] -cmd Command [cmd-options] + Usage: tcshqsub [qsub-options] [-cwd WorkDir] [-env EnvironmentPairs] \ + [-mod Modules] [-res Reservation] -cmd Command [cmd-options] - qsub-options, accepts options that can be passed to 'qsub' in a tcsh script. Check qsub man page for help on the PBS batch options. Here is the list of qsub options that are included at default: - -o LOGPATH/rdaqsub/ - -e LOGPATH/rdaqsub/ + -o LOGPATH/gdexqsub/ + -e LOGPATH/gdexqsub/ -A P43713000 -m a - -q regular + -q gdex -l walltime=6:00:00,select=1:node=1:mem=1gb - Option -cwd, set the working directory for the Command to be executed. If @@ -33,17 +33,17 @@ A tash script example: #!/bin/tcsh -#PBS -o /gpfs/u/home/rdadata/dssdb/log/rdaqsub/ -#PBS -e /gpfs/u/home/rdadata/dssdb/log/rdaqsub/ +#PBS -o /gpfs/u/home/gdexdata/dssdb/log/gdexqsub/ +#PBS -e /gpfs/u/home/gdexdata/dssdb/log/gdexqsub/ #PBS -A P43713000 -#PBS -q rda@casper-pbs +#PBS -q gdex@casper-pbs #PBS -m a #PBS -N dsrqst #PBS -l walltime=12:00:00 #PBS -l select=1:mem=20gb setenv HOME /gpfs/u/home/davestep -source /etc/profile.d/z00_modules.tsh -source /glade/u/apps/opt/conda/etc/profile.d/conda.tsh +source /etc/profile.d/z00_modules.csh +source /glade/u/apps/opt/conda/etc/profile.d/conda.csh source /gpfs/u/home/davestep/.tcshrc pwd; hostname; date @@ -56,7 +56,7 @@ module load conda module load grib-util module load wgrib2 -conda activate /glade/work/rdadata/conda-envs/pg-casper +conda activate /glade/work/gdexdata/conda-envs/pg-casper -echo /gpfs/u/home/rdadata/bin/dsrqst d628000 SP -RI 729708 -NP -b -d -/gpfs/u/home/rdadata/bin/dsrqst d628000 SP -RI 729708 -NP -b -d +echo /glade/work/gdexdata/conda-envs/pg-casper/bin/dsrqst d628000 SP -RI 729708 -NP -b -d +/glade/work/gdexdata/conda-envs/pg-casper/bin/dsrqst d628000 SP -RI 729708 -NP -b -d