rda => gdex bash/tcshqsub

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="[email protected]" },
 ]

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)
@@ -111,18 +111,18 @@ 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)
 
 #
 # 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
 

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

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)
@@ -111,18 +111,18 @@ 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)
 
 #
 # 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
 

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