[cig-commits] r5571 - in cs/pythia/trunk: mpi pyre/odb/fs
pyre/schedulers pyre/schedulers/scripts
pyre/schedulers/scripts/lsf pyre/schedulers/scripts/pbs
leif at geodynamics.org
leif at geodynamics.org
Fri Dec 8 16:41:17 PST 2006
Author: leif
Date: 2006-12-08 16:41:16 -0800 (Fri, 08 Dec 2006)
New Revision: 5571
Added:
cs/pythia/trunk/pyre/schedulers/SchedulerPBS.py
cs/pythia/trunk/pyre/schedulers/pbs.odb
cs/pythia/trunk/pyre/schedulers/scripts/pbs/
cs/pythia/trunk/pyre/schedulers/scripts/pbs/__vault__.odb
cs/pythia/trunk/pyre/schedulers/scripts/pbs/batch.sh.tmpl
Modified:
cs/pythia/trunk/mpi/Launcher.py
cs/pythia/trunk/pyre/odb/fs/CodecODB.py
cs/pythia/trunk/pyre/schedulers/SchedulerLSF.py
cs/pythia/trunk/pyre/schedulers/scripts/lsf/batch.sh.tmpl
Log:
Added support for PBS. This included adding 'os.environ' to the MPI
launcher macro substitutions, so that one can reference PBS_NODEFILE
as follows:
[CitcomS.launcher]
command = mpirun -np ${nodes} -machinefile ${PBS_NODEFILE}
Nuked all references to FileLocking (actually there was only one, in
CodecODB). This is the annoying code that prevented Pyre from working
on NFS-mounted filesystems (!). The locking seems to serve no
purpose, anyway.
Renamed 'scheduler.batch-command' to simply 'scheduler.command'. The
'batch-' was an anachonism: it was to avoid a name conflict with the
'command' property used for 'mpirun', back when Launcher and Scheduler
were the same thing.
Modified: cs/pythia/trunk/mpi/Launcher.py
===================================================================
--- cs/pythia/trunk/mpi/Launcher.py 2006-12-09 00:35:19 UTC (rev 5570)
+++ cs/pythia/trunk/mpi/Launcher.py 2006-12-09 00:41:16 UTC (rev 5571)
@@ -69,8 +69,11 @@
# 'ibrun' (the number of nodes is not given).
from pyre.util import expandMacros
+ from os import environ
args = self.command.split(' ')
- substitutions = {'nodes': '%d' % self.nodes }
+ substitutions = dict()
+ substitutions.update(environ) # to allow, for example, ${PBS_NODEFILE}
+ substitutions['nodes'] = '%d' % self.nodes
args = [expandMacros(arg, substitutions) for arg in args]
# use only the specific nodes specified explicitly
Modified: cs/pythia/trunk/pyre/odb/fs/CodecODB.py
===================================================================
--- cs/pythia/trunk/pyre/odb/fs/CodecODB.py 2006-12-09 00:35:19 UTC (rev 5570)
+++ cs/pythia/trunk/pyre/odb/fs/CodecODB.py 2006-12-09 00:41:16 UTC (rev 5571)
@@ -53,9 +53,6 @@
# public data
self.renderer = self._createRenderer()
- # private data
- self._locker = self._createLocker()
-
return
@@ -71,9 +68,7 @@
stream = file(shelf.name)
- self._locker.lock(stream, self._locker.LOCK_EX)
exec stream in shelf
- self._locker.unlock(stream)
return
@@ -85,11 +80,6 @@
weaver = Weaver()
return weaver
-
- def _createLocker(self):
- from FileLocking import FileLocking
- return FileLocking()
-
# version
__id__ = "$Id: CodecODB.py,v 1.1.1.1 2005/03/08 16:13:41 aivazis Exp $"
Modified: cs/pythia/trunk/pyre/schedulers/SchedulerLSF.py
===================================================================
--- cs/pythia/trunk/pyre/schedulers/SchedulerLSF.py 2006-12-09 00:35:19 UTC (rev 5570)
+++ cs/pythia/trunk/pyre/schedulers/SchedulerLSF.py 2006-12-09 00:41:16 UTC (rev 5571)
@@ -22,9 +22,8 @@
import pyre.inventory as pyre
- command = pyre.str("command", default="mpijob mpirun")
- batchCommand = pyre.str("batch-command", default="bsub")
- bsubOptions = pyre.list("bsub-options")
+ command = pyre.str("command", default="bsub")
+ bsubOptions = pyre.list("bsub-options")
def schedule(self, job):
@@ -53,7 +52,7 @@
import os
from popen2 import Popen4
- cmd = [self.batchCommand]
+ cmd = [self.command]
if self.wait:
cmd.append("-K")
self._info.log("spawning: %s" % ' '.join(cmd))
@@ -82,7 +81,7 @@
self._info.log("%s: %s" % (cmd[0], statusStr))
except IOError, e:
- self._error.log("%s: %s" % (self.batchCommand, e))
+ self._error.log("%s: %s" % (self.command, e))
return
# "[When given the -K option], bsub will exit with the same
Added: cs/pythia/trunk/pyre/schedulers/SchedulerPBS.py
===================================================================
--- cs/pythia/trunk/pyre/schedulers/SchedulerPBS.py 2006-12-09 00:35:19 UTC (rev 5570)
+++ cs/pythia/trunk/pyre/schedulers/SchedulerPBS.py 2006-12-09 00:41:16 UTC (rev 5571)
@@ -0,0 +1,108 @@
+#!/usr/bin/env python
+#
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+# California Institute of Technology
+# (C) 2006 All Rights Reserved
+#
+# {LicenseText}
+#
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+
+
+from BatchScheduler import BatchScheduler
+
+
+class SchedulerPBS(BatchScheduler):
+
+
+ name = "pbs"
+
+
+ import pyre.inventory as pyre
+
+ command = pyre.str("command", default="qsub")
+ qsubOptions = pyre.list("qsub-options")
+ ppn = pyre.int("ppn", default=1)
+
+
+ def schedule(self, job):
+ import os, sys
+ import pyre.util as util
+
+ # Fix-up the job.
+ if not job.task:
+ job.task = "jobname"
+ job.walltime = util.hms(job.dwalltime.value)
+ job.arguments = ' '.join(job.arguments)
+ job.resourceList = self.buildResourceList(job)
+
+ # Generate the main PBS batch script.
+ script = self.retrieveTemplate('batch.sh', ['schedulers', 'scripts', 'pbs'])
+ script.scheduler = self
+ script.job = job
+
+ if self.dry:
+ print script
+ return
+
+ try:
+ import os
+ from popen2 import Popen4
+
+ cmd = [self.command]
+ self._info.log("spawning: %s" % ' '.join(cmd))
+ child = Popen4(cmd)
+ self._info.log("spawned process %d" % child.pid)
+
+ print >> child.tochild, script
+ child.tochild.close()
+
+ for line in child.fromchild:
+ self._info.line(" " + line.rstrip())
+ status = child.wait()
+ self._info.log()
+
+ exitStatus = None
+ if (os.WIFSIGNALED(status)):
+ statusStr = "signal %d" % os.WTERMSIG(status)
+ elif (os.WIFEXITED(status)):
+ exitStatus = os.WEXITSTATUS(status)
+ statusStr = "exit %d" % exitStatus
+ else:
+ statusStr = "status %d" % status
+ self._info.log("%s: %s" % (cmd[0], statusStr))
+
+ except IOError, e:
+ self._error.log("%s: %s" % (self.command, e))
+ return
+
+ if exitStatus == 0:
+ pass
+ else:
+ sys.exit("%s: %s: %s" % (sys.argv[0], cmd[0], statusStr))
+
+ return
+
+
+ def buildResourceList(self, job):
+
+ resourceList = []
+ if self.ppn:
+ resourceList.append(
+ "nodes=%d:ppn=%d" % ((job.nodes / self.ppn) + (job.nodes % self.ppn and 1 or 0), self.ppn)
+ )
+ else:
+ resourceList.append(
+ "nodes=%d" % job.nodes
+ )
+
+ walltime = job.walltime
+ if max(walltime):
+ resourceList.append("walltime=%d:%02d:%02d" % walltime)
+
+ return resourceList
+
+
+# end of file
Added: cs/pythia/trunk/pyre/schedulers/pbs.odb
===================================================================
--- cs/pythia/trunk/pyre/schedulers/pbs.odb 2006-12-09 00:35:19 UTC (rev 5570)
+++ cs/pythia/trunk/pyre/schedulers/pbs.odb 2006-12-09 00:41:16 UTC (rev 5571)
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+#
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+# California Institute of Technology
+# (C) 2006 All Rights Reserved
+#
+# {LicenseText}
+#
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+
+
+def scheduler():
+ from pyre.schedulers.SchedulerPBS import SchedulerPBS
+ return SchedulerPBS()
+
+
+# end of file
Modified: cs/pythia/trunk/pyre/schedulers/scripts/lsf/batch.sh.tmpl
===================================================================
--- cs/pythia/trunk/pyre/schedulers/scripts/lsf/batch.sh.tmpl 2006-12-09 00:35:19 UTC (rev 5570)
+++ cs/pythia/trunk/pyre/schedulers/scripts/lsf/batch.sh.tmpl 2006-12-09 00:41:16 UTC (rev 5571)
@@ -49,4 +49,4 @@
@end if
# ~~~~ submit command ~~~~
-# ${scheduler.batchCommand} < [script]
+# ${scheduler.command} < [script]
Added: cs/pythia/trunk/pyre/schedulers/scripts/pbs/__vault__.odb
===================================================================
--- cs/pythia/trunk/pyre/schedulers/scripts/pbs/__vault__.odb 2006-12-09 00:35:19 UTC (rev 5570)
+++ cs/pythia/trunk/pyre/schedulers/scripts/pbs/__vault__.odb 2006-12-09 00:41:16 UTC (rev 5571)
@@ -0,0 +1,13 @@
+#!/usr/bin/env python
+#
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+# California Institute of Technology
+# (C) 2006 All Rights Reserved
+#
+# {LicenseText}
+#
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+
+# end of file
Added: cs/pythia/trunk/pyre/schedulers/scripts/pbs/batch.sh.tmpl
===================================================================
--- cs/pythia/trunk/pyre/schedulers/scripts/pbs/batch.sh.tmpl 2006-12-09 00:35:19 UTC (rev 5570)
+++ cs/pythia/trunk/pyre/schedulers/scripts/pbs/batch.sh.tmpl 2006-12-09 00:41:16 UTC (rev 5571)
@@ -0,0 +1,39 @@
+## -*- sh -*-
+#compiler-settings
+directiveStartToken = @
+#end compiler-settings
+ at from pyre.schedulers import BatchScriptTemplate
+ at extends BatchScriptTemplate
+ at implements respond
+ at set $self.substitutions = {'job.id': "${PBS_JOBID}"}
+#!${scheduler.shell}
+#PBS -S ${scheduler.shell}
+#PBS -N ${job.task}
+ at if $job.queue
+#PBS -q ${job.queue}
+ at end if
+ at if $self.stdout
+#PBS -o ${self.stdout}
+ at end if
+ at if $self.stderr
+#PBS -e ${self.stderr}
+ at end if
+ at if $job.resourceList
+#PBS -l @echo ','.join($job.resourceList)
+ at end if
+ at for option in $scheduler.qsubOptions
+#PBS ${option}
+ at end for
+
+cd \$PBS_O_WORKDIR
+${job.executable} @echo ' '.join($job.arguments)
+
+ at if $job.comments
+# ~~~~ comments ~~~~
+ at for line in $job.comments
+# ${line}
+ at end for
+ at end if
+
+# ~~~~ submit command ~~~~
+# ${scheduler.command} < [script]
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