[IPython-dev] 0.11rc1 : problem with tutorial for PBS in http://ipython.org/ipython-doc/dev/parallel/parallel_process.html
Johann Cohen-Tanugi
johann.cohentanugi at gmail.com
Mon Jul 4 11:07:33 EDT 2011
hi there, my problem is in the fact that a line seems to be added to the
template I am defining following the tutorial :
the template proposed in the tutorial is modified at runtime as :
#!/bin/sh
#PBS -t 1-4 <----------------- incorrect?
#PBS -V
#PBS -N ipengine
/usr/local/bin/python
/sps/glast/users/cohen/IPYDEV/ipython/IPython/parallel/apps/ipengineapp.py
profile_dir=/afs/in2p3.fr/home/t/tanugi/\
.ipython/profile_pbs
The problem I believe is in the job_array_template in :
class PBSLauncher(BatchSystemLauncher):
"""A BatchSystemLauncher subclass for PBS."""
submit_command = List(['qsub'], config=True,
help="The PBS submit command ['qsub']")
delete_command = List(['qdel'], config=True,
help="The PBS delete command ['qsub']")
job_id_regexp = Unicode(r'\d+', config=True,
help="Regular expresion for identifying the job ID [r'\d+']")
batch_file = Unicode(u'')
job_array_regexp = Unicode('#PBS\W+-t\W+[\w\d\-\$]+')
job_array_template = Unicode('#PBS -t 1-{n}')
queue_regexp = Unicode('#PBS\W+-q\W+\$?\w+')
queue_template = Unicode('#PBS -q {queue}')
I looked at the PBS doc for version 10 and 11 and I did not see any '-t'
option. When I try to run, I get :
[tanugi at ccali28 test_directory]$ ipcluster start profile=pbs n=4
[IPClusterStart] Using existing profile dir:
u'/afs/in2p3.fr/home/t/tanugi/.ipython/profile_pbs'
[IPClusterStart] Starting ipcluster with [daemon=False]
[IPClusterStart] Creating pid file:
/afs/in2p3.fr/home/t/tanugi/.ipython/profile_pbs/pid/ipcluster.pid
[IPClusterStart] Starting PBSControllerLauncher: ['qsub',
u'/afs/in2p3.fr/home/t/tanugi/.ipython/profile_pbs/pbs_controller']
[IPClusterStart] adding job array settings to batch script
[IPClusterStart] Writing instantiated batch script:
/afs/in2p3.fr/home/t/tanugi/.ipython/profile_pbs/pbs_controller
unknown -t option
ERROR:root:Error in periodic callback
Traceback (most recent call last):
File
"/sps/glast/users/cohen/IPYDEV/local/lib/python2.6/site-packages/zmq/eventloop/ioloop.py",
line 432, in _run
self.callback()
File
"/sps/glast/users/cohen/IPYDEV/ipython/IPython/parallel/apps/ipclusterapp.py",
line 364, in start_controller
self.profile_dir.location
File
"/sps/glast/users/cohen/IPYDEV/ipython/IPython/parallel/apps/launcher.py",
line 943, in start
return super(PBSControllerLauncher, self).start(1, profile_dir)
File
"/sps/glast/users/cohen/IPYDEV/ipython/IPython/parallel/apps/launcher.py",
line 902, in start
job_id = self.parse_job_id(output)
File
"/sps/glast/users/cohen/IPYDEV/ipython/IPython/parallel/apps/launcher.py",
line 854, in parse_job_id
raise LauncherError("Job id couldn't be determined: %s" % output)
LauncherError: Job id couldn't be determined:
Not sure yet about the traceback, but the "unknown -t option" is clear.
Furthermore, I wonder if it is really what we want to add lines to a
template file provided by the user?
best,
Johann
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