Hi,
Thanks a lot it actually helped. It is not exactly as straightforward in
drmaa.py but somehow I could manage.
However, it was not the problem. For some reason, the user needs to
write files from the node to job_working_directory/00X/XXXX/ and the
latter is not world-writable. I had to make everyone chmod everything to
777 to make it work. Did I miss something?
Best,
L-A
Le 24/04/2012 15:17, Alban Lermine a écrit :
Hi L-A,
I run Galaxy as real user on our cluster with pbs (free version).
We first configure LDAP authentification for having email account
related to unix account (just cut the @curie.fr)
Then I have modify pbs.py (in
<GALAXY_DIR>galaxy-dist/lib/galaxy/jobs/runners)
I have just disconnected the pbs submission through python library and
replace it by a system call (just like I send jobs to the cluster with
command line), here is the code used:
galaxy_job_id = job_wrapper.job_id
log.debug("(%s) submitting file %s" % ( galaxy_job_id, job_file ) )
log.debug("(%s) command is: %s" % ( galaxy_job_id, command_line ) )
# Submit job with system call instead of using python PBS library -
Permit to run jobs as .. with sudo -u cmd prefix
galaxy_job_idSTR = str(job_wrapper.job_id)
galaxy_tool_idSTR = str(job_wrapper.tool.id)
galaxy_job_name =
galaxy_job_idSTR+"_"+galaxy_tool_idSTR+"_"+job_wrapper.user
torque_options = runner_url.split("/")
queue = torque_options[3]
ressources = torque_options[4]
user_mail = job_wrapper.user.split("@")
username = user_mail[0]
torque_cmd = "sudo -u username echo "+"\""+command_line+"\" | qsub
-o "+ofile+" -e "+efile+" -M "+job_wrapper.user+" -N "+galaxy_job_name+"
-q "+queue+" "+ressources
submit_pbs_job = os.popen(torque_cmd)
job_id = submit_pbs_job.read().rstrip("\n")
#Original job launcher
#job_id = pbs.pbs_submit(c, job_attrs, job_file, pbs_queue_name, None)
pbs.pbs_disconnect(c)
Second thing I have done is to wait error and output file from torque in
the finish_job function (if not, I never receive the output, seems to be
your problem..), here is the code used:
def finish_job( self, pbs_job_state ):
"""
Get the output/error for a finished job, pass to
`job_wrapper.finish`
and cleanup all the PBS temporary files.
"""
ofile = pbs_job_state.ofile
efile = pbs_job_state.efile
job_file = pbs_job_state.job_file
# collect the output
try:
# With qsub system call, need to wait efile and ofile creation
at the end of the job execution before reading them
efileExists = os.path.isfile(efile)
ofileExists = os.path.isfile(ofile)
efileExistsSTR = str(efileExists)
ofileExistsSTR = str(ofileExists)
while efileExistsSTR == "False":
time.sleep( 1 )
efileExists = os.path.isfile(efile)
efileExistsSTR = str(efileExists)
while ofileExistsSTR == "False":
time.sleep( 1 )
ofileExists = os.path.isfile(ofile)
ofileExistsSTR = str(ofileExists)
# Back to original code
ofh = file(ofile, "r")
efh = file(efile, "r")
stdout = ofh.read( 32768 )
stderr = efh.read( 32768 )
except:
stdout = ''
stderr = 'Job output not returned by PBS: the output
datasets were deleted while the job was running, the job was manually
dequeued or there was a cluster error.'
log.debug(stderr)
* Last step is to allow galaxy user to run sudo
Hope it can help you finding your problem..
See you,
Alban
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