Le 24/04/2012 14:53, Louise-Amélie Schmitt a écrit :
> At first we thought it could be an ssh issue but submitting jobs and
> getting the output back isn't a problem when I do it from my personal
> user manually, so it's really related to Galaxy. We're using PBS Pro btw.
>
> And I'm still at loss... :(
>
> L-A
>
> Le 23/04/2012 15:42, zhengqiu cai a écrit :
>> I am having the same problem when I use condor as the scheduler
>> instead of sge.
>>
>> Cai
>>
>> --- 12年4月23日，周一, Louise-Amélie
>> Schmitt<louise-amelie.schm...@embl.de> 写道：
>>
>>> 发件人: Louise-Amélie Schmitt<louise-amelie.schm...@embl.de>
>>> 主题: [galaxy-dev] Error: Job output not returned from cluster
>>> 收件人: galaxy-dev@lists.bx.psu.edu
>>> 日期: 2012年4月23日,周一,下午5:09
>>> Hello everyone,
>>>
>>> I'm still trying to set up the job submission as the real
>>> user, and I get a mysterious error. The job obviously runs
>>> somewhere and when it ends it is in error state and displays
>>> the following message: "Job output not returned from
>>> cluster"
>>>
>>> In the Galaxy log I have the following lines when the job
>>> finishes running:
>>>
>>> galaxy.jobs.runners.drmaa DEBUG 2012-04-23 10:36:41,509
>>> (1455/9161620.pbs-master2.embl.de) state change: job
>>> finished, but failed
>>> galaxy.jobs.runners.drmaa DEBUG 2012-04-23 10:36:41,511 Job
>>> output not returned from cluster
>>> galaxy.jobs DEBUG 2012-04-23 10:36:41,547 finish(): Moved
>>> /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/galaxy_dataset_2441.dat
>>>
>>> to
>>> /g/funcgen/galaxy-dev/database/files/002/dataset_2441.dat
>>> galaxy.jobs DEBUG 2012-04-23 10:36:41,755 job 1455 ended
>>> galaxy.datatypes.metadata DEBUG 2012-04-23 10:36:41,755
>>> Cleaning up external metadata files
>>> galaxy.datatypes.metadata DEBUG 2012-04-23 10:36:41,768
>>> Failed to cleanup MetadataTempFile temp files from
>>> /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/metadata_out_HistoryDatasetAssociation_1606_npFIJM:
>>>
>>> No JSON object could be decoded: line 1 column 0 (char 0)
>>>
>>> The
>>> /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/
>>> directory is empty and
>>> /g/funcgen/galaxy-dev/database/files/002/dataset_2441.dat
>>> exists but is empty.
>>>
>>> Any ideas about what can go wrong there? Any lead would be
>>> immensely appreciated!
>>>
>>> Thanks,
>>> L-A
>>>
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>
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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
--
Alban Lermine
Unité 900 : Inserm - Mines ParisTech - Institut Curie
« Bioinformatics and Computational Systems Biology of Cancer »
11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France
Tel : +33 (0) 1 56 24 69 84
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