Hi Luca,
Could you send your job_conf.xml please? Also, is there any chance that you
modified run.sh to set DRMAA_LIBRARY_PATH there (which would override what
you set on the command line)?
--nate
On Thu, Apr 3, 2014 at 9:17 AM, Luca Toldo <lucatoldo(a)gmail.com> wrote:
Dear All,
after having discovered the mess in which I was, and the incomplete PBS
client installation, I've done the following:
*1) PBS Pro*
a) removed the incomplete pbs installation that I had
b) downloaded the latest version from vendor
c) installed it in //usr/pbs
d) configured
e) tested it --> worked well
*2) drma-pbs*
a) downloaded version 1.0.17
b) compiled it (./configure --with-pbs=/usr/pbs ) without any problem
c) installed it in /usr/local/lib
3) modified DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so
4) sh run.sh --stop
5) sh run.sh --daemon
Unfortunately, however when I launch a new job I always get the error
message
galaxy.jobs DEBUG 2014-04-03 15:13:44,306 (261) Working directory for job
is: /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261
galaxy.jobs.handler DEBUG 2014-04-03 15:13:44,321 (261) Dispatching to
drmaa runner
galaxy.jobs DEBUG 2014-04-03 15:13:44,434 (261) Persisting job
destination (destination id: pbs_default)
galaxy.jobs.handler INFO 2014-04-03 15:13:44,474 (261) Job dispatched
galaxy.tools.deps DEBUG 2014-04-03 15:13:44,659 Building dependency shell
command for dependency 'clustalw2'
galaxy.tools.deps WARNING 2014-04-03 15:13:44,660 Failed to resolve
dependency on 'clustalw2', ignoring
galaxy.jobs.runners.drmaa DEBUG 2014-04-03 15:13:45,050 (261) submitting
file
/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy_261.sh
galaxy.jobs.runners.drmaa DEBUG 2014-04-03 15:13:45,050 (261) command is:
python /opt/ngs/bin/galaxy-dist/tools/rgenetics/rgClustalw.py -i
"/data/imgt.fasta" -o
"/opt/ngs/bin/galaxy-dist/database/files/000/dataset_340.dat" -s
"ALIGNED"
-l "/opt/ngs/bin/galaxy-dist/database/files/000/dataset_341.dat" -t
"Clustal_run" -d "DNA" -f "CLUSTAL"; return_code=$?; cd
/opt/ngs/bin/galaxy-dist; /opt/ngs/bin/galaxy-dist/set_metadata.sh
./database/files
/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261 .
/opt/ngs/bin/galaxy-dist/universe_wsgi.ini
/opt/ngs/bin/galaxy-dist/database/tmp/tmpq4Rmdl
/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy.json
/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_in_HistoryDatasetAssociation_347_GsBRYB,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_kwds_HistoryDatasetAssociation_347_dFD5t0,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_out_HistoryDatasetAssociation_347_k0zCP6,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_results_HistoryDatasetAssociation_347_4LVIFs,,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_override_HistoryDatasetAssociation_347_jKfp0r
/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_in_HistoryDatasetAssociation_348_Fyy0tJ,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_kwds_HistoryDatasetAssociation_348_9vWiO3,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_out_HistoryDatasetAssociation_348_HL3EIj,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_results_HistoryDatasetAssociation_348_s1gqxk,,/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/metadata_override_HistoryDatasetAssociation_348_hyQkDF;
sh -c "exit $return_code"
galaxy.jobs.runners ERROR 2014-04-03 15:13:45,051 (261) Unhandled
exception calling queue_job
Traceback (most recent call last):
File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 62, in run_next
method(arg)
File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line
150, in queue_job
external_job_id = self.ds.runJob(jt)
File
"/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py", line
331, in runJob
_h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
File
"/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py", line
213, in c
return f(*(args + (error_buffer, sizeof(error_buffer))))
File
"/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py", line
90, in error_check
raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
InvalidAttributeValueException: code 14: Illegal attribute or resource
value: Illegal attribute or resource value
If from the commandline I do
qsub -q NGSq
/opt/ngs/bin/galaxy-dist/database/job_working_directory/000/261/galaxy_261.sh
then
I get 1695145.servername
...
What can I do now ?