Hi All,

Trying to setup a Galaxy cluster using Rocks Gridengine

OS is Centos 6.5.
psql (9.1.18)
shell bash

Getting error messages in paster.log below. I can submit jobs to Gridengine 
using qsub so this is not an issue. But when trying to "Upload File from you 
computer”, history indicates jobs does not complete.

Any help would be appreciated.

galaxy.tools.actions.upload_common DEBUG 2015-10-02 09:35:02,272 Changing 
ownership of /share/apps/galaxy/database/tmp/upload_file_data_xvpaYs with: 
/usr/bin/sudo -E /share/apps/galaxy/scripts/external_chown_script.py 
/share/apps/galaxy/database/tmp/upload_file_data_xvpaYs rpolich 507
galaxy.tools.actions.upload_common WARNING 2015-10-02 09:35:02,297 Changing 
ownership of uploaded file 
/share/apps/galaxy/database/tmp/upload_file_data_xvpaYs failed: sudo: no tty 
present and no askpass program specified

galaxy.tools.actions.upload_common DEBUG 2015-10-02 09:35:02,297 Changing 
ownership of /share/apps/galaxy/database/tmp/tmplIgC3n with: /usr/bin/sudo -E 
/share/apps/galaxy/scripts/external_chown_script.py 
/share/apps/galaxy/database/tmp/tmplIgC3n rpolich 507
galaxy.tools.actions.upload_common WARNING 2015-10-02 09:35:02,323 Changing 
ownership of uploaded file /share/apps/galaxy/database/tmp/tmplIgC3n failed: 
sudo: no tty present and no askpass program specified

galaxy.tools.actions.upload_common INFO 2015-10-02 09:35:02,357 tool upload1 
created job id 101
galaxy.tools.execute DEBUG 2015-10-02 09:35:02,423 Tool [upload1] created job 
[101] (332.351 ms)
206.124.61.6 - - [02/Oct/2015:09:34:59 -0500] "POST /api/tools HTTP/1.1" 200 - 
"http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac 
OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0"
206.124.61.6 - - [02/Oct/2015:09:35:02 -0500] "GET 
/api/histories/1fad1eaf5f4f1766/contents HTTP/1.1" 200 - 
"http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac 
OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0"
galaxy.jobs DEBUG 2015-10-02 09:35:02,676 (101) Working directory for job is: 
/share/apps/galaxy/database/job_working_directory/000/101
galaxy.jobs.handler DEBUG 2015-10-02 09:35:02,682 (101) Dispatching to drmaa 
runner
galaxy.jobs DEBUG 2015-10-02 09:35:02,894 (101) Persisting job destination 
(destination id: sge_default)
galaxy.jobs.runners DEBUG 2015-10-02 09:35:02,903 Job [101] queued (220.456 ms)
galaxy.jobs.handler INFO 2015-10-02 09:35:02,958 (101) Job dispatched
galaxy.jobs.command_factory INFO 2015-10-02 09:35:03,821 Built script 
[/share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh] for 
tool 
command[/share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh]
galaxy.jobs.runners DEBUG 2015-10-02 09:35:04,010 (101) command is: 
/share/apps/galaxy/database/job_working_directory/000/101/tool_script.sh; 
return_code=$?; python 
"/share/apps/galaxy/database/job_working_directory/000/101/set_metadata_QaaegG.py"
 "/share/apps/galaxy/database/tmp/tmpglze54" 
"/share/apps/galaxy/database/job_working_directory/000/101/galaxy.json" 
"/share/apps/galaxy/database/job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_71_7DAllZ,/share/apps/galaxy/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetAssociation_71_YiPkTL,/share/apps/galaxy/database/job_working_directory/000/101/metadata_out_HistoryDatasetAssociation_71_JbkolS,/share/apps/galaxy/database/job_working_directory/000/101/metadata_results_HistoryDatasetAssociation_71_d93tKG,/share/apps/galaxy/database/job_working_directory/000/101/galaxy_dataset_71.dat,/share/apps/galaxy/database/job_working_directory/000/101/metadata_override_HistoryDatasetAssociation_71_ih81Fj"
 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,074 (101) submitting file 
/share/apps/galaxy/database/job_working_directory/000/101/galaxy_101.sh
galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,075 (101) native 
specification is: -q galaxy.q -V
galaxy.jobs DEBUG 2015-10-02 09:35:04,075 (101) Changing ownership of working 
directory with: /usr/bin/sudo -E 
/share/apps/galaxy/scripts/external_chown_script.py 
/share/apps/galaxy/database/job_working_directory/000/101 rpolich 507
galaxy.jobs ERROR 2015-10-02 09:35:04,102 (101) Failed to change ownership of 
/share/apps/galaxy/database/job_working_directory/000/101, making 
world-writable instead
Traceback (most recent call last):
  File "/share/apps/galaxy/lib/galaxy/jobs/__init__.py", line 1649, in 
change_ownership_for_run
    self._change_ownership( self.user_system_pwent[0], str( 
self.user_system_pwent[3] ) )
  File "/share/apps/galaxy/lib/galaxy/jobs/__init__.py", line 1643, in 
_change_ownership
    assert p.returncode == 0
AssertionError
galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,102 (101) submitting with 
credentials: rpolich [uid: 1006]
galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:04,104 (101) Job script for 
external submission is: /share/apps/galaxy/database/gridengine/101.jt_json
galaxy.jobs.runners.drmaa INFO 2015-10-02 09:35:04,104 Running command 
['/usr/bin/sudo', '-E', '/share/apps/galaxy/scripts/drmaa_external_runner.py', 
'1006', '/share/apps/galaxy/database/gridengine/101.jt_json']
galaxy.jobs.runners.drmaa INFO 2015-10-02 09:35:04,308 (101) queued as 239
galaxy.jobs DEBUG 2015-10-02 09:35:04,375 (101) Persisting job destination 
(destination id: sge_default)
galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:05,462 (101/239) state change: 
job is queued and active
206.124.61.6 - - [02/Oct/2015:09:35:06 -0500] "GET 
/api/histories/1fad1eaf5f4f1766/contents HTTP/1.1" 200 - 
"http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac 
OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0"
206.124.61.6 - - [02/Oct/2015:09:35:10 -0500] "GET 
/api/histories/1fad1eaf5f4f1766/contents HTTP/1.1" 200 - 
"http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac 
OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0"
206.124.61.6 - - [02/Oct/2015:09:35:14 -0500] "GET 
/api/histories/1fad1eaf5f4f1766/contents HTTP/1.1" 200 - 
"http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac 
OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0"
galaxy.jobs.runners.drmaa DEBUG 2015-10-02 09:35:17,626 (101/239) state change: 
job is running
206.124.61.6 - - [02/Oct/2015:09:35:18 -0500] "GET 
/api/histories/1fad1eaf5f4f1766/contents HTTP/1.1" 200 - 
"http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac 
OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0"
galaxy.jobs.runners.drmaa INFO 2015-10-02 09:35:22,084 (101/239) job left DRM 
queue with following message: code 18: The job specified by the 'jobid' does 
not exist.
galaxy.jobs DEBUG 2015-10-02 09:35:22,212 (101) Changing ownership of working 
directory with: /usr/bin/sudo -E 
/share/apps/galaxy/scripts/external_chown_script.py 
/share/apps/galaxy/database/job_working_directory/000/101 galaxy 507
galaxy.jobs.runners ERROR 2015-10-02 09:35:22,240 (unknown) Unhandled exception 
calling finish_job
Traceback (most recent call last):
  File "/share/apps/galaxy/lib/galaxy/jobs/runners/__init__.py", line 100, in 
run_next
    method(arg)
  File "/share/apps/galaxy/lib/galaxy/jobs/runners/__init__.py", line 554, in 
finish_job
    job_state.job_wrapper.reclaim_ownership()
  File "/share/apps/galaxy/lib/galaxy/jobs/__init__.py", line 1657, in 
reclaim_ownership
    self._change_ownership( self.galaxy_system_pwent[0], str( 
self.galaxy_system_pwent[3] ) )
  File "/share/apps/galaxy/lib/galaxy/jobs/__init__.py", line 1643, in 
_change_ownership
    assert p.returncode == 0
AssertionError
206.124.61.6 - - [02/Oct/2015:09:35:22 -0500] "GET 
/api/histories/1fad1eaf5f4f1766/contents HTTP/1.1" 200 - 
"http://galaxy.txbiomedgenetics.org:8080/"; "Mozilla/5.0 (Macintosh; Intel Mac 
OS X 10.9; rv:40.0) Gecko/20100101 Firefox/40.0"

My job_conf.xml below….

<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is 
configured by default (if there is no explicit config). -->
<job_conf>
    <plugins>
        <plugin id="drmaa" type="runner" 
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
        <plugin id="local" type="runner" 
load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
    </plugins>
    <handlers>
        <handler id="main"/>
    </handlers>
    <destinations default="sge_default">
        <!--destination id="big_jobs" runner="drmaa">
            <param id="nativeSpecification">-P bignodes -R y -pe threads 
8</param>
        </destination-->
        <destination id="sge_default" runner="drmaa">
            <param id="nativeSpecification">-q galaxy.q -V</param>
        </destination>
        <destination id="local" runner="local"/>
    </destinations>
</job_conf>


Output from qacct -j

qname        galaxy.q
hostname     compute-1-1703.local
group        galaxy
owner        rpolich
project      NONE
department   defaultdepartment
jobname      g101_upload1_rpolich_txbiomed_org
jobnumber    239
taskid       undefined
account      sge
priority     0
qsub_time    Fri Oct  2 09:35:04 2015
start_time   Fri Oct  2 09:35:17 2015
end_time     Fri Oct  2 09:35:21 2015
granted_pe   NONE
slots        1
failed       0
exit_status  0
ru_wallclock 4
ru_utime     1.975
ru_stime     0.494
ru_maxrss    37792
ru_ixrss     0
ru_ismrss    0
ru_idrss     0
ru_isrss     0
ru_minflt    63746
ru_majflt    7
ru_nswap     0
ru_inblock   26720
ru_oublock   152
ru_msgsnd    0
ru_msgrcv    0
ru_nsignals  0
ru_nvcsw     6188
ru_nivcsw    522
cpu          2.469
mem          0.372
io           0.225
iow          0.000
maxvmem      463.258M
arid         undefined

Thank you,

Richard Polich
Systems Administrator
Department of Genetics
Texas Biomedical Research Institute
7620 NW Loop 410, San Antonio, TX 78227-5301
Phone:(210)258-9727
Email: rpol...@txbiomed.org<mailto:rpol...@txbiomed.org>

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