Hi John,

Yes, I came across a listing to enable this in /config/galaxy.ini for 
Gridengine. Peter van Heusden brought this error to my attention.  I have now 
commented this out and can now upload files.

#drmaa_external_runjob_script = 
/share/apps/galaxy/scripts/drmaa_external_runner.py
#drmaa_external_killjob_script = 
/share/apps/galaxy/scripts/drmaa_external_killer.py
#external_chown_script = /share/apps/galaxy/scripts/external_chown_script.py

Thank you very much,
Richard

On Oct 7, 2015, at 8:40 AM, John Chilton 
<jmchil...@gmail.com<mailto:jmchil...@gmail.com>> wrote:

Do you have drmaa_external_** options set in config/galaxy.ini? It
seems like maybe you do. I would try to get Galaxy working without
those first, just submitting everything as the Galaxy user.

-John

On Fri, Oct 2, 2015 at 4:05 PM, Richard Polich 
<rpol...@txbiomed.org<mailto:rpol...@txbiomed.org>> wrote:
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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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>

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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