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> 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 > > > ___________________________________________________________ > 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: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: http://galaxyproject.org/search/mailinglists/
