I am trying to get a Galaxy instance running on a Rocks cluster. I am able to run jobs with the local runner at this point, but I am having an issue with the drmaa runner that I haven't been able to fix. When I submit a job in Galaxy it is successfully submitted to the cluster and runs to completion according to qacct, but Galaxy just reports "failure running job".
Here's what is written to paster.log when I submit a job:
69.181.235.240 - - [19/Jan/2016:11:24:31 -0700] "GET
/api/histories/fb86c918c0d3d33b/contents?dataset_details=bae154fe2294752e%2C6fe732485990d2ac%2C604c4e6e60e997bc%2Cf015f1cb819ec50e%2C9f6f4b3cb6cf43eb%2C3d13d598882b6eb8%2C551006fddcb290ae%2C10b9bbc646c48387%2C7670dfdf35146bc5%2Ce0ec2cf59f1fc79e%2Cee30922e5e4854db%2C9e7a0ba216194210 HTTP/1.1" 200 - "https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" 69.181.235.240 - - [19/Jan/2016:11:24:38 -0700] "GET /tool_runner/data_source_redirect?tool_id=ucsc_table_direct1 HTTP/1.1" 302
- "https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64;
x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" galaxy.tools.actions.__init__ INFO 2016-01-19 11:24:42,801 Handled output (327.778 ms) galaxy.tools.actions.__init__ INFO 2016-01-19 11:24:43,236 Verified access to datasets (0.023 ms) galaxy.tools.execute DEBUG 2016-01-19 11:24:43,343 Tool [ucsc_table_direct1] created job [7019] (919.481 ms) 69.181.235.240 - - [19/Jan/2016:11:24:42 -0700] "POST /tool_runner HTTP/1.1" 200 - "https://genome.ucsc.edu/cgi-bin/hgTables" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" galaxy.jobs DEBUG 2016-01-19 11:24:44,056 (7019) Working directory for job is: /campusdata/galaxy/galaxy/database/job_working_directory/007/7019 galaxy.jobs.handler DEBUG 2016-01-19 11:24:44,070 (7019) Dispatching to sge runner galaxy.jobs DEBUG 2016-01-19 11:24:44,378 (7019) Persisting job destination (destination id: sge_default) galaxy.jobs.runners DEBUG 2016-01-19 11:24:44,403 Job [7019] queued (332.423 ms) galaxy.jobs.handler INFO 2016-01-19 11:24:44,444 (7019) Job dispatched 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET /api/genomes HTTP/1.1" 200 - "https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET /api/datatypes?extension_only=False& HTTP/1.1" 200 - " https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET /history/current_history_json HTTP/1.1" 200 - " https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" galaxy.jobs.runners DEBUG 2016-01-19 11:24:46,399 (7019) command is: python /campusdata/galaxy/galaxy/tools/data_source/data_source.py /campusdata/galaxy/galaxy/database/files/011/dataset_11361.dat 0; return_code=$?; python "/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/set_metadata_IaPURP.py" "/campusdata/galaxy/galaxy/database/tmp/tmp9Qt0cv" "/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/galaxy.json" "/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/metadata_in_HistoryDatasetAssociation_13512_oucw5s,/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/metadata_kwds_HistoryDatasetAssociation_13512_ZrUbrF,/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/metadata_out_HistoryDatasetAssociation_13512_twCvq7,/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/metadata_results_HistoryDatasetAssociation_13512_FO1cy9,/campusdata/galaxy/galaxy/database/files/011/dataset_11361.dat,/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/metadata_override_HistoryDatasetAssociation_13512_Z_cUTF" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:46,787 (7019) submitting file /campusdata/galaxy/galaxy/database/job_working_directory/007/7019/galaxy_7019.sh galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:46,808 (7019) native specification is: -R y -pe mpi 8 -q small.q galaxy.jobs DEBUG 2016-01-19 11:24:46,828 (7019) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /campusdata/galaxy/galaxy/database/job_working_directory/007/7019 eshell 100000 galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:47,020 (7019) submitting with credentials: eshell [uid: 38559] galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:47,129 (7019) Job script for external submission is: /campusdata/galaxy/galaxy/database/pbs/7019.jt_json galaxy.jobs.runners.drmaa INFO 2016-01-19 11:24:47,130 Running command ['/usr/bin/sudo', '-E', 'scripts/drmaa_external_runner.py', '38559', '/campusdata/galaxy/galaxy/database/pbs/7019.jt_json'] galaxy.jobs.runners.drmaa INFO 2016-01-19 11:24:47,981 (7019) queued as 116563 galaxy.jobs DEBUG 2016-01-19 11:24:48,198 (7019) Persisting job destination (destination id: sge_default) galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:48,823 (7019/116563) state change: job is queued and active 69.181.235.240 - - [19/Jan/2016:11:24:45 -0700] "GET /api/histories/fb86c918c0d3d33b/contents?dataset_details=bae154fe2294752e%2C6fe732485990d2ac%2C604c4e6e60e997bc%2Cf015f1cb819ec50e%2C9f6f4b3cb6cf43eb%2C3d13d598882b6eb8%2C551006fddcb290ae%2C10b9bbc646c48387%2C7670dfdf35146bc5%2Ce0ec2cf59f1fc79e%2Cee30922e5e4854db%2C9e7a0ba216194210 HTTP/1.1" 200 - "https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:53,532 (7019/116563) state change: job is running galaxy.jobs WARNING 2016-01-19 11:24:53,922 (7019) Ignoring state change from 'error' to 'running' for job that is already terminal 69.181.235.240 - - [19/Jan/2016:11:24:54 -0700] "GET /api/histories/fb86c918c0d3d33b/contents HTTP/1.1" 200 - " https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" 69.181.235.240 - - [19/Jan/2016:11:24:55 -0700] "GET /api/histories/fb86c918c0d3d33b HTTP/1.1" 200 - " https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" galaxy.jobs.runners.drmaa INFO 2016-01-19 11:25:06,240 (7019/116563) job left DRM queue with following message: code 18: The job specified by the 'jobid' does not exist. galaxy.jobs DEBUG 2016-01-19 11:25:06,412 (7019) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /campusdata/galaxy/galaxy/database/job_working_directory/007/7019 galaxy 59997 galaxy.jobs DEBUG 2016-01-19 11:25:06,622 (7019) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /campusdata/galaxy/galaxy/database/job_working_directory/007/7019 galaxy 59997
'qacct -j -o eshell' shows that job 7019 completed, though:
qname all.q
hostname campusrocks2-0-4.local group users owner eshell project NONE department defaultdepartment jobname g7019_ucsc_table_direct1_eshell_ucsc_edu jobnumber 116563 taskid undefined account sge priority 0 qsub_time Tue Jan 19 11:24:47 2016 start_time Tue Jan 19 11:24:53 2016 end_time Tue Jan 19 11:25:05 2016 granted_pe mpi slots 8 failed 0 exit_status 0 ru_wallclock 12 ru_utime 9.285 ru_stime 0.908 ru_maxrss 98384 ru_ixrss 0 ru_ismrss 0 ru_idrss 0 ru_isrss 0 ru_minflt 81778 ru_majflt 2 ru_nswap 0 ru_inblock 6728 ru_oublock 184 ru_msgsnd 0 ru_msgrcv 0 ru_nsignals 0 ru_nvcsw 13952 ru_nivcsw 301 cpu 10.192 mem 2.326 io 0.150 iow 0.000 maxvmem 448.820M arid undefined
Why does Galaxy not see the job after it has been submitted to the cluster?
Thanks in advance for your help!