Hi Eric, Here we use both solutions: Galaxy and RocksCluster. In Galaxy, you have to define your jobs in "config/job_conf.xml" and you should probably source a file (search for "environment" in your galaxy.ini) before the submit process. In fact, you could have to set a DRMAA_LIBRARY_PATH to load your drmaa library; see https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#DRMAA
Best, Remy 2016-01-19 20:28 GMT+01:00 Eric Shell <esh...@soe.ucsc.edu>: > 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! > > -- > Eric Shell > UNIX Software & Google Apps Administrator > Baskin School of Engineering > UC Santa Cruz > 831 459 4919 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. 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