December 2019 - galaxy-dev - lists.galaxyproject.org

Errors running jobs in Galaxy 16.01 with slurm-drmaa 1.1.0
by Philip Blood 29 Jan '20

29 Jan '20

Hi Folks, I'm trying to get an old instance of Galaxy (16.01) working for a user who needs to use it this week for a class he is teaching (so upgrading Galaxy is not an option at the moment). Due to a recent slurm upgrade on our compute system to slurm 18.08.8, we had to replace the old slurm-drmaa 1.0.7 library <http://apps.man.poznan.pl/trac/slurm-drmaa>, which doesn't work with with 18.08.8, with Nate's forked slurm-drmaa library version 1.1.0 <https://github.com/natefoo/slurm-drmaa>. That built fine with slurm 18.08.8 and (I think) we updated all the relevant pointers in the galaxy config to point to the new slurm-drmaa 1.1.0 library. However, now when I try to run jobs on our system I get errors (it worked fine before with slurm-drmaa 1.0.7 and the older version of slurm). So, I wanted to get a quick sanity check on whether this might be an issue with trying to use the new slurm-drmaa with an old version of Galaxy, 16.01, or if anyone has any other quick thoughts on troubleshooting this. The errors I get are below. Best, Phil *Short version (just the errors):* 198.91.54.159 - - [31/Aug/2019:16:31:28 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:30,366 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (2): No such file or directory* 198.91.54.159 - - [31/Aug/2019:16:31:32 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:35,372 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:37 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:40,377 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:41 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:45 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:45,383 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:49 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:50,388 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:53 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa ERROR 2019-08-31 16:31:55,393 (10) All attempts to submit job failed * *Full context:* 198.91.54.159 - - [31/Aug/2019:16:30:27 +0000] "GET /api/tools/squeue/build HTTP/1.1" 200 - "https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" galaxy.tools DEBUG 2019-08-31 16:30:30,142 Validated and populated state for tool request (4.081 ms) galaxy.tools.actions INFO 2019-08-31 16:30:30,285 Handled output (100.616 ms) galaxy.tools.actions INFO 2019-08-31 16:30:30,319 Verified access to datasets (0.005 ms) galaxy.tools.execute DEBUG 2019-08-31 16:30:30,368 Tool [squeue] created job [10] (206.086 ms) galaxy.tools.execute DEBUG 2019-08-31 16:30:30,376 Executed all jobs for tool request: (233.862 ms) 198.91.54.159 - - [31/Aug/2019:16:30:30 +0000] "POST /api/tools HTTP/1.1" 200 - "https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:30 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" galaxy.jobs DEBUG 2019-08-31 16:30:30,747 (10) Working directory for job is: /opt/packages/galaxy/galaxy01/database/job_working_directory/000/10 galaxy.jobs.handler DEBUG 2019-08-31 16:30:30,751 (10) Dispatching to slurm runner galaxy.jobs DEBUG 2019-08-31 16:30:30,774 (10) Persisting job destination (destination id: LM4) galaxy.jobs.runners DEBUG 2019-08-31 16:30:30,790 Job [10] queued (38.578 ms) galaxy.jobs.handler INFO 2019-08-31 16:30:30,818 (10) Job dispatched galaxy.tools.deps DEBUG 2019-08-31 16:30:31,012 Building dependency shell command for dependency 'slurm' galaxy.tools.deps DEBUG 2019-08-31 16:30:31,013 Find dependency slurm version None galaxy.tools.deps DEBUG 2019-08-31 16:30:31,013 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x1b38390> (isnull? True) galaxy.tools.deps DEBUG 2019-08-31 16:30:31,014 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7fc78c334750> (isnull? False) galaxy.jobs.command_factory INFO 2019-08-31 16:30:31,057 Built script [/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/tool_script.sh] for tool command[PACKAGE_BASE=/opt/packages/galaxy/galaxy01/tool_dependencies/slurm/18.08.8; export PACKAGE_BASE; . /opt/packages/galaxy/galaxy0 1/tool_dependencies/slurm/18.08.8/env.sh; echo "hostname:" > output; echo " " >> output; hostname >> output; echo " " >> output; env >> output; echo " " >> output; date >> output; echo " " >> output; echo "Uptime:" >> output; echo " " >> output; uptime >> output; echo " " >> output; echo "Module s:" >> output; echo " " >> output; module avail >> output 2>&1; echo " " >> output; echo "SLURM Queue Status" >> output; echo " " >> output; echo "If your job is running on the queues, it will be listed in the reports below:" >> output; echo " " >> output; echo " " >> output; echo "Normal Report: s queue" >> output; echo " " >> output; echo " " >> output; echo " " >> output; squeue >> output; date >> output; echo " " >> output; echo " " >> output; echo "*** Full Report: squeue -l ***" >> output; echo " " >> output; squeue -l >> output; echo " " >> output; echo " " >> output; date >> output; echo " " >> output; echo "Local: ${LOCAL}" >> output; echo "Ramdisk: ${RAMDISK}" >> output; workdir=`pwd`; echo "workdir is $workdir" >> output; cd $LOCAL; echo "i am in `pwd`" >> $workdir/output; cd $workdir; echo "i am in `pwd`" >> output; date >> output; echo " " >> output] galaxy.tools.deps DEBUG 2019-08-31 16:30:31,259 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2019-08-31 16:30:31,259 Find dependency samtools version None galaxy.tools.deps DEBUG 2019-08-31 16:30:31,259 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x1b38390> (isnull? True) galaxy.tools.deps DEBUG 2019-08-31 16:30:31,279 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7fc7b01e01d0> (isnull? False) galaxy.jobs.runners DEBUG 2019-08-31 16:30:31,284 (10) command is: /opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/tool_script.sh; return_code=$?; if [ -f /opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/output ] ; then cp /opt/packages/galaxy/galaxy01/databas e/job_working_directory/000/10/output /opt/packages/galaxy/galaxy01/database/files/000/dataset_10.dat ; fi; PACKAGE_BASE=/opt/packages/galaxy/galaxy01/tool_dependencies/samtools/0.1.19; export PACKAGE_BASE; . /opt/packages/galaxy/galaxy01/tool_dependencies/samtools/0.1.19/env.sh; python "/opt/packa ges/galaxy/galaxy01/database/job_working_directory/000/10/set_metadata_jGYkkM.py" "/opt/packages/galaxy/galaxy01/tmp/tmpxmB5GA" "/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/galaxy.json" "/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_in_HistoryD atasetAssociation_10_u2k7qq,/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_kwds_HistoryDatasetAssociation_10_2ZmSXR,/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_out_HistoryDatasetAssociation_10_shC78c,/opt/packages/galaxy/galaxy01/databa se/job_working_directory/000/10/metadata_results_HistoryDatasetAssociation_10_57x96D,/opt/packages/galaxy/galaxy01/database/files/000/dataset_10.dat,/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_override_HistoryDatasetAssociation_10_AEeOfc" 5242880; sh -c "exit $retur n_code" galaxy.jobs.runners.drmaa DEBUG 2019-08-31 16:30:31,356 (10) submitting file /opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/galaxy_10.sh galaxy.jobs.runners.drmaa DEBUG 2019-08-31 16:30:31,356 (10) native specification is: -p LM -C LM -N 1 -n 4 --ntasks-per-node=4 --mem=192500 -t 24:00:00 198.91.54.159 - - [31/Aug/2019:16:30:34 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:38 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:42 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:47 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:51 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:55 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:30:59 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:03 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:08 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:12 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:16 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:20 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:24 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:28 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:30,366 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (2): No such file or directory* 198.91.54.159 - - [31/Aug/2019:16:31:32 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:35,372 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:37 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:40,377 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:41 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" 198.91.54.159 - - [31/Aug/2019:16:31:45 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:45,383 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:49 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:50,388 (10) drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job error (0): No error* 198.91.54.159 - - [31/Aug/2019:16:31:53 +0000] "GET /api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - " https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0" *galaxy.jobs.runners.drmaa ERROR 2019-08-31 16:31:55,393 (10) All attempts to submit job failed *

3 4

BCC2020 and Galaxy Admin Training
by Dave Clements 19 Dec '19

19 Dec '19

Hello all, There are three things going on that are of general interest to the Galaxy and GMOD communities, and that have some urgency to them (and thus this mid-month email). BCC2020 Schedule Structure ----------------------- The Bioinformatics Community Conference (BCC2020, https://bcc2020.github.io/) will be held in July, in Toronto, right after ISMB in Montréal. This event brings together the BOSC and Galaxy communities into one gathering. If you are considering attending BCC2020, then the organizers would like your input on several scheduling choices, BY JANUARY 7: https://bcc2020.github.io/blog/poll BCC2020 Training Topic Nominations ------------------------ The training offered at BCC2020 is determined by the community. We are now accepting nominations for training sessions. Nominated topics will be voted on by the community. Please submit your ideas by JANUARY 17. https://bcc2020.github.io/blog/training-nom 2020 Galaxy Admin Training ----------------------- A week long workshop on setting up your own production-grade Galaxy instance will be held in Barcelona the first week of March. Registration is now open, and is, well, pretty darn cheap too. https://galaxyproject.org/events/2020-03-admin/ And, of course, there is a lot of other stuff going on too: https://galaxyproject.org/events/ Happy Holidays, and hope to see you in the new year! Dave C, on behalf of the BCC2020 and Galaxy Admin Training organizers -- https://galaxyproject.org/

1 0

December Galaxy News
by Dave Clements 09 Dec '19

09 Dec '19

Hello all, The December 2019 Galactic News is out! https://galaxyproject.org/news/2019-12-galaxy-update/ - 12 Upcoming Events - India, PAG, HTS, single cell/microbiome, Barcelona, and more - 191 new publications - Two new blog posts - g:Profiler, GalaxyP - Galaxy Platform News - Systems biology, Laniakea, OpenRefine, ... - Training material and doc updates - defining data types, citing GTN, Windows, account help, metatranscriptomics, Galaxy for everyone - Openings - with 5 organizations in Denmark, France, US, US, Germany - Releases - Galaxy 19.09 is out - And other news too Thanks for a superb year, and we are looking forward to an even better 2020. Dave C, on behalf of everyone -- https://galaxyproject.org/

1 0