Errors running jobs in Galaxy 16.01 with slurm-drmaa 1.1.0
by Philip Blood
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 *
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Hello and to whom it may concern.
As I point out in the matter, I am having trouble uploading information, particularly a BIOPROJECT that has already uploaded.
I am taking exactly the same steps that I previously used to load this database. I don't understand if Galaxy is not working properly today or what it can be.
I am loading it from: Download from web or upload from disk / Upload data as: Collection (s) / Load tabular data from: (pasted table).
Thank you in advance and sorry for the inconvenience
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Becario Doctoral
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?Hello,
Please could you help me to run this wrapper : RNA STAR Gapped-read mapper for RNA-seq data (Galaxy Version 2.7.2b)
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terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::at
/galaxydata/galaxy-prod/my_job_working_directory/000/282/282124/tool_script.sh: line 9: 48744 Aborted (core dumped) STAR --runThreadN ${GALAXY_SLOTS:-4}...
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Dear Community,
The Galaxy Committers team is pleased to announce the release of Galaxy 19.09.
The release announcement for developers and admins can be found at
https://docs.galaxyproject.org/en/master/releases/19.09_announce.html
and user facing release notes are at
https://docs.galaxyproject.org/en/master/releases/19.09_announce_user.html.
A few release highlights are:
Interactive Tools
----------------------
A new type of Galaxy tool has been implemented that allows interactive
experiences like Galaxy Interactive Environments (via a proxy and
Docker containers) but using plugins defined with Galaxy’s XML tool
syntax.
Workflow Invocation Reports
---------------------------
Workflows may now define Markdown templates with Galaxy-specific
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New Toolshed Client Interface
-----------------------------
This project drove numerous enhancements to the Tool Shed API,
including vastly improved search functionality. This interface has
been completely re-imagined and feels much more interactive.
Check out the release notes for a lot more details - there are many
more enhancements such as new interface elements, visualizations,
datatypes, and more. There are also important notes for Galaxy
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As announced last month, there will be a GMOD codefest held before the
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Several potential projects are described in this document:
https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-Vg...
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See you in San Diego!
Scott
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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Deleted Galaxy Account
by Horstmann, Cullen M
Good evening,
Upon trying to log onto my galaxy profile I received this message: "This account has been marked deleted, contact your local Galaxy administrator to restore the account." I was hoping I could re-gain access to this account because I have a lot of differential gene expression data on my account. Please let me know what I need to do to re-gain access at your earliest convenience.
Kind Regards,
Cullen Horstmann
Missouri State University
Master's in Biology
Graduate Researcher | Kim Lab
Teaching Assistant | Biology Department
4 months, 2 weeks
