Hi John and Marius, So, I am assuming I have some problem with my slurm configuration, does
that sounds accurate?
Maybe it would help to see that. I have a couple of complicated experiences with slurm config but up to now it is with Ubuntu 16.04 Xenial Best - Chris Christophe Antoniewski ARTbio <http://artbio.fr/> - Tel +33 1 44 2*7 70 05* Drosophila Genetics & Epigenetics <http://drosophile.org/> - Tel +33 1 44 2 *7 34 39*Mobile +33 6 68 60 51 50 https://twitter.com/ARTbio_IBPS https://twitter.com/drosofff 2017-11-07 21:09 GMT+01:00 John Letaw <letaw@ohsu.edu>:
Hi Marius.
Ok, this was pretty much how I read the code as well. My first instinct was to do exactly as you suggested, and add that declaration in group_vars/all. This does stop the error, but then I just get stuck with jobs that never run. So, I am assuming I have some problem with my slurm configuration, does that sounds accurate?
Thanks,
John
*From: *galaxy-dev <galaxy-dev-bounces@lists.galaxyproject.org> on behalf of Marius van den Beek <m.vandenbeek@gmail.com> *Date: *Tuesday, November 7, 2017 at 10:06 AM *To: *Christophe Antoniewski <drosofff@gmail.com> *Cc: *galaxy-dev <galaxy-dev@lists.galaxyproject.org> *Subject: *Re: [galaxy-dev] Fwd: Job Script Integrity with GalaxyKickStart (galaxy-dev Digest, Vol 137, Issue 5)
Hi John and Christophe,
What the job script integrity script does is checking that the script is ready to be executed, by setting the environment variable `ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ` to 1 and then executing the tool_script.sh script that contains the following check:
``` if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then exit 42 fi
```
So if the script is ready to execute it returns with the exit code 42. Now this can take a few seconds over NFS (I guess that'd be true for lustre as well). This check is being run 35 times with a sleep of .25 seconds.
Unfortunately there was a bug in galaxy that would skip the sleep, so the job integrity check would fail frequently. We fixed this in https://github.com/galaxyproject/galaxy/pull/4720 and this has been backported up to galaxy release 16.07, so if you just get to the latest galaxy commit on your branch it *may* work again.
Now this has been broken for a long time, and it has never worked for me on our current cluster. Should an update to galaxy not be enough,
you can disable this check with `check_job_script_integrity = False` in the galaxy.ini or by adding
`-e GALAXY_CONFIG_CHECK_JOB_SCRIPT_INTEGRITY=False` if you're running kickstart in docker.
I have not seen any drawback of disabling the integrity check on our cluster.
Good luck, Marius
On 7 November 2017 at 18:25, Christophe Antoniewski <drosofff@gmail.com> wrote:
Hi John,
Can you also raise an issue in https://github.com/ARTbio/ GalaxyKickStart/issues ?
In order to help, I will need to know the configuration of your GalaxyKickStart (the variables you modified in the playbook, group_vars and inventory_files).
Did you use the cloud_setup role ? In that case Enis Afgan https://github.com/afgane may help.
Best regards
Chris
Christophe Antoniewski
Institut de Biologie Paris Seine <http://www.ibps.upmc.fr/en> 9, Quai St Bernard <https://maps.google.com/?q=9,+Quai+St+Bernard&entry=gmail&source=g>, Boîte courrier 24 75252 Paris Cedex 05 ARTbio <http://artbio.fr/> Bâtiment B, 7e étage, porte 725
Tel +33 1 44 2 *7 70 05 *Mobile +33 6 68 60 51 50 <06%2068%2060%2051%2050>
Pour accéder à la Plateforme Bâtiment B, 7e étage, Porte 725 <https://www.google.com/maps/d/u/0/edit?mid=zmZz-3Vin5D0.kjRSV6vitXE8>
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2017-11-07 18:00 GMT+01:00 <galaxy-dev-request@lists.galaxyproject.org>:
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Today's Topics:
1. Job Script Integrity (John Letaw)
----------------------------------------------------------------------
Message: 1 Date: Tue, 7 Nov 2017 03:20:49 +0000 From: "John Letaw" <letaw@ohsu.edu> To: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Subject: [galaxy-dev] Job Script Integrity Message-ID: <FBF795C3-8F01-47EF-8033-F14DD8694328@ohsu.edu> Content-Type: text/plain; charset="utf-8"
Hi all,
I’m installing via GalaxyKickStart…
I’m getting the following error:
galaxy.jobs.runners ERROR 2017-11-06 19:14:05,263 (19) Failure preparing job Traceback (most recent call last): File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/ galaxy/jobs/runners/__init__.py", line 175, in prepare_job modify_command_for_container=modify_command_for_container File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/ galaxy/jobs/runners/__init__.py", line 209, in build_command_line container=container File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/ galaxy/jobs/command_factory.py", line 84, in build_command externalized_commands = __externalize_commands(job_wrapper, external_command_shell, commands_builder, remote_command_params) File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/ galaxy/jobs/command_factory.py", line 143, in __externalize_commands write_script(local_container_script, script_contents, config) File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/ galaxy/jobs/runners/util/job_script/__init__.py", line 112, in write_script _handle_script_integrity(path, config) File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/ galaxy/jobs/runners/util/job_script/__init__.py", line 147, in _handle_script_integrity raise Exception("Failed to write job script, could not verify job script integrity.") Exception: Failed to write job script, could not verify job script integrity. galaxy.model.metadata DEBUG 2017-11-06 19:14:05,541 Cleaning up external metadata files galaxy.model.metadata DEBUG 2017-11-06 19:14:05,576 Failed to cleanup MetadataTempFile temp files from /home/exacloud/lustre1/ galaxydev/galaxyuser/database/jobs/000/19/metadata_out_ HistoryDatasetAssociation_16_I8bhLX: No JSON object could be decoded
I would like to further understand what it means to not verify integrity of a job script. Does this just mean there is a permissions error? Ownership doesn’t match up?
Thanks, John