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-boun...@lists.galaxyproject.org> on behalf of
Marius van den Beek <m.vandenb...@gmail.com>
Date: Tuesday, November 7, 2017 at 10:06 AM
To: Christophe Antoniewski <droso...@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
<droso...@gmail.com<mailto:droso...@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, Boîte courrier 24
75252 Paris Cedex 05
ARTbio<http://artbio.fr/> Bâtiment B, 7e étage, porte 725
Tel +33 1 44 27 70 05
Mobile +33 6 68 60 51 50<tel: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>
[mage removed by sender.]
https://twitter.com/ARTbio_IBPS
2017-11-07 18:00 GMT+01:00
<galaxy-dev-requ...@lists.galaxyproject.org<mailto:galaxy-dev-requ...@lists.galaxyproject.org>>:
Send galaxy-dev mailing list submissions to
galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>
To subscribe or unsubscribe via the World Wide Web, visit
https://lists.galaxyproject.org/listinfo/galaxy-dev
or, via email, send a message with subject or body 'help' to
galaxy-dev-requ...@lists.galaxyproject.org<mailto:galaxy-dev-requ...@lists.galaxyproject.org>
You can reach the person managing the list at
galaxy-dev-ow...@lists.galaxyproject.org<mailto:galaxy-dev-ow...@lists.galaxyproject.org>
When replying, please edit your Subject line so it is more specific
than "Re: Contents of galaxy-dev digest..."
HEY! This is important! If you reply to a thread in a digest, please
1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the
original subject for the thread.
2. Strip out everything else in the digest that is not part of the thread you
are responding to.
Why?
1. This will keep the subject meaningful. People will have some idea from the
subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search
queries, but that aren't actually informative.
Today's Topics:
1. Job Script Integrity (John Letaw)
----------------------------------------------------------------------
Message: 1
Date: Tue, 7 Nov 2017 03:20:49 +0000
From: "John Letaw" <le...@ohsu.edu<mailto:le...@ohsu.edu>>
To:
"galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>"
<galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>>
Subject: [galaxy-dev] Job Script Integrity
Message-ID:
<fbf795c3-8f01-47ef-8033-f14dd8694...@ohsu.edu<mailto:fbf795c3-8f01-47ef-8033-f14dd8694...@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
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
<https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171107/66103ce8/attachment-0001.html>
------------------------------
Subject: Digest Footer
_______________________________________________
galaxy-dev mailing list
galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>
https://lists.galaxyproject.org/listinfo/galaxy-dev
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
------------------------------
End of galaxy-dev Digest, Vol 137, Issue 5
******************************************
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
