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 <[email protected]>
wrote:
> Hi John,
>
> Can you also raise an issue in https://github.com/ARTbio/G
> alaxyKickStart/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 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>
>
>
> https://twitter.com/ARTbio_IBPS
>
>
> 2017-11-07 18:00 GMT+01:00 <[email protected]>:
>
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>> 1. Job Script Integrity (John Letaw)
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>> ----------------------------------------------------------------------
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>> Message: 1
>> Date: Tue, 7 Nov 2017 03:20:49 +0000
>> From: "John Letaw" <[email protected]>
>> To: "[email protected]"
>> <[email protected]>
>> Subject: [galaxy-dev] Job Script Integrity
>> Message-ID: <[email protected]>
>> 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/galaxyd
>> ev/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
>>
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