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 - Tel +33 1 44 27 70 05
Drosophila Genetics & Epigenetics - Tel +33 1 44 27 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
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05
ARTbio Bâtiment B, 7e étage, porte 725 

Tel +33 1 44 27 70 05
Mobile +33 6 68 60 51 50

Pour accéder à la Plateforme
Bâtiment B, 7e étage, Porte 725

mage removed by sender.

https://twitter.com/ARTbio_IBPS

 

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

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