Hi Chris, Thanks for looking at this. We have spun up an Ubunutu 14.04 VM for this purpose, and have a lustre filesystem mounted for persistent data. Our SLURM cluster is already in place, so I have removed from the playbook most of what occurs in the galaxy-extras slurm task. I believe the only thing left are a couple of steps at the bottom of the task that deal with creating a job_conf.xml file. I have also changed things like the galaxy_user_name, gid, uid, galaxy_loc (on lustre), etc. The playbook does run to completion, and without error. We have confirmed that the ‘galaxyuser’ user can submit jobs to the scheduler, though haven’t had any luck getting this to work from the Galaxy instance.
I’m happy to give you any details you need, I feel like I am so close to getting this working… Thanks, John From: galaxy-dev <[email protected]> on behalf of Christophe Antoniewski <[email protected]> Date: Tuesday, November 7, 2017 at 9:25 AM To: "[email protected]" <[email protected]> Subject: [galaxy-dev] Fwd: Job Script Integrity with GalaxyKickStart (galaxy-dev Digest, Vol 137, Issue 5) 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 <[email protected]<mailto:[email protected]>>: Send galaxy-dev mailing list submissions to [email protected]<mailto:[email protected]> 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 [email protected]<mailto:[email protected]> You can reach the person managing the list at [email protected]<mailto:[email protected]> When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." 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Job Script Integrity (John Letaw) ---------------------------------------------------------------------- Message: 1 Date: Tue, 7 Nov 2017 03:20:49 +0000 From: "John Letaw" <[email protected]<mailto:[email protected]>> To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [galaxy-dev] Job Script Integrity Message-ID: <[email protected]<mailto:[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/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... 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