[slurm-users] Naive SLURM question: equivalent to LSF pre-exec
Cutts, Tim via slurm-users
Hi, I apologise if I’ve failed to find this in the documentation (and am happy to be told to RTFM) but a recent issue for one of my users resulted in a question I couldn’t answer.
LSF has a feature called a Pre-Exec where a script executes to check whether a node is ready to run a task. So, you can run arbitrary checks and go back to the queue if they fail.
For example, if I have some automounted filesystems, and I want to be able to check for failure of the automounted, in an LSF world, I can do:
bsub -E “test -f /nfs/someplace/file_I_know_exists” my_job.sh
What’s the equivalent in SLURM?
Thanks,
Tim
--
Tim Cutts
Scientific Computing Platform Lead
AstraZeneca
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Paul Edmon via slurm-users
You probably want the Prolog option: https://slurm.schedmd.com/slurm.conf.html#OPT_Prolog along with: https://slurm.schedmd.com/slurm.conf.html#OPT_ForceRequeueOnFail
-Paul Edmon-
Paul Raines via slurm-users
The Prolog will run with every job, not just "as asked for" by the user.
Also it runs as the root or slurm user, not the user who submitted.
For that one would use TaskProlog but at that point there is no
way to abort or requeue the job I think from TaskProlog
The Prolog script could check for environment var set by user
such as SLURM_USER_PROLOG that it will 'su' run as the submitting
user if it exists. Then if it returns a non-zero return value,
exit and return that value. Even with 'su' there are security
issues one has to think through here.
The requeing thing is a bit tricky. I would not necessarily
set ForceRequeueOnFail as some Prolog scripts probably really
want some jobs just cancelled. Also Prolog will put the node
in a drain state which is not necessarily what an admin wants
when a user's prolog script fails.
Not sure there is any good way to do this with safe requeing.
-- Paul Raines (http://help.nmr.mgh.harvard.edu)
On Wed, 14 Feb 2024 9:32am, Paul Edmon via slurm-users wrote:
> External Email - Use Caution
>
> You probably want the Prolog option:
> https://secure-web.cisco.com/1gA_zj13OnVqs4BaLrstiwdHEvx0FITE_aDl92-7hACgRFo_Ph48JPmpZ9c5eUdI5r38RRv4LyHRZxUazGd8Y_CxRcSjCSPq4HCIQJcE60NasvEWY9i9Xgqo6APDiT8QvHKHdYw50eQKRazhP2XS1g-wXOiOOw7uPptriVL5hqDIwKYoVSXAuGhHms65rMC17PKxnfoFr0MI86JHZ2ecT4U3sFwTTtV-dVm9VPNG-mQcT-61c-7jDh8mJ-iQFauaFo9p9qmU6XPonf41CieTMfOIcaTkNo9Z04YFmOY8hH-q1xTXVS-sc2AhU0kzQ5t_D/https%3A%2F%2Fslurm.schedmd.com%2Fslurm.conf.html%23OPT_Prolog
> along with:
> https://secure-web.cisco.com/1yoj7-l3lvo6_mD2LfIN7tNcHHzRekef8BenX_pB-l_Y7mzJdx9VNkuJnU8gyQGzWeU5PydyWg37_UnlJ-9STr9PxDBKHbmzaItEyH3XzeXO9cJY5-0NrAHcvRaBL76KveIqVKxkIAYjIwbmDtolahe9_FEuINl-B53wd6YYisn6loWpdYtQpL0z4Mjz4DZWuxs-GaRcoZRSUDqmseghEAlLBUJvKpdkAUBOA78xhWCIv6W7jJb75di-NmFX5h2R_GPJa9tdgTBgvdh3MS8FYTTnAH7R2hAK6X2iXoO6EsGmkWQP0l-8PCdsTreZ9bkkn/https%3A%2F%2Fslurm.schedmd.com%2Fslurm.conf.html%23OPT_ForceRequeueOnFail
>
> -Paul Edmon-
>
> On 2/14/2024 8:38 AM, Cutts, Tim via slurm-users wrote:
>>
>> Hi, I apologise if I’ve failed to find this in the documentation (and am
>> happy to be told to RTFM) but a recent issue for one of my users resulted
>> in a question I couldn’t answer.
>>
>> LSF has a feature called a Pre-Exec where a script executes to check
>> whether a node is ready to run a task. So, you can run arbitrary checks
>> and go back to the queue if they fail.
>>
>> For example, if I have some automounted filesystems, and I want to be
>> able to check for failure of the automounted, in an LSF world, I can do:
>>
>> bsub -E “test -f /nfs/someplace/file_I_know_exists” my_job.sh
>>
>> What’s the equivalent in SLURM?
>>
>> Thanks,
>>
>> Tim
>>
>> --
>>
>> *Tim Cutts*
>>
>> Scientific Computing Platform Lead
>>
>> AstraZeneca
>>
>> Find out more about R&D IT Data, Analytics & AI and how we can support
>> you by visiting ourService Catalogue
>> <https://secure-web.cisco.com/1rZFGGAYuCJMmirDSdCijgYo0A_aAByN6SOBZixUX1qDb_AQrhGzQNOOfxivOQjGgoJQ_3Eqm_BlvSd_99xvFZ3dhHGloY6L4ITdMvmqo5V3Ye9UUtqy5yyYPyNL3bZYq62Bru2u_9cx17-A7smV0ki_kxvPQzgh_zY_aVzr9oQDKFSBuIesGJY6WzLFQUWsMl8o_-8GjfGz-lOf7QVzLM8ztcMhWsdoRg3qA3rxJQKM3WO-9A9Hys1B8fjQm8Xowvab8kzZX7qb1fcySnuMAOo2Ya8A-MKnRn37j4izSFUyORtIHFCzfgpKVoGm5qGGY/https%3A%2F%2Fazcollaboration.sharepoint.com%2Fsites%2FCMU993>|
>>
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