I'm working on the Slurm integration in our Toil workflow runner project. I'm having a problem where an `sbatch` command to submit a job to Slurm can fail (with exit code 1 and message "sbatch: error: Batch job submission failed: Socket timed out on send/recv operation", in my case, but possibly in other ways), but the job can still actually have been submitted, and can still execute.
This causes a problem for Toil because right now, when it sees a submission attempt fail, it backs off and submits the job again a little later. But Toil can't handle multiple copies of the same job running at once, and if a submission appears to the client to have failed but actually succeeded, it's possible to get into that situation if you just submit again.
When an sbatch command fails, is it possible to detect cases where the cluster will still execute the job? (For example, is it guaranteed that the job ID will be available on standard output on the client if the job is going to execute on the cluster, no matter when in the client process it might get a socket disconnection, allowing the job to be inquired about later?) Do I maybe need to tag my jobs with unique identifiers myself so I can poll for them in the queue after a supposedly-failed submission?
Is it possible to write an idempotent sbatch command, where it can be run any number of times but will only actually submit one copy of the job?
Is the Slurm REST API somehow more transactional, or able to promise somehow that a job will not actually go into the queue without the client having acknowledged receipt of the job's assigned ID?
Thanks, -Adam
On 2026/02/18 01:56, Adam Novak via slurm-users wrote:
... Toil can't handle multiple copies of the same job running at once ... Is it possible to write an idempotent sbatch command, where it can be run any number of times but will only actually submit one copy of the job?
Could you not make use of the
--dependency=singleton
constraint, to achieve something close to what your meta-scheduler needs?
From the sbatch manpage:
singleton This job can begin execution after any previously launched jobs sharing the same job name and user have terminated. In other words, only one job by that name and owned by that user can be running or suspended at any point in time. In a federation, a singleton dependency must be fulfilled on all clusters unless DependencyParameters=disable_remote_singleton is used in slurm.conf.
You would still need to catch any queued dupe(s) that your meta-scheduler created but there wouldn't be two running at once.
That could probably help; I'd still want to make the job names unique to prevent multiple workflows under one user from delaying each other, but I'd be able to have something much closer to correct without a lot of second-guessing the submission return code.
On Tue, Feb 17, 2026 at 9:12 PM Kevin Buckley via slurm-users < slurm-users@lists.schedmd.com> wrote:
On 2026/02/18 01:56, Adam Novak via slurm-users wrote:
... Toil can't handle multiple copies of the same job running at once ... Is it possible to write an idempotent sbatch command, where it can be run any number of times but will only actually submit one copy of the job?
Could you not make use of the
--dependency=singleton
constraint, to achieve something close to what your meta-scheduler needs?
From the sbatch manpage:
singleton This job can begin execution after any previously launched jobssharing the same job name and user have terminated. In other words, only one job by that name and owned by that user can be running or suspended at any point in time. In a federation, a singleton dependency must be fulfilled on all clusters unless DependencyParameters=disable_remote_singleton is used in slurm.conf.
You would still need to catch any queued dupe(s) that your meta-scheduler created but there wouldn't be two running at once.
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Another option, probably better, would be to use WCKeys. See for example how https://github.com/WFU-HPC/OOD-MultitenantApps solved a very similar problem exploiting WCKeys (and other things)
On Wed, Feb 18, 2026 at 9:08 AM Adam Novak via slurm-users < slurm-users@lists.schedmd.com> wrote:
That could probably help; I'd still want to make the job names unique to prevent multiple workflows under one user from delaying each other, but I'd be able to have something much closer to correct without a lot of second-guessing the submission return code.
On Tue, Feb 17, 2026 at 9:12 PM Kevin Buckley via slurm-users < slurm-users@lists.schedmd.com> wrote:
On 2026/02/18 01:56, Adam Novak via slurm-users wrote:
... Toil can't handle multiple copies of the same job running at once ... Is it possible to write an idempotent sbatch command, where it can be
run
any number of times but will only actually submit one copy of the job?
Could you not make use of the
--dependency=singleton
constraint, to achieve something close to what your meta-scheduler needs?
From the sbatch manpage:
singleton This job can begin execution after any previously launched jobssharing the same job name and user have terminated. In other words, only one job by that name and owned by that user can be running or suspended at any point in time. In a federation, a singleton dependency must be fulfilled on all clusters unless DependencyParameters=disable_remote_singleton is used in slurm.conf.
You would still need to catch any queued dupe(s) that your meta-scheduler created but there wouldn't be two running at once.
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-- Adam Novak (He/Him) Senior Software Engineer Computational Genomics Lab UC Santa Cruz Genomics Institute "Revealing life’s code."
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