[slurm-users] ticking time bomb? launching too many jobs in parallel

Tue Aug 27 16:38:34 UTC 2019

Hi Paul,

Your comment confirms my worst fear, that I should either implement job
arrays or stick to a sequential for loop.

My problem with job arrays is that, as far as I understand them, they
cannot be used with singleton to set a max job limit.

I use singleton to limit the number of jobs a user can be running at a
time. For example if the limit is 3 jobs per user and the user launches 10
jobs, the sbatch submissions via my scripts may look this:
sbatch --job-name=job1 [OPTIONS SET1] Dependency=singleton my.sbatch
sbatch --job-name=job2 [OTHER  SET1] Dependency=singleton my.sbatch
sbatch --job-name=job3 [OTHER SET1] Dependency=singleton my.sbatch
sbatch --job-name=job1 [OTHER SET1 Dependency=singleton my.sbatch
sbatch --job-name=job2 [OTHER  SET1 ] Dependency=singleton my.sbatch
sbatch --job-name=job3 [OTHER  SET2] Dependency=singleton my.sbatch2
sbatch --job-name=job1 [OTHER  SET2] Dependency=singleton my.sbatch2
sbatch --job-name=job2 [OTHER  SET2 ] Dependency=singleton my.sbatch2
sbatch --job-name=job2 [OTHER  SET2 ] Dependency=singleton my.sbatch2
sbatch --job-name=job1 [OTHER  SET2 ] Dependency=singleton my.sbatch 2

This way, at most 3 jobs will run at a time (ie a job with name job1, a job
with name job2, and job with name job3).

Notice that my example has two option sets provided to sbatch, so the
example would be suitable for conversion to two Job Arrays.

This is the problem I can't obercome.

In the job array documentation, I see
A maximum number of simultaneously running tasks from the job array may be
specified using a "%" separator. For example "--array=0-15%4" will limit
the number of simultaneously running tasks from this job array to 4.

But this '%' separator cannot specify a max number of tasks over two (or
more) separate job arrays, as far as I can tell.

And the job array element names cannot be made to modulo rotate in the way
they do in my above example.

Perhaps I need to play more with job arrays, and try harder to find a
solution to limit number of jobs across multiple arrays. Or ask this
question in a separate post, since it's a bit off topic.

In any case, thanks so much for answer my question. I think it answer my
original post perfectly :)

Regards,
Guillaume.

On Tue, Aug 27, 2019 at 10:08 AM Paul Edmon <pedmon at cfa.harvard.edu> wrote:

> At least for our cluster we generally recommend that if you are submitting
> large numbers of jobs you either use a job array or you just for loop over
> the jobs you want to submit.  A fork bomb is definitely not recommended.
> For highest throughput submission a job array is your best bet as in one
> submission it will generate thousands of jobs which then the scheduler can
> handle sensibly.  So I highly recommend using job arrays.
>
> -Paul Edmon-
> On 8/27/19 3:45 AM, Guillaume Perrault Archambault wrote:
>
> Hi Paul,
>
> Thanks a lot for your suggestion.
>
> The cluster I'm using has thousands of users, so I'm doubtful the admins
> will change this setting just for me. But I'll mention it to the support
> team I'm working with.
>
> I was hoping more for something that can be done on the user end.
>
> Is there some way for the user to measure whether the scheduler is in RPC
> saturation? And then if it is, I could make sure my script doesn't launch
> too many jobs in parallel.
>
> Sorry if my question is too vague, I don't understand the backend of the
> SLURM scheduler too well, so my questions are using the limited terminology
> of a user.
>
> My concern is just to make sure that my scripts don't send out more
> commands (simultaneously) than the scheduler can handle.
>
> For example, as an extreme scenario, suppose a user forks off 1000 sbatch
> commands in parallel, is that more than the scheduler can handle? As a
> user, how can I know whether it is?
>
> Regards,
> Guillaume.
>
>
>
> On Mon, Aug 26, 2019 at 10:15 AM Paul Edmon <pedmon at cfa.harvard.edu>
> wrote:
>
>> We've hit this before due to RPC saturation.  I highly recommend using
>> max_rpc_cnt and/or defer for scheduling.  That should help alleviate this
>> problem.
>>
>> -Paul Edmon-
>> On 8/26/19 2:12 AM, Guillaume Perrault Archambault wrote:
>>
>> Hello,
>>
>> I wrote a regression-testing toolkit to manage large numbers of SLURM
>> jobs and their output (the toolkit can be found here
>> <https://github.com/gobbedy/slurm_simulation_toolkit/> if anyone is
>> interested).
>>
>> To make job launching faster, sbatch commands are forked, so that
>> numerous jobs may be submitted in parallel.
>>
>> We (the cluster admin and myself) are concerned that this may cause
>> unresponsiveness for other users.
>>
>> I cannot say for sure since I don't have visibility over all users of the
>> cluster, but unresponsiveness doesn't seem to have occurred so far. That
>> being said, the fact that it hasn't occurred yet doesn't mean it won't in
>> the future. So I'm treating this as a ticking time bomb to be fixed asap.
>>
>> My questions are the following:
>> 1) Does anyone have experience with large numbers of jobs submitted in
>> parallel? What are the limits that can be hit? For example is there some
>> hard limit on how many jobs a SLURM scheduler can handle before blacking
>> out / slowing down?
>> 2) Is there a way for me to find/measure/ping this resource limit?
>> 3) How can I make sure I don't hit this resource limit?
>>
>> From what I've observed, parallel submission can improve submission time
>> by a factor at least 10x. This can make a big difference in users'
>> workflows.
>>
>> For that reason I would like to keep the option of launching jobs
>> sequentially as a last resort.
>>
>> Thanks in advance.
>>
>> Regards,
>> Guillaume.
>>
>>
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