Hi, I'm trying to figure out how to deal with a mix of few- and many-cpu jobs. By that I mean most jobs use 128 cpus, but sometimes there are jobs with only 16. As soon as that job with only 16 is running, the scheduler splits the next 128 cpu jobs into 96+16 each, instead of assigning a full 128 cpu node to them. Is there a way for the administrator to achieve preferring full nodes? The existence of pack_serial_at_end makes me believe there is not, because that basically is what I needed, apart from my serial jobs using 16 cpus instead of 1. Gerhard
Hi Gerhard, Gerhard Strangar via slurm-users <slurm-users@lists.schedmd.com> writes:
Hi,
I'm trying to figure out how to deal with a mix of few- and many-cpu jobs. By that I mean most jobs use 128 cpus, but sometimes there are jobs with only 16. As soon as that job with only 16 is running, the scheduler splits the next 128 cpu jobs into 96+16 each, instead of assigning a full 128 cpu node to them. Is there a way for the administrator to achieve preferring full nodes? The existence of pack_serial_at_end makes me believe there is not, because that basically is what I needed, apart from my serial jobs using 16 cpus instead of 1.
Gerhard
This may well not be relevant for your case, but we actively discourage the use of full nodes for the following reasons: - When the cluster is full, which is most of the time, MPI jobs in general will start much faster if they don't specify the number of nodes and certainly don't request full nodes. The overhead due to the jobs being scattered across nodes is often much lower than the additional waiting time incurred by requesting whole nodes. - When all the cores of a node are requested, all the memory of the node becomes unavailable to other jobs, regardless of how much memory is requested or indeed how much is actually used. This holds up jobs with low CPU but high memory requirements and thus reduces the total throughput of the system. These factors are important for us because we have a large number of single core jobs and almost all the users, whether doing MPI or not, significantly overestimate the memory requirements of their jobs. Cheers, Loris -- Dr. Loris Bennett (Herr/Mr) FUB-IT (ex-ZEDAT), Freie Universität Berlin
Agree with that. Plus, of course, even if the jobs run a bit slower by not having all the cores on a single node, they will be scheduled sooner, so the overall turnaround time for the user will be better, and ultimately that's what they care about. I've always been of the view, for any scheduler, that the less you try to constrain it the better. It really depends on what you're trying to optimise for, but generally speaking I try to optimise for maximum utilisation and throughput, unless I have a specific business case that needs to prioritise particular workloads, and then I'll compromise on throughput to get the urgent workload through sooner. Tun ________________________________ From: Loris Bennett via slurm-users <slurm-users@lists.schedmd.com> Sent: 09 April 2024 06:51 To: slurm-users@lists.schedmd.com <slurm-users@lists.schedmd.com> Cc: Gerhard Strangar <g.s@arcor.de> Subject: [slurm-users] Re: Avoiding fragmentation Hi Gerhard, Gerhard Strangar via slurm-users <slurm-users@lists.schedmd.com> writes:
Hi,
I'm trying to figure out how to deal with a mix of few- and many-cpu jobs. By that I mean most jobs use 128 cpus, but sometimes there are jobs with only 16. As soon as that job with only 16 is running, the scheduler splits the next 128 cpu jobs into 96+16 each, instead of assigning a full 128 cpu node to them. Is there a way for the administrator to achieve preferring full nodes? The existence of pack_serial_at_end makes me believe there is not, because that basically is what I needed, apart from my serial jobs using 16 cpus instead of 1.
Gerhard
This may well not be relevant for your case, but we actively discourage the use of full nodes for the following reasons: - When the cluster is full, which is most of the time, MPI jobs in general will start much faster if they don't specify the number of nodes and certainly don't request full nodes. The overhead due to the jobs being scattered across nodes is often much lower than the additional waiting time incurred by requesting whole nodes. - When all the cores of a node are requested, all the memory of the node becomes unavailable to other jobs, regardless of how much memory is requested or indeed how much is actually used. This holds up jobs with low CPU but high memory requirements and thus reduces the total throughput of the system. These factors are important for us because we have a large number of single core jobs and almost all the users, whether doing MPI or not, significantly overestimate the memory requirements of their jobs. Cheers, Loris -- Dr. Loris Bennett (Herr/Mr) FUB-IT (ex-ZEDAT), Freie Universität Berlin -- slurm-users mailing list -- slurm-users@lists.schedmd.com To unsubscribe send an email to slurm-users-leave@lists.schedmd.com ________________________________ AstraZeneca UK Limited is a company incorporated in England and Wales with registered number:03674842 and its registered office at 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA. This e-mail and its attachments are intended for the above named recipient only and may contain confidential and privileged information. If they have come to you in error, you must not copy or show them to anyone; instead, please reply to this e-mail, highlighting the error to the sender and then immediately delete the message. For information about how AstraZeneca UK Limited and its affiliates may process information, personal data and monitor communications, please see our privacy notice at www.astrazeneca.com<https://www.astrazeneca.com>
I wrote a little blog post on this topic a few years back: https://www.rc.fas.harvard.edu/blog/cluster-fragmentation/ It's a vexing problem, but as noted by the other responders it is something that depends on your cluster policy and job performance needs. Well written MPI code should be able to scale well even when given non-optimal topologies. You might also look at Node Weights (https://slurm.schedmd.com/slurm.conf.html#OPT_Weight). We use them on mosaic partitions so that the latest hardware is left available for larger jobs needing more performance. You can also use it to force jobs to one side of the partition, though generally the scheduler does this automatically. -Paul Edmon- On 4/9/24 6:45 AM, Cutts, Tim via slurm-users wrote:
Agree with that. Plus, of course, even if the jobs run a bit slower by not having all the cores on a single node, they will be scheduled sooner, so the overall turnaround time for the user will be better, and ultimately that's what they care about. I've always been of the view, for any scheduler, that the less you try to constrain it the better. It really depends on what you're trying to optimise for, but generally speaking I try to optimise for maximum utilisation and throughput, unless I have a specific business case that needs to prioritise particular workloads, and then I'll compromise on throughput to get the urgent workload through sooner.
Tun ------------------------------------------------------------------------ *From:* Loris Bennett via slurm-users <slurm-users@lists.schedmd.com> *Sent:* 09 April 2024 06:51 *To:* slurm-users@lists.schedmd.com <slurm-users@lists.schedmd.com> *Cc:* Gerhard Strangar <g.s@arcor.de> *Subject:* [slurm-users] Re: Avoiding fragmentation Hi Gerhard,
Gerhard Strangar via slurm-users <slurm-users@lists.schedmd.com> writes:
Hi,
I'm trying to figure out how to deal with a mix of few- and many-cpu jobs. By that I mean most jobs use 128 cpus, but sometimes there are jobs with only 16. As soon as that job with only 16 is running, the scheduler splits the next 128 cpu jobs into 96+16 each, instead of assigning a full 128 cpu node to them. Is there a way for the administrator to achieve preferring full nodes? The existence of pack_serial_at_end makes me believe there is not, because that basically is what I needed, apart from my serial jobs using 16 cpus instead of 1.
Gerhard
This may well not be relevant for your case, but we actively discourage the use of full nodes for the following reasons:
- When the cluster is full, which is most of the time, MPI jobs in general will start much faster if they don't specify the number of nodes and certainly don't request full nodes. The overhead due to the jobs being scattered across nodes is often much lower than the additional waiting time incurred by requesting whole nodes.
- When all the cores of a node are requested, all the memory of the node becomes unavailable to other jobs, regardless of how much memory is requested or indeed how much is actually used. This holds up jobs with low CPU but high memory requirements and thus reduces the total throughput of the system.
These factors are important for us because we have a large number of single core jobs and almost all the users, whether doing MPI or not, significantly overestimate the memory requirements of their jobs.
Cheers,
Loris
-- Dr. Loris Bennett (Herr/Mr) FUB-IT (ex-ZEDAT), Freie Universität Berlin
-- slurm-users mailing list -- slurm-users@lists.schedmd.com To unsubscribe send an email to slurm-users-leave@lists.schedmd.com ------------------------------------------------------------------------
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This e-mail and its attachments are intended for the above named recipient only and may contain confidential and privileged information. If they have come to you in error, you must not copy or show them to anyone; instead, please reply to this e-mail, highlighting the error to the sender and then immediately delete the message. For information about how AstraZeneca UK Limited and its affiliates may process information, personal data and monitor communications, please see our privacy notice at www.astrazeneca.com <https://www.astrazeneca.com>
Hi Gerhard, I am not sure if this counts as administrative measure, but we do highly encourage our users to always explicitely specify --nodes=n together with --ntasks-per-node=m (rather than just --ntasks=n*m and omitting --nodes option, which may lead to cores allocated here and there and everywhere as long as network topology allows this). I do understand Loris' and Tim's arguments, but for certain reasons we have configured single user node access policy (ExclusiveUser=YES), which allows multiple jobs to share a node, but only jobs owned by one and the same user. So we also try to avoid fragmentation whenever possible and want users to pack their jobs as densely as possible on the nodes in order to leave as many nodes as possible available for others. For us, this works reasonably well in terms of core utilization because we have almost no users who submit only one or two few-core jobs at a time but usually whole bunches of such jobs (sometimes hundreds) at once of which multiple jobs then simultaneously run on the individual nodes. That keeps the waste of unallocated cores on individual nodes within acceptable limits for us. Best regards Jürgen * Loris Bennett via slurm-users <slurm-users@lists.schedmd.com> [240409 07:51]:
Hi Gerhard,
Gerhard Strangar via slurm-users <slurm-users@lists.schedmd.com> writes:
Hi,
I'm trying to figure out how to deal with a mix of few- and many-cpu jobs. By that I mean most jobs use 128 cpus, but sometimes there are jobs with only 16. As soon as that job with only 16 is running, the scheduler splits the next 128 cpu jobs into 96+16 each, instead of assigning a full 128 cpu node to them. Is there a way for the administrator to achieve preferring full nodes? The existence of pack_serial_at_end makes me believe there is not, because that basically is what I needed, apart from my serial jobs using 16 cpus instead of 1.
Gerhard
This may well not be relevant for your case, but we actively discourage the use of full nodes for the following reasons:
- When the cluster is full, which is most of the time, MPI jobs in general will start much faster if they don't specify the number of nodes and certainly don't request full nodes. The overhead due to the jobs being scattered across nodes is often much lower than the additional waiting time incurred by requesting whole nodes.
- When all the cores of a node are requested, all the memory of the node becomes unavailable to other jobs, regardless of how much memory is requested or indeed how much is actually used. This holds up jobs with low CPU but high memory requirements and thus reduces the total throughput of the system.
These factors are important for us because we have a large number of single core jobs and almost all the users, whether doing MPI or not, significantly overestimate the memory requirements of their jobs.
Cheers,
Loris
-- Dr. Loris Bennett (Herr/Mr) FUB-IT (ex-ZEDAT), Freie Universität Berlin
-- slurm-users mailing list -- slurm-users@lists.schedmd.com To unsubscribe send an email to slurm-users-leave@lists.schedmd.com
-- Jürgen Salk Scientific Software & Compute Services (SSCS) Kommunikations- und Informationszentrum (kiz) Universität Ulm Telefon: +49 (0)731 50-22478 Telefax: +49 (0)731 50-22471
Various options that might help reduce job fragmentation. Turn up debugging on slurmctld and add the DebugFlags like TraceJobs, SelectType, and Steps. With debugging set high enough one can see a good bit of the logic in regard to node selection. CR_LLN Schedule resources to jobs on the least loaded nodes (based upon the number of idle CPUs). This is generally only recommended for an environment with serial jobs as idle resources will tend to be highly fragmented, result- ing in parallel jobs being distributed across many nodes. Note that node Weight takes precedence over how many idle resources are on each node. Also see the partition con- figuration parameter LLN use the least loaded nodes in selected partitions. Explore node weights. If your nodes are not identical apply node weights to sort your nodes in the order of how you wish them to be selected; on the other hand, even for homogenous nodes you might try sets of weights to have the scheduler within a given scheduling cycle consider a smaller number of nodes of a weight before then considering the next number of nodes of the next weight. The number of nodes within a weight set might be no smaller than 1/3 or 1/4 of the total partition size. YMMV based on for instance ratio of serial jobs to MPI jobs, job length, etc. I have seen evidence that node allocation progresses roughly this way. Turn on backfill and educate users to better fit both their job resource requirements and the job runtime. This will allow backfill to work more efficiently. Note that backfill choices are made within a given set of job within a partition. CR_Pack_Nodes If a job allocation contains more resources than will be used for launching tasks (e.g. if whole nodes are allo- cated to a job), then rather than distributing a job's tasks evenly across its allocated nodes, pack them as tightly as possible on these nodes. For example, consider a job allocation containing two entire nodes with eight CPUs each. If the job starts ten tasks across those two nodes without this option, it will start five tasks on each of the two nodes. With this option, eight tasks will be started on the first node and two tasks on the second node. This can be superseded by "NoPack" in srun's "--distribution" option. CR_Pack_Nodes only applies when the "block" task distribution method is used. pack_serial_at_end If used with the select/cons_res or select/cons_tres plug- in, then put serial jobs at the end of the available nodes rather than using a best fit algorithm. This may reduce resource fragmentation for some workloads. reduce_completing_frag This option is used to control how scheduling of resources is performed when jobs are in the COMPLETING state, which influences potential fragmentation. If this option is not set then no jobs will be started in any partition when any job is in the COMPLETING state for less than CompleteWait seconds. If this option is set then no jobs will be started in any individual partition that has a job in COM- PLETING state for less than CompleteWait seconds. In addition, no jobs will be started in any partition with nodes that overlap with any nodes in the partition of the completing job. This option is to be used in conjunction with CompleteWait. -----Original Message----- From: Gerhard Strangar via slurm-users <slurm-users@lists.schedmd.com> Sent: Tuesday, April 9, 2024 12:53 AM To: slurm-users@lists.schedmd.com Subject: [slurm-users] Avoiding fragmentation Hi, I'm trying to figure out how to deal with a mix of few- and many-cpu jobs. By that I mean most jobs use 128 cpus, but sometimes there are jobs with only 16. As soon as that job with only 16 is running, the scheduler splits the next 128 cpu jobs into 96+16 each, instead of assigning a full 128 cpu node to them. Is there a way for the administrator to achieve preferring full nodes? The existence of pack_serial_at_end makes me believe there is not, because that basically is what I needed, apart from my serial jobs using 16 cpus instead of 1. Gerhard -- slurm-users mailing list -- slurm-users@lists.schedmd.com To unsubscribe send an email to slurm-users-leave@lists.schedmd.com
participants (6)
-
Cutts, Tim -
Gerhard Strangar -
Juergen Salk -
Loris Bennett -
Paul Edmon -
Williams, Jenny Avis