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Re: [slurm-users] [BULK] slurm-users Digest, Vol 75, Issue 26
by Jason Macklin 18 Jan '24

18 Jan '24

If you run "scontrol show jobid <jobid>" of your pending job with the "(Resources)" tag you may see more about what is unavailable to your job. Slurm default configs can cause an entire compute node of resources to be "allocated" to a running job regardless of whether it needs all of them or not so you may need to alter one or both of the following settings to allow more than one job to run on a single node at once. You'll find these in your slurm.conf. Don't forget to "scontrol reconf"… [View More] and even potentially restart both "slurmctld" & "slurmd" on your nodes if you do end up making changes. SelectType=select/cons_tres SelectTypeParameters=CR_Core_Memory I hope this helps. Kind regards, Jason ---- Jason Macklin Manager Cyberinfrastructure, Research Cyberinfrastructure 860.837.2142 t | 860.202.7779 m jason.macklin(a)jax.org The Jackson Laboratory Maine | Connecticut | California | Shanghai www.jax.org<http://www.jax.org> The Jackson Laboratory: Leading the search for tomorrow's cures ________________________________ From: slurm-users <slurm-users-bounces(a)lists.schedmd.com> on behalf of slurm-users-request(a)lists.schedmd.com <slurm-users-request(a)lists.schedmd.com> Sent: Thursday, January 18, 2024 9:46 AM To: slurm-users(a)lists.schedmd.com <slurm-users(a)lists.schedmd.com> Subject: [BULK] slurm-users Digest, Vol 75, Issue 26 Send slurm-users mailing list submissions to slurm-users(a)lists.schedmd.com To subscribe or unsubscribe via the World Wide Web, visit https://lists.schedmd.com/cgi-bin/mailman/listinfo/slurm-users or, via email, send a message with subject or body 'help' to slurm-users-request(a)lists.schedmd.com You can reach the person managing the list at slurm-users-owner(a)lists.schedmd.com When replying, please edit your Subject line so it is more specific than "Re: Contents of slurm-users digest..." Today's Topics: 1. Re: Need help with running multiple instances/executions of a batch script in parallel (with NVIDIA HGX A100 GPU as a Gres) (Baer, Troy) ---------------------------------------------------------------------- Message: 1 Date: Thu, 18 Jan 2024 14:46:48 +0000 From: "Baer, Troy" <troy(a)osc.edu> To: Slurm User Community List <slurm-users(a)lists.schedmd.com> Subject: Re: [slurm-users] Need help with running multiple instances/executions of a batch script in parallel (with NVIDIA HGX A100 GPU as a Gres) Message-ID: <CH0PR01MB6924127AF471DED69151805BCF712(a)CH0PR01MB6924.prod.exchangelabs.com> Content-Type: text/plain; charset="utf-8" Hi Hafedh, Your job script has the sbatch directive ??gpus-per-node=4? set. I suspect that if you look at what?s allocated to the running job by doing ?scontrol show job <jobid>? and looking at the TRES field, it?s been allocated 4 GPUs instead of one. Regards, --Troy From: slurm-users <slurm-users-bounces(a)lists.schedmd.com> On Behalf Of Kherfani, Hafedh (Professional Services, TC) Sent: Thursday, January 18, 2024 9:38 AM To: Slurm User Community List <slurm-users(a)lists.schedmd.com> Subject: Re: [slurm-users] Need help with running multiple instances/executions of a batch script in parallel (with NVIDIA HGX A100 GPU as a Gres) Hi Noam and Matthias, Thanks both for your answers. I changed the ?#SBATCH --gres=gpu:?4? directive (in the batch script) with ?#SBATCH --gres=gpu:?1? as you suggested, but it didn?t make a difference, as running Hi Noam and Matthias, Thanks both for your answers. I changed the ?#SBATCH --gres=gpu:4? directive (in the batch script) with ?#SBATCH --gres=gpu:1? as you suggested, but it didn?t make a difference, as running this batch script 3 times will result in the first job to be in a running state, while the second and third jobs will still be in a pending state ? [slurmtest@c-a100-master test-batch-scripts]$ cat gpu-job.sh #!/bin/bash #SBATCH --job-name=gpu-job #SBATCH --partition=gpu #SBATCH --nodes=1 #SBATCH --gpus-per-node=4 #SBATCH --gres=gpu:1 # <<<< Changed from ?4? to ?1? #SBATCH --tasks-per-node=1 #SBATCH --output=gpu_job_output.%j #SBATCH --error=gpu_job_error.%j hostname date sleep 40 pwd [slurmtest@c-a100-master test-batch-scripts]$ sbatch gpu-job.sh Submitted batch job 217 [slurmtest@c-a100-master test-batch-scripts]$ squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 217 gpu gpu-job slurmtes R 0:02 1 c-a100-cn01 [slurmtest@c-a100-master test-batch-scripts]$ sbatch gpu-job.sh Submitted batch job 218 [slurmtest@c-a100-master test-batch-scripts]$ sbatch gpu-job.sh Submitted batch job 219 [slurmtest@c-a100-master test-batch-scripts]$ squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 219 gpu gpu-job slurmtes PD 0:00 1 (Priority) 218 gpu gpu-job slurmtes PD 0:00 1 (Resources) 217 gpu gpu-job slurmtes R 0:07 1 c-a100-cn01 Basically I?m seeking for some help/hints on how to tell Slurm, from the batch script for example: ?I want only 1 or 2 GPUs to be used/consumed by the job?, and then I run the batch script/job a couple of times with sbatch command, and confirm that we can indeed have multiple jobs using a GPU and running in parallel, at the same time. Makes sense ? Best regards, Hafedh From: slurm-users <slurm-users-bounces(a)lists.schedmd.com<mailto:slurm-users-bounces@lists.schedmd.com>> On Behalf Of Bernstein, Noam CIV USN NRL (6393) Washington DC (USA) Sent: jeudi 18 janvier 2024 2:30 PM To: Slurm User Community List <slurm-users(a)lists.schedmd.com<mailto:slurm-users@lists.schedmd.com>> Subject: Re: [slurm-users] Need help with running multiple instances/executions of a batch script in parallel (with NVIDIA HGX A100 GPU as a Gres) On Jan 18, 2024, at 7:31 AM, Matthias Loose <m.loose(a)mindcode.de<mailto:m.loose@mindcode.de>> wrote: Hi Hafedh, Im no expert in the GPU side of SLURM, but looking at you current configuration to me its working as intended at the moment. You have defined 4 GPUs and start multiple jobs each consuming 4 GPUs each. So the jobs wait for the ressource the be free again. I think what you need to look into is the MPS plugin, which seems to do what you are trying to achieve: https://slurm.schedmd.com/gres.html#MPS_Management<https://urldefense.com/v3/__https:/slurm.schedmd.com/gres.html*MPS_Manageme…> I agree with the first paragraph. How many GPUs are you expecting each job to use? I'd have assumed, based on the original text, that each job is supposed to use 1 GPU, and the 4 jobs were supposed to be running side-by-side on the one node you have (with 4 GPUs). If so, you need to tell each job to request only 1 GPU, and currently each one is requesting 4. If your jobs are actually supposed to be using 4 GPUs each, I still don't see any advantage to MPS (at least in what is my usual GPU usage pattern): all the jobs will take longer to finish, because they are sharing the fixed resource. If they take turns, at least the first ones finish as fast as they can, and the last one will finish no later than it would have if they were all time-sharing the GPUs. I guess NVIDIA had something in mind when they developed MPS, so I guess our pattern may not be typical (or at least not universal), and in that case the MPS plugin may well be what you need. [View Less]

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slurm.conf
by LEROY Christine 208562 18 Jan '24

18 Jan '24

Hello all, Is there an env variable in SLURM to tell where the slurm.conf is? We would like to have on the same client node, 2 type of possible submissions to address 2 different cluster. Thanks in advance, Christine

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What happens if GPU GRES exceeding number of GPUs per node
by Purwanto, Wirawan 18 Jan '24

18 Jan '24

Hi, In my HPC center, I found a SLURM job that was submitted with --gres=gpu:6 whereas the cluster has only four GPUs per node each. It is a parallel job. Here are some relevant field printout: AllocCPUS 30 AllocGRES gpu:6 AllocTRES billing=30,cpu=30,gres/gpu=6,node=3 CPUTime 1-01:23:00 CPUTimeRAW 91380 Elapsed 00:50:46 … [View More]

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Strict GrpTRESMins limit
by Kamil Wilczek 17 Jan '24

17 Jan '24

Dear All, I tried to implement a strict limit on the GrpTRESMins for each user. The effect I'm trying to achieve is that after the limit of GPU minutes is reached, no new jobs can be run. No decay, no automatic resource replenishment. After the limit on GPU minutes is reached, each user should ask for more minutes. But despite exceeding the limits users *can* run new jobs. * When I'm adding a user to the cluster I set: sacctmgr --immediate add user name=... ... QOS=2gpu2d … [View More]

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Suspend/Resume request limit
by 김종록 17 Jan '24

17 Jan '24

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preemptable queue
by Davide DelVento 12 Jan '24

12 Jan '24

I would like to add a preemptable queue to our cluster. Actually I already have. We simply want jobs submitted to that queue be preempted if there are no resources available for jobs in other (high priority) queues. Conceptually very simple, no conditionals, no choices, just what I wrote. However it does not work as desired. This is the relevant part: grep -i Preemp /opt/slurm/slurm.conf #PreemptType = preempt/partition_prio PartitionName=regular DefMemPerCPU=4580 Default=True Nodes=node[01-… [View More]

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Re: [slurm-users] sacct --name --status filtering
by Drucker, Daniel 11 Jan '24

11 Jan '24

Yes, that makes sense. Thank you! The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over … [View More]

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sacct --name --status filtering
by Drucker, Daniel 10 Jan '24

10 Jan '24

What am I misunderstanding about how sacct filtering works here? I would have expected the second command to show the exact same results as the first. [root@mickey ddrucker]# sacct --starttime $(date -d "7 days ago" +"%Y-%m-%d") -X --format JobID,JobName,State,Elapsed --name zsh JobID JobName State Elapsed ------------ ---------- ---------- ---------- 257713 zsh COMPLETED 00:01:02 257714 zsh COMPLETED 00:04:01 257715 zsh … [View More]

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Re: [slurm-users] sacct --name --status filtering
by Drucker, Daniel 10 Jan '24

10 Jan '24

> All I can say is that this has to do with --starttime and that you have to read the manual really carefully about how they interact, including when you have --endtime set. It’s a bit fiddly and annoying, IMO, and I can never quite remember how it works. Oh, I think I understand. --starttime actually behaves differently when --state is present: If states are given with the '-s' option then only jobs in this state at this time will be returned. So is there a way to do what I want? I … [View More]

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Cleanup of old clusters in database
by Jeffrey R. Lang 10 Jan '24

10 Jan '24

We have shuttered two clusters and need to remove them from the database. To do this, do we remove the table spaces associated with the cluster names from the Slurm database? Thanks, Jeff

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