- slurm-users - lists.schedmd.com

Avoiding fragmentation
by Gerhard Strangar 10 Apr '24

10 Apr '24

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, … [View More]

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Nodes required for job are down, drained or reserved
by Alison Peterson 09 Apr '24

09 Apr '24

Hi everyone, I'm conducting some tests. I've just set up SLURM on the head node and haven't added any compute nodes yet. I'm trying to test it to ensure it's working, but I'm encountering an error: 'Nodes required for the job are DOWN, DRAINED, or reserved for jobs in higher priority partitions. Any guidance will be appreciated thank you! -- *Alison Peterson* IT Research Support Analyst *Information Technology* apeterson5(a)sdsu.edu <mfarley(a)sdsu.edu> O: 619-594-3364 *San Diego State … [View More]

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DefCpuPerGPU and multiple partitions
by Ansgar Esztermann-Kirchner 09 Apr '24

09 Apr '24

Hello List, does anyone have experience with DefCpuPerGPU and jobs requesting multiple partitions? I would expect Slurm to select a partition from those requested by the job, then assign CPUs based on that partition's DefCpuPerGPU. But according to my observations, it appears that (at least sometimes), DefCpuPerGPU from another partition (also requested by the job, but not selected to execute it) is used to assign CPUs. I haven't done extensive testing to determine whether there's a pattern to … [View More]

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Elastic Computing: Is it possible to incentivize grouping power_up calls?
by Xaver Stiensmeier 09 Apr '24

09 Apr '24

Dear slurm user list, we make use of elastic cloud computing i.e. node instances are created on demand and are destroyed when they are not used for a certain amount of time. Created instances are set up via Ansible. If more than one instance is requested at the exact same time, Slurm will pass those into the resume script together and one Ansible call will handle all those instances. However, more often than not workflows will request multiple instances within the same second, but not at the … [View More]

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Slurm User Group 2024 Call for Papers
by Victoria Hobson 08 Apr '24

08 Apr '24

Slurm User Group (SLUG) 2024 is set for September 12-13 at the University of Oslo in Oslo, Norway. Registration information and a high-level schedule can be found here: https://slug24.splashthat.com/ We invite all interested attendees to submit a presentation abstract to be given at SLUG. Presentation content can be in the form of a tutorial, technical presentation or site report. SLUG 2024 is sponsored and organized by the University of Oslo and SchedMD. This international event is open to … [View More]

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How to reinstall / reconfigure Slurm?
by Shooktija S N 08 Apr '24

08 Apr '24

Hi, I am setting up Slurm on our lab's 3 node cluster and I have run into a problem while adding GPUs (each node has an NVIDIA 4070 ti) as a GRES. There is an error at the 'debug' log level in slurmd.log that says that the GPU is file-less and is being removed from the final GRES list. This error according to some older posts on this forum might be fixed by reinstalling / reconfiguring Slurm with the right flag (the '--with-nvml' flag according to this <https://groups.google.com/g/slurm-… [View More]

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No SLURM_SHARDS_ON_NODE in prolog/epilog
by Thomas Green - Staff in University IT, Research Technologies / Staff Technoleg Gwybodaeth, Technolegau Ymchwil 05 Apr '24

05 Apr '24

Hi, I have found that SLURM_SHARDS_ON_NODE is not an environment variable in prolog or epilog. Is ther ea reason for this? I thought it would be handy to know if shards have been requested in a prolog/epilog. Tom -- Thomas Green Senior Programmer ARCCA, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB Tel: +44 (0)29 208 79269 Fax: +44 (0)29 208 70734 Email: greent10(a)cardiff.ac.uk<mailto:greent10@cardiff.ac.uk> Web: http://www.… [View More]

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Suggestions for Partition/QoS configuration
by thomas.hartmann＠th-ht.de 04 Apr '24

04 Apr '24

Hi, we're testing possible slurm configurations on a test system right now. Eventually, it is going to serve ~1000 users. We're going to have some users who are going to run lots of short jobs (a couple of minutes to ~4h) and some users that run jobs that are going to run for days or weeks. I want to avoid a situation in which a group of users basically saturates the whole cluster with jobs that run for a week or two and nobody could run any short jobs anymore. I also would like to favor short … [View More]

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Re: [EXT] Re: SLURM configuration help
by Renfro, Michael 04 Apr '24

04 Apr '24

Yep, from your scontrol show node output: CfgTRES=cpu=64,mem=2052077M,billing=64 AllocTRES=cpu=1,mem=2052077M The running job (77) has allocated 1 CPU and all the memory on the node. That’s probably due to the partition using the default DefMemPerCPU value [1], which is unlimited. Since all our nodes are shared, and our workloads vary widely, we set our DefMemPerCPU value to something considerably lower than mem_in_node/cores_in_node . That way, most jobs will leave some memory available by … [View More]default, and other jobs can use that extra memory as long as CPUs are available. [1] https://slurm.schedmd.com/slurm.conf.html#OPT_DefMemPerCPU From: Alison Peterson <apeterson5(a)sdsu.edu> Date: Thursday, April 4, 2024 at 11:58 AM To: Renfro, Michael <Renfro(a)tntech.edu> Subject: Re: [EXT] Re: [slurm-users] SLURM configuration help External Email Warning This email originated from outside the university. Please use caution when opening attachments, clicking links, or responding to requests. ________________________________ Here is the info: sma@cusco:/data/work/sma-scratch/tohoku_wOcean$ scontrol show node cusco NodeName=cusco Arch=x86_64 CoresPerSocket=32 CPUAlloc=1 CPUTot=64 CPULoad=0.02 AvailableFeatures=(null) ActiveFeatures=(null) Gres=gpu:4 NodeAddr=cusco NodeHostName=cusco Version=19.05.5 OS=Linux 5.4.0-172-generic #190-Ubuntu SMP Fri Feb 2 23:24:22 UTC 2024 RealMemory=2052077 AllocMem=2052077 FreeMem=1995947 Sockets=2 Boards=1 State=MIXED ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A Partitions=mainpart BootTime=2024-03-01T17:06:26 SlurmdStartTime=2024-03-01T17:06:53 CfgTRES=cpu=64,mem=2052077M,billing=64 AllocTRES=cpu=1,mem=2052077M CapWatts=n/a CurrentWatts=0 AveWatts=0 ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s sma@cusco:/data/work/sma-scratch/tohoku_wOcean$ squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 78 mainpart CF1090_w sma PD 0:00 1 (Resources) 77 mainpart CF0000_w sma R 0:26 1 cusco sma@cusco:/data/work/sma-scratch/tohoku_wOcean$ scontrol show job 78 JobId=78 JobName=CF1090_wOcean500m.shell UserId=sma(1008) GroupId=myfault(1001) MCS_label=N/A Priority=4294901720 Nice=0 Account=(null) QOS=(null) JobState=PENDING Reason=Resources Dependency=(null) Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0 RunTime=00:00:00 TimeLimit=01:00:00 TimeMin=N/A SubmitTime=2024-04-04T09:55:34 EligibleTime=2024-04-04T09:55:34 AccrueTime=2024-04-04T09:55:34 StartTime=2024-04-04T10:55:28 EndTime=2024-04-04T11:55:28 Deadline=N/A SuspendTime=None SecsPreSuspend=0 LastSchedEval=2024-04-04T09:55:58 Partition=mainpart AllocNode:Sid=newcusco:2450574 ReqNodeList=(null) ExcNodeList=(null) NodeList=(null) SchedNodeList=cusco NumNodes=1 NumCPUs=1 NumTasks=1 CPUs/Task=1 ReqB:S:C:T=0:0:*:* TRES=cpu=1,node=1,billing=1 Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=* MinCPUsNode=1 MinMemoryNode=0 MinTmpDiskNode=0 Features=(null) DelayBoot=00:00:00 OverSubscribe=YES Contiguous=0 Licenses=(null) Network=(null) Command=/data/work/sma-scratch/tohoku_wOcean/CF1090_wOcean500m.shell WorkDir=/data/work/sma-scratch/tohoku_wOcean StdErr=/data/work/sma-scratch/tohoku_wOcean/slurm-78.out StdIn=/dev/null StdOut=/data/work/sma-scratch/tohoku_wOcean/slurm-78.out Power= On Thu, Apr 4, 2024 at 8:57 AM Renfro, Michael <Renfro(a)tntech.edu<mailto:Renfro@tntech.edu>> wrote: What does “scontrol show node cusco” and “scontrol show job PENDING_JOB_ID” show? On one job we currently have that’s pending due to Resources, that job has requested 90 CPUs and 180 GB of memory as seen in its ReqTRES= value, but the node it wants to run on only has 37 CPUs available (seen by comparing its CfgTRES= and AllocTRES= values). From: Alison Peterson via slurm-users <slurm-users(a)lists.schedmd.com<mailto:slurm-users@lists.schedmd.com>> Date: Thursday, April 4, 2024 at 10:43 AM To: slurm-users(a)lists.schedmd.com<mailto:slurm-users@lists.schedmd.com> <slurm-users(a)lists.schedmd.com<mailto:slurm-users@lists.schedmd.com>> Subject: [slurm-users] SLURM configuration help External Email Warning This email originated from outside the university. Please use caution when opening attachments, clicking links, or responding to requests. ________________________________ I am writing to seek assistance with a critical issue on our single-node system managed by Slurm. Our jobs are queued and marked as awaiting resources, but they are not starting despite seeming availability. I'm new with SLURM and my only experience was a class on installing it so I have no experience, running it or using it. Issue Summary: Main Problem: Jobs submitted only one run and the second says NODELIST(REASON) (Resources). I've checked that our single node has enough RAM (2TB) and CPU's (64) available. # COMPUTE NODES NodeName=cusco CPUs=64 Sockets=2 CoresPerSocket=32 ThreadsPerCore=1 RealMemory=2052077 Gres=gpu:1,gpu:1,gpu:1,gpu:1 PartitionName=mainpart Default=YES MinNodes=1 DefaultTime=00:60:00 MaxTime=UNLIMITED AllowAccounts=ALL Nodes=ALL State=UP OverSubscribe=Force System Details: We have a single-node setup with Slurm as the workload manager. The node appears to have sufficient resources for the queued jobs. Troubleshooting Performed: Configuration Checks: I have verified all Slurm configurations and the system's resource availability, which should not be limiting job execution. Service Status: The Slurm daemon slurmdbd is active and running without any reported issues. System resource monitoring shows no shortages that would prevent job initiation. Any guidance and help will be deeply appreciated! -- Alison Peterson IT Research Support Analyst Information Technology apeterson5(a)sdsu.edu<mailto:mfarley@sdsu.edu> O: 619-594-3364 San Diego State University | SDSU.edu<http://sdsu.edu/> 5500 Campanile Drive | San Diego, CA 92182-8080 Error! Filename not specified. -- Alison Peterson IT Research Support Analyst Information Technology apeterson5(a)sdsu.edu<mailto:mfarley@sdsu.edu> O: 619-594-3364 San Diego State University | SDSU.edu<http://sdsu.edu/> 5500 Campanile Drive | San Diego, CA 92182-8080 [Image removed by sender.] [View Less]

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SLURM configuration help
by Alison Peterson 04 Apr '24

04 Apr '24

I am writing to seek assistance with a critical issue on our single-node system managed by Slurm. Our jobs are queued and marked as awaiting resources, but they are not starting despite seeming availability. I'm new with SLURM and my only experience was a class on installing it so I have no experience, running it or using it. Issue Summary: Main Problem: Jobs submitted only one run and the second says *NODELIST(REASON) (Resources*). I've checked that our single node has enough RAM (2TB) and … [View More]

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Slurm 23.11 - Unknown system variable 'wsrep_on'
by Russell Jones 04 Apr '24

04 Apr '24

Hi all, I am working on upgrading a Slurm cluster from 20 -> 23. I was successfully able to upgrade to 22, however now that I am trying to go from 22 to 23, starting slurmdbd results in the following error being logged: error: mysql_query failed: 1193 Unknown system variable 'wsrep_on' When trying to start slurmctld, I get: [2024-04-02T15:09:52.439] Couldn't find tres gres/gpumem in the database, creating. [2024-04-02T15:09:52.439] Couldn't find tres gres/gpuutil in the database, … [View More]

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scrun: Failed to run the container due to GID mapping configuration
by Toshiki Sonoda (Fujitsu) 04 Apr '24

04 Apr '24

Dear All, We set up scrun (slurm 23.11.5) integrated with rootless podman, referring to the official documentation. https://slurm.schedmd.com/containers.html#podman-scrun https://slurm.schedmd.com/scrun.html#SECTION_Example-%3CB%3Escrun.lua%3C/B%… However, runc/crun prints the error message and fails to run the container. Looking at the error message from runc, it seems that there is a problem with the GID mapping configuration. - runc [hoge@slm-master hoge]$ podman run centos echo "Hello … [View More]

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File-less NVIDIA GeForce 4070 Ti being removed from GRES list
by Shooktija S N 02 Apr '24

02 Apr '24

Hi, I am trying to set up Slurm (version 22.05) on a 3 node cluster each having an NVIDIA GeForce RTX 4070 Ti GPU. I tried to follow along with the GRES setup tutorial on the Schedmd website and added the following (Gres=gpu:RTX4070TI:1) to the Node configuration in /etc/slurm/slurm.conf: NodeName=server[1-3] RealMemory=128636 Sockets=1 CoresPerSocket=64 ThreadsPerCore=2 State=UNKNOWN Gres=gpu:RTX4070TI:1 I do not have a gres.conf. However, I see this line at the debug log level in /var/log/… [View More]

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PMIxDirectConn Setting
by efweber＠uwe.nsa.gov 28 Mar '24

28 Mar '24

Hi, The documentation for mpi.conf says: PMIxDirectConn={true|false} Disable direct launching of tasks. Default is "true". I'm finding this a bit confusing. Does true really mean that Direct Connection is disabled? I would have thought true meant enabled. Thanks

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Incorrect hyperthreading with Slurm 23.11
by Guillaume COCHARD 27 Mar '24

27 Mar '24

Hello, We have upgraded our cluster to Slurm 23.11.1 then, a few weeks later, to 23.11.4. Since then, Slurm doesn't detect hyperthreaded CPUs. We have downgraded our test cluster, the issue is not present with Slurm 22.05 (we had skipped Slurm 23.02). For example, we are working with this node: $ slurmd -C NodeName=node03 CPUs=40 Boards=1 SocketsPerBoard=2 CoresPerSocket=10 ThreadsPerCore=2 RealMemory=128215 It is defined like this in slurm.conf: SelectTypeParameters=CR_CPU_Memory … [View More]TaskPlugin=task/cgroup,task/affinity NodeName=node03 CPUs=40 RealMemory=150000 Feature=htc MemSpecLimit=5000 NodeSet=htc Feature=htc PartitionName=htc Default=YES MinNodes=0 MaxNodes=1 Nodes=htc DefMemPerCPU=1000 State=UP LLN=Yes MaxMemPerNode=142000 So no oversubscribing, 20 cores and 40 CPUs thanks to hyperthreading. Until the updgrade, Slurm was allocating those 40 CPUs: when launching 40 jobs of 1 CPU, each of those job would use one 1 CPU. This is the expected behavior. Since the upgrade, we can still launch those 40 jobs, but only the first half of the CPUs will be used (CPUs 0 to 19 according to htop). Each of those CPUs is used by 2 jobs, and the second half of the CPUs (#20 to 39) stay completely idle. When launching 40 stress processes directly in the node without using Slurm all the CPUs are used. When allocating a specific CPU with srun, it works until CPU #19 and then an error occurs even if the allocation includes all the CPUs of the node: #SBATCH --ntasks=1 #SBATCH --cpus-per-task=40 # Works for 0 to 19 srun --cpu-bind=v,map_cpu:19 stress.py # Doesn't work (20 to 39) srun --cpu-bind=v,map_cpu:20 stress.py # Output: srun: error: CPU binding outside of job step allocation, allocated CPUs are: 0x00000FFFFF. srun: error: Task launch for StepId=57194.0 failed on node node03: Unable to satisfy cpu bind request srun: error: Application launch failed: Unable to satisfy cpu bind request srun: Job step aborted This behaviour concerns all our nodes, some of which have been restarted recently and others have not. This causes the jobs to be frequently interrupted, augmenting the difference between the system real time and user+system times and making the jobs slower. We have been peering the documentation but, from what we understand, our configuration seems correct. In particular, as advised by the documentation[1], we don't set up ThreadsPerCore in slurm.conf. Are we missing something, or is there a regression or a change in Slurm configuration since the version 23.11? Thank you, Guillaume [1] : https://slurm.schedmd.com/slurm.conf.html#OPT_ThreadsPerCore [View Less]

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FairShare priority questions
by Long, Daniel S. 27 Mar '24

27 Mar '24

Hi, I’m trying to set up multifactor priority on our cluster and am having some trouble getting it to behave the way I’d like. My main issues seem to revolve around FairShare. We have multiple projects on our cluster and multiple users in those projects (and some users are in multiple projects, of course). I would like the FairShare to be based only on the project associated with the job; if user A and user B both submit jobs on project C, the FairShare should be identical. However, it looks … [View More]

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Slurm releases move to a six-month cycle
by Tim Wickberg 26 Mar '24

26 Mar '24

Slurm major releases are moving to a six month release cycle. This change starts with the upcoming Slurm 24.05 release this May. Slurm 24.11 will follow in November 2024. Major releases then continue every May and November in 2025 and beyond. There are two main goals of this change: - Faster delivery of newer features and functionality for customers. - "Predictable" release timing, especially for those sites that would prefer to upgrade during an annual system maintenance window. SchedMD … [View More]

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controller backup slurmctld error while takeover
by Miriam Olmi 26 Mar '24

26 Mar '24

Dear all, I am having trouble finalizing the configuration of the backup controller for my slurm cluster. In principle, if no job is running everything seems fine: both the slurmctld services on the primary and the backup controller are running and if I stop the service on the primary controller after 10s more or less (SlurmctldTimeout = 10 sec) the backup controller takes over. Also, if I run the sinfo or squeue command during the 10s of inactivity, the shell stay pending but it … [View More]

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cgroups_exporter for slurm on rhel9 (cgroups-v2)
by Saluja, Prabhjyot 25 Mar '24

25 Mar '24

Hi All, We are currently trying to set up cgroup_exporter <https://github.com/treydock/cgroup_exporter> for slurm. It's been working smoothly with cgroups.v1 and slurm-22.05.7. However, we're facing some challenges with RHEL-9, slurm-23.11.1 and cgroups.v2. The cgroup_exporter isn't capturing the slurm cgroup job information. I'm reaching out to see if any other sites have managed to make this work. If you're using a different exporter that's working for your site, could you please let us … [View More]

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Slurm version 23.11.5 is now available
by Tim McMullan 21 Mar '24

21 Mar '24

We are pleased to announce the availability of Slurm version 23.11.5. The 23.11.5 release includes some important fixes related to newer features as well as some database fixes. The most noteworthy fixes include fixing the sattach command (which only worked for root and SlurmUser after 23.11.0) and fixing an issue while constructing the new lineage database entries. This last change will also perform a query during the upgrade from any prior 23.11 version to fix existing databases. … [View More]Slurm can be downloaded from https://www.schedmd.com/downloads.php . -Tim > * Changes in Slurm 23.11.5 > ========================== > -- Fix Debian package build on systems that are not able to query the systemd > package. > -- data_parser/v0.0.40 - Emit a warning instead of an error if a disabled > parser is invoked. > -- slurmrestd - Improve handling when content plugins rely on parsers > that haven't been loaded. > -- Fix old pending jobs dying (Slurm version 21.08.x and older) when upgrading > Slurm due to "Invalid message version" errors. > -- Have client commands sleep for progressively longer periods when backed off > by the RPC rate limiting system. > -- slurmctld - Ensure agent queue is flushed correctly at shutdown time. > -- slurmdbd - correct lineage construction during assoc table conversion for > partition based associations. > -- Add new RPCs and API call for faster querying of job states from slurmctld. > -- slurmrestd - Add endpoint '/slurm/{data_parser}/jobs/state'. > -- squeue - Add `--only-job-state` argument to use faster query of job states. > -- Make a job requesting --no-requeue, or JobRequeue=0 in the slurm.conf, > supersede RequeueExit[Hold]. > -- Add sackd man page to the Debian package. > -- Fix issues with tasks when a job was shrinked more than once. > -- Fix reservation update validation that resulted in reject of correct > updates of reservation when the reservation was running jobs. > -- Fix possible segfault when the backup slurmctld is asserting control. > -- Fix regression introduced in 23.02.4 where slurmctld was not properly > tracking the total GRES selected for exclusive multi-node jobs, potentially > and incorrectly bypassing limits. > -- Fix tracking of jobs typeless GRES count when multiple typed GRES with the > same name are also present in the job allocation. Otherwise, the job could > bypass limits configured for the typeless GRES. > -- Fix tracking of jobs typeless GRES count when request specification has a > typeless GRES name first and then typed GRES of different names (i.e. > --gres=gpu:1,tmpfs:foo:2,tmpfs:bar:7). Otherwise, the job could bypass > limits configured for the generic of the typed one (tmpfs in the example). > -- Fix batch step not having SLURM_CLUSTER_NAME filled in. > -- slurmstepd - Avoid error during `--container` job cleanup about > RunTimeQuery never being configured. Results in cleanup where job steps not > fully started. > -- Fix nodes not being rebooted when using salloc/sbatch/srun "--reboot" flag. > -- Send scrun.lua in configless mode. > -- Fix rejecting an interactive job whose extra constraint request cannot > immediately be satisfied. > -- Fix regression in 23.11.0 when parsing LogTimeFormat=iso8601_ms that > prevented milliseconds from being printed. > -- Fix issue where you could have a gpu allocated as well as a shard on that > gpu allocated at the same time. > -- Fix slurmctld crashes when using extra constraints with job arrays. > -- sackd/slurmrestd/scrun - Avoid memory leak on new unix socket connection. > -- The failed node field is filled when a node fails but does not time out. > -- slurmrestd - Remove requiring job script field and job component script > fields to both be populated in the `POST /slurm/v0.0.40/job/submit` > endpoint as there can only be one batch step script for a job. > -- slurmrestd - When job script is provided in '.jobs[].script' and '.script' > fields, the '.script' field's value will be used in the > `POST /slurm/v0.0.40/job/submit` endpoint. > -- slurmrestd - Reject HetJob submission missing or empty batch script for > first Het component in the `POST /slurm/v0.0.40/job/submit` endpoint. > -- slurmrestd - Reject job when empty batch script submitted to the > POST /slurm/v0.0.40/job/submit` endpoint. > -- Fix pam_slurm and pam_slurm_adopt when using auth/slurm. > -- slurmrestd - Add 'cores_per_socket' field to > `POST /slurm/v0.0.40/job/submit` endpoint. > -- Fix srun and other Slurm commands running within a "configless" salloc when > salloc itself fetched the config. > -- Enforce binding with shared gres selection if requested. > -- Fix job allocation failures when the requested tres type or name ends in > "gres" or "license". > -- accounting_storage/mysql - Fix lineage string construction when adding a > user association with a partition. > -- Fix sattach command. > -- Fix ReconfigFlags. Due how reconfig was changed in 23.11, they will also > be used to influence the slurmctld startup as well. > -- Fix starting slurmd in configless mode if MUNGE support was disabled. -- Tim McMullan Release Management, Support, and Development SchedMD LLC - Commercial Slurm Development and Support [View Less]

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Re: Lua script
by Gestió Servidors 21 Mar '24

21 Mar '24

Hello, I answer about my question: * What is the contents of your /etc/slurm/job_submit.lua file? function slurm_job_submit(job_desc, part_list, submit_uid) if (job_desc.user_id == 1008) then slurm.log_info("Trabajo sometido por druiz") if (job_desc['partition'] == "nodo.q") then if (job_desc['time_limit'] > 345600) # 345600 seconds == 4 days # nodo.q partition … [View More]

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Re: Lua script
by Gestió Servidors 20 Mar '24

20 Mar '24

Hello, after adding "EnforcePartLimits=ALL" in slurm.conf and restarting slurmctld daemon, job continues being accepted... so I don't undertand where I'm doing some wrong. My slurm.conf is this: ControlMachine=my_server MailProg=/bin/mail MpiDefault=none ProctrackType=proctrack/linuxproc ReturnToService=2 SlurmctldPidFile=/var/run/slurmctld.pid SlurmctldPort=6817 SlurmdPidFile=/var/run/slurmd.pid SlurmdPort=6818 SlurmdSpoolDir=/var/spool/slurmd SlurmUser=slurm SlurmdUser=root AuthType=auth/… [View More]

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Node CPU Allocation and Effective CPU Allocation for Running Jobs
by Muhammad Akhdhor 18 Mar '24

18 Mar '24

Hi Everyone, We have a SLURM cluster of three different types of nodes. One partition consists of nodes that have a large number of CPUs, 256 CPUs on each node. I'm trying to find out the current CPU allocation on some of those nodes but part of the information I gathered seems to be incorrect. If I use "*scontrol show node <node-name>*", I get this for the CPU info: RealMemory=450000 AllocMem=262144 FreeMem=235397 Sockets=2 Boards=1 State=ALLOCATED ThreadsPerCore=2 TmpDisk=0 Weight=1 … [View More]

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Slurm suspend preemption not working
by Verma, Nischey (HPC ENG,RAL,LSCI) 15 Mar '24

15 Mar '24

Hi All, we are trying to implement preemption in one of our partitions so we can run priority jobs on it and suspend the ones running on the partition and resume once the priority job is done. We have read through the Slurm documentation and did the configuration, but somehow we can not make it work. We tried other preemption like cancel which works fine, but Suspend isn't working. The jobs with higher priority which should suspend other jobs stays as pending and waiting for resources. We are … [View More]using a QOS to assign priority to the job and also configuring the QOS so it can preempt certain other QOSs. this is the output of our scontrol show config : AccountingStorageBackupHost = (null) AccountingStorageEnforce = associations,limits,qos AccountingStorageHost = -Some-server- AccountingStorageExternalHost = (null) AccountingStorageParameters = (null) AccountingStoragePort = 6819 AccountingStorageTRES = cpu,mem,energy,node,billing,fs/disk,vmem,pages AccountingStorageType = accounting_storage/slurmdbd AccountingStorageUser = N/A AccountingStoreFlags = job_comment,job_env,job_extra,job_script AcctGatherEnergyType = (null) AcctGatherFilesystemType = (null) AcctGatherInterconnectType = (null) AcctGatherNodeFreq = 0 sec AcctGatherProfileType = (null) AllowSpecResourcesUsage = No AuthAltTypes = (null) AuthAltParameters = (null) AuthInfo = (null) AuthType = auth/munge BatchStartTimeout = 10 sec BcastExclude = /lib,/usr/lib,/lib64,/usr/lib64 BcastParameters = (null) BOOT_TIME = 2024-03-15T13:32:05 BurstBufferType = (null) CliFilterPlugins = (null) ClusterName = cluster CommunicationParameters = (null) CompleteWait = 0 sec CoreSpecPlugin = (null) CpuFreqDef = Unknown CpuFreqGovernors = OnDemand,Performance,UserSpace CredType = cred/munge DebugFlags = (null) DefMemPerCPU = 3500 DependencyParameters = (null) DisableRootJobs = Yes EioTimeout = 60 EnforcePartLimits = ALL Epilog = (null) EpilogMsgTime = 2000 usec EpilogSlurmctld = (null) ExtSensorsType = (null) ExtSensorsFreq = 0 sec FairShareDampeningFactor = 1 FederationParameters = (null) FirstJobId = 1 GetEnvTimeout = 2 sec GresTypes = gpu GpuFreqDef = (null) GroupUpdateForce = 1 GroupUpdateTime = 600 sec HASH_VAL = Match HealthCheckInterval = 300 sec HealthCheckNodeState = ANY HealthCheckProgram = /usr/sbin/nhc InactiveLimit = 0 sec InteractiveStepOptions = --interactive --preserve-env --pty $SHELL JobAcctGatherFrequency = 30 JobAcctGatherType = jobacct_gather/linux JobAcctGatherParams = (null) JobCompHost = localhost JobCompLoc = (null) JobCompParams = (null) JobCompPort = 0 JobCompType = (null) JobCompUser = root JobContainerType = (null) JobDefaults = (null) JobFileAppend = 0 JobRequeue = 1 JobSubmitPlugins = lua KillOnBadExit = 0 KillWait = 30 sec LaunchParameters = (null) Licenses = (null) LogTimeFormat = iso8601_ms MailDomain = (null) MailProg = /bin/mail MaxArraySize = 1001 MaxBatchRequeue = 5 MaxDBDMsgs = 20024 MaxJobCount = 10000 MaxJobId = 67043328 MaxMemPerNode = UNLIMITED MaxNodeCount = 6 MaxStepCount = 40000 MaxTasksPerNode = 512 MCSPlugin = (null) MCSParameters = (null) MessageTimeout = 10 sec MinJobAge = 300 sec MpiDefault = pmix_v2 MpiParams = (null) NEXT_JOB_ID = 3626 NodeFeaturesPlugins = (null) OverTimeLimit = 0 min PluginDir = /usr/lib64/slurm PlugStackConfig = (null) PowerParameters = (null) PowerPlugin = (null) PreemptMode = GANG,SUSPEND PreemptParameters = (null) PreemptType = preempt/qos PreemptExemptTime = 00:00:00 PrEpParameters = (null) PrEpPlugins = prep/script PriorityParameters = (null) PrioritySiteFactorParameters = (null) PrioritySiteFactorPlugin = (null) PriorityDecayHalfLife = 7-00:00:00 PriorityCalcPeriod = 00:05:00 PriorityFavorSmall = No PriorityFlags = PriorityMaxAge = 7-00:00:00 PriorityUsageResetPeriod = NONE PriorityType = priority/multifactor PriorityWeightAge = 0 PriorityWeightAssoc = 0 PriorityWeightFairShare = 0 PriorityWeightJobSize = 0 PriorityWeightPartition = 0 PriorityWeightQOS = 5000 PriorityWeightTRES = (null) PrivateData = none ProctrackType = proctrack/cgroup Prolog = (null) PrologEpilogTimeout = 65534 PrologSlurmctld = (null) PrologFlags = (null) PropagatePrioProcess = 0 PropagateResourceLimits = ALL PropagateResourceLimitsExcept = (null) RebootProgram = /etc/slurm/slurmupdate.sh ReconfigFlags = (null) RequeueExit = (null) RequeueExitHold = (null) ResumeFailProgram = (null) ResumeProgram = (null) ResumeRate = 300 nodes/min ResumeTimeout = 60 sec ResvEpilog = (null) ResvOverRun = 0 min ResvProlog = (null) ReturnToService = 1 SchedulerParameters = bf_max_job_user=2 SchedulerTimeSlice = 30 sec SchedulerType = sched/backfill ScronParameters = (null) SelectType = select/cons_tres SelectTypeParameters = CR_CORE_MEMORY SlurmUser = slurm(888) SlurmctldAddr = (null) SlurmctldDebug = info SlurmctldHost[0] = -some-server- SlurmctldLogFile = /var/log/slurm/slurmctld.log SlurmctldPort = 6817 SlurmctldSyslogDebug = (null) SlurmctldPrimaryOffProg = (null) SlurmctldPrimaryOnProg = (null) SlurmctldTimeout = 120 sec SlurmctldParameters = (null) SlurmdDebug = info SlurmdLogFile = /var/log/slurm/slurmd.log SlurmdParameters = (null) SlurmdPidFile = /var/run/slurmd.pid SlurmdPort = 6818 SlurmdSpoolDir = /var/spool/slurm SlurmdSyslogDebug = (null) SlurmdTimeout = 300 sec SlurmdUser = root(0) SlurmSchedLogFile = (null) SlurmSchedLogLevel = 0 SlurmctldPidFile = /var/run/slurmctld.pid SLURM_CONF = /etc/slurm/slurm.conf SLURM_VERSION = 23.11.1 SrunEpilog = (null) SrunPortRange = 0-0 SrunProlog = (null) StateSaveLocation = /var/spool/slurmctld SuspendExcNodes = (null) SuspendExcParts = (null) SuspendExcStates = (null) SuspendProgram = (null) SuspendRate = 60 nodes/min SuspendTime = INFINITE SuspendTimeout = 30 sec SwitchParameters = (null) SwitchType = (null) TaskEpilog = (null) TaskPlugin = task/cgroup,task/affinity TaskPluginParam = none TaskProlog = (null) TCPTimeout = 2 sec TmpFS = /tmp TopologyParam = (null) TopologyPlugin = topology/default TrackWCKey = No TreeWidth = 16 UsePam = No UnkillableStepProgram = (null) UnkillableStepTimeout = 60 sec VSizeFactor = 0 percent WaitTime = 0 sec X11Parameters = (null) Cgroup Support Configuration: AllowedRAMSpace = 100.0% AllowedSwapSpace = 0.0% CgroupMountpoint = /sys/fs/cgroup CgroupPlugin = autodetect ConstrainCores = yes ConstrainDevices = yes ConstrainRAMSpace = yes ConstrainSwapSpace = no EnableControllers = no IgnoreSystemd = no IgnoreSystemdOnFailure = no MaxRAMPercent = 100.0% MaxSwapPercent = 100.0% MemorySwappiness = (null) MinRAMSpace = 30 MB MPI Plugins Configuration: PMIxCliTmpDirBase = (null) PMIxCollFence = (null) PMIxDebug = 0 PMIxDirectConn = yes PMIxDirectConnEarly = no PMIxDirectConnUCX = no PMIxDirectSameArch = no PMIxEnv = (null) PMIxFenceBarrier = no PMIxNetDevicesUCX = (null) PMIxTimeout = 300 PMIxTlsUCX = (null) the partition is configured like: PartitionName=test-partition AllowGroups=sysadmin,users AllowAccounts=ALL AllowQos=ALL AllocNodes=ALL Default=NO QoS=N/A DefaultTime=NONE DisableRootJobs=YES ExclusiveUser=NO GraceTime=0 Hidden=NO MaxNodes=UNLIMITED MaxTime=UNLIMITED MinNodes=0 LLN=NO MaxCPUsPerNode=UNLIMITED MaxCPUsPerSocket=UNLIMITED Nodes=vserv-[275-277] PriorityJobFactor=1 PriorityTier=100 RootOnly=NO ReqResv=NO OverSubscribe=FORCE:1 OverTimeLimit=NONE PreemptMode=GANG,SUSPEND State=UP TotalCPUs=32 TotalNodes=4 SelectTypeParameters=NONE JobDefaults=(null) DefMemPerNode=UNLIMITED MaxMemPerNode=UNLIMITED TRES=cpu=32,mem=304933M,node=4,billing=32 Our QOS looks like this: | Name | Priority | GraceTime | Preempt | PreemptMode | Flags | UsageFactor | MaxTRESPU | MaxJobsPU | MaxSubmitPU |-----------|----------|-----------|-----------|-------------|-----------------|-------------|-----------------|-----------|----------- | normal | 50 | 00:00:00 | | cluster | | 1.000000 | | 20 | 50 | preempter | 1000 | 00:00:00 | preempted | gang,suspe+| | 1.000000 | | | | preempted | 0 | 00:00:00 | | gang,suspe+ | OverPartQOS | 1.000000 | cpu=100,node=10 | | I can provide more configs if needed. Do you guys see anything strange? Or any property to be set? This is the state of the queue: |JOBID | QOS | ST | TIME | NODELIST(REASON) | PARTITION | PRIORITY | | ---------------- ----------- --------- ----------- ---------------------- ----------------- ----------| | 3629 | preempted | PD | 0:00 | (Resources) | test-partition | 1 | | 3627 | preempted | R | 0:20 | vserv-276 | test-partition | 1 | | 3628 | preempted | R | 0:20 | vserv-277 | test-partition | 1 | | 3626 | preempted | R | 0:27 | vserv-275 | test-partition | 1 | | 3630 | preempter | PD | 0:00 | (Resources) | test-partition | 5000 | any advice is welcomed. Regards, Nischey Verma Nischey Verma [View Less]

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Issues with Slurm 23.11.1
by Fokke Dijkstra 15 Mar '24

15 Mar '24

Dear all, Since the upgrade from Slurm 22.05 to 23.11.1 we are having problems with the communication between the slurmctld and slurmd processes. We are running a cluster with 183 nodes and almost 19000 cores. Unfortunately some nodes are in a different network preventing full internode communication. A network topology and setting TopologyParam RouteTree have been used to make sure no slurmd communication happens between nodes on different networks. In the new Slurm version we see the … [View More]following issues, which did not appear in 22.05: 1. slurmd processes acquire many network connections in CLOSE-WAIT (or CLOSE_WAIT depending on the tool used) causing the processes to hang, when trying to restart slurmd. When checking for CLOSE-WAIT processes we see the following behaviour: Recv-Q Send-Q Local Address:Port Peer Address:Port Process 1 0 10.5.2.40:6818 10.5.0.43:58572 users:(("slurmd",pid=1930095,fd=72),("slurmd",pid=1930067,fd=72)) 1 0 10.5.2.40:6818 10.5.0.43:58284 users:(("slurmd",pid=1930095,fd=8),("slurmd",pid=1930067,fd=8)) 1 0 10.5.2.40:6818 10.5.0.43:58186 users:(("slurmd",pid=1930095,fd=22),("slurmd",pid=1930067,fd=22)) 1 0 10.5.2.40:6818 10.5.0.43:58592 users:(("slurmd",pid=1930095,fd=76),("slurmd",pid=1930067,fd=76)) 1 0 10.5.2.40:6818 10.5.0.43:58338 users:(("slurmd",pid=1930095,fd=19),("slurmd",pid=1930067,fd=19)) 1 0 10.5.2.40:6818 10.5.0.43:58568 users:(("slurmd",pid=1930095,fd=68),("slurmd",pid=1930067,fd=68)) 1 0 10.5.2.40:6818 10.5.0.43:58472 users:(("slurmd",pid=1930095,fd=69),("slurmd",pid=1930067,fd=69)) 1 0 10.5.2.40:6818 10.5.0.43:58486 users:(("slurmd",pid=1930095,fd=38),("slurmd",pid=1930067,fd=38)) 1 0 10.5.2.40:6818 10.5.0.43:58316 users:(("slurmd",pid=1930095,fd=29),("slurmd",pid=1930067,fd=29)) The first IP address is that of the compute node, the second that of the node running slurmctld. The nodes can communicate using these IP addresses just fine. 2. slurmd cannot be properly restarted [2024-01-18T10:45:26.589] slurmd version 23.11.1 started [2024-01-18T10:45:26.593] error: Error binding slurm stream socket: Address already in use [2024-01-18T10:45:26.593] fatal: Unable to bind listen port (6818): Address already in use This is probably because of the processes being in CLOSE-WAIT, which can only be killed using signal -9. 3. We see jobs stuck in completing CG state, probably due to communication issues between slurmctld and slurmd. The slurmctld sends repeated kill requests but those do not seem to be acknowledged by the client. This happens more often in large job arrays, or generally when many jobs start at the same time. However, this could be just a biased observation (i.e., it is more noticeable on large job arrays because there are more jobs to fail in the first place). 4. Since the new version we also see messages like: [2024-01-17T09:58:48.589] error: Failed to kill program loading user environment [2024-01-17T09:58:48.590] error: Failed to load current user environment variables [2024-01-17T09:58:48.590] error: _get_user_env: Unable to get user's local environment, running only with passed environment The effect of this is that the users run with the wrong environment and can’t load the modules for the software that is needed by their jobs. This leads to many job failures. The issue appears to be somewhat similar to the one described at: https://bugs.schedmd.com/show_bug.cgi?id=18561 In that case the site downgraded the slurmd clients to 22.05 which got rid of the problems. We’ve now downgraded the slurmd on the compute nodes to 23.02.7 which also seems to be a workaround for the issue. Does anyone know of a better solution? Kind regards, Fokke Dijkstra -- Fokke Dijkstra <f.dijkstra(a)rug.nl> <f.dijkstra(a)rug.nl> Team High Performance Computing Center for Information Technology, University of Groningen Postbus 11044, 9700 CA Groningen, The Netherlands [View Less]

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Overhead of multiple concurrent job steps
by Mehta, Kshitij 15 Mar '24

15 Mar '24

Hello, We have a use case in which we need to launch multiple concurrently running MPI applications inside a job allocation. Most supercomputing facilities limit the number of concurrent job steps as they incur an overhead with the global Slurm scheduler. Some frameworks, such as the Flux framework from LLNL, claim to mitigate this issue by starting an instance of their own scheduler inside an allocation, which then acts as the resource manager for the compute nodes in the allocation. Out of … [View More]

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Jobs being denied for GrpCpuLimit despite having enough resource
by Simon Andrews 14 Mar '24

14 Mar '24

Our cluster has developed a strange intermittent behaviour where jobs are being put into a pending state because they aren't passing the AssocGrpCpuLimit, even though the user submitting has enough cpus for the job to run. For example: $ squeue -o "%.6i %.9P %.8j %.8u %.2t %.10M %.7m %.7c %.20R" JOBID PARTITION NAME USER ST TIME MIN_MEM MIN_CPU NODELIST(REASON) 799 normal hostname andrewss PD 0:00 2G 5 (AssocGrpCpuLimit) ..so the job isn't running, … [View More]

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We're Live! Check out the new SchedMD.com now!
by Victoria Hobson 13 Mar '24

13 Mar '24

Our website has gone through some much needed change and we'd love for you to explore it! The new SchedMD.com is equipped with the latest information about Slurm, your favorite workload manager, and details about SchedMD services, support, and training offerings. Toggle through our Industries pages (https://www.schedmd.com/slurm-industries/) to learn more about how Slurm can service your specific site needs. Why Slurm? (https://www.schedmd.com/slurm/why-slurm/) gives you all the basics around … [View More]

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Slurm Utilities
by Paul Edmon 13 Mar '24

13 Mar '24

Just wanted to share some slurm utilities that we've written at Harvard FASRC that maybe useful to the community. seff-account: https://github.com/fasrc/seff-account Creates job statistics summaries for users and accounts similar to what seff and seff-array does. showq: https://github.com/fasrc/slurm_showq A slurm version of the Moab showq command lsload: https://github.com/fasrc/lsload A slurm version of the LSF lsload command scalc: https://github.com/fasrc/scalc&… [View More]

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Re: SLURM in K8s, any advice?
by LEAVY Alan 13 Mar '24

13 Mar '24

I'm a little late to this party but would love to establish contact with others using slurm in Kubernetes. I recently joined a research institute in Vienna (IIASA) and I'm getting to grips with slurm and Kubernetes (my previous role was data engineering / fintech). My current setup sounds like what Urban described in this thread, back in Nov 22. It has some rough edges though. Right now, I'm trying to upgrade to slurm-23.11.4 in Ubuntu 23.10 containers. I'm having trouble with the cgroup/v2 … [View More]

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Shards distribution over multiple GPUs
by Francois Broquedis 12 Mar '24

12 Mar '24

Hi all, We're trying to enable sharding on our compute cluster. On this cluster: - ensicompute-1 comes with 1 NVIDIA V100 GPU ; - ensicompute-13 comes with 3 NVIDIA A40 GPUs ; - all other nodes (for now, ensicompute-11 and ensicompute-12, but several others will come) come with 3 NVIDIA RTX 6000 GPUs. To enable sharding, I followed these steps: 1. [slurm.conf] Add "shard" to GresTypes ; 2. [slurm.conf] Add "shard:N" to Gres for each node. For testing purposes, I have set N to 9, so each GPU … [View More]can execute up to 3 jobs concurrently: NodeName=ensicompute-[11-12] Gres=gpu:Quadro:3,shard:9 CPUs=40 RealMemory=128520 Sockets=2 CoresPerSocket=10 ThreadsPerCore=2 State=UNKNOWN Feature=gpu,ht 3. [gres.conf] Declare the shards after the definition of the GPUs GRES. For step 3, I tried different things, leading to different outcomes: a. Define a global number of shards, for the entire host: Name=shard Count=9 ==> This way, sharding seems to work ok, but all the jobs are executed on GPU#0. If running 12 jobs for example, 9 of them are assigned to GPU#0 and start executing, while 3 of them remain in a pending state. No job is assigned to GPU#1 or GPU#2. b. Define a per-GPU number of shards, associated to the device file representing the GPU: Name=shard Count=3 File=/dev/nvidia0 Name=shard Count=3 File=/dev/nvidia1 Name=shard Count=3 File=/dev/nvidia2 ==> In this case, the slurmd service fails to start on the compute node. The error message found in /var/log/slurmd.log is "fatal: Invalid GRES record for shard, count does not match File value". c. Don't define anything about shards in gres.conf. ==> Same behavior than in a.: all jobs are executed on GPU#0. I attach to this message the full content of the slurm.conf and gres.conf files. What is the proper way to configure sharding in a cluster with several GPUs per node? Is there a way to specify how many shards should be allocated to each GPU? Cheers, François === slurm.conf === # slurm.conf file generated by configurator.html. # Put this file on all nodes of your cluster. # See the slurm.conf man page for more information. # ClusterName=ensimag SlurmctldHost=nash ProctrackType=proctrack/cgroup SlurmctldPidFile=/var/run/slurmctld.pid SlurmctldPort=6817 SlurmdPidFile=/var/run/slurmd.pid SlurmdPort=6818 SlurmdSpoolDir=/var/spool/slurmd SlurmUser=slurm #SlurmdUser=root StateSaveLocation=/var/spool/slurmctld TaskPlugin=task/affinity,task/cgroup ReturnToService=2 # # # TIMERS InactiveLimit=0 KillWait=30 MinJobAge=300 SlurmctldTimeout=120 SlurmdTimeout=300 Waittime=0 # # # SCHEDULING SchedulerType=sched/backfill SelectType=select/cons_tres # # # LOGGING AND ACCOUNTING JobCompType=jobcomp/none JobAcctGatherFrequency=30 SlurmctldDebug=info SlurmctldLogFile=/var/log/slurmctld.log SlurmdDebug=info SlurmdLogFile=/var/log/slurmd.log # # # COMPUTE NODES GresTypes=gpu,shard NodeName=ensicompute-1 Gres=gpu:Tesla:1,shard:3 CPUs=40 RealMemory=128520 Sockets=2 CoresPerSocket=10 ThreadsPerCore=2 State=UNKNOWN Feature=gpu,ht NodeName=ensicompute-13 Gres=gpu:A40:3,shard:9 CPUs=40 RealMemory=128520 Sockets=2 CoresPerSocket=10 ThreadsPerCore=2 State=UNKNOWN Feature=gpu,ht NodeName=ensicompute-[11-12] Gres=gpu:Quadro:3,shard:9 CPUs=40 RealMemory=128520 Sockets=2 CoresPerSocket=10 ThreadsPerCore=2 State=UNKNOWN Feature=gpu,ht PartitionName=compute Nodes=ALL Default=YES MaxTime=INFINITE State=UP === gres.conf === AutoDetect=off # ensicompute-1 NodeName=ensicompute-1 Name=gpu Type=Tesla File=/dev/nvidia0 NodeName=ensicompute-1 Name=shard Count=3 File=/dev/nvidia0 # ensicompute-11 NodeName=ensicompute-11 Name=gpu Type=Quadro File=/dev/nvidia0 NodeName=ensicompute-11 Name=gpu Type=Quadro File=/dev/nvidia1 NodeName=ensicompute-11 Name=gpu Type=Quadro File=/dev/nvidia2 NodeName=ensicompute-11 Name=shard Count=3 File=/dev/nvidia0 NodeName=ensicompute-11 Name=shard Count=3 File=/dev/nvidia1 NodeName=ensicompute-11 Name=shard Count=3 File=/dev/nvidia2 # ensicompute-12 NodeName=ensicompute-12 Name=gpu Type=Quadro File=/dev/nvidia0 NodeName=ensicompute-12 Name=gpu Type=Quadro File=/dev/nvidia1 NodeName=ensicompute-12 Name=gpu Type=Quadro File=/dev/nvidia2 NodeName=ensicompute-12 Name=shard Count=3 File=/dev/nvidia0 NodeName=ensicompute-12 Name=shard Count=3 File=/dev/nvidia1 NodeName=ensicompute-12 Name=shard Count=3 File=/dev/nvidia2 # ensicompute-13 NodeName=ensicompute-13 Name=gpu Type=A40 File=/dev/nvidia0 NodeName=ensicompute-13 Name=gpu Type=A40 File=/dev/nvidia1 NodeName=ensicompute-13 Name=gpu Type=A40 File=/dev/nvidia2 NodeName=ensicompute-13 Name=shard Count=3 File=/dev/nvidia0 NodeName=ensicompute-13 Name=shard Count=3 File=/dev/nvidia1 NodeName=ensicompute-13 Name=shard Count=3 File=/dev/nvidia2 -- François Broquedis, Ingénieur Service Informatique Grenoble INP - Ensimag, bureau E208 681 rue de la Passerelle BP 72, 38402 Saint Martin d'Hères CEDEX Tél.: +33 (0)4 76 82 72 78 [View Less]

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Re: user_name attribute missing in job response from slurm rest api method jobs
by Acartürk, Ayhan 11 Mar '24

11 Mar '24

Sorry... my previous message should have been a reply to the post by Filip Holka from March, 25th 2022: https://lists.schedmd.com/pipermail/slurm-users/2022-March/008543.html Best wishes, Ayhan Acartürk

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Re: user_name attribute missing in job response from slurm rest api method jobs
by Acartürk, Ayhan 11 Mar '24

11 Mar '24

Hello together, we have the same problem here. All jobs delivered by the api endpoint /slurm/v0.0.36/jobs have a user_id attached but no user_name. Currently, we solve this issue by an extra call for each job_id to the api endpoint /slurmdb/v.0.0.36/job/{job_id}. Any idea where to search for a possible solution is highly appreciated. Best wishes, Ayhan Acartürk

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Problem building slurm with PMIx
by Patrick Begou 11 Mar '24

11 Mar '24

Hi ! I manage a small CentOS8 cluster using slurm slurm-20.11.7-1 and OpenMPI built from sources. - I know this OS is not maintained any more and I need to negotiate downtime to reinstall - I know Slurm 20.11.7 has security issue (I've built it from source some years ago with rpmbuild -ta --with mysql --with hwloc slurm-20.11.7.tar.bz) and I should update. All was running fine until I add a GPU Node and Nvidia sdk. This SDK provides an openMPI3 implementation GPU aware but I'm … [View More]unable to launch an intranode parallel job with it using srun: -------------------------------------------------------------------------- The application appears to have been direct launched using "srun", but OMPI was not built with SLURM's PMI support and therefore cannot execute. There are several options for building PMI support under SLURM, depending upon the SLURM version you are using: version 16.05 or later: you can use SLURM's PMIx support. This requires that you configure and build SLURM --with-pmix. Versions earlier than 16.05: you must use either SLURM's PMI-1 or PMI-2 support. SLURM builds PMI-1 by default, or you can manually install PMI-2. You must then build Open MPI using --with-pmi pointing to the SLURM PMI library location. Please configure as appropriate and try again. -------------------------------------------------------------------------- I check with "srun --mpi=list" and got no pmx. srun: MPI types are... srun: pmi2 srun: cray_shasta srun: none So I decide to build the rpms from slurm-20.11.9.tar.bz2 as I had done previously for 20.11.7 and update. I've first installed pmix-2.1.1-1 from src as I had no pmix-devel rpm in my local CentOS8 repo: rpm --rebuild pmix-2.1.1-1.el8.src.rpm dnf install pmix-devel-2.1.1-1.el8.x86_64.rpm pmix-2.1.1-1.el8.x86_64.rpm Then build Slurm from slurm-20.11.9.tar.bz2 (just changing python3 to python38 in the spec file) rpmbuild -ta --with mysql --with hwloc --with pmix slurm-20.11.9.tar.bz2 And the try to install these package on the GPU node dnf install slurm-slurmd-20.11.9-1.el8.x86_64.rpm slurm-20.11.9-1.el8.x86_64.rpm slurm-devel-20.11.9-1.el8.x86_64.rpm slurm-libpmi-20.11.9-1.el8.x86_64.rpm But I get this strange error: Error: Problem: conflicting requests - nothing provides pmix = 20.11.9 needed by slurm-slurmd-20.11.9-1.el8.x86_64 (try to add '--skip-broken' to skip uninstallable packages or '--nobest' to use not only best candidate packages) Why this request on PMIX with the slurm version number ? Am I wrong somewhere ? Thanks for your help Patrick [View Less]

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FairShare value is always 0.
by Zacarias Benta 07 Mar '24

07 Mar '24

Hi guys, We've just setup our new cluster and are facing some issues regading fairshare calculation. Our slurm directive regarding priority calculation are defines as follows: PriorityType=priority/multifactor PriorityFlags=MAX_TRES PriorityDecayHalfLife=14-0 PriorityFavorSmall=NO PriorityMaxAge=14-0 PriorityWeightAge=1000 PriorityWeightJobSize=1000 PriorityWeightPartition=10000000 PriorityWeightQOS=10000000 PriorityWeightTRES=CPU=2000,Mem=4000 PriorityWeightFairshare=100000 The partition … [View More]we are submitinh out jobs to is setup as follows: PartitionName=mypartPriority=1000TRESBillingWeights="CPU=1.0,Mem=0.25G"Default=YESMaxTime=96:0:0DefMemPerCPU=5333Nodes=node[001-036] MaxNodes=20 Whenever we take a look at the fairshare value using sshare -l we see the following output: AccountUserRawSharesNormSharesRawUsageNormUsageEffectvUsageFairShareLevelFSGrpTRESMinsTRESRunMins ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- root10.0000002687245970.0000000.000000cpu=1098201,mem=5856709132,en+ rootroot10.10000000.0000000.0000000.000000cpu=0,mem=0,energy=0,node=0,b+ group110.10000000.0000000.000000cpu=0,mem=0,energy=0,node=0,b+ group210.10000000.0000000.000000cpu=0,mem=0,energy=0,node=0,b+ group310.1000002687245970.0000000.000000cpu=1098201,mem=5856709132,en+ group410.10000000.0000000.000000cpu=0,mem=0,energy=0,node=0,b+ group510.10000000.0000000.000000cpu=0,mem=0,energy=0,node=0,b+ group610.10000000.0000000.000000cpu=0,mem=0,energy=0,node=0,b+ group710.10000000.0000000.000000cpu=0,mem=0,energy=0,node=0,b+ group810.10000000.0000000.000000cpu=0,mem=0,energy=0,node=0,b+ group910.10000000.0000000.000000cpu=0,mem=0,energy=0,node=0,b+ We think it is really weird that the FairShare value is 0 for the root account and "NULL" for all other groups, even the one who had the greatest raw usage. While taking a look at the data for our users we see the following: AccountUserRawSharesNormSharesRawUsageEffectvUsageFairShare ------------------------------------------------------------------------------------- root10.0000002689837210.000000 rootroot10.10000000.0000000.000000 group310.1000002689837210.000000 group3user110.090909121093740.0000000.000000 group3user210.09090900.0000000.000000 group3user310.09090900.0000000.000000 group3user410.09090900.0000000.000000 group3user510.09090900.0000000.000000 group3user610.09090900.0000000.000000 group3user710.09090900.0000000.000000 group3user810.0909092088245970.0000000.000000 group3user910.09090900.0000000.000000 group3user1010.09090900.0000000.000000 group3user1110.090909480497500.0000000.000000 group410.10000000.000000 group4user1310.0000004994520.0000000.000000 group510.10000000.000000 group5user1410.00000015396030.0000000.000000 This is a weird behavior, since user1, user8, user11, user13 and user14 are the ones who have more RawUsage and the FairShare value is the same for all of them, including the users that have no yet submited any job. We also noticed that in the slurmctld log there is the fillowing error message that appears with some regularity [2024-03-07T16:38:13.260] error: _append_list_to_array: unable to append NULL list to assoc list. [2024-03-07T16:38:13.260] error: _calc_tree_fs: unable to calculate fairshare on empty tree The error above looks like it is coming from: https://github.com/SchedMD/slurm/blob/b11bf689b270f1f5dfe4b0cd54c4fa84b4af3… Are we missing any setting on slurm.conf? This is kind of strange, because we have another cluster with pretty much the same configuration and the FairShare is calculated without any problems. Any help would be appreciated. -- Cumprimentos / Best Regards, Zacarias Benta LIP/INCD @ UMINHO ---------------------------------------------- / Use linux, and may the source be with you. / ---------------------------------------------- \ __ -=(o '. '.-.\ /| \\ '| || _\_):,_ [View Less]

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Slurm management of dual-node server trays?
by Ole Holm Nielsen 07 Mar '24

07 Mar '24

We're in the process of installing some racks with Lenovo SD665 V3 [1] water-cooled servers. A Lenovo DW612S chassis contains 6 1U trays with 2 SD665 V3 servers mounted side-by-side in each tray. Lenovo delivers SD665 V3 servers including water-cooled NVIDIA InfiniBand "SharedIO" adapters [2] so that one node is the Primary including a PCIe adapter, and the other is Auxiliary with just a cable to the Primary's adapter. Obviously, servicing 2 "Siamese twin" Slurm nodes requires a bit of … [View More]

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Re: Lua script
by Paul Raines 06 Mar '24

06 Mar '24

Alternativelly consider setting EnforcePartLimits=ALL in slurm.conf -- Paul Raines (http://help.nmr.mgh.harvard.edu) 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 … [View More]

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Re: Lua script
by Gestió Servidors 06 Mar '24

06 Mar '24

And how can I reject the job inside the lua script?

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Lua script
by Gestió Servidors 06 Mar '24

06 Mar '24

Hello, I'm writing a small lua script that for modify "TimeLimit" of a submited job if user has configured a TimeLimit bigger that configured in the partition. So, is TimeLimit for partition is, for example, 4 hours (04:00:00) and user submit his/her job with a TimeLimit of 5 hours, lua script modify this submit and forces "TimeLimit" to 4 hours for avoiding that job remains at queue in state "pending" with reason "Partition Time Limit...". I have written these lines: function … [View More]

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Slurm billback and sreport
by Chip Seraphine 05 Mar '24

05 Mar '24

Hello, I am attempting to implement a billback model and finding myself stymied by the way that sreport handles job arrays. Basically, when a user submits a large array, their usage includes time that jobs in the back of the array spend waiting their turn. (My #1 user in “sreport user topusage” shows more “used” cpu*minutes than the cluster physically _has_ during that interval.) However, jobs that are idle pending resources are simply regarded as pending; as a result, a “polite” user … [View More]

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Is SWAP memory mandatory for SLURM
by John Joseph 04 Mar '24

04 Mar '24

Dear All, Good morning I do have a 4 node SLURM instance up and running. Like to know if I disable the SWAP memory, will it effect the SLURM performance Is SWAP a mandatory requirement, I have each node more RAM, if my phsicall RAM is more, is there any need for the SWAP thanks Joseph John

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What is "eligible time"
by Oren Shani 04 Mar '24

04 Mar '24

Hi All, Can someone shed some light on the exact meaning of the "eligible time" attribute in the slurm accounter, or to be more exact on the time between when the jobs becomes "eligible" to the time it actually starts to run? I understand that "eligible time" refers to the time in which the job becomes a candidate for running and that one case in which it will still not run, is that it waits for resources to become available. But are there any other conditions for a job to keep waiting at this … [View More]

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Question about IB and Ethernet networks
by Dan Healy 04 Mar '24

04 Mar '24

Hi Fellow Slurm Users, This question is not slurm-specific, but it might develop into that. My question relates to understanding how *typical* HPCs are designed in terms of networking. To start, is it typical for there to be a high speed Ethernet *and* Infiniband networks (meaning separate switches, NICs)? I know you can easily setup IP over IB, but is IB usually fully reserved for MPI messages? I’m tempted to spec all new HPCs with only a high speed (200Gbps) IB network, and use IPoIB for … [View More]

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How to get usage data for a QOS
by thomas.hartmann＠th-ht.de 01 Mar '24

01 Mar '24

Hi, so, I figured out that I can give some users priority access for a specific amount of TRES by creating a qos with the GrpTRESMins property and the DenyOnLimit,NoDecay flags. This works nicely. However, I would like to know, how much of this has already been consumed and I have not yet found a way to do this. Like: How can I get the amount of TRES/TRES minutes consumed for a certain QOS? Thanks a lot! Thomas

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MinTRES in QoS and power saving
by Stefan Walter 01 Mar '24

01 Mar '24

I am running a GPU cluster where nodes are mostly off to save on electricity. I have run into the problem that if I set 'MinTRES=gres/gpu=1' in the QoS for user-account associations, waking up nodes on-demand stops working for these users. Jobs are allocated on all running nodes but if a user starts a job that would require a node to be woken up, it remains pending with 'QOSMinGRES'. In the verbose logs, such a job will show this: debug3: TRES Weight: cpu = 1.000000 * 0.000000 = 0.000000 … [View More]

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pty jobs are killed when another job on the same node terminates
by Thomas Hartmann 01 Mar '24

01 Mar '24

Hi, when I start an interactive job like this: srun --pty --mem=3G -c2 bash And then I schedule and run other jobs (can be interactive or non interactive) and one of these jobs that runs on the same node terminates, the interactive job gets killed with this message: srun: error: node01.abc.at: task 0: Killed I attached our slurm config. Does anybody have an idea what is going on here or where I could look to debug? I'm quite new to slurm, so I don't know all the places to look... … [View More]

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GPU shards not exclusive
by Reed Dier 29 Feb '24

29 Feb '24

I seem to have run into an edge case where I’m able to oversubscribe a specific subset of GPUs on one host in particular. Slurm 22.05.8 Ubuntu 20.04 cgroups v1 (ProctrackType=proctrack/cgroup) It seems to be partly a corner case with a couple of caveats. This host has 2 different GPU types in the same host. All GPUs are configured with 6 shards/gpu. > NodeName=gpu03 CPUs=88 RealMemory=768000 Sockets=2 CoresPerSocket=22 ThreadsPerCore=2 State=… [View More]UNKNOWN Feature=avx512 Gres=gpu:rtx:2,gpu:p40:6,shard:48 My gres.conf is auto-nvml, with nothing else in the file. > AutoDetect=nvml Schedule and select from slurm.conf > SchedulerType=sched/backfill > SelectType=select/cons_tres > SelectTypeParameters=CR_CPU_Memory > GresTypes=gpu,shard Here’s a copy of slurmd’s log starting up with debug logging: https://pastebin.com/fbriTAZD <https://pastebin.com/fbriTAZD> I checked there to make sure that it was allocating an even 6 shards per GPU as intended, and it did. The only thing odd about the rtx cards is that they have an NVLink bridge between them, but I wouldn’t expect that to have any impact with respect to shards. So far it only appears to manifest if anything is using the named gpu (--gres gpu:rtx:1), but not as a general gres (--gres gpu:1). It also doesn’t occur with any count of named p40 gres either, only with the rtx gres. The below was as “high” as I was able to capture it oversubscribed in very quick testing. You can see there are 2 rtx and 43 shards allocated, which should be an impossible number, if we correctly assume an rtx==6 shards, and with 48 total shards, that should reduce the available pool of shards to 36 shards. > NodeName=gpu03 Arch=x86_64 CoresPerSocket=22 > CPUAlloc=88 CPUEfctv=88 CPUTot=88 CPULoad=0.27 > AvailableFeatures=avx512 > ActiveFeatures=avx512 > Gres=gpu:p40:6(S:0),gpu:rtx:2(S:0),shard:p40:36(S:0),shard:rtx:12(S:0) > NodeAddr=gpu03 NodeHostName=gpu03 Version=22.05.8 > OS=Linux 5.4.0-164-generic #181-Ubuntu SMP Fri Sep 1 13:41:22 UTC 2023 > RealMemory=768000 AllocMem=45056 FreeMem=563310 Sockets=2 Boards=1 > State=ALLOCATED+RESERVED ThreadsPerCore=2 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A > Partitions=gpu,gpu-prod > BootTime=2024-02-02T14:17:07 SlurmdStartTime=2024-02-14T16:28:17 > LastBusyTime=2024-02-14T16:38:03 > CfgTRES=cpu=88,mem=750G,billing=88,gres/gpu=8,gres/gpu:p40=6,gres/gpu:rtx=2,gres/shard=48 > AllocTRES=cpu=88,mem=44G,gres/gpu=2,gres/gpu:rtx=2,gres/shard=43 > CapWatts=n/a > CurrentWatts=0 AveWatts=0 > ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s The above is 1 rtx:2 jobs, and 43 shard:1 jobs, which is as many as I can seem to push through with the given cpu cores on the system, I expect if there were 98-100 cores I could completely oversubscribe it. If I do (1) rtx:2 + (24) shard:2 it actually limits it correctly to 36 shards, which is odd because the case that caused us to discover this was when 2 rtx:1 jobs were running for multiple days, and somehow shards got scheduled on those gpus. > AllocTRES=cpu=40,mem=20G,gres/gpu=2,gres/gpu:rtx=2,gres/shard=36 If I flip it around to shards before rtx, then I’m unable to oversubscribe it. If I add any P40 jobs before the rtx and then shard jobs, also unable to oversubscribe. This sounded familiar to Bug 16484 <https://bugs.schedmd.com/show_bug.cgi?id=16484> although they claimed it was resolved by using auto-nvml which would preclude this node. Here’s my very simple bash script that just srun's a sleep 20 so that it runs long enough to observe it. > #!/bin/bash > #rtx 2 > for((i=1;i<=1;++i)) ; > do > srun --gres gpu:rtx:2 --reservation=shardtest -J "RTX $i" sleep 20 & > done > sleep 1 > #shard 48 > for((i=1;i<=43;++i)) ; > do > srun --gres shard:1 --reservation=shardtest -J "shard $i" sleep 20 & > done > sleep 5 ; scontrol show node gpu03 Curious if anyone has any ideas beyond try a newer release? Thanks, Reed [View Less]

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sbatch and cgroup v2
by Dietmar Rieder 29 Feb '24

29 Feb '24

Hi, I'm new to slrum, but maybe someone can help me: I'm trying to restrict the CPU usage to the actually requested/allocated resources using cgroup v2. For this I made the following settings in slurmd.conf: ProctrackType=proctrack/cgroup TaskPlugin=task/cgroup,task/affinity And in cgroup.conf CgroupPlugin=cgroup/v2 CgroupAutomount=yes ConstrainCores=yes ConstrainRAMSpace=yes ConstrainDevices=yes AllowedRAMSpace=98 cgroup v2 seems to be active on the compute node: # mount | grep … [View More]cgroup cgroup2 on /sys/fs/cgroup type cgroup2 (rw,nosuid,nodev,noexec,relatime,nsdelegate,memory_recursiveprot) # cat /sys/fs/cgroup/cgroup.subtree_control cpuset cpu io memory pids # cat /sys/fs/cgroup/system.slice/cgroup.subtree_control cpuset cpu io memory pids Now, when I use sbatch to submit the following test script, the python script which is started from the batch script is utilizing all CPUs (96) at 100% on the allocated node, although I only ask for 4 cpus (--cpus-per-task=4). I'd expect that the task can not use more that these 4. #!/bin/bash #SBATCH --output=/local/users/appadmin/test-%j.log #SBATCH --job-name=test #SBATCH --chdir=/local/users/appadmin #SBATCH --cpus-per-task=4 #SBATCH --ntasks=1 #SBATCH --nodes=1 #SBATCH --mem=64gb #SBATCH --time=4:00:00 #SBATCH --partition=standard #SBATCH --gpus=0 #SBATCH --export #SBATCH --get-user-env=L export PATH=/usr/local/bioinf/jupyterhub/bin:/usr/local/bioinf/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/bioinf/miniforge/condabin source .bashrc conda activate test python test.py The python code in test.py is the following using the cpu_load_generator package from [1]: #!/usr/bin/env python import sys from cpu_load_generator import load_single_core, load_all_cores, from_profile load_all_cores(duration_s=120, target_load=1) # generates load on all cores Interestingly, when I use srun to launch an interactive job, and run the python script manually, I see with top that only 4 cpus are running at 100%. And I also python errors thrown when the script tries to start the 5th process (which makes sense): File "/usr/local/bioinf/miniforge/envs/test/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/usr/local/bioinf/miniforge/envs/test/lib/python3.12/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/usr/local/bioinf/miniforge/envs/test/lib/python3.12/site-packages/cpu_load_generator/_interface.py", line 24, in load_single_core process.cpu_affinity([core_num]) File "/usr/local/bioinf/miniforge/envs/test/lib/python3.12/site-packages/psutil/__init__.py", line 867, in cpu_affinity self._proc.cpu_affinity_set(list(set(cpus))) File "/usr/local/bioinf/miniforge/envs/test/lib/python3.12/site-packages/psutil/_pslinux.py", line 1714, in wrapper return fun(self, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/bioinf/miniforge/envs/test/lib/python3.12/site-packages/psutil/_pslinux.py", line 2213, in cpu_affinity_set cext.proc_cpu_affinity_set(self.pid, cpus) OSError: [Errno 22] Invalid argument What am I missing, why are the CPU resources not restricted when I use sbatch? Thanks for any input or hint Dietmar [1]: https://pypi.org/project/cpu-load-generator/ [View Less]

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slurmdbd error - Symbol `slurm_conf' has different size in shared object
by Miriam Olmi 29 Feb '24

29 Feb '24

Hi all, I am having some issue with the new version of slurm 23.11.0-1. I had already installed and configured slurm 23.02.3-1 on my cluster and all the services were active and running properly. Following the instructions of the official SLURM webpage, for the moment I upgrated only the slurmdbd service. In principle the cluster should be able to work properly if the slurmdbd has a higher version with respect to slurmctld and slurmd. Unfortunately the slurmdbd service fails to start … [View More]

2 4

salloc+srun vs just srun
by wdennis＠nec-labs.com 28 Feb '24

28 Feb '24

Hi list, In our institution, our instructions to users who want to spawn an interactive job (for us, a bash shell) have always been to do "srun ..." from the login node, which has always been working well for us. But when we had a recent Slurm training, the SchedMD folks advised us to use "salloc" and then "srun" to do interactive jobs. I tried this today, "salloc" gave me a shell on a server, the same as srun does, but then when I tried to "srun [programname]" it hung there with no output. Of … [View More]

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