October 2024 - slurm-users - lists.schedmd.com

Dependency jobs
by adam＠bramblecfd.com 17 Oct '24

17 Oct '24

Hi Slurm Users, I am trying to figure out if there is a way you can check if a running job has any jobs queued up after it that depend on the current running job, I know you can show job info and find what dependency a job is waiting for, But more after checking if there are jobs waiting on the current job to complete using the job ID, Many Thanks, Adam

3 2

AllowAccounts partition setting
by Marko Markoc 16 Oct '24

16 Oct '24

Hi All, At one point, when we were running slurm 22, we set up a few new partitions with `AllowAccounts` setting enabled. We limit access to these partitions only to a few accounts. We manually create these accounts and users using the `sacctmgr` command. At that time, everything was working. Only users in these accounts were able to run jobs in that partition. Few months ago we upgraded slurm to 23.02.7 but just a couple of days ago we noticed that anyone could submit jobs to these partitions. In addition to that, you can provide any value to the `--account` directive and slurm will accept and record it in the job accounting database. In our initial testing, you could only provide `--account` value that has been previously created. I'm still looking into this but I wanted to check if there was any change in version 23 that could have impacted this? I don't remember seeing anything in release notes. Thanks, Marko

6 8

Problem with nodes with 1 gpu
by Jörg Striewski 16 Oct '24

16 Oct '24

i cannot send jobs to nodes with one gpu, i don't find the bug in my configuration. can someone help me ? in slurm.conf GresTypes=gpu is set this are some nodes in slurm.conf NodeName=gpu-[001-003] CPUs=8 SocketsPerBoard=1 CoresPerSocket=4 RealMemory=31000 Gres=gpu:1080:1 NodeName=gpu-[010-019] CPUs=16 SocketsPerBoard=1 CoresPerSocket=8 RealMemory=64000 Gres=gpu:1080:2 the partition for this gpu nodes is # General GPU partitions PartitionName=GPU Nodes=gpu-[001-003,010-019] AllowAccounts=staff PreemptMode=REQUEUE PriorityTier=0 DefMemPerGPU=32000 DefCpuPerGPU=8 CpuBind=none TRESBillingWeights="GRES/gpu=1000" GraceTime=300 this are the entries for some nodes in gres.conf NodeName=gpu-[001-003] Name=gpu Type=1080 File=/dev/nvidia0 NodeName=gpu-[010-019] Name=gpu Type=1080 File=/dev/nvidia[0-1] when i send a job with sbatch to gpu-001 #SBATCH --job-name=hello #SBATCH --ntasks-per-node=1 #SBATCH --output=hello_%A.out #SBATCH --time=00:10:00 #SBATCH --mail-type=ALL #SBATCH --mail-user=striewski(a)ismll.de #SBATCH --partition=GPU #SBATCH --nodelist=gpu-001 #SBATCH --gres=gpu:1 [...] i get the error sbatch: error: Batch job submission failed: Requested node configuration is not available when i send the job to a node with 2 gpu's it runs with no error, just setting --nodelist=gpu-12 has someone a hint what i made wrong ? Mit freundlichen Grüßen / kind regards -- Jörg Striewski Information Systems and Machine Learning Lab (ISMLL) Institute of Computer Science University of Hildesheim Germany post address: Universitätsplatz 1, D-31141Hildesheim, Germany visitor address: Samelsonplatz 1, D-31141 Hildesheim,Germany Tel.(+49) 05121 / 883-40392 http://www.ismll.uni-hildesheim.de

2 2

unsuscribe
by LEROY Christine 208562 15 Oct '24

15 Oct '24

unsuscribe

1 0

How does --nodes=min[-max] determine number of nodes to allocate?
by Declan Valters 08 Oct '24

08 Oct '24

Hi, I am trying to understand how Slurm determines the actual number of nodes to allocate to a job specified with -nodes=min[-max] I've been trying to follow the source code through on Github - could anyone point me in the right area(s)/source files/functions to look at to understand the program logic behind this. Many thanks in advance, Declan The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

2 1

Jobs not getting scheduled, no priority calculation, but still in queue?
by Cutts, Tim 07 Oct '24

07 Oct '24

Something odd is going on on our cluster. User has a lot of pending jobs in a job array (a few thousand). squeue -u kmnx005 -r -t PD | head -5 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 3045324_875 core run_scp_ kmnx005 PD 0:00 1 (JobArrayTaskLimit) 3045324_876 core run_scp_ kmnx005 PD 0:00 1 (JobArrayTaskLimit) 3045324_877 core run_scp_ kmnx005 PD 0:00 1 (JobArrayTaskLimit) 3045324_878 core run_scp_ kmnx005 PD 0:00 1 (JobArrayTaskLimit) None are getting scheduled. But when I ask SLURM what that job’s priority is, it produces no output: $ sprio -j 3045324 JOBID PARTITION PRIORITY SITE AGE FAIRSHARE JOBSIZE PARTITION QOS TRES Any clues what’s going on here? -- Tim Cutts Scientific Computing Platform Lead AstraZeneca Find out more about R&D IT Data, Analytics & AI and how we can support you by visiting our Service Catalogue<https://azcollaboration.sharepoint.com/sites/CMU993> | ________________________________ 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>

2 3

SLURM GRES reservation not working properly on 24.05.1
by Minulakshmi S 07 Oct '24

07 Oct '24

Hello, *Issue 1:* I am using slurm version 24.05.1 , my slurmd has a single node where I connect multiple gres by enabling the overscribe feature. I am able to use the advance reservation of gres only using *gres** name* (tres=gres/gpu:*SYSTEM12*). i.e while in reservation period , if other users submits job with SYSTEM12 , then slurm places this job in queue *user1@host$ srun --gres=gpu:SYSTEM12:1 hostname* *srun: job 333 queued and waiting for resources * but when other users just submit a job without any system name , slurm jobs goes through on that gres immediately even though it is reserved. *user1@host$ srun --gres=gpu:1 hostname * *mylinux.wbi.com <http://mylinux.wbi.com/> * Also I can see GresUsed in busy mode using "*scontrol show node -d*" , this means the job is running on Gres/GPU and not on cpu etc. Same way , job submission based on Feature "rev1 in my case" is also going through even though it is reserved for other users in multiple partition slurm. *snippet of slurm.conf file* NodeName=cluster01 NodeAddr=cluster Port=6002CPUs=8 Boards=1 SocketsPerBoard=1 CoresPerSocket=8 ThreadsPerCore=2 Feature="rev1" Gres=gpu:SYSTEM12:1 RealMemory=64171 State=IDLE *Issue 2:* while execution , Slurm o/p's some extra prints in the srun output user1@host$ srun --gres=gpu:1 hostname srun: error: extract_net_cred: net_cred not provided srun: error: Malformed RPC of type RESPONSE_NODE_ALIAS_ADDRS(3017) received srun: error: slurm_unpack_received_msg: [mylinux.wbi.com]:41242] Header lengths are longer than data received *mylinux.wbi.com <http://mylinux.wbi.com/>* Regards, MS

1 1

Slurmctld process error 'double free or corruption' on RHEL 9 (Rocky Linux)
by William VINCENT 07 Oct '24

07 Oct '24

Hello I am writing to report an issue with the Slurmctld process on our RHEL 9 (Rocky Linux) . Twice in the past 5 days, the Slurmctld process has encountered an error that resulted in the service stopping. The error message displayed was "double free or corruption (out)". This error has caused significant disruption to our jobs, and we are concerned about its recurrence. We have tried troubleshooting the issue, but we have not been able to identify the root cause of the problem. We would appreciate any assistance or guidance you can provide to help us resolve this issue. Please let us know if you need any additional information or if there are any specific steps we should take to diagnose the problem further. Thank you for your attention to this matter. Best regards, _________________________ Jul 09 22:12:01 admin slurmctld[711010]: double free or corruption (fasttop) Jul 09 22:12:01 admin systemd[1]: slurmctld.service: Main process exited, code=killed, status=6/ABRT Jul 09 22:12:01 admin systemd[1]: slurmctld.service: Failed with result 'signal'. Jul 09 22:12:01 admin systemd[1]: slurmctld.service: Consumed 11min 26.451s CPU time. ..... Jul 14 10:15:01 admin slurmctld[1633720]: double free or corruption (out) Jul 14 10:15:02 admin systemd[1]: slurmctld.service: Main process exited, code=killed, status=6/ABRT Jul 14 10:15:02 admin systemd[1]: slurmctld.service: Failed with result 'signal'. Jul 14 10:15:02 admin systemd[1]: slurmctld.service: Consumed 7min 27.596s CPU time. _________________________ slurmctld -V slurm 22.05.9 ________________________ cat /etc/slurm/slurm.conf |grep -v '#' ClusterName=xxx SlurmctldHost=admin SlurmctldParameters=enable_configless SlurmUser=slurm AuthType=auth/munge CryptoType=crypto/munge SlurmctldPort=6817 StateSaveLocation=/var/spool/slurmctld SlurmctldLogFile=/var/log/slurm/slurmctld.log SlurmctldDebug=verbose DebugFlags=NO_CONF_HASH SlurmdPort=6818 SlurmdSpoolDir=/var/spool/slurmd SlurmdLogFile=/var/log/slurm/slurmd.log SlurmdDebug=verbose SchedulerType=sched/backfill SelectType=select/cons_tres SelectTypeParameters=CR_Core,CR_LLN DefMemPerCPU=1024 MaxMemPerCPU=4096 GresTypes=gpu ProctrackType=proctrack/cgroup JobAcctGatherType=jobacct_gather/cgroup JobAcctGatherFrequency=15 JobCompType=jobcomp/none TaskPlugin=task/cgroup LaunchParameters=use_interactive_step AccountingStorageType=accounting_storage/slurmdbd AccountingStorageHost=admin AccountingStoragePort=6819 AccountingStorageEnforce=associations AccountingStorageTRES=gres/gpu MailProg=/usr/bin/mailx EnforcePartLimits=YES MaxArraySize=200000 MaxJobCount=500000 MpiDefault=none ReturnToService=2 SwitchType=switch/none TmpFS=/tmpslurm/ UsePAM=1 InactiveLimit=0 KillWait=30 MessageTimeout=30 MinJobAge=300 SlurmctldTimeout=120 SlurmdTimeout=300 Waittime=0 PriorityType=priority/multifactor PriorityFlags=FAIR_TREE,MAX_TRES PriorityDecayHalfLife=1-0 PriorityWeightFairshare=10000 NodeName=xxx NodeHostname=xxx CPUs=4 Sockets=4 RealMemory=3500 TmpDisk=1 CoresPerSocket=1 ThreadsPerCore=1 State=DRAIN NodeName=xxx NodeHostname=xxx CPUs=2 Sockets=2 RealMemory=1700 TmpDisk=1 CoresPerSocket=1 ThreadsPerCore=1 State=DRAIN NodeName=xxx NodeHostname=xxx CPUs=4 Sockets=4 RealMemory=1700 TmpDisk=1 CoresPerSocket=1 ThreadsPerCore=1 State=DRAIN NodeName=xxx NodeHostname=xxx CPUs=4 Sockets=4 RealMemory=3500 TmpDisk=1 CoresPerSocket=1 ThreadsPerCore=1 State=DRAIN NodeName=r9nc-24-[1-12] NodeHostname=r9nc-24-[1-12] Sockets=2 CoresPerSocket=12 ThreadsPerCore=1 CPUs=24 RealMemory=180000 State=UNKNOWN NodeName=r9nc-48-[1-4] NodeHostname=r9nc-48-[1-4] Sockets=2 CoresPerSocket=24 ThreadsPerCore=1 CPUs=48 RealMemory=480000 State=UNKNOWN NodeName=r9ng-1080-[1-7] NodeHostname=r9ng-1080-[1-7] Sockets=2 CoresPerSocket=10 ThreadsPerCore=1 CPUs=20 RealMemory=180000 State=UNKNOWN Gres=gpu:1080ti:4 NodeName=r9ng-1080-8 NodeHostname=r9ng-1080-8 Sockets=2 CoresPerSocket=10 ThreadsPerCore=1 CPUs=20 RealMemory=176687 State=UNKNOWN Gres=gpu:1080ti:1 PartitionName=24CPUNodes Nodes=r9nc-24-[1-12] State=UP MaxTime=UNLIMITED OverSubscribe=NO MaxMemPerCPU=7500 DefMemPerCPU=7500 TRESBillingWeights="CPU=1.0,Mem=0.125G" Default=YES PartitionName=48CPUNodes Nodes=r9nc-48-[1-4] State=UP MaxTime=UNLIMITED OverSubscribe=NO MaxMemPerCPU=10000 DefMemPerCPU=8000 TRESBillingWeights="CPU=1.0,Mem=0.125G" PartitionName=GPUNodes Nodes=r9ng-1080-[1-7] State=UP MaxTime=UNLIMITED OverSubscribe=NO MaxMemPerCPU=9000 DefMemPerCPU=9000 PartitionName=GPUNodes1080-dev Nodes=r9ng-1080-8 State=UP MaxTime=UNLIMITED OverSubscribe=NO MaxMemPerCPU=9000 DefMemPerCPU=9000 Hidden=Yes _________________________ sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST 24CPUNodes* up infinite 12 idle r9nc-24-[1-12] 48CPUNodes up infinite 2 idle r9nc-48-[1-2] GPUNodes up infinite 4 idle r9ng-1080-[4-7] GPUNodes1080-dev up infinite 1 idle r9ng-1080-8 -- William VINCENT Administrateur systèmes et réseaux

4 15

license server redundancy
by Yves Kondoszek 03 Oct '24

03 Oct '24

Hello. I'm configuring a cluster that will run jobs that use FlexLM licenses. We have what I believe is a quite standard configuration of license servers - though I haven't found anything in the documentation or in the mailing list archives - that often provide the same features across several servers; for example, the license token "simulation" will be available at let's say 1717@server1, 1717@server2 and 4000@server3 . FlexLM clients support those through a path-style environment variable, typically LM_LICENSE_FILE=1717@server1:1717@server2:4000@server3 . Now, I have set up Slurm for remote dynamic licenses and update them live through "LastConsumed" from lmstat requests, so that Slurm is aware of some users checking them out externally (out of Slurm control). But my problem is that the documentation clearly states that: "When submitting jobs to remote licenses, the name and server must be used." So I have to specifically choose a server: $ sbatch -L simulation@server2 script.sh instead of telling Slurm to just use whatever license is available on any of the servers. Does any of you have any experience with redundant FlexLM licenses through several servers? Is there a way Slurm could support this?

1 0

GPU Accounting
by Emyr James 03 Oct '24

03 Oct '24

We have a node with 8 H100 GPUs that are split into MIG instances. We are using cgroups. This seems to work fine. Users can do something like sbatch --gres="gpu:1g.10gb:1"... and the job starts on the node with the gpus and cuda visible devices and the pytorch debug shows that the cgroup only gives them the gpu they asked for. In the accounting database, jobs in the job table always have the "gres_used" column be empty. I'd expect to see "gpu:1g.10gb:1" appearing for the job above. I have this set in slurm.conf AccountingStorageTRES=gres/gpu How can I see what gres was requested with the job ? At the moment I only see something like this in AllocTres billing=1,cpu=1,gres/gpu=1,mem=8G,node=1 and can't see any way to see what the specific MIG gpu asked for was. This is related to the email from Richard Lefebvre dated 7th June 2023 entitled "Billing/accounting for MIGs is not working". As far as I can see this got no replies. We are running slurm version 23.11.6. Regards, Emyr James Head of Scientific IT CRG - Centre for Genomic Regulation

2 1

2024

slurm-users October 2024 ----- 2024 ----- December 2024 November 2024 October 2024 September 2024 August 2024 July 2024 June 2024 May 2024 April 2024 March 2024 February 2024 January 2024

slurm-users October 2024