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Recover Batch Script Error
by Jason Simms 16 Feb '24

16 Feb '24

Hello all, I've used the "scontrol write batch_script" command to output the job submission script from completed jobs in the past, but for some reason, no matter which job I specify, it tells me it is invalid. Any way to troubleshoot this? Alternatively, is there another way - even if a manual database query - to recover the job script, assuming it exists in the database? sacct --jobs=38960 JobID JobName Partition Account AllocCPUS State ExitCode ------------ ---------- ---------- ---------- ---------- ---------- -------- 38960 amr_run_v+ tsmith2lab tsmith2lab 72 COMPLETED 0:0 38960.batch batch tsmith2lab 40 COMPLETED 0:0 38960.extern extern tsmith2lab 72 COMPLETED 0:0 38960.0 hydra_pmi+ tsmith2lab 72 COMPLETED 0:0 scontrol write batch_script 38960 job script retrieval failed: Invalid job id specified Warmest regards, Jason -- *Jason L. Simms, Ph.D., M.P.H.* Manager of Research Computing Swarthmore College Information Technology Services (610) 328-8102 Schedule a meeting: https://calendly.com/jlsimms

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Need help managing licence
by Sylvain MARET 16 Feb '24

16 Feb '24

Hello everyone ! Recently our users bought a cplex dynamic license and want to use it on our slurm cluster. I've installed the paid version of cplex within modules so authorized user can load it with a simple module load cplex/2111 command but I don't know how to manage and ensure slurm doesn't launch a job if 20 people are already running code with this license. How do you guys manage paid licenses on your cluster ? Any advice would be appreciated ! Regards, Sylvain Maret

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MPI/PMIx Issues after 23.11 Update
by Oliver Smith 16 Feb '24

16 Feb '24

Hi all, We’re running a small slurm dev cluster on Ubuntu and are facing issues with MPI/PMIx after upgrading slurm from 23.02.5 to 23.11.3. The first job step to use MPI within a job fails roughly 80% of the time but following attempts to use MPI within the same job work fine. For the failing job step we see this error after hitting the MPI timeout: slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_reset_if_to: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:741: 0x55a03f8d7a90: collective timeout seq=0 slurmstepd: error: mpi/pmix_v4: pmixp_coll_log: hpc-d-msh-01a02 [1]: pmixp_coll.c:286: Dumping collective state slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:759: 0x55a03f8d7a90: COLL_FENCE_RING state seq=0 slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:762: my peerid: 1:hpc-d-msh-01a02 slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:769: neighbor id: next 0:hpc-d-msh-01a01, prev 0:hpc-d-msh-01a01 slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:778: Context ptr=0x55a03f8d7b08, #0, in-use=0 slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:778: Context ptr=0x55a03f8d7b40, #1, in-use=0 slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:778: Context ptr=0x55a03f8d7b78, #2, in-use=1 slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:787: seq=0 contribs: loc=1/prev=1/fwd=0 slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:791: neighbor contribs [2]: slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:824: done contrib: hpc-d-msh-01a01 slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:826: wait contrib: - slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:828: status=PMIXP_COLL_RING_FINILIZE slurmstepd: error: mpi/pmix_v4: pmixp_coll_ring_log: hpc-d-msh-01a02 [1]: pmixp_coll_ring.c:831: buf (offset/size): 0/33362 [hpc-d-msh-01a01.tds.hpc.barf1.com:47652] pml_ucx.c:178 Error: Failed to receive UCX worker address: Not found (-13) [hpc-d-msh-01a01.tds.hpc.barf1.com:47652] pml_ucx.c:477 Error: Failed to resolve UCX endpoint for rank 31 [hpc-d-msh-01a01:47652] *** An error occurred in MPI_Send [hpc-d-msh-01a01:47652] *** reported by process [683360612,0] [hpc-d-msh-01a01:47652] *** on communicator MPI_COMM_WORLD [hpc-d-msh-01a01:47652] *** MPI_ERR_OTHER: known error not in list [hpc-d-msh-01a01:47652] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, [hpc-d-msh-01a01:47652] *** and potentially your MPI job) slurmstepd: error: *** STEP 1890.0 ON hpc-d-msh-01a01 CANCELLED AT 2024-02-14T16:14:52 *** OpenMPI/PMIx versions have not changed and downgrading slurm to 23.02.5 seems to resolve the issue. We’d appreciate any pointers anyone might have. Thanks Oli This email comprises confidential information of Mercedes-Benz Grand Prix Limited ("MGP") unless it contains an explicit statement to the contrary made by an authorised representative of MGP. Contracts may only be concluded on behalf of MGP by its authorised signatories and not solely by email communication. No employee, agent, contractor, consultant and/or other representative of MGP is authorised to conclude any legally binding agreement on behalf of MGP by email alone without the express prior written confirmation of two authorised signatories of MGP. Mercedes-Benz Grand Prix Limited. Registered in England No. 787446. Registered Office at Mercedes-Benz Grand Prix Limited, Operations Centre, Brackley, Northants NN13 7BD. Note: The MGP Legal Department also acts on behalf of Mercedes-Benz Motorsport Limited ("MBM") and the above notice applies mutatis mutandis in respect of all email communications of MBM. MBM: Mercedes-Benz Motorsport Limited. Registered in England No. 13057973. Registered office at Mercedes-Benz Motorsport Limited, Lauda Drive, Brackley, Northants NN13 7BD. Please consider the environment before printing this email.

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slurmctld: slurm_bufs_sendto(msg_type=SRUN_STEP_SIGNAL) failed: Connection reset by peer
by Rike-Benjamin Schuppner 15 Feb '24

15 Feb '24

Hi, I am getting the following error in the logs whenever I run a few srun jobs in a batch. Jan 25 11:24:03 slurmctl.XYZ slurmctld[272961]: slurmctld: debug: _send_timeout: Socket POLLERR: Connection reset by peer Jan 25 11:24:03 slurmctl.XYZ slurmctld[272961]: slurmctld: error: slurm_send_node_msg: [socket:[921897]] slurm_bufs_sendto(msg_type=SRUN_STEP_SIGNAL) failed: Connection reset by peer Jan 25 11:24:03 slurmctl.XYZ slurmctld[272961]: slurmctld: debug: laying out the 1 tasks on 1 hosts compute2 dist 1 The slurm version is 23.11.3 and an example sbatch file is: #!/bin/bash #SBATCH --job-name=slurm_test #SBATCH --mem=1gb #SBATCH --time=00:05:00 #SBATCH --output=slurm_test_%j.log pwd; hostname; date srun --exclusive -c1 -N1 -n1 bash -c "hostname ; sleep 10" & srun --exclusive -c1 -N1 -n1 bash -c "hostname ; sleep 10" & wait The more sruns I have in the script (&-backgrounded or not), the more the error shows up. Is there anything I could do to fix this error? Best /rike

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Naive SLURM question: equivalent to LSF pre-exec
by Cutts, Tim 14 Feb '24

14 Feb '24

Hi, I apologise if I’ve failed to find this in the documentation (and am happy to be told to RTFM) but a recent issue for one of my users resulted in a question I couldn’t answer. LSF has a feature called a Pre-Exec where a script executes to check whether a node is ready to run a task. So, you can run arbitrary checks and go back to the queue if they fail. For example, if I have some automounted filesystems, and I want to be able to check for failure of the automounted, in an LSF world, I can do: bsub -E “test -f /nfs/someplace/file_I_know_exists” my_job.sh What’s the equivalent in SLURM? Thanks, Tim -- 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>

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job_submit.lua - uid in Docker cluster
by Loris Bennett 14 Feb '24

14 Feb '24

Hi, Having used https://github.com/giovtorres/slurm-docker-cluster successfully a couple of years ago to develop a job_submit.lua plugin, I am trying to do this again. However, the plugin which works on our current cluster (CentOS 7.9, Slurm 23.02.7) fails in the Docker cluster (Rocky 8.9, Slurm 23.02.7) with error: job_submit/lua: /etc/slurm/job_submit.lua: /usr/share/lua/5.3/posix/deprecated.lua:453: bad argument #1 to 'getpwuid' (int expected, got number) which occurs when submit_user = posix.getpasswd(submit_user.uid) The problems is that 'submit_user.uid' has the value 0.0 and is thus not an integer. The only user within the Docker cluster is 'root'. Has anyone come across this issue? Is it to do with the Docker environment or the difference in the OS versions (Lua 5.1.4 vs. 5.3.4, lua-posix 32 vs. 33.3.1)? Cheers, Loris -- Dr. Loris Bennett (Herr/Mr) FUB-IT (ex-ZEDAT), Freie Universität Berlin

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Increasing SlurmdTimeout beyond 300 Seconds
by Andrew Baughan (ITCS - Staff) 12 Feb '24

12 Feb '24

Hi, We've been experiencing issues with network saturation on our older nodes caused by storage (GPFS) backups. This causes slurmctld to loose contact with slurmd on some compute nodes and for user jobs to be killed. While the longer term solution is to replace these and upgrade the network, I'm wondering if there are any ramifications, beyond nodes with genuine issues taking longer to get marked down, by increasing SlurmdTimeout. We've already applied a modest increase which has helped but not resolved the issue and wondering if we should push it further in the interim. Kind Regards Andy Baughan HPC Systems Developer

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simple question, I guess… from a newbie sysadmin
by Richard Randriatoamanana 12 Feb '24

12 Feb '24

Hi, I am trying to help a sysadmin colleague (and to understand for myself) trying to configure a new slurm server and he struggles to understand if there is an alternative way to config slurm managing job policy submission per user without necessarily installing an accounting mariadb service. I said no but maybe I misunderstand slurm admin configuration. Thanks in advance for feedback. Bests, Richard — Sent from my rotary and brandy phone ! Apologies for typos and any spelling errors

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Question on using a suffix with "squeue --Format=FORMAT"
by urbanjost 10 Feb '24

10 Feb '24

I do not see how to use the suffix for the --Format option of the squeue(1) command. The description does not indicate how to tell the end of the size and period components and the beginning of the suffix, but assuming the suffix must being with something other than a period or numeric character I found all suffix values produce a null separator. A wanted to use --Format somewhat like --format=%all, producing all fields. As the --Format did not have an equivalent descriptor, (ie. something like --Format=All ) it looked like it would be required to list all the allowed keywords with a suffix of "|", which from the description I assumed would be as simple as a longer version of something like thi: squeue --Format='STDOUT:|,STDERR:|,STDIN:|,WorkDir:|' Given the description: -O, --Format=<output_format> Specify the information to be displayed. Also see the -o, --format=<output_format> option described above (which supports greater flexibility in formatting, but does not support access to all fields because we ran out of letters). Requests a comma separated list of job information to be displayed. The format of each field is "type[:[.][size][suffix]]" size Minimum field size. If no size is specified, 20 char‐ acters will be allocated to print the information. . Indicates the output should be right justified and size must be specified. By default output is left justified. suffix Arbitrary string to append to the end of the field. Note that many of these type specifications are valid only for jobs while others are valid only for job steps. Valid type specifications include: Even something like this produces no error but the suffix is always a null string: squeue --Format='STDOUT:SUFFIX,STDERR:SUFFIXSTDIN:SUFFIXWorkDir:SUFFIX So if I want to generate output with squeue --Format=FORMAT with a vertical line character between the output fields what is the proper syntax? A test bash(1) script where I could not get the SUFFIX variable to work as expected ... #!/bin/bash #@(#) Build value for squeue --Format='FORMAT' that includes all available fields with a vertical bar separating each field GOODNAMES='' BADNAMES='' SUFFIX='SUFFIX' GOODNAMES='' BADNAMES='' SUFFIX='1000:|' GOODNAMES='' BADNAMES='' SUFFIX='|' for NAME in STDOUT Account AccrueTime admin_comment AllocNodes AllocSID ArrayJobID ArrayTaskID AssocID BatchFlag BatchHost BoardsPerNode BurstBuffer BurstBufferState Cluster ClusterFeature Command Comment Container ContainerID Contiguous Cores CoreSpec CPUFreq cpus-per-task cpus-per-tres Deadline DelayBal Licenses MaxCPUs MaxNodes MCSLabel mem-per-tres MinCpus MinMemory MinTime Mintition PendingTime PreemptTime Prefer Priority PriorityLong Profile QOS Reason Riable SiblingsViableRaw Sockets SPerBoard StartTime State StateCompact STDERR STres-per-node tres-per-socket tres-per-step tres-per-task UserID UserName Wait4Sw do if squeue --Format="$NAME" >/dev/null then GOODNAMES="$GOODNAMES${NAME}:${SUFFIX}," else BADNAMES="$BADNAMES${NAME}," fi done 2>&1 #FORMAT=$(tr --squeeze-repeats ' ' ' '<<<$GOODNAMES) FORMAT=${GOODNAMES%%,} # trim off trailing comma read r c < <(stty size) # get screen width for use with cut(1) # try it squeue --Format="$FORMAT"|column -t|cut -c 1-$c # echo it echo "$FORMAT" exit Sent with [Proton Mail](https://proton.me/) secure email.

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question on sbatch --prefer
by Alan Stange 10 Feb '24

10 Feb '24

Hello all, I'm somewhat new to Slurm, but long time user of other batch systems. Assume we have a simple cluster of uniform racks of systems with no special resources, and our jobs are all single cpu tasks. Lets say I have a long running job in the cluster, which needs to spawn a helper process into the cluster. We have a strong preference for this helper to run on the same cluster node as the original job, but if that node is already scheduled full, then we want this new task to be scheduled on another systems without any delay. The problem I have is that the --nodelist doesn't solve this, and, as far as I can tell, there's no option with --prefer to specify a node name as a resource, without creating a gres for every hostname in the cluster. It seems like what I'm trying to do should be achievable, but having read though the documentation and searched the archives of this list, I'm not seeing a solution. I'm hoping someone here has some experience with this and can point me in the right direction. Sincerely, Alan

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