- slurm-users - lists.schedmd.com

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 16 Feb '24

16 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 11 Feb '24

11 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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Compilation question
by Sylvain MARET 10 Feb '24

10 Feb '24

Hello everyone ! I'm trying to compile slurm 22.05.11 on Rocky linux 8.7 with freeipmi support I've seen the documentation so I've done the configure step : ./configure --with-pmix=$PMIXHOME --with-ucx=$UCXHOME --with-nvml=$NVMLHOME --prefix=$SLURMHOME --with-freeipmi=/usr but when I run make I end up with the following error : /bin/sh ../../../../../libtool --tag=CC --mode=link gcc -DNUMA_VERSION1_COMPATIBILITY -g -O2 -fno-omit-frame-pointer -pthread -ggdb3 -Wall -g -O1 -fno-strict-aliasing -export-dynamic -L/usr/lib64 -lhdf5_hl -lhdf5 -lsz -lz -ldl -lm -o sh5util sh5util.o -Wl,-rpath=/softs/batch/slurm/22.05.11/lib/slurm -L../../../../../src/api/.libs -lslurmfull -ldl ../libhdf5_api.la -lpthread -lm -lresolv libtool: link: gcc -DNUMA_VERSION1_COMPATIBILITY -g -O2 -fno-omit-frame-pointer -pthread -ggdb3 -Wall -g -O1 -fno-strict-aliasing -o .libs/sh5util sh5util.o -Wl,-rpath=/softs/batch/slurm/22.05.11/lib/slurm -Wl,--export-dynamic -L/usr/lib64 -L../../../../../src/api/.libs /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so ../.libs/libhdf5_api.a -lhdf5_hl -lhdf5 -lsz -lz -ldl -lpthread -lm -lresolv -pthread -Wl,-rpath -Wl,/softs/batch/slurm/22.05.11/lib/slurm sh5util.o:(.init_array+0x0): undefined reference to `__nv_init_env' sh5util.o:(.init_array+0x8): undefined reference to `__flushz' sh5util.o:(.init_array+0x10): undefined reference to `__daz' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_list_transfer_unique' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_sort_key_pairs' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_xstrchr' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_unsetenvp' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_list_sort' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_list_for_each' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `__builtin__pgi_isnanld' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_get_extra_conf_path' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `__blt_pgi_ctzll' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_running_in_slurmctld' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `__c_mcopy1' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `__blt_pgi_clzll' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_list_create' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_list_count' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `__builtin_va_gparg1' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_destroy_config_key_pair' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_xfree_ptr' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_getenvp' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_free_buf' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_get_log_level' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `__c_mset8' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_xstrdup_printf' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_list_delete_first' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_list_append' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_error' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_init_buf' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_log_var' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_s_p_parse_file' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_xstrdup' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_fatal' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `__blt_pgi_popcountll' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_xstrcmp' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_s_p_hashtbl_destroy' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_s_p_hashtbl_create' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_setenvpf' /softs/batch/slurm/slurm-22.05.11/src/api/.libs/libslurmfull.so: undefined reference to `slurm_list_destroy' collect2: error: ld returned 1 exit status What can I do to resolve these undefined reference error ? Regards, Sylvain Maret

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Re: Selecting only a subset of GPU's from all available GPU's
by Minulakshmi S 10 Feb '24

10 Feb '24

Hi Loris, I have different kind of GPU's in same node , and I beleive feature applies to particular node , and cant be applied to only a few GPU's connected to a single node. On Mon, 18 Dec 2023, 12:14 Loris Bennett, <loris.bennett(a)fu-berlin.de> wrote: > Hi Minu, > > Minulakshmi S <minulakshmi.s(a)gmail.com> writes: > > > I'm submitting jobs to a cluster via SLURM scheduler, and let's say I > have access to 8 GPUs in my cluster in same node. They are GPUs of type > A,B,C,D,E,F,G,H. I > > would like to submit a job that requests the use of GPUs of type A or B > or C but NOT of type D/E/F/G/H. So I need some type of OR logic with the > --gres flag. > > > > Eg : When I request GPU of type A , I can do sbatch –gres=gpu:TypeA:1, > I need to input a subset of GPU’s and let slurm schedule job utilizing one > of the GPU > > from this allowed list. > > > > Regards > > Minu > > Assuming the GPUs within a node are all of the same type, could you define > a feature for each GPU type, assign the features to the appropriate > nodes, and then run the job with > > --contraint=gpu_TypeA --gres=gpu:1 > > ? > > This is obviously rather clunky and it would be much nicer if > multiple GPUs types passed to '--gres' were ORed. > > Cheers, > > Loris > > -- > Dr. Loris Bennett (Herr/Mr) > ZEDAT, Freie Universität Berlin >

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Memory used per node
by Gerhard Strangar 09 Feb '24

09 Feb '24

Hello, I'm wondering if there's a way to tell how much memory my job is using per node. I'm doing #SBATCH -n 256 srun solver inputfile When I run sacct -o maxvmsize, the result apparently is the maxmimum VSZ of the largest solver process, not the maximum of the sum of them all (unlike when calling mpirun instead). When I sstat -o TresUsageInMax, I get the memory summed up over all nodes being used. Can I get the maximum VSZ per node? Gerhard

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Could not find group with gid even when they exist
by Nic Lewis 09 Feb '24

09 Feb '24

After upgrading to version 23.11.3 we started to get slammed with the following log messages from slurmctld "error: validate_group: Could not find group with gid <id>" This spans a handful of groups and repeats constantly, drowning out just about everything else. Attempting to do a lookup on the group shows that they exist on the scheduler node, same for all the submission and compute nodes. As far as I can tell, slurm should be able to locate the group in question. Jobs submitted from users within those groups go through just fine. They get scheduled, run, and clean up no problem. I'm at a loss on where to look next.

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Relative QOS limits in sacctmgr?
by Chip Seraphine 09 Feb '24

09 Feb '24

Hello, TL,DR: How does the relative QOS flag work? I have a QOS and I want it to be collectively restricted to 50% of the reachable cores in the cluster. I’ve been managing this by dividing my core count to 2 to get N, and doing ‘sacctmgr update qos foobar set MaxTRES=cpu=N’. That’s fine, except that N changes frequently as worker nodes come and go, so I have an hourly cronjob that enforces this. The problem with *that* is the values you back out with ‘sacctmgr show qos’ are often in different units than you input (e.g. gigs instead of megs of ram), which means I need to do some annoying parsing, will miss minor rounding errors, etc. (Using JSON solves that problem but introduces others that I do not want to deal with.) So while looking for a better way I noticed that QOSs support a flag called “relative”, which says “the QOS limits will be treated as percentages of a cluster/partition instead of absolutes”. Perfect! However, it’s not very clear to me what that means in practice. For example, with the “relative” flag set, the MaxTRES units still seem to work the same, expect metric suffices (“G”, ”M”, etc) and won’t accept periods. Is anyone actually using this flag, and if so can you tell me what attributes it affects, and in what way? -- Chip Seraphine Grid Operations For support please use help-grid in email or slack. This e-mail and any attachments may contain information that is confidential and proprietary and otherwise protected from disclosure. If you are not the intended recipient of this e-mail, do not read, duplicate or redistribute it by any means. Please immediately delete it and any attachments and notify the sender that you have received it by mistake. Unintended recipients are prohibited from taking action on the basis of information in this e-mail or any attachments. The DRW Companies make no representations that this e-mail or any attachments are free of computer viruses or other defects.

1 0

Is there a way to list allocated/unallocated resources defined in a QoS?
by Alastair Neil 09 Feb '24

09 Feb '24

Slurm version 23.02.07 If I have a QoS defined that has a set number of say GPU devices set in the GrpTRES. Is there an easy way to generate a list of how much of the defined quota is allocated or conversely un-allocated? e.g.: Name|Priority|GraceTime|Preempt|PreemptExemptTime|PreemptMode|Flags|UsageThres|UsageFactor|GrpTRES|GrpTRESMins|GrpTRESRunMins|GrpJobs|GrpSubmit|GrpWall|MaxTRES|MaxTRESPerNode|MaxTRESMins|MaxWall|MaxTRESPU|MaxJobsPU|MaxSubmitPU|MaxTRESPA|MaxJobsPA|MaxSubmitPA|MinTRES| normal|0|00:00:00|||cluster|||1.000000|||||||||||cpu=3000,gres/gpu=20||||||| dept1|1|00:00:00|||cluster|||1.000000|cpu=256,gres/gpu:1g.10gb=16,gres/gpu:2g.20gb=8,gres/gpu:3g.40gb=8,gres/gpu:a100.80gb=8||||||||||||||||| dept2|1|00:00:00|||cluster|||1.000000|cpu=256,gres/gpu:1g.10gb=0,gres/gpu:2g.20gb=0,gres/gpu:3g.40gb=0,gres/gpu:a100.80gb=16||||||||||||||||| So dept1 and dept2 qos are set on the same partition. How can a user with access to one or other see if there are available resources in the partition?

2 1

Errors upgrading to 23.11.0
by Xaver Stiensmeier 08 Feb '24

08 Feb '24

Dear slurm-user list, I got this error: Unable to start service slurmctld: Job for slurmctld.service failed because the control process exited with error code.\nSee \"systemctl status slurmctld.service\" and \"journalctl -xeu slurmctld.service\" for details. but in slurmctld.service I see nothing suspicious: slurmctld.service - Slurm controller daemon Loaded: loaded (/lib/systemd/system/slurmctld.service; enabled; vendor preset: enabled) Drop-In: /etc/systemd/system/slurmctld.service.d └─override.conf Active: active (running) since Wed 2024-02-07 15:50:56 UTC; 19min ago Main PID: 51552 (slurmctld) Tasks: 21 (limit: 9363) Memory: 10.4M CPU: 1min 16.088s CGroup: /system.slice/slurmctld.service ├─51552 /usr/sbin/slurmctld --systemd └─51553 "slurmctld: slurmscriptd" "" "" "" "" "" "" Feb 07 15:58:21 cluster-master-2vt2bqh7ahec04c slurmctld[51552]: slurmctld: sched: _slurm_rpc_allocate_resources JobId=3 NodeList=(null) usec=959 Feb 07 15:58:23 cluster-master-2vt2bqh7ahec04c slurmctld[51552]: slurmctld: _job_complete: JobId=3 WTERMSIG 2 Feb 07 15:58:23 cluster-master-2vt2bqh7ahec04c slurmctld[51552]: slurmctld: _job_complete: JobId=3 cancelled by interactive user Feb 07 15:58:23 cluster-master-2vt2bqh7ahec04c slurmctld[51552]: slurmctld: _job_complete: JobId=3 done Feb 07 15:58:23 cluster-master-2vt2bqh7ahec04c slurmctld[51552]: slurmctld: _slurm_rpc_complete_job_allocation: JobId=3 error Job/step already completing or completed Feb 07 15:58:42 cluster-master-2vt2bqh7ahec04c slurmctld[51552]: slurmctld: sched: _slurm_rpc_allocate_resources JobId=4 NodeList=cluster-master-2vt2bqh7ahec04c,cluster-worker-2vt2bqh7ahec04c-2 usec=512 Feb 07 16:06:04 cluster-master-2vt2bqh7ahec04c slurmctld[51553]: slurmctld: error: _run_script: JobId=0 resumeprog exit status 1:0 Feb 07 16:09:33 cluster-master-2vt2bqh7ahec04c slurmctld[51552]: slurmctld: _job_complete: JobId=4 WTERMSIG 2 Feb 07 16:09:33 cluster-master-2vt2bqh7ahec04c slurmctld[51552]: slurmctld: _job_complete: JobId=4 done Feb 07 16:09:33 cluster-master-2vt2bqh7ahec04c slurmctld[51552]: slurmctld: _slurm_rpc_complete_job_allocation: JobId=4 error Job/step already completing or completed I am unsure how to debug this further. It might be coming from a previous problem I tried to fix (basically a few deprecated keys in the configuration). I will try to restart the entire cluster with the added changes to rule out any follow up errors, but maybe it's something obvious a fellow list user can see. Best regards, Xaver

2 2

sinfo gresused shard count wrong/incomplete
by Reed Dier 07 Feb '24

07 Feb '24

I have a bash script that grabs current statistics from sinfo to ship into a time series database to use for Grafana dashboards. We recently began using shards with our gpus, and I’m seeing some unexpected behavior with the data reported from sinfo. > $ sinfo -h -O "NodeHost:5 ,GresUsed:100 ,Gres:100" | grep gpu03 > gpu03 gpu:p40:0(IDX:N/A),gpu:rtx:0(IDX:N/A),shard:p40:1(IDX:1),shard:rtx:0(IDX:N/A) gpu:p40:6(S:0),gpu:rtx:2(S:0),shard:p40:36(S:0),shard:rtx:12(S:0) > > $ scontrol show node gpu03 > NodeName=gpu03 Arch=x86_64 CoresPerSocket=22 > CPUAlloc=52 CPUEfctv=88 CPUTot=88 CPULoad=43.67 > AvailableFeatures=avx,avx512,largeMemory,matlab > ActiveFeatures=avx,avx512,largeMemory,matlab > 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=425984 FreeMem=116850 Sockets=2 Boards=1 > State=MIXED ThreadsPerCore=2 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A > Partitions=gpu > BootTime=2024-02-02T14:17:07 SlurmdStartTime=2024-02-05T12:33:50 > LastBusyTime=2024-02-07T09:48:50 > CfgTRES=cpu=88,mem=750G,billing=88,gres/gpu=8,gres/gpu:p40=6,gres/gpu:rtx=2,gres/shard=48 > AllocTRES=cpu=52,mem=416G,gres/shard=21 > CapWatts=n/a > CurrentWatts=0 AveWatts=0 > ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s Specifically, we can see there are 48 total shards on this specific node, 36 of type p40, 12 of type rtx. From control, I can see that 21 shards are in use, and from nvidia-smi I can see that the breakdown of shards per gpu index is: [0]p40:4/6 [1]p40:6/6 [2]rtx:4/6 [3]rtx:3/6 [4]p40:4/6 [5]p40:0/6 [6]p40:0/6 [7]p40:0/6 So, I can tell that what “GresUsed” is reporting is actually an entire gpu’s worth of shards used, and the index of that specific entire GPU consumed. However, what it doesn’t show is the amount of specific gres/shard actually used, or more succinctly, I can’t seem to extrapolate that there are 21 shards in use. Right now my script says there is 1 shard out of 48 used, because I’m scraping for the num of shards in use, which is reporting the value of entire GPUs used by shards, and anything less than 100% is rounded to 0.. So, given that I’m on 22.05.8, maybe its better in 23.02.X which I’m hoping to move to within the next month. However I can’t seem to find anything in the release notes for 23.02 or 23.11 that would imply that sinfo reports (my) expected value of the actual count of shards used, Does anyone have any ideas for how I might be able to achieve what I’m looking for using sinfo, or should I instead try to use the sinfo json parser which has a “tres_used” field, that doesn’t appear to be accessible outside of the json output? > { > "architecture": "x86_64", > "burstbuffer_network_address": "", > "boards": 1, > "boot_time": 1706901428, > "comment": "", > "cores": 22, > "cpu_binding": 0, > [SNIP] > "tres": "cpu=88,mem=750G,billing=88,gres/gpu=8,gres/gpu:p40=6,gres/gpu:rtx=2,gres/shard=48", > "slurmd_version": "22.05.8", > "alloc_memory": 284380, > "alloc_cpus": 62, > "idle_cpus": 26, > "tres_used": "cpu=62,mem=284380M,gres/gpu=7,gres/gpu:p40=5,gres/gpu:rtx=2,gres/shard=17", > "tres_weighted": 62 > }, Any ideas appreciated. Thanks, Reed

1 0

Re: Restricting local disk storage of jobs
by Tim Schneider 07 Feb '24

07 Feb '24

Hey Jeffrey, thanks for this suggestion! This is probably the way to go if one can find a way to access GRES in the prolog. I read somewhere that people were calling scontrol to get this information, but this seems a bit unclean. Anyway, if I find some time I will try it out. Best, Tim On 2/6/24 16:30, Jeffrey T Frey wrote: > Most of my ideas have revolved around creating file systems on-the-fly > as part of the job prolog and destroying them in the epilog. The > issue with that mechanism is that formatting a file system (e.g. > mkfs.<type>) can be time-consuming. E.g. formatting your local > scratch SSD as an LVM PV+VG and allocating per-job volumes, you'd > still need to run a e.g. mkfs.xfs and mount the new file system. > > > ZFS file system creation is much quicker (basically combines the LVM + > mkfs steps above) but I don't know of any clusters using ZFS to manage > local file systems on the compute nodes :-) > > > One /could/ leverage XFS project quotas. E.g. for Slurm job 2147483647: > > > *[root@r00n00 /]# mkdir /tmp-alloc/slurm-2147483647* > *[root@r00n00 /]# xfs_quota -x -c 'project -s -p > /tmp-alloc/slurm-2147483647 2147483647' /tmp-alloc* > Setting up project 2147483647 (path /tmp-alloc/slurm-2147483647)... > Processed 1 (/etc/projects and cmdline) paths for project > 2147483647 with recursion depth infinite (-1). > *[root@r00n00 /]# xfs_quota -x -c 'limit -p bhard=1g 2147483647' > /tmp-alloc* > *[root@r00n00 /]# cd /tmp-alloc/slurm-2147483647* > *[root@r00n00 slurm-2147483647]# dd if=/dev/zero of=zeroes bs=5M > count=1000* > dd: error writing ‘zeroes’: No space left on device > 205+0 records in > 204+0 records out > 1073741824 bytes (1.1 GB) copied, 2.92232 s, 367 MB/s > > : > > [root@r00n00 /]# rm -rf /tmp-alloc/*slurm-2147483647* > [root@r00n00 /]# *xfs_quota -x -c 'limit -p bhard=0 2147483647' > /tmp-alloc* > > > Since Slurm jobids max out at 0x03FFFFFF (and 2147483647 = 0x7FFFFFFF) > we have an easy on-demand project id to use on the file system. Slurm > tmpfs plugins have to do a mkdir to create the per-job directory, > adding two xfs_quota commands (which run in more or less O(1) time) > won't extend the prolog by much. Likewise, Slurm tmpfs plugins have to > scrub the directory at job cleanup, so adding another xfs_quota > command will not do much to change their epilog execution times. The > main question is "where does the tmpfs plugin find the quota limit for > the job?" > > > > > >> On Feb 6, 2024, at 08:39, Tim Schneider via slurm-users >> <slurm-users(a)lists.schedmd.com> wrote: >> >> Hi, >> >> In our SLURM cluster, we are using the job_container/tmpfs plugin to >> ensure that each user can use /tmp and it gets cleaned up after them. >> Currently, we are mapping /tmp into the nodes RAM, which means that >> the cgroups make sure that users can only use a certain amount of >> storage inside /tmp. >> >> Now we would like to use of the node's local SSD instead of its RAM >> to hold the files in /tmp. I have seen people define local storage as >> GRES, but I am wondering how to make sure that users do not exceed >> the storage space they requested in a job. Does anyone have an idea >> how to configure local storage as a proper tracked resource? >> >> Thanks a lot in advance! >> >> Best, >> >> Tim >> >> >> -- >> slurm-users mailing list -- slurm-users(a)lists.schedmd.com >> To unsubscribe send an email to slurm-users-leave(a)lists.schedmd.com >

2 1

scheme for protected GPU jobs from preemption
by Paul Raines 06 Feb '24

06 Feb '24

After using just Fairshare for over a year on our GPU cluster, we have decided it is not working for us for what we really want to achieve among our groups. We have decided to look at preemption. What we want is for users to NOT have a #job/GPU maximum (if they are only person on the cluster they should be able to use it all), but if another user comes to the "full" cluster they should immediately be able to run some jobs. Thus preemption is needed. In our scheme we want * users to have N protected GPU jobs that cannot be preempted where N is the number of GPUs allocated. * N may not be the same for all users. Some priviledged users get more. * jobs pending in the queue will have lower priority dependent on the number of GPUs allocated to running jobs. Maybe doable somehow with PriorityWeightJobSize though not sure how. * Jobs over N are subject to preemption (and requeued if --requeue is given) with shortest running jobs of the user with most unprotected GPUs preempted first. * another complication is we have a variety of different GPUs and users may ask for specific ones which can limit what unprotected GPU jobs are available for preemption My first attempt to do this in SLURM was to just create two partitions, GPU and GPU-req, with different PriorityTier values and the later partition have PreemptMode=REQUEUE. But N would be set by a MaxTRES on the first partition and be the same for everyone and we need it to be INDEPENDENT for each user. Also users would have to "think" about which partition to submit jobs to. And users want their longest running "unprotected" job to be able to be PROMOTED to a "protected" jobs automatically when a "protected" job finishes. However slurm does not allow running jobs to move between partitions. I am trying to figure out QOS pre-emption which might solve the independent N per user issue but I don't think it will solve the promotion issue. Any ideas how this scheme might be possible in SLURM? Otherwise I might have to write a complicated cron job that tries to do it all "outside" of SLURM issuing scontrol commands. --------------------------------------------------------------- Paul Raines http://help.nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129 USA The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

1 0

Restricting local disk storage of jobs
by Tim Schneider 06 Feb '24

06 Feb '24

Hi, In our SLURM cluster, we are using the job_container/tmpfs plugin to ensure that each user can use /tmp and it gets cleaned up after them. Currently, we are mapping /tmp into the nodes RAM, which means that the cgroups make sure that users can only use a certain amount of storage inside /tmp. Now we would like to use of the node's local SSD instead of its RAM to hold the files in /tmp. I have seen people define local storage as GRES, but I am wondering how to make sure that users do not exceed the storage space they requested in a job. Does anyone have an idea how to configure local storage as a proper tracked resource? Thanks a lot in advance! Best, Tim

3 2

Re: [ext] Restricting local disk storage of jobs
by Tim Schneider 06 Feb '24

06 Feb '24

Hi Magnus, I understand. Thanks a lot for your suggestion. Best, Tim On 06.02.24 15:34, Hagdorn, Magnus Karl Moritz wrote: > Hi Tim, > in the end the InitScript didn't contain anything useful because > > slurmd: error: _parse_next_key: Parsing error at unrecognized key: > InitScript > > At this stage I gave up. This was with SLURM 23.02. My plan was to > setup the local scratch directory with XFS and then get the script to > apply a project quota, ie quota attached to the directory. > > I would start by checking if slurm recognises the InitScript option. > > Regards > magnus > > On Tue, 2024-02-06 at 15:24 +0100, Tim Schneider wrote: >> Hi Magnus, >> >> thanks for your reply! If you can, would you mind sharing the >> InitScript >> of your attempt at getting it to work? >> >> Best, >> >> Tim >> >> On 06.02.24 15:19, Hagdorn, Magnus Karl Moritz wrote: >>> Hi Tim, >>> we are using the container/tmpfs plugin to map /tmp to a local NVMe >>> drive which works great. I did consider setting up directory >>> quotas. I >>> thought the InitScript [1] option should do the trick. Alas, I >>> didn't >>> get it to work. If I remember correctly, slurm complained about the >>> option being present. In the end we recommend our users to make >>> exclusive use a node if they are going to use a lot of local >>> scratch >>> space. I don't think this happens very often if at all. >>> Regards >>> magnus >>> >>> [1] >>> https://slurm.schedmd.com/job_container.conf.html#OPT_InitScript >>> >>> >>> On Tue, 2024-02-06 at 14:39 +0100, Tim Schneider via slurm-users >>> wrote: >>>> Hi, >>>> >>>> In our SLURM cluster, we are using the job_container/tmpfs plugin >>>> to >>>> ensure that each user can use /tmp and it gets cleaned up after >>>> them. >>>> Currently, we are mapping /tmp into the nodes RAM, which means >>>> that >>>> the >>>> cgroups make sure that users can only use a certain amount of >>>> storage >>>> inside /tmp. >>>> >>>> Now we would like to use of the node's local SSD instead of its >>>> RAM >>>> to >>>> hold the files in /tmp. I have seen people define local storage >>>> as >>>> GRES, >>>> but I am wondering how to make sure that users do not exceed the >>>> storage >>>> space they requested in a job. Does anyone have an idea how to >>>> configure >>>> local storage as a proper tracked resource? >>>> >>>> Thanks a lot in advance! >>>> >>>> Best, >>>> >>>> Tim >>>> >>>>

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Re: [ext] Restricting local disk storage of jobs
by Tim Schneider 06 Feb '24

06 Feb '24

Hi Magnus, thanks for your reply! If you can, would you mind sharing the InitScript of your attempt at getting it to work? Best, Tim On 06.02.24 15:19, Hagdorn, Magnus Karl Moritz wrote: > Hi Tim, > we are using the container/tmpfs plugin to map /tmp to a local NVMe > drive which works great. I did consider setting up directory quotas. I > thought the InitScript [1] option should do the trick. Alas, I didn't > get it to work. If I remember correctly, slurm complained about the > option being present. In the end we recommend our users to make > exclusive use a node if they are going to use a lot of local scratch > space. I don't think this happens very often if at all. > Regards > magnus > > [1] > https://slurm.schedmd.com/job_container.conf.html#OPT_InitScript > > > On Tue, 2024-02-06 at 14:39 +0100, Tim Schneider via slurm-users wrote: >> Hi, >> >> In our SLURM cluster, we are using the job_container/tmpfs plugin to >> ensure that each user can use /tmp and it gets cleaned up after them. >> Currently, we are mapping /tmp into the nodes RAM, which means that >> the >> cgroups make sure that users can only use a certain amount of storage >> inside /tmp. >> >> Now we would like to use of the node's local SSD instead of its RAM >> to >> hold the files in /tmp. I have seen people define local storage as >> GRES, >> but I am wondering how to make sure that users do not exceed the >> storage >> space they requested in a job. Does anyone have an idea how to >> configure >> local storage as a proper tracked resource? >> >> Thanks a lot in advance! >> >> Best, >> >> Tim >> >>

2 1

Starting a job after a file is created in previous job (dependency looking for soluton)
by Amjad Syed 06 Feb '24

06 Feb '24

Hello I have the following scenario: I need to submit a sequence of up to 400 jobs where the even jobs depend on the preceeding odd job to finish and every odd job depends on the presence of a file generated by the preceding even job (availability of the file for the first of those 400 jobs is guaranteed). If I just submit all those jobs via a loop using dependencies, then I end up with a lot of pending jobs who might later not even run because no output file has been produced by the preceding jobs. Is there a way to pause the submission loop until the required file has been generated so that at most two jobs are submitted at the same time? Here is a sample submission script showing what I want to achieve. for i in {1..200}; do FILE=GHM_paramset_${i}.dat # How can I pause the submission loop until the FILE has been created???? #if test -f "$FILE"; then jobid4=$(sbatch --parsable --dependency=afterok:$jobid3 job4_sub $i) jobid3=$(sbatch --parsable --dependency=afterok:$jobid4 job3_sub $i) #fi done Any help will be appreciated Amjad

3 2

SLURM configuration for LDAP users
by Richard Chang 05 Feb '24

05 Feb '24

Hi, I am a little new to this, so please pardon my ignorance. I have configured slurm in my cluster and it works fine with local users. But I am not able to get it working with LDAP/SSSD authentication. User logins using ssh are working fine. An LDAP user can login to the login, slurmctld and compute nodes, but when they try to submit jobs, slurmctld logs an error about invalid account or partition for user. Someone said we need to add the user manually into the database using the sacctmgr command. But I am not sure we need to do this for each and every LDAP user. Yes, it does work if we add the LDAP user manually using sacctmgr. But I am not convinced this manual way is the way to do. The documentation is not very clear about using LDAP accounts. Saw somewhere in the list about using UsePAM=1 and copying or creating a softlink for slurm PAM module under /etc/pam.d . But it didn't work for me. Saw somewhere else that we need to specifying LaunchParameters=enable_nss_slurm in the slurm.conf file and put slurm keyword in passwd/group entry in the /etc/nsswitch.conf file. Did these, but didn't help either. I am bereft of ideas at present. If anyone has real world experience and can advise, I will be grateful. Thank you, Richard

4 4

timeout of get_user_env does not obey time limit
by urbanjost 03 Feb '24

03 Feb '24

If I use the sbatch(1) option --export=NONE or wipe the environment with "env -i /usr/bin/sbatch ..." or use --export=NIL then the environment is not properly constructed and I see the message in the /var/log/*slurm* files: [2024-02-03T11:50:33.052] _get_user_env: get env for user jsu here [2024-02-03T11:52:33.152] timeout waiting for /bin/su to complete [2024-02-03T11:52:34.152] error: Failed to load current user environment variables [2024-02-03T11:52:34.153] error: _get_user_env: Unable to get user's local environment, running only with passed environment This occurs at 120 seconds not matter if I add --get-user-env=3600 or adjust many slurm.conf time-related parameters. It is easy to reproduce by adding "sleep 100" into a .cshrc file and sbatch(1) the file #!/bin/csh #SBATCH --export=NONE --propagate=NONE --get-user-env=3600L printenv HOME printenv USER printenv PATH env I have adjust MANY time-related limits in the slurm.conf file to no avail. When the system is unresponsive or heavily loaded or users have prologues that set up complex environments via module commands (which can be notoriously slow) the jobs are failing or producing errors. If I configure Slurm so that jobs that timeout requeue instead of running then a user with a slow login setup can submit a large number of jobs and basically close down a cluster because this option not only requeues jobs that fail but puts the node it occurred on in a DRAIN state. We see this as very dangerous as by defaults jobs proceed to execute even when their environment is not properly constructed. I can see that "slurmrestd getenv" and the procedure get_user_env(3c) are involved, but a preliminary scan of the code looked like the --get-user-env=NNNN value was being parsed, and I did not see a reason the setup always times out at 120 seconds (at least on my system). Does anyone know how to get the time allowed to get the default user environment to use the value on the --get-user-env option when no environment is being exported to a job? This is showing up sporadically and causing intermittent failures that are very confusing and disturbing to the users it occurs with. Sent with [Proton Mail](https://proton.me/) secure email.

1 0

selecting job-specific log messages
by urbanjost 03 Feb '24

03 Feb '24

log files use many strings to identify job, including not having a jobID in the message NUMBER=$SLURM_JOBID egrep "\.\<$NUMBER\>\] |\<$NUMBER\>\.batch|jobid \<$NUMBER\>|JObId=\<$NUMBER\>|job id \<$NUMBER\>|job\.\<$NUMBER\>|job \<$NUMBER\>|jobid \[\<$NUMBER\>\]|task_p_slurmd_batch_request: \<$NUMBER\>" /var/log/slurm* Even that misses cruciall data that does not even contain the jobid [2024-02-03T11:50:33.052] _get_user_env: get env for user jsu here [2024-02-03T11:52:33.152] timeout waiting for /bin/su to complete [2024-02-03T11:52:34.152] error: Failed to load current user environment variables [2024-02-03T11:52:34.153] error: _get_user_env: Unable to get user's local environment, running only with passed environment It would be very useful if all messages related to a job had a consistent string in them for grepping the log files; even better might be a command like "scontrol show jobid=NNNN log_messages But I could not find what I wanted (an easy way to find all daemon log messages related to a specific job). I would find it particularly useful if there were a way to automatically append such information to the stdout of the job at job termination so users would automatically get information about job failures or warnings. Is there such a feature available I have missed? Sent with [Proton Mail](https://proton.me/) secure email.

1 0

after upgrade to 23.11.1 nodes stuck in completion state
by Paul Raines 01 Feb '24

01 Feb '24

I finally had downtime on our cluster running 20.11.3 and decided to upgrade SLURM. All daemons were stopped on nodes and master. Rocky 8 Linux OS was updated but not changed configuration-wise in anyway. On the master, when I first installed 23.11.1 and tried to run slurmdbd -D -vvv at the command line, it balked as the more than 2 major version jump. I then installed 22.05.6 and run slurmdbd -D -vvv which took a long time but completed fine. I reinstalled 23.11.1 and did slurmdbd -D --vvv which went quick. I stopped it then ran slurmdbd normally with systemctl. When I ran slurmctld it complained about incompatable state files. I didn't care about loosing state so ran with the -i option to ignore. Seemed happy. I then started up slurmd on my various GPU and non-GPU nodes. I ran a test interactive job just to see if I would get a shell with expected SLURM environment on the nodes and it worked. Except on the GPU nodes I got errors about not being able to get/set GPU frequences. I removed GpuFreqDef=medium from slurm.conf and that went away. I had my people start running jobs last night. This morning I come in and see a lot of nodes are stuck in completing state. All these are GPU nodes. For example on node 'sevilla' squeue reports JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 3679433 lcna100 sjob_123 sg1526 CG 8:29 1 sevilla 3679432 lcna100 sjob_123 sg1526 CG 8:35 1 sevilla 3679431 lcna100 sjob_123 sg1526 CG 8:42 1 sevilla In the slurmd.log on sevilla I see every minute the lines: [2024-01-28T09:37:52.003] debug2: Start processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug2: Processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug: _rpc_terminate_job: uid = 1150 JobId=3679432 [2024-01-28T09:37:52.004] debug2: Start processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug2: Processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug: _rpc_terminate_job: uid = 1150 JobId=3679431 [2024-01-28T09:37:52.004] debug2: Finish processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug2: Start processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug2: Processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug: _rpc_terminate_job: uid = 1150 JobId=3679433 [2024-01-28T09:37:52.004] debug2: Finish processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug2: Finish processing RPC: REQUEST_TERMINATE_JOB Back at the time 3679433 was cancelled by the user I see [2024-01-28T00:27:48.658] debug2: Start processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T00:27:48.658] debug2: Processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T00:27:48.658] debug: _rpc_terminate_job: uid = 1150 JobId=3679433 [2024-01-28T00:27:48.658] debug: credential for job 3679433 revoked [2024-01-28T00:27:48.658] debug: _rpc_terminate_job: sent SUCCESS for 3679433, waiting for prolog to finish [2024-01-28T00:27:48.658] debug: Waiting for job 3679433's prolog to complete On sevilla itself there are no processes currently running for user sg1526 so no sign of these jobs. There ARE processes running for user mu40 though [root@sevilla ~]# pgrep -f slurm_script | xargs -n1 pstree -p | grep ^slurm slurm_script(30691)---starter-suid(30764)-+-python3(30784)-+-{python3}(30817) slurm_script(30861)---starter-suid(30873)-+-python3(30888)-+-{python3}(30915) slurm_script(30963)---starter-suid(30975)-+-python3(30992)-+-{python3}(31020) [root@sevilla ~]# strings /proc/30691/cmdline /bin/sh /var/slurm/spool/d/job3679220/slurm_script /usr/bin/sacct -p --jobs=3679220 --format=JobID,User,ReqTRES,NodeList,Start,End,Elapsed,CPUTime,State,ExitCode JobID|User|ReqTRES|NodeList|Start|End|Elapsed|CPUTime|State|ExitCode| 3679220|mu40|billing=6,cpu=3,gres/gpu=1,mem=32G,node=1|sevilla|2024-01-27T22:33:27|2024-01-27T23:26:39|00:53:12|02:39:36|NODE_FAIL|1:0| 3679220.batch|||sevilla|2024-01-27T22:33:27|2024-01-27T23:26:39|00:53:12|02:39:36|CANCELLED|| 3679220.extern|||sevilla|2024-01-27T22:33:27|2024-01-27T23:26:39|00:53:12|02:39:36|CANCELLED|| The slurmd.log has at the time it started lines like: [2024-01-27T22:33:28.679] [3679220.batch] debug2: gpu/nvml: _get_gpuutil: Couldn't find pid 30691, probably hasn't started yet or has already finished [2024-01-27T22:33:58.092] [3679220.extern] debug2: gpu/nvml: _get_gpuutil: Couldn't find pid 30650, probably hasn't started yet or has already finished [2024-01-27T22:33:58.166] [3679220.batch] debug2: profile signaling type Task [2024-01-27T22:33:58.168] [3679220.batch] debug2: gpu/nvml: _get_gpuutil: Couldn't find pid 30691, probably hasn't started yet or has already finished [2024-01-27T22:33:58.170] [3679220.batch] debug2: gpu/nvml: _get_gpuutil: Couldn't find pid 30764, probably hasn't started yet or has already finished [2024-01-27T22:33:58.172] [3679220.batch] debug2: gpu/nvml: _get_gpuutil: Couldn't find pid 30784, probably hasn't started yet or has already finished ... [2024-01-27T22:46:39.018] debug: _step_connect: connect() failed for /var/slurm/spool/d/sevilla_3679220.4294967292: Connection refused [2024-01-27T22:46:39.018] debug: Cleaned up stray socket /var/slurm/spool/d/sevilla_3679220.4294967292 [2024-01-27T22:46:39.018] debug: _step_connect: connect() failed for /var/slurm/spool/d/sevilla_3679220.4294967291: Connection refused [2024-01-27T22:46:39.018] debug: Cleaned up stray socket /var/slurm/spool/d/sevilla_3679220.4294967291 [2024-01-27T22:46:39.018] _handle_stray_script: Purging vestigial job script /var/slurm/spool/d/job3679220/slurm_script then later at the time of termination [2024-01-27T23:26:39.042] debug: _rpc_terminate_job: uid = 1150 JobId=3679220 [2024-01-27T23:26:39.042] debug: credential for job 3679220 revoked [2024-01-27T23:26:39.042] debug2: No steps in jobid 3679220 to send signal 998 [2024-01-27T23:26:39.043] debug2: No steps in jobid 3679220 to send signal 18 [2024-01-27T23:26:39.043] debug2: No steps in jobid 3679220 to send signal 15 [2024-01-27T23:26:39.044] debug2: set revoke expiration for jobid 3679220 to 1706416119 UTS [2024-01-27T23:26:39.044] debug: Waiting for job 3679220's prolog to complete [2024-01-27T23:26:39.044] debug: Finished wait for job 3679220's prolog to complete [2024-01-27T23:26:39.068] debug: completed epilog for jobid 3679220 [2024-01-27T23:26:39.071] debug: JobId=3679220: sent epilog complete msg: rc = 0 So I have a node stuck in 'comp' state that claims to have jobs completing that are definite NOT running on the box BUT there are jobs running on the box that SLURM thinks are done --------------------------------------------------------------- Paul Raines http://help.nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129 USA Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

4 7

Why is Slurm 20 the latest RPM in RHEL 8/Fedora repo?
by Robert Kudyba 31 Jan '24

31 Jan '24

According to these links: https://rpmfind.net/linux/rpm2html/search.php?query=slurm https://src.fedoraproject.org/rpms/slurm Why doesn't RHEL 8 get a newer version? Can someone update the repo maintainer Philip Kovacs <https://src.fedoraproject.org/user/pkfed> < pkfed(a)fedoraproject.org>? There was a ticket at https://bugzilla.redhat.com/show_bug.cgi?id=1912491 but no movement on RHEL 8.

5 4

Mailing list upgrade - slurm-users list paused
by Tim Wickberg 30 Jan '24

30 Jan '24

Hey folks - The mailing list will be offline for about an hour as we upgrade the host, upgrade the mailing list software, and change the mail configuration around. As part of these changes, the "From: " field will no longer be the original sender, but instead use the mailing list ID itself. This is to comply with DMARC sending options, and allow us to start DKIM signing messages to ensure deliverability once Google and Yahoo impose new policy changes in February. This is the last post on the current (mailman2) list. I'll send a welcome message on the upgraded (mailman3) list once finished, and when the list is open to new traffic again. - Tim -- Tim Wickberg Chief Technology Officer, SchedMD LLC Commercial Slurm Development and Support

1 1

Testing to SchedMD folks
by Tim Wickberg 30 Jan '24

30 Jan '24

Hey - this is hopefully a final test before the list is re-enabled for everyone. - Tim

1 0

Socket timed out - tuning
by Reed Dier 29 Jan '24

29 Jan '24

Hoping someone can help point me towards some tweaks to help prevent denial-of-service issues. > sbatch: error: Batch job submission failed: Socket timed out on send/recv operation Root cause is understood, issues with shared storage for the slurmctld’s was impacted, leading to an increase in write latency to the StateSaveLocation. Then with a large enough avalanche of job submissions, things the RPC’s would stack up and stop responding. I’ve been running well with some tweaks sourced from the “high-throughput” guide <https://slurm.schedmd.com/high_throughput.html>. > SchedulerParameters=max_rpc_cnt=400,\ > sched_min_interval=50000,\ > sched_max_job_start=300,\ > batch_sched_delay=6 > KillWait=30 > MessageTimeout=30 I’m assuming that I was running into batch_sched_delay because looking at sdiag after the fact, it was averaging .2s, and total time is 5.5h out of 16h8m18s at the time of the sdiag sample. > ******************************************************* > sdiag output at Thu Jan 25 11:08:18 2024 (1706198898) > Data since Wed Jan 24 19:00:00 2024 (1706140800) > ******************************************************* > REQUEST_SUBMIT_BATCH_JOB ( 4003) count:98400 ave_time:201442 total_time:19821991013 Currently on 22.05.8, but hoping to get to 23.02.7 soon™, and I think this could possible resolve the issue well enough if I’m reading it correctly from the release notes <https://slurm.schedmd.com/archive/slurm-23.02-latest/news.html>? > HIGHLIGHTS > ========== > -- slurmctld - Add new RPC rate limiting feature. This is enabled through > SlurmctldParameters=rl_enable, otherwise disabled by default. > rl_enable <https://slurm.schedmd.com/slurm.conf.html#OPT_rl_enable>Enable per-user RPC rate-limiting support. Client-commands will be told to back off and sleep for a second once the limit has been reached. This is implemented as a "token bucket", which permits a certain degree of "bursty" RPC load from an individual user before holding them to a steady-state RPC load established by the refill period and rate. But given that the hardware seems to be well over provisioned, CPU never drops below 5% idle, it feels like there is more room to squeeze some optimization out of here that I’m missing in the interim, and hoping to get a better overall understanding in the process. I scrape the DBD Agent queue size from sdiag every 30s and the largest value I saw was 115, which is much higher than normal, but should be well below MaxDBDMsgs, where the minimum value is 10000. I would really hope that I didn’t potentially hit a 30s MessageTimeout value, but I guess thats on the table all well, not knowing if that would potentially trigger the sbatch submission failure like that. Just moving the max_rpc_cnt value up seems like an easy button, but also seems like it could have some adverse effects for backfill scheduling, and may be diminishing returns for actually keeping RPCs flowing? > Setting max_rpc_cnt to more than 256 will be only useful to let backfill continue scheduling work after locks have been yielded (i.e. each 2 seconds) if there are a maximum of MAX(max_rpc_cnt/10, 20) RPCs in the queue. i.e. max_rpc_cnt=1000, the scheduler will be allowed to continue after yielding locks only when there are less than or equal to 100 pending RPCs. Obviously, fix the storage is the real solution, but hoping that there may be more goodness to unlock, even if it is as simple as “upgrade to 23.02”. Appreciate any insight, Reed

1 0

Two jobs each with a different partition running on same node?
by Loris Bennett 29 Jan '24

29 Jan '24

Hi, I seem to remember that in the past, if a node was configured to be in two partitions, the actual partition of the node was determined by the partition associated with the jobs running on it. Moreover, at any instance where the node was running one or more jobs, the node could only actually be in a single partition. Was this indeed the case and is it still the case with version Slurm 23.02.7? Cheers, Loris -- Dr. Loris Bennett (Herr/Mr) FUB-IT (ex-ZEDAT), Freie Universität Berlin

2 1

srun only runs one job on a node
by Rike-Benjamin Schuppner 27 Jan '24

27 Jan '24

Hi, Not sure if I do not understand the scheduling algorithm correctly of if this is a bug. The bug seems similar to the one described and fixed here https://github.com/SchedMD/slurm/commit/6a2c99edbf96e50463cc2f16d8e5eb955c8… Given the node definition: NodeName=cluster01 CPUs=8 Boards=1 SocketsPerBoard=1 CoresPerSocket=4 ThreadsPerCore=2 RealMemory=64283 NodeName=cluster02 CPUs=8 Boards=1 SocketsPerBoard=1 CoresPerSocket=4 ThreadsPerCore=2 RealMemory=128814 PartitionName=DEFAULT MaxTime=2-0 MaxNodes=2 PartitionName=mini Nodes=cluster01,cluster02 State=UP and the batch script: for i in {1..6} do srun --exclusive --mem=100 --threads-per-core=1 -N1 -c1 -n1 bash -c 'echo $(hostname) $(date); sleep 10 ; echo done $(hostname) $(date)' & done wait When run with: time sbatch --wait --partition=mini --ntasks=10 --cpus-per-task=1 --mem=1000 mini.slurm I get the following log after 2m 18s: cluster01 Sat Jan 27 02:05:12 PM CET 2024 cluster01 Sat Jan 27 02:05:12 PM CET 2024 cluster01 Sat Jan 27 02:05:13 PM CET 2024 cluster01 Sat Jan 27 02:05:13 PM CET 2024 cluster02 Sat Jan 27 02:05:13 PM CET 2024 done cluster01 Sat Jan 27 02:05:22 PM CET 2024 done cluster01 Sat Jan 27 02:05:22 PM CET 2024 done cluster01 Sat Jan 27 02:05:23 PM CET 2024 done cluster01 Sat Jan 27 02:05:23 PM CET 2024 done cluster02 Sat Jan 27 02:05:23 PM CET 2024 srun: Job 650 step creation temporarily disabled, retrying (Requested nodes are busy) srun: Step created for StepId=650.6 cluster01 Sat Jan 27 02:07:14 PM CET 2024 done cluster01 Sat Jan 27 02:07:24 PM CET 2024 So apparently I am getting 4 sruns on cluster01 (why not 6 when I have 8 CPUs?), but only 1 is scheduled on cluster02. Then it is exhausted and waits endlessly long (almost 2 minutes?) before scheduling again. The step log tells me: slurmctld: debug: laying out the 1 tasks on 1 hosts cluster01 dist 1 slurmctld: STEPS: _step_alloc_lps: JobId=650 StepId=4 node 0 (cluster01) gres_cpus_alloc=0 tasks=1 cpus_per_task=1 slurmctld: STEPS: _pick_step_cores: step JobId=650 StepId=4 requires 1 cores on node 0 with cpus_per_core=1, available cpus from job: 8 slurmctld: STEPS: _pick_step_core: alloc Node:0 Socket:0 Core:3 slurmctld: STEPS: step alloc on job node 0 (cluster01) used 4 of 8 CPUs slurmctld: STEPS: _slurm_rpc_job_step_create: JobId=650 StepId=4 cluster01 usec=5502 slurmctld: STEPS: _pick_step_nodes: JobId=650 Currently running steps use 4 of allocated 8 CPUs on node cluster01 slurmctld: STEPS: _pick_step_nodes: JobId=650 Currently running steps use 1 of allocated 2 CPUs on node cluster02 slurmctld: STEPS: _mark_busy_nodes: JobId=650 StepId=0 has nodes cluster01 slurmctld: STEPS: _mark_busy_nodes: JobId=650 StepId=1 has nodes cluster02 slurmctld: STEPS: _mark_busy_nodes: JobId=650 StepId=2 has nodes cluster01 slurmctld: STEPS: _mark_busy_nodes: JobId=650 StepId=3 has nodes cluster01 slurmctld: STEPS: _mark_busy_nodes: JobId=650 StepId=4 has nodes cluster01 slurmctld: STEPS: _pick_step_nodes: step pick 1-1 nodes, avail:cluster[01-02] idle: picked:NONE slurmctld: STEPS: _pick_step_nodes: step picked 0 of 1 nodes slurmctld: STEPS: Picked nodes cluster01 when accumulating from cluster01 slurmctld: debug: laying out the 1 tasks on 1 hosts cluster01 dist 1 slurmctld: STEPS: _step_alloc_lps: JobId=650 StepId=5 node 0 (cluster01) gres_cpus_alloc=0 tasks=1 cpus_per_task=1 slurmctld: STEPS: _pick_step_cores: step JobId=650 StepId=5 requires 1 cores on node 0 with cpus_per_core=1, available cpus from job: 8 slurmctld: STEPS: unable to pick step cores for job node 0 (cluster01): Requested nodes are busy slurmctld: STEPS: Deallocating 100MB of memory on node 0 (cluster01) now used: 400 of 1000 slurmctld: STEPS: step dealloc on job node 0 (cluster01) used: 4 of 8 CPUs slurmctld: STEPS: _slurm_rpc_job_step_create for JobId=650: Requested nodes are busy So why is it unable to allocate on cluster02? And why does its need to when it is only using 4 of 8 CPUs on cluster01 anyway? Now if I change to --ntasks=8, the algorithm doesn’t even schedule cluster02 at all: cluster01 Sat Jan 27 02:15:30 PM CET 2024 cluster01 Sat Jan 27 02:15:30 PM CET 2024 cluster01 Sat Jan 27 02:15:30 PM CET 2024 cluster01 Sat Jan 27 02:15:30 PM CET 2024 done cluster01 Sat Jan 27 02:15:40 PM CET 2024 done cluster01 Sat Jan 27 02:15:40 PM CET 2024 done cluster01 Sat Jan 27 02:15:40 PM CET 2024 done cluster01 Sat Jan 27 02:15:40 PM CET 2024 srun: Job 651 step creation temporarily disabled, retrying (Requested nodes are busy) srun: Step created for StepId=651.6 cluster01 Sat Jan 27 02:17:35 PM CET 2024 srun: Job 651 step creation temporarily disabled, retrying (Requested nodes are busy) srun: Step created for StepId=651.7 cluster01 Sat Jan 27 02:17:36 PM CET 2024 done cluster01 Sat Jan 27 02:17:45 PM CET 2024 done cluster01 Sat Jan 27 02:17:46 PM CET 2024 Thanks for your help. Best /rike

1 0

LuaSQLite3 with slurm-lua-spank
by Jackson, Gary L. 26 Jan '24

26 Jan '24

What do I need to do to use the LuaSQLite3 library with Lua SPANK? For what it’s worth, I don’t know anything about Lua. -- Gary

1 0

sinfo: error: resolve_ctls_from_dns_srv: res_nsearch error: Unknown host
by Michael Lewis 26 Jan '24

26 Jan '24

Hi All, I’m trying to get slurm-23.11.3 running on Ubuntu 20.04 and running on a stand alone system. I’m running into an issue I can not find the answer to. After compiling and installing when I fire up slurmctld and slurmd I get an error from sinfo: sinfo: error: resolve_ctls_from_dns_srv: res_nsearch error: Unknown host sinfo: error: fetch_config: DNS SRV lookup failed sinfo: error: _establish_config_source: failed to fetch config sinfo: fatal: Could not establish a configuration source I looks like a DNS issue but the system has no issue resolving to its hostname or localhost. The slurm.conf file is also being read properly as I have the logs directed to a place convenient to me. I see lots have had these same issues but cannot find a clear resolution. I have slurm running on a stand alone system in another lab with and identical setup without issue. Any advice would be greatly appreciated. Thanks, Mike

2 2

Database cluster
by Daniel L'Hommedieu 26 Jan '24

26 Jan '24

Community: What do you do to ensure database reliability in your SLURM environment? We can have multiple controllers and multiple slurmdbds, but my understanding is that slurmdbd can be configured with a single MySQL server, so what do you do? Do you have that “single MySQL server” be a cluster, such as Percona XtraDB? Do you use MySQL replication, then manually switch to slurmdbd to a replication slave if the master goes down? Do you do something else? Thanks. Daniel

6 7

Problem using Podman with scrun on SLURM 23.11.3
by Marcus Lauer 25 Jan '24

25 Jan '24

I am getting an unusual error when trying to run Podman containers using scrun on SLURM 23.11.3 (and 23.11.1 previously). In short, Podman works when not configured to use scrun, but when configured to use scrun it fails. Podman gives this error: scrun: fatal: Unable to request job allocation: Job cannot be submitted without the current working directory specified. The slurmctld logs show this error: _slurm_rpc_allocate_resources: Job cannot be submitted without the current working directory specified. The scrun command does not appear to have a --chdir option so the working directory must be detected automatically, and this appears to be failing. Perhaps someone has encountered this or a similar error before? If anyone has seen this before I would love to hear about your experiences. A bit more detail in case anyone is interested. This is a two-node test system with one head node and one compute node, both running Rocky Linux 8.9. I have created /etc/containers/storage.conf and containers.conf files which are identical to the ones in the SLURM Containers Guide except that I set the rootless_storage_path to the same value as the graphroot in storage.conf. When I get rid of the /etc/containers/containers.conf file I can run containers on the head node. The backing store is ext4, though I have tried NFS (which had other problems). I have tried the vfs and overlay storage drivers but get the same results. On the SLURM side I created an oci.conf which is the same as the "oci.conf example for crun using run (suggested)" from the SLURM Container Guide. I'm using crun because I have forced cgroup v2 on both systems ( systemd.unified_cgroup_hierarchy=1 on the kernel cmdline) and crun seems to support cgroup v2 better. I am using an scrun.lua which is similar to the one in the scrun manual page with some paths modified for my setup. I should also mention that sbatch jobs run just fine and srun works as well. the test cluster seems to be working fine in general. -- Marcus Lauer Systems Administrator CETS Group, Research Support

1 0

Question about CPUs and cores
by Gestió Servidors 25 Jan '24

25 Jan '24

Hi, I want to run a simple test that uses one node and four cores. Also, in my script, I execute a binary that reports me in what core is running one of the four tasks. These are my files: * submit script: #!/bin/bash #SBATCH --job-name=test_jobs # Job name #SBATCH --output=test_job_%j.out # Output file (using array index) #SBATCH --error=test_job_%j.err # Error file (using array index) #SBATCH --ntasks=4 #SBATCH --ntasks-per-core=1 #SBATCH --cpus-per-task=1 # Number of CPU cores per task echo "START : $(date)" srun -n1 -c1 check_cores >> output_small.txt & srun -n1 -c1 check_cores >> output_small.txt & srun -n1 -c1 check_cores >> output_small.txt & srun -n1 -c1 check_cores >> output_small.txt & # Wait for all jobs to finish before exiting the job submission script wait echo "END : $(date)" * check_cores.c file: #include <stdio.h> #include<unistd.h> struct pstat { int pid; //process id char tcomm[256];//filename of the executable char state[2]; //state (R is running, S is sleeping, D is sleeping in an //uninterruptible wait, Z is zombie, T is traced or stopped) int ppid;// process id of the parent process int pgrp;// pgrp of the process int sid;// session id int tty_nr;// tty the process uses int tty_pgrp;// pgrp of the tty int flags;// task flags int min_flt;// number of minor faults int cmin_flt;// number of minor faults with child's int maj_flt;// number of major faults int cmaj_flt;// number of major faults with child's int utime;// user mode jiffies int stime;// kernel mode jiffies int cutime;// user mode jiffies with child's int cstime;// kernel mode jiffies with child's int priority;// priority level int nice;// nice level int num_threads;// number of threads int it_real_value;// (obsolete, always 0) int start_time;// time the process started after system boot int vsize;// virtual memory size int rss;// resident set memory size int rsslim;// current limit in bytes on the rss int start_code;// address above which program text can run int end_code;// address below which program text can run int start_stack;// address of the start of the stack int esp;// current value of ESP int eip;// current value of EIP int pending;// bitmap of pending signals int blocked;// bitmap of blocked signals int sigign;// bitmap of ignored signals int sigcatch;// bitmap of catched signals int wchan;// address where process went to sleep int i0;// (place holder) int i1;// (place holder) int exit_signal;// signal to send to parent thread on exit int task_cpu;// which CPU the task is scheduled on int rt_priority;// realtime priority int policy;// scheduling policy (man sched_setscheduler) int blkio_ticks;// time spent waiting for block IO int gtime;// guest time of the task in jiffies int cgtime;// guest time of the task children in jiffies } p ; int main() { char name[256]; char state[8]; FILE* f = fopen("/proc/self/stat", "r"); char hostname[1024]; gethostname(hostname, 1024); fscanf(f, "%d%s%s%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d%d", &p.pid, &p.tcomm, &p.state, &p.ppid, &p.pgrp, &p.sid, &p.tty_nr, &p.tty_pgrp, &p.flags, &p.min_flt, &p.cmin_flt, &p.maj_flt, &p.cmaj_flt, &p.utime, &p.stime, &p.cutime, &p.cstime, &p.priority, &p.nice, &p.num_threads, &p.it_real_value, &p.start_time, &p.vsize, &p.rss, &p.rsslim, &p.start_code, &p.end_code, &p.start_stack, &p.esp, &p.eip, &p.pending, &p.blocked, &p.sigign, &p.sigcatch, &p.wchan, &p.i0, &p.i1, &p.exit_signal, &p.task_cpu, &p.rt_priority, &p.policy, &p.blkio_ticks, &p.gtime, &p.cgtime); sleep (15); printf("HOST %s\n", hostname); printf("CPU %d\n", p.task_cpu); return 0; } When I run this script, I should receive an output like this: HOST clus04.hpc.local CPU 0 HOST clus04.hpc.local CPU 7 HOST clus04.hpc.local CPU 1 HOST clus04.hpc.local CPU 6 because system has scheduled my job in node "clus04.hpc.local" (a node with two 6-cores processors) and has reserved cores 0-1 of each processor. However, the real output I receive is HOST clus04.hpc.local CPU 1 HOST clus04.hpc.local CPU 1 HOST clus04.hpc.local CPU 1 HOST clus04.hpc.local CPU 6 (and others outputs where there are one CPU repeated), so it seems SLURMs is reserving correctly four cores but, then, process is running two or more times in the same core. Slurmctld.log file in server shows this information: [...] [2024-01-25T09:38:42.867] DEBUG: JobId=206129 node clus04 vpus 1 cpus 4 [2024-01-25T09:38:42.867] ==================== [2024-01-25T09:38:42.867] JobId=206129 nhosts:1 ncpus:4 node_req:1 nodes=clus04 [2024-01-25T09:38:42.867] Node[0]: [2024-01-25T09:38:42.867] Mem(MB):0:0 Sockets:2 Cores:6 CPUs:4:0 [2024-01-25T09:38:42.867] Socket[0] Core[0] is allocated [2024-01-25T09:38:42.867] Socket[0] Core[1] is allocated [2024-01-25T09:38:42.867] Socket[1] Core[0] is allocated [2024-01-25T09:38:42.867] Socket[1] Core[1] is allocated [2024-01-25T09:38:42.867] -------------------- [2024-01-25T09:38:42.867] cpu_array_value[0]:4 reps:1 [2024-01-25T09:38:42.867] ==================== [2024-01-25T09:38:42.867] DEBUG: Dump job_resources: nhosts 1 cb 0-1,6-7 [...] [2024-01-25T09:38:58.213] _job_complete: JobId=206129 WEXITSTATUS 0 [2024-01-25T09:38:58.213] deallocate_nodes: JobId=206129 [2024-01-25T09:38:58.213] DEBUG: Dump job_resources: nhosts 1 cb 0-1,6-7 [2024-01-25T09:38:58.213] _job_complete: JobId=206129 done And slurmd.log file in node clus04 shows this information: [...] [2024-01-25T09:38:30.685] [206129.batch] debug: task/cgroup: job abstract cores are '0-1,6-7' [2024-01-25T09:38:30.685] [206129.batch] debug: task/cgroup: step abstract cores are '0-1,6-7' [2024-01-25T09:38:30.685] [206129.batch] debug: task/cgroup: job physical cores are '0-1,6-7' [2024-01-25T09:38:30.685] [206129.batch] debug: task/cgroup: step physical cores are '0-1,6-7' [...] [2024-01-25T09:38:30.883] [206129.1] debug: task/cgroup: job abstract cores are '0-1,6-7' [2024-01-25T09:38:30.883] [206129.1] debug: task/cgroup: step abstract cores are '0-1,6-7' [2024-01-25T09:38:30.883] [206129.1] debug: task/cgroup: job physical cores are '0-1,6-7' [2024-01-25T09:38:30.883] [206129.1] debug: task/cgroup: step physical cores are '0-1,6-7' [...] [2024-01-25T09:38:30.911] [206129.0] debug: task/cgroup: job abstract cores are '0-1,6-7' [2024-01-25T09:38:30.911] [206129.0] debug: task/cgroup: step abstract cores are '0-1,6-7' [2024-01-25T09:38:30.911] [206129.0] debug: task/cgroup: job physical cores are '0-1,6-7' [2024-01-25T09:38:30.911] [206129.0] debug: task/cgroup: step physical cores are '0-1,6-7' [...] [2024-01-25T09:38:30.912] [206129.2] debug: task/cgroup: job abstract cores are '0-1,6-7' [2024-01-25T09:38:30.912] [206129.2] debug: task/cgroup: step abstract cores are '0-1,6-7' [2024-01-25T09:38:30.912] [206129.2] debug: task/cgroup: job physical cores are '0-1,6-7' [2024-01-25T09:38:30.912] [206129.2] debug: task/cgroup: step physical cores are '0-1,6-7' [...] [2024-01-25T09:38:30.922] [206129.3] debug: task/cgroup: job abstract cores are '0-1,6-7' [2024-01-25T09:38:30.922] [206129.3] debug: task/cgroup: step abstract cores are '0-1,6-7' [2024-01-25T09:38:30.922] [206129.3] debug: task/cgroup: job physical cores are '0-1,6-7' [2024-01-25T09:38:30.922] [206129.3] debug: task/cgroup: step physical cores are '0-1,6-7' It seems that SLURM is reserving me correctly four cores for my job but, when inside my script I run four "srun", then each srun can freely take one of the four reserved cores, not exactly one to each task. What am I doing wrong? Thanks a lot!

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Slurm version 23.11.3 is now available
by Tim McMullan 24 Jan '24

24 Jan '24

We are pleased to announce the availability of Slurm version 23.11.3. The 23.11.3 fixes a single issue related to the new Debian package support. For 23.11.2, the debian changelog was not updated correctly and would generate packages as 23.11.1. This release will correctly generate 23.11.3 packages, with no other changes. Slurm can be downloaded from https://www.schedmd.com/downloads.php . -Tim > * Changes in Slurm 23.11.3 > ========================== > -- Fix debian/changelog file to reflect the correct version so the packages > are generated correctl. -- Tim McMullan Release Management, Support, and Development SchedMD LLC - Commercial Slurm Development and Support

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Re: [slurm-users] slurmstepd: error: load_ebpf_prog: BPF load error (No space left on device). Please check your system limits (MEMLOCK).
by Tim Schneider 24 Jan '24

24 Jan '24

Hi, I just tested with 23.02.7-1 and the issue is gone. So it seems like the patch got released. Best, Tim On 1/24/24 16:55, Stefan Fleischmann wrote: > On Wed, 24 Jan 2024 12:37:04 -0300 Cristóbal Navarro > <cristobal.navarro.g(a)gmail.com> wrote: >> Many thanks >> One question? Do we have to apply this patch (and recompile slurm i >> guess) only on the compute-node with problems? >> Also, I noticed the patch now appears as "obsolete", is that ok? > We have Slurm installed on a NFS share, so what I did was to recompile > it and then I only replaced the library lib/slurm/cgroup_v2.so. Good > enough for now, I've been planning to update to 23.11 anyway soon. > > I suppose it's marked as obsolete because the patch went into a > release. According to the info in the bug report it should have been > included in 23.02.4. > > Cheers, > Stefan > >> On Wed, Jan 24, 2024 at 9:52 AM Stefan Fleischmann <sfle(a)kth.se> >> wrote: >> >>> Turns out I was wrong, this is not a problem in the kernel at all. >>> It's a known bug that is triggered by long bpf logs, see here >>> https://bugs.schedmd.com/show_bug.cgi?id=17210 >>> >>> There is a patch included there. >>> >>> Cheers, >>> Stefan >>> >>> On Tue, 23 Jan 2024 15:28:59 +0100 Stefan Fleischmann <sfle(a)kth.se> >>> wrote: >>>> I don't think there is much for SchedMD to do. As I said since it >>>> is working fine with newer kernels there doesn't seem to be any >>>> breaking change in cgroup2 in general, but only a regression >>>> introduced in one of the latest updates in 5.15. >>>> >>>> If Slurm was doing something wrong with cgroup2, and it >>>> accidentally worked until this recent change, then other kernel >>>> versions should show the same behavior. But as far as I can tell >>>> it still works just fine with newer kernels. >>>> >>>> Cheers, >>>> Stefan >>>> >>>> On Tue, 23 Jan 2024 15:20:56 +0100 >>>> Tim Schneider <tim.schneider1(a)tu-darmstadt.de> wrote: >>>> >>>>> Hi, >>>>> >>>>> I have filed a bug report with SchedMD >>>>> (https://bugs.schedmd.com/show_bug.cgi?id=18623), but the >>>>> support told me they cannot invest time in this issue since I >>>>> don't have a support contract. Maybe they will look into it >>>>> once it affects more people or someone important enough. >>>>> >>>>> So far, I have resorted to using 5.15.0-89-generic, but I am >>>>> also a bit concerned about the security aspect of this choice. >>>>> >>>>> Best, >>>>> >>>>> Tim >>>>> >>>>> On 23.01.24 14:59, Stefan Fleischmann wrote: >>>>>> Hi! >>>>>> >>>>>> I'm seeing the same in our environment. My conclusion is that >>>>>> it is a regression in the Ubuntu 5.15 kernel, introduced with >>>>>> 5.15.0-90-generic. Last working kernel version is >>>>>> 5.15.0-89-generic. I have filed a bug report here: >>>>>> https://bugs.launchpad.net/bugs/2050098 >>>>>> >>>>>> Please add yourself to the affected users in the bug report >>>>>> so it hopefully gets more attention. >>>>>> >>>>>> I've tested with newer kernels (6.5, 6.6 and 6.7) and the >>>>>> problem does not exist there. 6.5 is the latest hwe kernel >>>>>> for 22.04 and would be an option for now. Reverting back to >>>>>> 5.15.0-89 would work as well, but I haven't looked into the >>>>>> security aspects of that. >>>>>> >>>>>> Cheers, >>>>>> Stefan >>>>>> >>>>>> On Mon, 22 Jan 2024 13:31:15 -0300 >>>>>> cristobal.navarro.g at gmail.com wrote: >>>>>> >>>>>>> Hi Tim and community, >>>>>>> We are currently having the same issue (cgroups not working >>>>>>> it seems, showing all GPUs on jobs) on a GPU-compute node >>>>>>> (DGX A100) a couple of days ago after a full update (apt >>>>>>> upgrade). Now whenever we launch a job for that partition, >>>>>>> we get the error message mentioned by Tim. As a note, we >>>>>>> have another custom GPU-compute node with L40s, on a >>>>>>> different partition, and that one works fine. Before this >>>>>>> error, we always had small differences in kernel version >>>>>>> between nodes, so I am not sure if this can be the problem. >>>>>>> Nevertheless, here is the info of our nodes as well. >>>>>>> >>>>>>> *[Problem node]* The DGX A100 node has this kernel >>>>>>> cnavarro at nodeGPU01:~$ uname -a >>>>>>> Linux nodeGPU01 5.15.0-1042-nvidia #42-Ubuntu SMP Wed Nov 15 >>>>>>> 20:28:30 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux >>>>>>> >>>>>>> *[Functioning node]* The Custom GPU node (L40s) has this >>>>>>> kernel cnavarro at nodeGPU02:~$ uname -a >>>>>>> Linux nodeGPU02 5.15.0-91-generic #101-Ubuntu SMP Tue Nov 14 >>>>>>> 13:30:08 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux >>>>>>> >>>>>>> *And the login node *(slurmctld) >>>>>>> ? ~ uname -a >>>>>>> Linux patagon-master 5.15.0-91-generic #101-Ubuntu SMP Tue >>>>>>> Nov 14 13:30:08 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux >>>>>>> >>>>>>> Any ideas what we should check? >>>>>>> >>>>>>> On Thu, Jan 4, 2024 at 3:03?PM Tim Schneider <tim.schneider1 >>>>>>> at tu-darmstadt.de> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> I am using SLURM 22.05.9 on a small compute cluster. Since I >>>>>>>> reinstalled two of our nodes, I get the following error when >>>>>>>> launching a job: >>>>>>>> >>>>>>>> slurmstepd: error: load_ebpf_prog: BPF load error (No space >>>>>>>> left on device). Please check your system limits (MEMLOCK). >>>>>>>> >>>>>>>> Also the cgroups do not seem to work properly anymore, as I >>>>>>>> am able to see all GPUs even if I do not request them, >>>>>>>> which is not the case on the other nodes. >>>>>>>> >>>>>>>> One difference I found between the updated nodes and the >>>>>>>> original nodes (both are Ubuntu 22.04) is the kernel >>>>>>>> version, which is "5.15.0-89-generic #99-Ubuntu SMP" on the >>>>>>>> functioning nodes and "5.15.0-91-generic #101-Ubuntu SMP" >>>>>>>> on the updated nodes. I could not figure out how to install >>>>>>>> the exact first kernel version on the updated nodes, but I >>>>>>>> noticed that when I reinstall 5.15.0 with this tool: >>>>>>>> https://github.com/pimlie/ubuntu-mainline-kernel.sh, the >>>>>>>> error message disappears. However, once I do that, the >>>>>>>> network driver does not function properly anymore, so this >>>>>>>> does not seem to be a good solution. >>>>>>>> >>>>>>>> Has anyone seen this issue before or is there maybe >>>>>>>> something else I should take a look at? I am also happy to >>>>>>>> just find a workaround such that I can take these nodes >>>>>>>> back online. >>>>>>>> >>>>>>>> I appreciate any help! >>>>>>>> >>>>>>>> Thanks a lot in advance and best wishes, >>>>>>>> >>>>>>>> Tim >>>>>>>> >>>>>>>> >>>>>>>> >>>> >>> >>

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Re: [slurm-users] slurmstepd: error: load_ebpf_prog: BPF load error (No space left on device). Please check your system limits (MEMLOCK).
by Cristóbal Navarro 24 Jan '24

24 Jan '24

Many thanks One question? Do we have to apply this patch (and recompile slurm i guess) only on the compute-node with problems? Also, I noticed the patch now appears as "obsolete", is that ok? On Wed, Jan 24, 2024 at 9:52 AM Stefan Fleischmann <sfle(a)kth.se> wrote: > Turns out I was wrong, this is not a problem in the kernel at all. It's > a known bug that is triggered by long bpf logs, see here > https://bugs.schedmd.com/show_bug.cgi?id=17210 > > There is a patch included there. > > Cheers, > Stefan > > On Tue, 23 Jan 2024 15:28:59 +0100 Stefan Fleischmann <sfle(a)kth.se> > wrote: > > I don't think there is much for SchedMD to do. As I said since it is > > working fine with newer kernels there doesn't seem to be any breaking > > change in cgroup2 in general, but only a regression introduced in one > > of the latest updates in 5.15. > > > > If Slurm was doing something wrong with cgroup2, and it accidentally > > worked until this recent change, then other kernel versions should > > show the same behavior. But as far as I can tell it still works just > > fine with newer kernels. > > > > Cheers, > > Stefan > > > > On Tue, 23 Jan 2024 15:20:56 +0100 > > Tim Schneider <tim.schneider1(a)tu-darmstadt.de> wrote: > > > > > Hi, > > > > > > I have filed a bug report with SchedMD > > > (https://bugs.schedmd.com/show_bug.cgi?id=18623), but the support > > > told me they cannot invest time in this issue since I don't have a > > > support contract. Maybe they will look into it once it affects more > > > people or someone important enough. > > > > > > So far, I have resorted to using 5.15.0-89-generic, but I am also a > > > bit concerned about the security aspect of this choice. > > > > > > Best, > > > > > > Tim > > > > > > On 23.01.24 14:59, Stefan Fleischmann wrote: > > > > Hi! > > > > > > > > I'm seeing the same in our environment. My conclusion is that it > > > > is a regression in the Ubuntu 5.15 kernel, introduced with > > > > 5.15.0-90-generic. Last working kernel version is > > > > 5.15.0-89-generic. I have filed a bug report here: > > > > https://bugs.launchpad.net/bugs/2050098 > > > > > > > > Please add yourself to the affected users in the bug report so it > > > > hopefully gets more attention. > > > > > > > > I've tested with newer kernels (6.5, 6.6 and 6.7) and the problem > > > > does not exist there. 6.5 is the latest hwe kernel for 22.04 and > > > > would be an option for now. Reverting back to 5.15.0-89 would work > > > > as well, but I haven't looked into the security aspects of that. > > > > > > > > Cheers, > > > > Stefan > > > > > > > > On Mon, 22 Jan 2024 13:31:15 -0300 > > > > cristobal.navarro.g at gmail.com wrote: > > > > > > > >> Hi Tim and community, > > > >> We are currently having the same issue (cgroups not working it > > > >> seems, showing all GPUs on jobs) on a GPU-compute node (DGX A100) > > > >> a couple of days ago after a full update (apt upgrade). Now > > > >> whenever we launch a job for that partition, we get the error > > > >> message mentioned by Tim. As a note, we have another custom > > > >> GPU-compute node with L40s, on a different partition, and that > > > >> one works fine. Before this error, we always had small > > > >> differences in kernel version between nodes, so I am not sure if > > > >> this can be the problem. Nevertheless, here is the info of our > > > >> nodes as well. > > > >> > > > >> *[Problem node]* The DGX A100 node has this kernel > > > >> cnavarro at nodeGPU01:~$ uname -a > > > >> Linux nodeGPU01 5.15.0-1042-nvidia #42-Ubuntu SMP Wed Nov 15 > > > >> 20:28:30 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > > > >> > > > >> *[Functioning node]* The Custom GPU node (L40s) has this kernel > > > >> cnavarro at nodeGPU02:~$ uname -a > > > >> Linux nodeGPU02 5.15.0-91-generic #101-Ubuntu SMP Tue Nov 14 > > > >> 13:30:08 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > > > >> > > > >> *And the login node *(slurmctld) > > > >> ? ~ uname -a > > > >> Linux patagon-master 5.15.0-91-generic #101-Ubuntu SMP Tue Nov 14 > > > >> 13:30:08 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > > > >> > > > >> Any ideas what we should check? > > > >> > > > >> On Thu, Jan 4, 2024 at 3:03?PM Tim Schneider <tim.schneider1 at > > > >> tu-darmstadt.de> wrote: > > > >> > > > >>> Hi, > > > >>> > > > >>> I am using SLURM 22.05.9 on a small compute cluster. Since I > > > >>> reinstalled two of our nodes, I get the following error when > > > >>> launching a job: > > > >>> > > > >>> slurmstepd: error: load_ebpf_prog: BPF load error (No space left > > > >>> on device). Please check your system limits (MEMLOCK). > > > >>> > > > >>> Also the cgroups do not seem to work properly anymore, as I am > > > >>> able to see all GPUs even if I do not request them, which is not > > > >>> the case on the other nodes. > > > >>> > > > >>> One difference I found between the updated nodes and the > > > >>> original nodes (both are Ubuntu 22.04) is the kernel version, > > > >>> which is "5.15.0-89-generic #99-Ubuntu SMP" on the functioning > > > >>> nodes and "5.15.0-91-generic #101-Ubuntu SMP" on the updated > > > >>> nodes. I could not figure out how to install the exact first > > > >>> kernel version on the updated nodes, but I noticed that when I > > > >>> reinstall 5.15.0 with this tool: > > > >>> https://github.com/pimlie/ubuntu-mainline-kernel.sh, the error > > > >>> message disappears. However, once I do that, the network driver > > > >>> does not function properly anymore, so this does not seem to be > > > >>> a good solution. > > > >>> > > > >>> Has anyone seen this issue before or is there maybe something > > > >>> else I should take a look at? I am also happy to just find a > > > >>> workaround such that I can take these nodes back online. > > > >>> > > > >>> I appreciate any help! > > > >>> > > > >>> Thanks a lot in advance and best wishes, > > > >>> > > > >>> Tim > > > >>> > > > >>> > > > >>> > > > -- Cristóbal A. Navarro

2 1

slurm-config on NFS-volume
by Werf, C.G. van der (Carel) 24 Jan '24

24 Jan '24

Hi, Among other clusters, I have a simple cluster with 2 nodes, running slurm. 1 node runs : mysqld, slurmdbd, slurmctld and slurmd. The other node, only runs slurmd. Slurm config is in node1: /etc/slurm. A copy of the config is in node2:/etc/slurm. This slurm configuration runs ok. But, as I am normally used to configure on a shared location, where there is only 1 copy of the config, I tried to change the current setup by moving the slurm-config to a shared (NFS) disk. So on both nodes : /etc/slurm -> nfs-server:/shared/etc/slurm But, I have tried several ways... The slurmctld and slurmd daemons will not start when I refer to this "nfs-shared" location. Any ideas what is missing here ? Authorizations seem ok. With Regards, | Carel van der Werf | | Developer/Administrator Linux | ICT-Bèta | Department of Science | Utrecht University |

3 3

error: Couldn't find the specified plugin name for cred/munge looking at all files
by Jesse Aiton 24 Jan '24

24 Jan '24

Hello Slurm Folks, I have a weird issue where on the same server, which acts as both a controller and a node, slurmctld can’t find cred_munge.so slurmctld: debug3: Trying to load plugin /app/slurm-24.0.8/lib/slurm/cred_munge.so slurmctld: debug4: /app/slurm-24.0.8/lib/slurm/cred_munge.so: Does not exist or not a regular file. slurmctld: error: Couldn't find the specified plugin name for cred/munge looking at all files slurmctld: error: cannot open plugin directory /app/slurm-24.0.8/lib/slurm slurmctld: error: cannot find cred plugin for cred/munge slurmctld: error: cannot create cred context for cred/munge slurmctld: fatal: failed to initialize cred plugin But slurmd can: slurmd: debug3: Trying to load plugin /app/slurm-24.0.8/lib/slurm/cred_munge.so slurmd: debug3: plugin_load_from_file->_verify_syms: found Slurm plugin name:Munge credential signature plugin type:cred/munge version:0x180800 slurmd: cred/munge: init: Munge credential signature plugin loaded slurmd: debug3: Success. This is on Ubuntu 20.04 and happens both with Slurm 20.11.09 and 24.0.8 Thank you, Jesse # slurm.conf file generated by configurator easy.html. # Put this file on all nodes of your cluster. # See the slurm.conf man page for more information. # ClusterName=prod-cluster SlurmctldHost=controller # #MailProg=/bin/mail #MpiDefault= #MpiParams=ports=#-# ProctrackType=proctrack/cgroup ReturnToService=1 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 #SwitchType= TaskPlugin=task/affinity,task/cgroup # # # TIMERS #KillWait=30 #MinJobAge=300 #SlurmctldTimeout=120 #SlurmdTimeout=300 # # # SCHEDULING SchedulerType=sched/backfill SelectType=select/cons_tres # # # LOGGING AND ACCOUNTING #AccountingStorageType= #JobAcctGatherFrequency=30 #JobAcctGatherType= #SlurmctldDebug=info SlurmctldLogFile=/var/log/slurmctld.log #SlurmdDebug=info SlurmdLogFile=/var/log/slurmd.log # # # COMPUTE NODES NodeName=controller CPUs=1 State=UNKNOWN NodeName=node CPUs=1 State=UNKNOWN PartitionName=prod-part Nodes=ALL Default=YES MaxTime=INFINITE State=UP

3 5

Slurm version 23.11.2 is now available
by Tim McMullan 23 Jan '24

23 Jan '24

We are pleased to announce the availability of Slurm version 23.11.2. The 23.11.2 release includes a number of fixes to stability and various bug fixes. Some notable changes include several fixes to the new scontrol reconfigure method, including one that could result in jobs getting cancelled prematurely, a couple errors that resulted in the backup slurmctld stopping on fail-back, and an issue during upgrades with older MySQL versions with a small max_allowed_packet value for sites with a large number of associations. Slurm can be downloaded from https://www.schedmd.com/downloads.php . -Tim > * Changes in Slurm 23.11.2 > ========================== > -- slurmrestd - Reject single http query with multiple path requests. > -- Fix launching Singularity v4.x containers with srun --container by setting > .process.terminal to true in generated config.json when step has > pseudoterminal (--pty) requested. > -- Fix loading in dyanmic/cloud node jobs after net_cred expired. > -- Fix cgroup null path error on slurmd/slurmstepd tear down. > -- data_parser/v0.0.40 - Prevent failure if accounting is disabled, instead > issue a warning if needed data from the database can not be retrieved. > -- openapi/slurmctld - Prevent failure if accounting is disabled. > -- Prevent slurmscriptd processing delays from blocking other threads in > slurmctld while trying to launch various scripts. This is additional work > for a fix in 23.02.6. > -- Fix memory leak when receiving alias addrs from controller. > -- scontrol - Accept `scontrol token lifespan=infinite` to create tokens that > effectively do not expire. > -- Avoid errors when Slurmdb accounting disabled when '--json' or '--yaml' is > invoked with CLI commands and slurmrestd. Add warnings when query would > have populated data from Slurmdb instead of errors. > -- Fix slurmctld memory leak when running job with --tres-per-task=gres:shard:# > -- Fix backfill trying to start jobs outside of backfill window. > -- Fix oversubscription on partitions with PreemptMode=OFF. > -- Preserve node reason on power up if the node is downed or drained. > -- data_parser/v0.0.40 - Avoid aborting when invoking a not implemented > parser. > -- data_parser/v0.0.40 - Fix how nice values are parsed for job submissions. > -- data_parser/v0.0.40 - Fix regression where parsing error did not result in > invalid request being rejected. > -- Fix segfault in front-end node registration. > -- Prevent jobs using none typed gpus from being killed by the controller after > a reconfig or restart. > -- Fix deadlock situation in the dbd when adding associations. > -- Update default values of text/blob columns when updating from old mysql > versions in more situations. This improves a previous fix to handle an > uncommon case when upgrading mysql/mariadb. > -- Fix rpmbuild in openSUSE/SLES due to incorrect mariadb dependency. > -- Fix compilation on RHEL 7. > -- When upgrading the slurmdbd to 23.11, avoid generating a query to update > the association table that is larger than max_allowed_packet which would > result in an upgrade failure. > -- Fix rare deadlock when a dynamic node registers at the same time that a > once per minute background task occurs. > -- Fix build issue on 32-bit systems. > -- data_parser/v0.0.40 - Fix enumerated strings in OpenAPI specification not > have type field specified. > -- Improve scontrol show job -d information of used shared gres (shard/mps) > topology. > -- Allow Slurm to compile without MUNGE if --without-munge is used as an > argument to configure. > -- accounting_storage/mysql - Fix usage query to use new lineage column > instead of lft/rgt. > -- slurmrestd - Improve handling of missing parsers when content plugins > expect parsers not loaded. > -- slurmrestd - Correct parsing of StepIds when querying jobs. > -- slurmrestd - Improve error from parsing failures of lists. > -- slurmrestd - Improve parsing of singular values for lists. > -- accounting_storage/mysql - Fix PrivateData=User when listing associations. > -- Disable sorting of dynamic nodes to avoid issues when restarting with > heterogenous jobs that cause jobs to abort on restart. > -- Don't allow deletion of non-dynamic nodes. > -- accounting_storage/mysql - Fix issue adding partition based associations. > -- Respect non-"slurm" settings for I_MPI_HYDRA_BOOTSTRAP and HYDRA_BOOTSTRAP > and avoid injecting the --external-launcher option which will cause > mpirun/mpiexec to fail with an unexpected argument error. > -- Fix bug where scontrol hold would change node count for jobs with > implicitly defined node counts. > -- data_parser/v0.0.40 - Fix regression of support for "hold" in > job description. > -- Avoid sending KILL RPCs to unresolvable POWERING_UP and POWERED_DOWN nodes. > -- data_parser/v0.0.38 - Fix several potential NULL dereferences that could > cause slurmrestd to crash. > -- Add --gres-flags=one-task-per-sharing. Do not allow different tasks in to be > allocated shared gres from the same sharing gres. > -- Add SelectTypeParameters=ENFORCE_BINDING_GRES and ONE_TASK_PER_SHARING_GRES. > This gives default behavior for a job's --gres-flags. > -- Alter the networking code to try connecting to the backup controllers > if the DNS lookup for the primary SlurmctldHost fails. > -- Alter the name resolution to only log at verbose() in client commands > on failures. This allows for HA setups where the DNS entries are withdrawn > for some SlurmctldHost entries without flooding the user with errors. > -- Prevent slurmscriptd PID leaks when running slurmctld in foreground mode. > -- Open all slurmctld listening ports at startup, and persist throughout. > This also changes the backup slurmctld process to open the SlurmctldPort > range, instead of only the first. > -- Fix backup slurmctld shutting down instead of resuming standby duty if it > took control. > -- Fix race condition that delayed the primary slurmctld resuming when taking > control from a backup controller. > -- srun - Ensure processed messages are meant for this job in case of a > rapidly-reused TCP port. > -- srun - Prevent step launch failure while waiting for step allocation if > a stray message is received. > -- Fix backup slurmctld to be able to respond to configless config file > requests correctly. > -- Fix slurmctld crashing when recovering from a failed reconfigure. > -- Fix slurmscriptd operation after recovering from a failed reconfigure. -- Tim McMullan Release Management, Support, and Development SchedMD LLC - Commercial Slurm Development and Support

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GPU devices mapping with job's cgroup in cgroups v2 using eBPF
by Mahendra Paipuri 23 Jan '24

23 Jan '24

Hello all, Happy new year! We have recently upgraded the cgroups on our SLURM cluster to v2. In cgroups v1, the interface `/devices.list` used to have the information of which device has been attached to that particular cgroup. From my understanding, cgroups v2 use eBPF to manage devices and so as SLURM to manage the GPUs. I was looking for a way to be able to programatically determine the job cgroups to device mapping and I came across this thread ( https://bugzilla.redhat.com/show_bug.cgi?id=1717396) which has a similar discussion in the context of VMs. So, I have used `bpftool` to inspect the job cgroups. An example output: ``` # /tmp/bpftool cgroup list /sys/fs/cgroup/system.slice/slurmstepd.scope/job_1956132 ID AttachType AttachFlags Name ``` When I add `effective` flag, I see the attached eBPF program ``` # /tmp/bpftool cgroup list /sys/fs/cgroup/system.slice/slurmstepd.scope/job_1956132 effective ID AttachType Name 4197 cgroup_device Slurm_Cgroup_v2 ``` >From my understand, `effective` flag shows the inherited eBPF programs as well. So, my question is at which level of cgroups the eBPF program is attached? I tried to inspect at various levels but all of them returned none. Then looking into translated byte code of eBPF program, I get the following ``` # /tmp/bpftool prog dump xlated id 4197 0: (61) r2 = *(u32 *)(r1 +0) 1: (54) w2 &= 65535 2: (61) r3 = *(u32 *)(r1 +0) 3: (74) w3 >>= 16 4: (61) r4 = *(u32 *)(r1 +4) 5: (61) r5 = *(u32 *)(r1 +8) 6: (55) if r2 != 0x2 goto pc+4 7: (55) if r4 != 0xc3 goto pc+3 8: (55) if r5 != 0x0 goto pc+2 9: (b7) r0 = 0 10: (95) exit 11: (55) if r2 != 0x2 goto pc+4 12: (55) if r4 != 0xc3 goto pc+3 13: (55) if r5 != 0x1 goto pc+2 14: (b7) r0 = 0 15: (95) exit 16: (55) if r2 != 0x2 goto pc+4 17: (55) if r4 != 0xc3 goto pc+3 18: (55) if r5 != 0x2 goto pc+2 19: (b7) r0 = 0 20: (95) exit 21: (55) if r2 != 0x2 goto pc+4 22: (55) if r4 != 0xc3 goto pc+3 23: (55) if r5 != 0x3 goto pc+2 24: (b7) r0 = 1 25: (95) exit 26: (b7) r0 = 1 27: (95) exit ``` >From the output, it is clear that GPU:3 (among 0,1,2,3) is the one that is attached to that job's cgroup. However, I was looking for a way to dump eBPF maps that can directly provide the major, minor numbers and permissions of device as discussed in the comment (https://bugzilla.redhat.com/show_bug.cgi?id=1717396#c5). When I inspect eBPF program, I dont see any maps associated. ``` # /tmp/bpftool prog list id 4197 4197: cgroup_device name Slurm_Cgroup_v2 tag 1a261c8a913ff67c gpl loaded_at 2024-01-02T08:19:56+0100 uid 0 xlated 224B jited 142B memlock 4096B ``` So, my second question is how can I get a similar information as `map dump` that can give us the device's major minor numbers directly instead of parsing the byte code from `prog dump`? I am still discovering the eBPF ecosystem so if I am missing something very obvious, please let me know. I would really appreciate that. Cheers! Regards Mahendra

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Re: [slurm-users] slurmstepd: error: load_ebpf_prog: BPF load error (No space left on device). Please check your system limits (MEMLOCK).
by Tim Schneider 23 Jan '24

23 Jan '24

Hi, I have filed a bug report with SchedMD (https://bugs.schedmd.com/show_bug.cgi?id=18623), but the support told me they cannot invest time in this issue since I don't have a support contract. Maybe they will look into it once it affects more people or someone important enough. So far, I have resorted to using 5.15.0-89-generic, but I am also a bit concerned about the security aspect of this choice. Best, Tim On 23.01.24 14:59, Stefan Fleischmann wrote: > Hi! > > I'm seeing the same in our environment. My conclusion is that it is a > regression in the Ubuntu 5.15 kernel, introduced with 5.15.0-90-generic. > Last working kernel version is 5.15.0-89-generic. I have filed a bug > report here: https://bugs.launchpad.net/bugs/2050098 > > Please add yourself to the affected users in the bug report so it > hopefully gets more attention. > > I've tested with newer kernels (6.5, 6.6 and 6.7) and the problem does > not exist there. 6.5 is the latest hwe kernel for 22.04 and would be an > option for now. Reverting back to 5.15.0-89 would work as well, but I > haven't looked into the security aspects of that. > > Cheers, > Stefan > > On Mon, 22 Jan 2024 13:31:15 -0300 > cristobal.navarro.g at gmail.com wrote: > >> Hi Tim and community, >> We are currently having the same issue (cgroups not working it seems, >> showing all GPUs on jobs) on a GPU-compute node (DGX A100) a couple >> of days ago after a full update (apt upgrade). Now whenever we launch >> a job for that partition, we get the error message mentioned by Tim. >> As a note, we have another custom GPU-compute node with L40s, on a >> different partition, and that one works fine. >> Before this error, we always had small differences in kernel version >> between nodes, so I am not sure if this can be the problem. >> Nevertheless, here is the info of our nodes as well. >> >> *[Problem node]* The DGX A100 node has this kernel >> cnavarro at nodeGPU01:~$ uname -a >> Linux nodeGPU01 5.15.0-1042-nvidia #42-Ubuntu SMP Wed Nov 15 20:28:30 >> UTC 2023 x86_64 x86_64 x86_64 GNU/Linux >> >> *[Functioning node]* The Custom GPU node (L40s) has this kernel >> cnavarro at nodeGPU02:~$ uname -a >> Linux nodeGPU02 5.15.0-91-generic #101-Ubuntu SMP Tue Nov 14 13:30:08 >> UTC 2023 x86_64 x86_64 x86_64 GNU/Linux >> >> *And the login node *(slurmctld) >> ? ~ uname -a >> Linux patagon-master 5.15.0-91-generic #101-Ubuntu SMP Tue Nov 14 >> 13:30:08 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux >> >> Any ideas what we should check? >> >> On Thu, Jan 4, 2024 at 3:03?PM Tim Schneider <tim.schneider1 at >> tu-darmstadt.de> wrote: >> >>> Hi, >>> >>> I am using SLURM 22.05.9 on a small compute cluster. Since I >>> reinstalled two of our nodes, I get the following error when >>> launching a job: >>> >>> slurmstepd: error: load_ebpf_prog: BPF load error (No space left on >>> device). Please check your system limits (MEMLOCK). >>> >>> Also the cgroups do not seem to work properly anymore, as I am able >>> to see all GPUs even if I do not request them, which is not the >>> case on the other nodes. >>> >>> One difference I found between the updated nodes and the original >>> nodes (both are Ubuntu 22.04) is the kernel version, which is >>> "5.15.0-89-generic #99-Ubuntu SMP" on the functioning nodes and >>> "5.15.0-91-generic #101-Ubuntu SMP" on the updated nodes. I could >>> not figure out how to install the exact first kernel version on the >>> updated nodes, but I noticed that when I reinstall 5.15.0 with this >>> tool: https://github.com/pimlie/ubuntu-mainline-kernel.sh, the >>> error message disappears. However, once I do that, the network >>> driver does not function properly anymore, so this does not seem to >>> be a good solution. >>> >>> Has anyone seen this issue before or is there maybe something else I >>> should take a look at? I am also happy to just find a workaround >>> such that I can take these nodes back online. >>> >>> I appreciate any help! >>> >>> Thanks a lot in advance and best wishes, >>> >>> Tim >>> >>> >>>

2 1

Need help with running multiple instances/executions of a batch script in parallel (with NVIDIA HGX A100 GPU as a Gres)
by Kherfani, Hafedh (Professional Services, TC) 23 Jan '24

23 Jan '24

Hello Experts, I'm a new Slurm user (so please bare with me :) ...). Recently we've deployed Slurm version 23.11 on a very simple cluster, which consists of a Master node (acting as a Login & Slurmdbd node as well), a Compute Node which has a NVIDIA HGX A100-SXM4-40GB GPU, detected as 4 x GPU's: GPU [0-4], and a Storage Array presenting/sharing the NFS disk (where users' home directories will be created as well). The problem is that I've never been able to run a simple/dummy batch script in a parallel way using the 4 GPU's. In fact, running the same command "sbatch gpu-job.sh" multiple times shows that only one single job is running, while the other jobs are in a pending state: [slurmtest@c-a100-master test-batch-scripts]$ sbatch gpu-job.sh Submitted batch job 214 [slurmtest@c-a100-master test-batch-scripts]$ sbatch gpu-job.sh Submitted batch job 215 [slurmtest@c-a100-master test-batch-scripts]$ sbatch gpu-job.sh Submitted batch job 216 [slurmtest@c-a100-master test-batch-scripts]$ squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 216 gpu gpu-job slurmtest PD 0:00 1 (None) 215 gpu gpu-job slurmtest PD 0:00 1 (Priority) 214 gpu gpu-job slurmtest PD 0:00 1 (Priority) 213 gpu gpu-job slurmtest PD 0:00 1 (Priority) 212 gpu gpu-job slurmtest PD 0:00 1 (Resources) 211 gpu gpu-job slurmtest R 0:14 1 c-a100-cn01 PS: CPU jobs (i.e. using the default debug partition, without call the GPU Gres) can be run in parallel. The issue with running parallel jobs is only seen when using the GPU's as Gres. I've tried many combinations of settings in gres.conf and slurm.conf, many (if not most) of these combinations would result in error messages in slurmctld and slurmd logs. The current gres.conf and slurm.conf contents is shown below. Even though it doesn't give errors when restarting slurmctld and slurmd services (on master and compute nodes, resp.), but as I said, it doesn't allow jobs to be executed in parallel. Batch script contents shared below as well, in order to give more clarity on what I'm trying to do: [root@c-a100-master slurm]# cat gres.conf | grep -v "^#" NodeName=c-a100-cn01 AutoDetect=nvml Name=gpu Type=A100 File=/dev/nvidia[0-3] [root@c-a100-master slurm]# cat slurm.conf | grep -v "^#" | egrep -i "AccountingStorageTRES|GresTypes|NodeName|partition" GresTypes=gpu AccountingStorageTRES=gres/gpu NodeName=c-a100-cn01 Gres=gpu:A100:4 CPUs=64 Boards=1 SocketsPerBoard=1 CoresPerSocket=32 ThreadsPerCore=2 RealMemory=515181 State=UNKNOWN PartitionName=debug Nodes=ALL Default=YES MaxTime=INFINITE State=UP PartitionName=gpu Nodes=ALL MaxTime=10:0:0 [slurmtest@c-a100-master test-batch-scripts]$ cat gpu-job.sh #!/bin/bash #SBATCH --job-name=gpu-job #SBATCH --partition=gpu #SBATCH --nodes=1 #SBATCH --gpus-per-node=4 #SBATCH --gres=gpu:4 #SBATCH --tasks-per-node=1 #SBATCH --output=gpu_job_output.%j # Output file name (replaces %j with job ID) #SBATCH --error=gpu_job_error.%j # Error file name (replaces %j with job ID) hostname date sleep 40 pwd Any help on which changes need to be made to the config files (mainly slurm.conf and gres.cong) and/or the batch script, so that multiple jobs can be in a "Running" state at the same time (in parallel) ? Thanks in advance for your help ! Best regards, Hafedh Kherfani

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propose environment variables SLURM_STDOUT, SLURM_STDERR, SLURM_STDIN
by urbanjost 22 Jan '24

22 Jan '24

RE: Placing the full pathname of the job stdout in an environment variable Would others find it useful if new variables were added that contained the full pathnames of the standard input, error and input files of batch jobs? ## SYNOPSIS Proposed new environment variables SLURM_STDOUT,SLURM_STDERR, and SLURM_STDIN pointing to the full pathnames of the output, error output, and input files of a task would be a useful feature for batch jobs in particular. ## PROBLEM There are cases where it is desirable to have a job process the standard files (stdin, stdout, stderr) from a batch job from within the job instead of later via an epilog or via post-processing. Just a few examples where the job might want to reference the full pathname of stdout: * copy the file to a remote machine (via scp(1), for example) * move the file from local or scratch space to permanent globally accessible storage * remove the file depending on completion status * mail the output * archive it * post-process it Slurm commands like scontrol(1) and squeue(1) can help you locate the file names. But the names returned do not always expand all the macros allowed when specifying the names, and require calling a Slurm command (which might overload Slurm if millions of jobs are submitted or cause problems if Slurm is not responding for any reason(?)). For example: #!/bin/bash # Minimalist submit script for sbatch(1) #SBATCH --nodes 1-1 --ntasks=1 --time 0-0:1:00 --chdir=/tmp #SBATCH --output=stdout.%j #SBATCH --error=stderr.%A:%a:%J:%j:%N:%n:%s:%t:%u.out # query filenames via squeue(1) export SLURM_STDOUT=$(squeue --noheader --Format=STDOUT: --job=$SLURM_JOBID) export SLURM_STDERR=$(squeue --noheader --Format=STDERR: --job=$SLURM_JOBID) # PS: Current documentation for squeue(1) does not explicitly tell the # user a null size works. # query filenames via scontrol(1) declare -x $(scontrol show job=$SLURM_JOBID|grep StdOut) declare -x $(scontrol show job=$SLURM_JOBID|grep StdErr) cat <<EOF SLURM_STDOUT=$SLURM_STDOUT SLURM_STDERR=$SLURM_STDERR StdOut=$StdOut StdErr=$StdErr EOF ls stdout.* stderr.* The resulting output shows either none or some macros are expanded by the commands (and I am not sure all commands will always return a full pathname(?)) SLURM_STDOUT=/home/urbanjs/venus/V600/stdout.%j SLURM_STDERR=/home/urbanjs/venus/V600/stderr.%A:%a:%J:%j:%N:%n:%s:%t:%u.out StdOut=/home/urbanjs/venus/V600/stdout.96 StdErr=/home/urbanjs/venus/V600/stderr.96:4294967294:%J:96:%N:%n:%s:%t:urbanjs.out stderr.96:4294967294:96:96:mercury:0:4294967294:0:urbanjs.out stdout.96 One currently available work-around would be that the user just avoid the filename macros and always specify the filenames using a standard convention (which would obviously have to be specific to a specific platform). This is error-prone as it requires the user to strictly follow a protocol where the pathnames are specified that can be overridden by command-line options on sbatch(1) and so-on. Alternatively instead of the new environment variables Slurm could have a command option that returns the fully expanded names always expanding the macros. But if you query Slurm you have to worry about scaleability. Is it OK for a 100 000, jobs to query Slurm simulataneously via squeue(1) or scontrol(1)? What happens if for external reasons the Slurm daemons are down or not responding? As a current work-around using commands like realpath(1), stat(1), ls(1),find(1),and getting pids with fuser(1), pidof(1), and ps(1) become attractive. I find using the realpath(1) command at the top of the job and $SLURM_TASK_ID works the best. realpath(1) may not be available on all platforms(?) as well as the /proc/$PID/fd/1 file, in which case the other commands might be used to the same effect but it would be nice to have a simple standard way that does not require calling a command. The proposed environment variables seem the most obvious solution. # do this early in the job in case the user changes or closes # file descriptor 1 ... export SLURM_STDOUT=$(realpath /proc/$SLURM_TASK_PID/fd/1) # create softlink OUTPUT to stdout of job ln -s -f $SLURM_STDOUT OUTPUT # now user can do things like mailx(1) or scp(1) the OUTPUT file. Other reasons I might want to know the stdout pathname are to minimize network traffic and filespace on central servers. I might specify the output of a job goes to scratch or local storage or a memory-resident file system and move it all to a location on another system or a long-term archive instead of a central area that might be filled by other jobs or that I have a quota on, etc. So since the stdout might not be easily accessible from my other sessions also having something like "scontrol write batch_stdout=$SLURM_JOBID" that shows the stdout of the job would also be useful. Note the LSF job scheduler bpeek(1) command allows for a tail(1)-like interface to the job stdout to support the stdout not being accessible from all system access points, just as described. The current situation where in typical usage the output file is often in a globally mounted area and I can just access it from other nodes with grep(1), tail(1), and so on covers many users needs in simple cluster configurations; but there are several scenarios as described above primarily encountered by people running many thousands of single-node jobs where assigning output to a local scratch device and then selectively processing at job termination is preferable. As mentioned, those users can specify such a local name with "#SBATCH --output" and then, knowing it, process it as desired but having something like $SLURM_STDOUT being the full pathname to the file is much more generic. ## SUMMARY So adding the variables creates an ability for users to reliably access the standard files of a job with a low-load scalable method; and being a SLURM_* module it could be much more reliably accessed via prolog and epilog scripts and module(1) scripts as well. ## PS: Related to this would be instead of just --chdir a --mkdir and --scratch #SBATCH option would be useful that expanded file macros that would be similar to --chdir but would make sure the directory existed (using only user privelages) and a --scratch that would do the same as --mkdir but remove the directory at job termination. urbanjs@mercury:~/SLURM/proposals$ Sent with [Proton Mail](https://proton.me/) secure email.

3 2

slurmstepd: error: load_ebpf_prog: BPF load error (No space left on device). Please check your system limits (MEMLOCK).
by Tim Schneider 22 Jan '24

22 Jan '24

Hi, I am using SLURM 22.05.9 on a small compute cluster. Since I reinstalled two of our nodes, I get the following error when launching a job: slurmstepd: error: load_ebpf_prog: BPF load error (No space left on device). Please check your system limits (MEMLOCK). Also the cgroups do not seem to work properly anymore, as I am able to see all GPUs even if I do not request them, which is not the case on the other nodes. One difference I found between the updated nodes and the original nodes (both are Ubuntu 22.04) is the kernel version, which is "5.15.0-89-generic #99-Ubuntu SMP" on the functioning nodes and "5.15.0-91-generic #101-Ubuntu SMP" on the updated nodes. I could not figure out how to install the exact first kernel version on the updated nodes, but I noticed that when I reinstall 5.15.0 with this tool: https://github.com/pimlie/ubuntu-mainline-kernel.sh, the error message disappears. However, once I do that, the network driver does not function properly anymore, so this does not seem to be a good solution. Has anyone seen this issue before or is there maybe something else I should take a look at? I am also happy to just find a workaround such that I can take these nodes back online. I appreciate any help! Thanks a lot in advance and best wishes, Tim

2 1

2025

2024

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