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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

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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

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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.

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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.

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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.

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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.

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Mailing list upgrade - slurm-users list paused
by Tim Wickberg 31 Jan '24

31 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

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Testing to SchedMD folks
by Tim Wickberg 31 Jan '24

31 Jan '24

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

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Socket timed out - tuning
by Reed Dier 30 Jan '24

30 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

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