- slurm-users - lists.schedmd.com

Cleanup of old clusters in database
by Jeffrey R. Lang 10 Jan '24

10 Jan '24

We have shuttered two clusters and need to remove them from the database. To do this, do we remove the table spaces associated with the cluster names from the Slurm database? Thanks, Jeff

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Re: [slurm-users] DBD_SEND_MULT_MSG - invalid uid error (Timony, Mick)
by Craig Stark 10 Jan '24

10 Jan '24

All good ideas Mick – - I've restarted slurmd on all nodes – no effect - Ran this on all nodes: #!/bin/bash uname -n id slurm id 59999 scontrol show config | grep SlurmUser All show slurm being that 59999 user. - The firewalld already has the internal network interface being used set to the trusted zone I get a bit more info out of setting the slurmctld to debug level, but I'm not sure what to make of it TBH. I'm not sure what "_handle_mult_rc_ret: PERSIST_RC is 2002 from DBD_SEND_MULT_MSG(1474)" is trying to tell me. Jan 10 10:48:26 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid Jan 10 10:48:31 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid Jan 10 10:48:35 kirby slurmctld[461138]: slurmctld: debug: accounting_storage/slurmdbd: _handle_mult_rc_ret: PERSIST_RC is 2002 from DBD_SEND_MULT_MSG(1474): DBD_SEND_MULT_MSG message from invalid uid Jan 10 10:48:36 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid Jan 10 10:48:41 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid Jan 10 10:48:46 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid Jan 10 10:48:46 kirby slurmctld[461138]: slurmctld: debug: sched/backfill: _attempt_backfill: beginning Jan 10 10:48:46 kirby slurmctld[461138]: slurmctld: debug: sched/backfill: _attempt_backfill: no jobs to backfill Jan 10 10:48:51 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid Jan 10 10:48:53 kirby slurmctld[461138]: slurmctld: debug: accounting_storage/slurmdbd: _handle_mult_rc_ret: PERSIST_RC is 2002 from DBD_SEND_MULT_MSG(1474): DBD_SEND_MULT_MSG message from invalid uid Jan 10 10:48:56 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid Jan 10 10:49:01 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid Jan 10 10:49:06 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid Jan 10 10:49:11 kirby slurmctld[461138]: slurmctld: debug: accounting_storage/slurmdbd: _handle_mult_rc_ret: PERSIST_RC is 2002 from DBD_SEND_MULT_MSG(1474): DBD_SEND_MULT_MSG message from invalid uid Jan 10 10:49:11 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid Jan 10 10:49:16 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid Jan 10 10:49:17 kirby slurmctld[461138]: slurmctld: debug: sched: Running job scheduler for full queue. Jan 10 10:49:21 kirby slurmctld[461138]: slurmctld: error: DBD_SEND_MULT_JOB_START message from invalid uid A bit more info / another possible clue. While "sacctmgr list Account" or "sacctmgr list user" shows expected account groups and users, "sreport user top start=12/1/23" and "sreport cluster utilization start=12/1/23" both report empty tables. Craig Stark, Ph.D. Professor, Department of Neurobiology and Behavior Director, Facility for Imaging and Brain Research (FIBRE) Director, Campus Center for Neuroimaging (CCNI) School of Biological Sciences, University of California, Irvine cestark(a)uci.edu<mailto:cestark@uci.edu>

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Beginner admin question: Prioritization within a partition based on time limit
by Kenneth Chiu 09 Jan '24

09 Jan '24

I'm just learning about slurm. I understand that different different partitions can be prioritized separately, and can have different max time limits. I was wondering whether or not there was a way to have a finer-grained prioritization based on the time limit specified by a job, within a single partition. Or perhaps this is already happening by default? Would the backfill scheduler be best for this?

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job_container/tmpfs and srun.
by Phill Harvey-Smith 09 Jan '24

09 Jan '24

Hi all, On our setup we are using job_container/tmpfs to give each job it's own temp space. Since our compute nodes have reasonably sized disks for tasks that do a lot of disk I/O on user's data we have asked users to copy their data to the local disk at the beginning of the task and (if needed) copy it back at the end. This saves lots of NFS thrashing slowing down both the task and the NFS servers. However some of our users are having problems with this, their initial sbatch script will create a temp directory in their private /tmp copy their data to it and then try to srun a program. The srun will fall over as it doesn't seem to have have access to the copied data. I suspect this is because the srun task is getting it's own private /tmp. So my question is, is there a way to have the srun task inherit the /tmp of the initial sbatch? I'll include a sample of the script our user is using below. If any further information is required please feel free to ask. Cheers. Phill. #!/usr/bin/bash #SBATCH --nodes 1 #SBATCH --ntasks-per-node=1 #SBATCH --cpus-per-task=1 #SBATCH --time=00:00:10 #SBATCH --mem-per-cpu=3999 #SBATCH --output=script_out.log #SBATCH --error=script_error.log # The above options puts the STDOUT and STDERR of sbatch in # log files prefixed with 'script_'. # Create a randomly-named directory under /tmp jobtmpdir=$(mktemp -d) # Register a function to try and cleanup in case of job failure cleanup_handler() { echo "Cleaning up ${jobtmpdir}" rm -rf ${jobtmpdir} } trap 'cleanup_handler' SIGTERM EXIT # Change working directory to this directory cd ${jobtmpdir} # Copy the executable and input files from # where the job was submitted to the temporary directory. cp ${SLURM_SUBMIT_DIR}/a.out . cp ${SLURM_SUBMIT_DIR}/input.txt . # Run the executable, handling the collection of stdout # and stderr ourselves by redirecting to file srun ./a.out 2> task_error.log > task_out.log # Copy output data back to the submit directory. cp output.txt ${SLURM_SUBMIT_DIR} cp task_out.log ${SLURM_SUBMIT_DIR} cp task_error.log ${SLURM_SUBMIT_DIR} # Cleanup cd ${SLURM_SUBMIT_DIR} cleanup_handler

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Re: [slurm-users] DBD_SEND_MULT_MSG - invalid uid error
by Craig Stark 08 Jan '24

08 Jan '24

This ticket with SchedMD implies it's a munged issue: https://urldefense.com/v3/__https://bugs.schedmd.com/show_bug.cgi?id=1293__… Is the munge daemon running on all systems? If it is, are all servers running a network time daemon such chronyd or ntpd and the time is in sync on all hosts? Thanks Mick, munge is seemingly running on all systems (systemctl status munge). I do get a warning about the munge file changing on disk, but I'm pretty sure that's from warewulf sync'ing files every minute. A sha256sum on the munge.key file on the compute nodes and host node says they're the same, so I think I can put that aside. The management node runs chrony and the compute nodes sync to the management node. [root@kirby uber]# chronyc tracking Reference ID : 4A06A849 (t2.time.gq1.yahoo.com) Stratum : 3 Ref time (UTC) : Mon Jan 08 22:26:44 2024 System time : 0.000032525 seconds slow of NTP time Last offset : -0.000021390 seconds RMS offset : 0.000055729 seconds Frequency : 38.797 ppm slow Residual freq : +0.001 ppm Skew : 0.018 ppm Root delay : 0.033342984 seconds Root dispersion : 0.000524800 seconds Update interval : 256.8 seconds Leap status : Normal vs [root@sonic01 ~]# chronyc tracking Reference ID : C0A80102 (warewulf) Stratum : 4 Ref time (UTC) : Mon Jan 08 22:31:02 2024 System time : 0.000000120 seconds slow of NTP time Last offset : -0.000000092 seconds RMS offset : 0.000014737 seconds Frequency : 47.495 ppm slow Residual freq : +0.000 ppm Skew : 0.066 ppm Root delay : 0.033458963 seconds Root dispersion : 0.000283949 seconds Update interval : 64.2 seconds Leap status : Normal So, the compute node is talking to the host and the host is talking to generic NTP sources. "date" shows the same time on the compute nodes

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Re: [slurm-users] DBD_SEND_MULT_MSG - invalid uid error
by Craig Stark 08 Jan '24

08 Jan '24

3rd time trying to get this to come through to the list - hopefully this time works. I've been running SLURM for several years now, but in setting it up on a new cluster, I'm hitting a recurring issue. I'm using a MariaDB and configured it just as I had in my several-year-ago setup and in the docs. There's a "slurm" user (59999) on the OS (Rocky 9), that's on all the nodes, and I've added the slurm@localhost as instructed (grant all on slurm_acct_db.* TO 'slurm'@'localhost' identified by 'PASSWORD'). But, I keep getting things like this: ``` Dec 22 14:22:07 kirby slurmdbd[14518]: slurmdbd: error: DBD_SEND_MULT_MSG message from invalid uid 59999 Dec 22 14:22:07 kirby slurmdbd[14518]: slurmdbd: error: Processing last message from connection 7(192.168.1.2) uid(59999) Dec 22 14:22:07 kirby slurmdbd[14518]: slurmdbd: error: CONN:7 DBD_REGISTER_CTLD message from invalid uid 59999 Dec 22 14:22:07 kirby slurmdbd[14518]: slurmdbd: error: CONN:7 Security violation, DBD_REGISTER_CTLD Dec 22 14:22:07 kirby slurmdbd[14518]: slurmdbd: error: Processing last message from connection 7(192.168.1.2) uid(59999) ``` I'm a total SQL noob, but can at least verify that the user is in there: MariaDB [(none)]> SELECT User, Host, Password FROM mysql.user; +-------------+-----------+-------------------------------------------+ | User | Host | Password | +-------------+-----------+-------------------------------------------+ | mariadb.sys | localhost | | | root | localhost | invalid | | mysql | localhost | invalid | | slurm | localhost | *D6665ECF4F3CB12BCA836117F7727B6D0B78D644 | +-------------+-----------+-------------------------------------------+ 4 rows in set (0.002 sec) Any thoughts as to where I might look to fix this? Craig

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Multifactor fair-share with single account
by Kamil Wilczek 08 Jan '24

08 Jan '24

Dear All, I have a question regarding the fair-share factor of the multifactor priority algorithm. My current understanding is that the fair-share makes sure that different *accounts* have a fair share of the computational power. But what if my organisation structure is flat and I have only one account where all my user reside. Is fair-share algorithm working in this situation -- does it take into account users (associations) from this single account, and tries to assing a fair-factor to each user? Or each user from this account have the same fair-factor at each iteration? And what if I have, say 3 accounts, but I do not wan't to calculate fair-share between accounts, but between all associations from all 3 accounts? In other words, is there a fair-share factor for users/associations instead of accounts? Kind regards -- Kamil Wilczek [https://keys.openpgp.org/] [D415917E84B8DA5A60E853B6E676ED061316B69B]

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Tool for profiling resource usage by slurm jobs
by Nicolas Granger 08 Jan '24

08 Jan '24

Hi all, Happy new year everyone! I've been looking for a simple tool that reports how much resources are actually consumed by a job to help my colleagues and I adjust job requirements. I could not find such a tool, or the ones mentioned on this ML were not easy to install and use, so I have written a new one: https://github.com/CEA-LIST/sprofile It's a simple python script which parses cgroup and nvml data from the nvidia driver. It reports duration, cpu load, peak RAM, GPU load and peak GPU memory like so: |-- sprofile report (node03) -- Time: 0:00:03 / 1:00:00 CPU load: 2.0 / 4.0 RAM peak mem: 7G / 8G GPU load: 0.2 / 2.0 GPU peak mem: 7G / 40G| The requirements are to use the slurm cgroup plugin and to enable accounting on the GPU (nvidia-smi --accounting-mode=1). I hope you find this useful and let me know I you find bugs or want to contribute. Regards, Nicolas Granger

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A fairshare policy that spans multiple clusters
by David Baker 05 Jan '24

05 Jan '24

Hello, We are soon to install new Slurm cluster at our site. That means that we will have a total of three clusters running Slurm. Only two, that is the new clusters, will share a common file system. The original cluster has its own file system is independent of the new arrivals. If possible, we would like to try to prevent users from making significant user of all the clusters and get a 'triple whammy'. In other words, is there any way to share the fairshare information between the clusters so that a user's use of one of the clusters impacts their usage on the other clusters – if that makes sense. Does anyone have any thoughts on this question, please? Am I correct in thinking that federating clusters is related to my question? Do I gather correctly, however, that federation only works if there is a common database on a shared file system? Best regards, David

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slurmdb endpoints for slurmrestd
by Jackson, Gary L. 05 Jan '24

05 Jan '24

I get an HTTP 404 when I try to GET /slurmdb/v0.0.39/clusters or any other /slurmdb endpoint. I get this against multiple versions of Slurm, including 23.11.1. Using GET against /slurm/v0.0.39/ping works just fine. Is there something I need to do to turn slurmdb endpoints on? -- Gary

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