- slurm-users - lists.schedmd.com

srun weirdness
by Dj Merrill 17 May '24

17 May '24

I'm running into a strange issue and I'm hoping another set of brains looking at this might help. I would appreciate any feedback. I have two Slurm Clusters. The first cluster is running Slurm 21.08.8 on Rocky Linux 8.9 machines. The second cluster is running Slurm 23.11.6 on Rocky Linux 9.4 machines. This works perfectly fine on the first cluster: $ srun --mem=32G --pty /bin/bash srun: job 93911 queued and waiting for resources srun: job 93911 has been allocated resources and on the resulting shell on the compute node: $ /mnt/local/ollama/ollama help and the ollama help message appears as expected. However, on the second cluster: $ srun --mem=32G --pty /bin/bash srun: job 3 queued and waiting for resources srun: job 3 has been allocated resources and on the resulting shell on the compute node: $ /mnt/local/ollama/ollama help fatal error: failed to reserve page summary memory runtime stack: runtime.throw({0x1240c66?, 0x154fa39a1008?}) runtime/panic.go:1023 +0x5c fp=0x7ffe6be32648 sp=0x7ffe6be32618 pc=0x4605dc runtime.(*pageAlloc).sysInit(0x127b47e8, 0xf8?) runtime/mpagealloc_64bit.go:81 +0x11c fp=0x7ffe6be326b8 sp=0x7ffe6be32648 pc=0x456b7c runtime.(*pageAlloc).init(0x127b47e8, 0x127b47e0, 0x128d88f8, 0x0) runtime/mpagealloc.go:320 +0x85 fp=0x7ffe6be326e8 sp=0x7ffe6be326b8 pc=0x454565 runtime.(*mheap).init(0x127b47e0) runtime/mheap.go:769 +0x165 fp=0x7ffe6be32720 sp=0x7ffe6be326e8 pc=0x451885 runtime.mallocinit() runtime/malloc.go:454 +0xd7 fp=0x7ffe6be32758 sp=0x7ffe6be32720 pc=0x434f97 runtime.schedinit() runtime/proc.go:785 +0xb7 fp=0x7ffe6be327d0 sp=0x7ffe6be32758 pc=0x464397 runtime.rt0_go() runtime/asm_amd64.s:349 +0x11c fp=0x7ffe6be327d8 sp=0x7ffe6be327d0 pc=0x49421c If I ssh directly to the same node on that second cluster (skipping Slurm entirely), and run the same "/mnt/local/ollama/ollama help" command, it works perfectly fine. My first thought was that it might be related to cgroups. I switched the second cluster from cgroups v2 to v1 and tried again, no difference. I tried disabling cgroups on the second cluster by removing all cgroups references in the slurm.conf file but that also made no difference. My guess is something changed with regards to srun between these two Slurm versions, but I'm not sure what. Any thoughts on what might be happening and/or a way to get this to work on the second cluster? Essentially I need a way to request an interactive shell through Slurm that is associated with the requested resources. Should we be using something other than srun for this? Thank you, -Dj

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Slurm DB upgrade failure behavior
by Yuengling, Philip J. 17 May '24

17 May '24

Hi everyone, I'm writing up some Ansible code to manage Slurm software updates, and I haven't found any documentation about slurmdbd behavior if the mysql/mariadb database doesn't upgrade successfully. What I do know is that if it is sucessful I can expect to see "Conversion done: success!" in the slurmdbd log. This is good, but minor updates do not update the database as far as I know. If the Slurm database cannot upgrade upon an update, does it always shut down with a fatal error? What other behaviors should I look for if there is a failure? Cheers, Phil Y

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Removing safely a node
by Ratnasamy, Fritz 17 May '24

17 May '24

Hi, What is the "official" process to remove nodes safely? I have drained the nodes so jobs are completed and put them in down state after they are completely drained. I edited the slurm.conf file to remove the nodes. After some time, I can see that the nodes were removed from the partition with the command sinfo However, I was told I might need to restart the service slurmctld, do you know if it is necessary? Should I also run scontrol reconfig? Best, *Fritz Ratnasamy* Data Scientist Information Technology

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memory high water mark reporting
by Emyr James 16 May '24

16 May '24

Hi, We are trying out slurm having been running grid engine for a long while. In grid engine, the cgroups peak memory and max_rss are generated at the end of a job and recorded. It logs the information from the cgroup hierarchy as well as doing a getrusage call right at the end on the parent pid of the whole job "container" before cleaning up. With slurm it seems that the only way memory is recorded is by the acct gather polling. I am trying to add something in an epilog script to get the memory.peak but It looks like the cgroup hierarchy has been destroyed by the time the epilog is run. Where in the code is the cgroup hierarchy cleared up ? Is there no way to add something in so that the accounting is updated during the job cleanup process so that peak memory usage can be accurately logged ? I can reduce the polling interval from 30s to 5s but don't know if this causes a lot of overhead and in any case this seems to not be a sensible way to get values that should just be determined right at the end by an event rather than using polling. Many thanks, Emyr

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Best practice for jobs resuming from suspended state
by Paul Jones 16 May '24

16 May '24

Hi, We use PreemptMode and PriorityTier within Slurm to suspend low priority jobs when more urgent work needs to be done. This generally works well, but on occasion resumed jobs fail to restart - which is to say Slurm sets the job status to running but the actual code doesn't recover from being suspended. Technically everything is working as expected, but I wondered if there was any best practice to pass onto users about how to cope with this state? Obviously not a direct Slurm question, but wondered if others had experience with this and any advice on how best to limit the impact? Thanks, Paul --

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Executing srun -n X where X is greater than total CPU in entire cluster
by Dan Healy 16 May '24

16 May '24

Hi there, SLURM community, I swear I've done this before, but now it's failing on a new cluster I'm deploying. We have 6 compute nodes with 64 cpu each (384 CPU total). When I run `srun -n 500 hostname`, the task gets queued since there's not 500 available CPU. Wasn't there an option that allows for this to be run where the first 384 tasks execute, and then the remaining execute when resources free up? Here's my conf: # Slurm Cgroup Configs used on controllers and workersslurm_cgroup_config: CgroupAutomount: yes ConstrainCores: yes ConstrainRAMSpace: yes ConstrainSwapSpace: yes ConstrainDevices: yes# Slurm conf file settingsslurm_config: AccountingStorageType: "accounting_storage/slurmdbd" AccountingStorageEnforce: "limits" AuthAltTypes: "auth/jwt" ClusterName: "cluster" AccountingStorageHost : "{{ hostvars[groups['controller'][0]].ansible_hostname }}" DefMemPerCPU: 1024 InactiveLimit: 120 JobAcctGatherType: "jobacct_gather/cgroup" JobCompType: "jobcomp/none" MailProg: "/usr/bin/mail" MaxArraySize: 40000 MaxJobCount: 100000 MinJobAge: 3600 ProctrackType: "proctrack/cgroup" ReturnToService: 2 SelectType: "select/cons_tres" SelectTypeParameters: "CR_Core_Memory" SlurmctldTimeout: 30 SlurmctldLogFile: "/var/log/slurm/slurmctld.log" SlurmdLogFile: "/var/log/slurm/slurmd.log" SlurmdSpoolDir: "/var/spool/slurm/d" SlurmUser: "{{ slurm_user.name }}" SrunPortRange: "60000-61000" StateSaveLocation: "/var/spool/slurm/ctld" TaskPlugin: "task/affinity,task/cgroup" UnkillableStepTimeout: 120 -- Thanks, Daniel Healy

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_refresh_assoc_mgr_qos_list: no new list given back keeping cached one
by joao.damas＠syngenta.com 16 May '24

16 May '24

Hi all, We are doing a simple setup for a Slurm cluster (version 23.11.6). We follow the documentation and we are trying a setup still without accounting or slurmdbd. The slurm.conf is really simple: ``` ClusterName=Develop SlurmctldHost=head # Slurm configuration AuthType=auth/munge CryptoType=crypto/munge SlurmctldLogFile=/var/log/slurm/slurmctld.log SlurmctldPidFile=/var/run/slurmctld.pid SlurmctldPort=6817 SlurmdLogFile=/var/log/slurm/slurmd.log SlurmdPidFile=/var/run/slurmd.pid SlurmdPort=6818 SlurmdSpoolDir=/var/spool/slurmd SlurmUser=slurm StateSaveLocation=/var/spool/slurmctld # Nodes NodeName=worker1 CoresPerSocket=2 Sockets=1 ThreadsPerCore=1 NodeName=worker2 CoresPerSocket=2 Sockets=1 ThreadsPerCore=1 # Partitions PartitionName=develop Default=YES MaxTime=UNLIMITED Nodes="worker1,worker2" ``` When running a simple `srun sleep 10`, all works well and the log file shows: [2024-05-15T12:34:12.741] sched: _slurm_rpc_allocate_resources JobId=1 NodeList=worker1 usec=549 [2024-05-15T12:34:22.775] _job_complete: JobId=1 WEXITSTATUS 0 [2024-05-15T12:34:22.775] _job_complete: JobId=1 done But when creating a scrip with the same sleep command, and submiting using `sbatch test.sh`, the log shows: [2024-05-15T12:35:39.916] _slurm_rpc_submit_batch_job: JobId=2 InitPrio=1 usec=368 [2024-05-15T12:35:40.000] error: _refresh_assoc_mgr_qos_list: no new list given back keeping cached one. [2024-05-15T12:35:40.000] sched: JobId=2 has invalid account [2024-05-15T12:35:40.145] sched/backfill: _start_job: Started JobId=2 in develop on worker1 [2024-05-15T12:35:50.172] _job_complete: JobId=2 WEXITSTATUS 0 [2024-05-15T12:35:50.172] _job_complete: JobId=2 done We have the same account with the UID and GID, as said in the documentation. Looking at the function that seems to spit out that error (https://github.com/SchedMD/slurm/blob/e9f28ede27795f525e62f998cb2d40931d884…), it appears like there should be some accounting setup? We do not have slurmdbd setup and the documentation states we should test basic functionality before implementing that daemon. Any tips? Thanks in advance. João

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Location of Slurm source packages?
by Jeffrey Layton 15 May '24

15 May '24

Good morning, I have an Ubuntu 22.04 server where I installed Slurm from the Ubuntu packages. I now want to install pyxis but it says I need the Slurm sources. In Ubuntu 22.04, is there a package that has the source code? How to download the sources I need from github? Thanks! Jeff

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Re: Location of Slurm source packages?
by Lloyd Brown 15 May '24

15 May '24

Jeff, I'm not sure what version is in the Ubuntu packages, as I don't think they're provided by SchedMD, and I'm having trouble finding the right one on packages.ubuntu.com. Having said that, SchedMD is pretty good about using tags in their github repo (https://github.com/schedmd/slurm), to represent the releases. For example, the "slurm-23-11-6-1" tag corresponds to release 23.11.6. It's pretty straightforward to clone the repo, and do something like "git checkout -b MY_LOCAL_BRANCH_NAME TAG_NAME" to get the version you're after. Lloyd -- Lloyd Brown HPC Systems Administrator Office of Research Computing Brigham Young University http://rc.byu.edu On 5/15/24 08:35, Jeffrey Layton via slurm-users wrote: > Good morning, > > I have an Ubuntu 22.04 server where I installed Slurm from the Ubuntu > packages. I now want to install pyxis but it says I need the Slurm > sources. In Ubuntu 22.04, is there a package that has the source code? > How to download the sources I need from github? > > Thanks! > > Jeff

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Re: Location of Slurm source packages?
by Lloyd Brown 15 May '24

15 May '24

Jeff, Dang. That's really old. I'm not sure I would run one that old, to be honest. Too many missing security fixes and added features. It's never been that hard to do a 'git clone' and the normal configure/make/make install process with slurm. Someone else made me aware of this, in case it's easier: https://slurm.schedmd.com/quickstart_admin.html#debuild Lloyd On 5/15/24 08:57, Jeffrey Layton wrote: > Lloyd, > > Good to hear from you! I was hoping to avoid the use of git but that > may be the only way. The version is 21.08.5. I checked the "old" > packages from SchedMD and they begin part way through 2024 so that > won't work. > > I'm very surprised Ubuntu let a package through without a source > package for it. I'm hoping I'm not seeing the tree through the forest > in finding that package. > > Thanks for the help! > > Jeff > > > On Wed, May 15, 2024 at 10:54 AM Lloyd Brown via slurm-users > <slurm-users(a)lists.schedmd.com> wrote: > > Jeff, > > I'm not sure what version is in the Ubuntu packages, as I don't > think they're provided by SchedMD, and I'm having trouble finding > the right one on packages.ubuntu.com > <http://packages.ubuntu.com>. Having said that, SchedMD is pretty > good about using tags in their github repo > (https://github.com/schedmd/slurm), to represent the releases. > For example, the "slurm-23-11-6-1" tag corresponds to release > 23.11.6. It's pretty straightforward to clone the repo, and do > something like "git checkout -b MY_LOCAL_BRANCH_NAME TAG_NAME" to > get the version you're after. > > > Lloyd > > -- > Lloyd Brown > HPC Systems Administrator > Office of Research Computing > Brigham Young University > http://rc.byu.edu > > On 5/15/24 08:35, Jeffrey Layton via slurm-users wrote: >> Good morning, >> >> I have an Ubuntu 22.04 server where I installed Slurm from the >> Ubuntu packages. I now want to install pyxis but it says I need >> the Slurm sources. In Ubuntu 22.04, is there a package that has >> the source code? How to download the sources I need from github? >> >> Thanks! >> >> Jeff > > > -- > slurm-users mailing list -- slurm-users(a)lists.schedmd.com > To unsubscribe send an email to slurm-users-leave(a)lists.schedmd.com > -- Lloyd Brown HPC Systems Administrator Office of Research Computing Brigham Young University http://rc.byu.edu

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