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jobs dropping
by Mihai Ciubancan 24 Oct '24

24 Oct '24

Hello, We are trying to run some PiconGPU codes on a machine with 8x100H, susing slurm. But the jobs don't run, and are not in the queue. In slurmd logs I have: [2024-10-24T09:50:40.934] CPU_BIND: _set_batch_job_limits: Memory extracted from credential for StepId=1079.batch job_mem_limit= 648000 [2024-10-24T09:50:40.934] Launching batch job 1079 for UID 1009 [2024-10-24T09:50:40.938] debug: acct_gather_energy/none: init: AcctGatherEnergy NONE plugin loaded [2024-10-24T09:50:40.938] debug: acct_gather_profile/none: init: AcctGatherProfile NONE plugin loaded [2024-10-24T09:50:40.938] debug: acct_gather_interconnect/none: init: AcctGatherInterconnect NONE plugin loaded [2024-10-24T09:50:40.938] debug: acct_gather_filesystem/none: init: AcctGatherFilesystem NONE plugin loaded [2024-10-24T09:50:40.939] debug: gres/gpu: init: loaded [2024-10-24T09:50:41.022] [1079.batch] debug: cgroup/v2: init: Cgroup v2 plugin loaded [2024-10-24T09:50:41.026] [1079.batch] debug: CPUs:192 Boards:1 Sockets:2 CoresPerSocket:48 ThreadsPerCore:2 [2024-10-24T09:50:41.026] [1079.batch] debug: jobacct_gather/cgroup: init: Job accounting gather cgroup plugin loaded [2024-10-24T09:50:41.026] [1079.batch] CPU_BIND: Memory extracted from credential for StepId=1079.batch job_mem_limit=648000 step_mem_limit=648000 [2024-10-24T09:50:41.027] [1079.batch] debug: laying out the 8 tasks on 1 hosts mihaigpu2 dist 2 [2024-10-24T09:50:41.027] [1079.batch] gres_job_state gres:gpu(7696487) type:(null)(0) job:1079 flags: [2024-10-24T09:50:41.027] [1079.batch] total_gres:8 [2024-10-24T09:50:41.027] [1079.batch] node_cnt:1 [2024-10-24T09:50:41.027] [1079.batch] gres_cnt_node_alloc[0]:8 [2024-10-24T09:50:41.027] [1079.batch] gres_bit_alloc[0]:0-7 of 8 [2024-10-24T09:50:41.027] [1079.batch] debug: Message thread started pid = 459054 [2024-10-24T09:50:41.027] [1079.batch] debug: Setting slurmstepd(459054) oom_score_adj to -1000 [2024-10-24T09:50:41.027] [1079.batch] debug: switch/none: init: switch NONE plugin loaded [2024-10-24T09:50:41.027] [1079.batch] debug: task/cgroup: init: core enforcement enabled [2024-10-24T09:50:41.027] [1079.batch] debug: task/cgroup: task_cgroup_memory_init: task/cgroup/memory: total:2063720M allowed:100%(enforced), swap:0%(permissive), max:100%(2063720M) max+swap:100%(4127440M) min:30M kmem:100%(2063720M permissive) min:30M [2024-10-24T09:50:41.027] [1079.batch] debug: task/cgroup: init: memory enforcement enabled [2024-10-24T09:50:41.027] [1079.batch] debug: task/cgroup: init: Tasks containment cgroup plugin loaded [2024-10-24T09:50:41.027] [1079.batch] cred/munge: init: Munge credential signature plugin loaded [2024-10-24T09:50:41.027] [1079.batch] debug: job_container/none: init: job_container none plugin loaded [2024-10-24T09:50:41.030] [1079.batch] debug: spank: opening plugin stack /etc/slurm/plugstack.conf [2024-10-24T09:50:41.030] [1079.batch] debug: task/cgroup: task_cgroup_cpuset_create: job abstract cores are '0-63' [2024-10-24T09:50:41.030] [1079.batch] debug: task/cgroup: task_cgroup_cpuset_create: step abstract cores are '0-63' [2024-10-24T09:50:41.030] [1079.batch] debug: task/cgroup: task_cgroup_cpuset_create: job physical CPUs are '0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,96,98,100,102,104,106,108,110,112,114,116,118,120,122,124,126,128,130,132,134,136,138,140,142,144,146,148,150,152,154,156,158' [2024-10-24T09:50:41.030] [1079.batch] debug: task/cgroup: task_cgroup_cpuset_create: step physical CPUs are '0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,96,98,100,102,104,106,108,110,112,114,116,118,120,122,124,126,128,130,132,134,136,138,140,142,144,146,148,150,152,154,156,158' [2024-10-24T09:50:41.031] [1079.batch] task/cgroup: _memcg_initialize: job: alloc=648000MB mem.limit=648000MB memsw.limit=unlimited [2024-10-24T09:50:41.031] [1079.batch] task/cgroup: _memcg_initialize: step: alloc=648000MB mem.limit=648000MB memsw.limit=unlimited [2024-10-24T09:50:41.064] [1079.batch] debug levels are stderr='error', logfile='debug', syslog='quiet' [2024-10-24T09:50:41.064] [1079.batch] starting 1 tasks [2024-10-24T09:50:41.064] [1079.batch] task 0 (459058) started 2024-10-24T09:50:41 [2024-10-24T09:50:41.069] [1079.batch] _set_limit: RLIMIT_NOFILE : reducing req:1048576 to max:131072 [2024-10-24T09:51:23.066] debug: _rpc_terminate_job: uid = 64030 JobId=1079 [2024-10-24T09:51:23.067] debug: credential for job 1079 revoked [2024-10-24T09:51:23.067] [1079.batch] debug: Handling REQUEST_SIGNAL_CONTAINER [2024-10-24T09:51:23.067] [1079.batch] debug: _handle_signal_container for StepId=1079.batch uid=64030 signal=18 [2024-10-24T09:51:23.068] [1079.batch] Sent signal 18 to StepId=1079.batch [2024-10-24T09:51:23.068] [1079.batch] debug: Handling REQUEST_SIGNAL_CONTAINER [2024-10-24T09:51:23.068] [1079.batch] debug: _handle_signal_container for StepId=1079.batch uid=64030 signal=15 [2024-10-24T09:51:23.068] [1079.batch] error: *** JOB 1079 ON mihaigpu2 CANCELLED AT 2024-10-24T09:51:23 *** [2024-10-24T09:51:23.069] [1079.batch] Sent signal 15 to StepId=1079.batch [2024-10-24T09:51:23.069] [1079.batch] debug: Handling REQUEST_STATE [2024-10-24T09:51:23.071] [1079.batch] task 0 (459058) exited. Killed by signal 15. [2024-10-24T09:51:23.090] [1079.batch] debug: Handling REQUEST_STATE [2024-10-24T09:51:23.141] [1079.batch] debug: Handling REQUEST_STATE [2024-10-24T09:51:23.241] [1079.batch] debug: Handling REQUEST_STATE [2024-10-24T09:51:23.741] [1079.batch] debug: Handling REQUEST_STATE [2024-10-24T09:51:24.073] [1079.batch] debug: signaling condition [2024-10-24T09:51:24.073] [1079.batch] debug: jobacct_gather/cgroup: fini: Job accounting gather cgroup plugin unloaded [2024-10-24T09:51:24.073] [1079.batch] debug: task/cgroup: fini: Tasks containment cgroup plugin unloaded [2024-10-24T09:51:24.073] [1079.batch] debug: get_exit_code task 0 killed by cmd [2024-10-24T09:51:24.073] [1079.batch] job 1079 completed with slurm_rc = 0, job_rc = 15 [2024-10-24T09:51:24.075] [1079.batch] debug: Message thread exited [2024-10-24T09:51:24.154] [1079.batch] done with job Anyone have any idea what could be the problem? Thank you, Mihai

2 1

Randomly draining nodes
by Nacereddine Laddaoui 24 Oct '24

24 Oct '24

Hello everyone, I’ve recently encountered an issue where some nodes in our cluster enter a drain state randomly, typically after completing long-running jobs. Below is the output from the |sinfo| command showing the reason *“Prolog error”* : |root@controller-node:~# sinfo -R REASON USER TIMESTAMP NODELIST Prolog error slurm 2024-09-24T21:18:05 node[24,31] | When checking the |slurmd.log| files on the nodes, I noticed the following errors: |[2024-09-24T17:18:22.386] [217703.extern] error: _handle_add_extern_pid_internal: Job 217703 can't add pid 3311892 to jobacct_gather plugin in the extern_step. **(repeated 90 times)** [2024-09-24T17:18:22.917] [217703.extern] error: _handle_add_extern_pid_internal: Job 217703 can't add pid 3313158 to jobacct_gather plugin in the extern_step. ... [2024-09-24T21:17:45.162] launch task StepId=217703.0 request from UID:54059 GID:1600 HOST:<SLURMCTLD_IP> PORT:53514 [2024-09-24T21:18:05.166] error: Waiting for JobId=217703 REQUEST_LAUNCH_PROLOG notification failed, giving up after 20 sec [2024-09-24T21:18:05.166] error: slurm_send_node_msg: [(null)] slurm_bufs_sendto(msg_type=RESPONSE_SLURM_RC_MSG) failed: Unexpected missing socket error [2024-09-24T21:18:05.166] error: _rpc_launch_tasks: unable to send return code to address:port=<SLURMCTLD_IP>:53514 msg_type=6001: No such file or directory | If you know how to solve these errors, please let me know. I would greatly appreciate any guidance or suggestions for further troubleshooting. Thank you in advance for your assistance. Best regards, -- Télécom Paris <https://www.telecom-paris.fr> *Nacereddine LADDAOUI* Ingénieur de Recherche et de Développement 19 place Marguerite Perey CS 20031 91123 Palaiseau Cedex Site web Télécom Paris <https://www.telecom-paris.fr>X Télécom Paris <https://twitter.com/TelecomParis_>Facebook Télécom Paris <https://www.facebook.com/TelecomParis>LinkedIn Télécom Paris <https://www.linkedin.com/school/telecom-paris/>Instagram Télécom Paris <https://www.instagram.com/telecom_paris/>Blog Télécom Paris <https://imtech.wp.imt.fr> Une école de l'IMT <https://www.imt.fr>

6 9

loss of "unchangeable" node features
by Laura Hild 23 Oct '24

23 Oct '24

Has anyone else noticed, somewhere between versions 22.05.11 and 23.11.9, losing fixed Features defined for a node in slurm.conf, and instead now just having those controlled by a NodeFeaturesPlugin like node_features/knl_generic?

1 0

Slurm version 24.05.4 is now available (CVE-2024-48936)
by Tim Wickberg 23 Oct '24

23 Oct '24

Slurm version 24.05.4 is now available and includes a fix for a recently discovered security issue with the new stepmgr subsystem. SchedMD customers were informed on October 9th and provided a patch on request; this process is documented in our security policy. [1] A mistake in authentication handling in stepmgr could permit an attacker to execute processes under other users' jobs. This is limited to jobs explicitly running with --stepmgr, or on systems that have globally enabled stepmgr through "SlurmctldParameters=enable_stepmgr" in their configuration. CVE-2024-48936. Downloads are available at https://www.schedmd.com/downloads.php . Release notes follow below. - Tim [1] https://www.schedmd.com/security-policy/ -- Tim Wickberg Chief Technology Officer, SchedMD LLC Commercial Slurm Development and Support > * Changes in Slurm 24.05.4 > ========================== > -- Fix generic int sort functions. > -- Fix user look up using possible unrealized uid in the dbd. > -- Fix FreeBSD compile issue with tls/none plugin. > -- slurmrestd - Fix regressions that allowed slurmrestd to be run as SlurmUser > when SlurmUser was not root. > -- mpi/pmix fix race conditions with het jobs at step start/end which could > make srun to hang. > -- Fix not showing some SelectTypeParameters in scontrol show config. > -- Avoid assert when dumping removed certain fields in JSON/YAML. > -- Improve how shards are scheduled with affinity in mind. > -- Fix MaxJobsAccruePU not being respected when MaxJobsAccruePA is set > in the same QOS. > -- Prevent backfill from planning jobs that use overlapping resources for the > same time slot if the job's time limit is less than bf_resolution. > -- Fix memory leak when requesting typed gres and --[cpus|mem]-per-gpu. > -- Prevent backfill from breaking out due to "system state changed" every 30 > seconds if reservations use REPLACE or REPLACE_DOWN flags. > -- slurmrestd - Make sure that scheduler_unset parameter defaults to true even > when the following flags are also set: show_duplicates, skip_steps, > disable_truncate_usage_time, run_away_jobs, whole_hetjob, > disable_whole_hetjob, disable_wait_for_result, usage_time_as_submit_time, > show_batch_script, and or show_job_environment. Additionaly, always make > sure show_duplicates and disable_truncate_usage_time default to true when > the following flags are also set: scheduler_unset, scheduled_on_submit, > scheduled_by_main, scheduled_by_backfill, and or job_started. This effects > the following endpoints: > 'GET /slurmdb/v0.0.40/jobs' > 'GET /slurmdb/v0.0.41/jobs' > -- Ignore --json and --yaml options for scontrol show config to prevent mixing > output types. > -- Fix not considering nodes in reservations with Maintenance or Overlap flags > when creating new reservations with nodecnt or when they replace down nodes. > -- Fix suspending/resuming steps running under a 23.02 slurmstepd process. > -- Fix options like sprio --me and squeue --me for users with a uid greater > than 2147483647. > -- fatal() if BlockSizes=0. This value is invalid and would otherwise cause the > slurmctld to crash. > -- sacctmgr - Fix issue where clearing out a preemption list using > preempt='' would cause the given qos to no longer be preempt-able until set > again. > -- Fix stepmgr creating job steps concurrently. > -- data_parser/v0.0.40 - Avoid dumping "Infinity" for NO_VAL tagged "number" > fields. > -- data_parser/v0.0.41 - Avoid dumping "Infinity" for NO_VAL tagged "number" > fields. > -- slurmctld - Fix a potential leak while updating a reservation. > -- slurmctld - Fix state save with reservation flags when a update fails. > -- Fix reservation update issues with parameters Accounts and Users, when > using +/- signs. > -- slurmrestd - Don't dump warning on empty wckeys in: > 'GET /slurmdb/v0.0.40/config' > 'GET /slurmdb/v0.0.41/config' > -- Fix slurmd possibly leaving zombie processes on start up in configless when > the initial attempt to fetch the config fails. > -- Fix crash when trying to drain a non-existing node (possibly deleted > before). > -- slurmctld - fix segfault when calculating limit decay for jobs with an > invalid association. > -- Fix IPMI energy gathering with multiple sensors. > -- data_parser/v0.0.39 - Remove xassert requiring errors and warnings to have a > source string. > -- slurmrestd - Prevent potential segfault when there is an error parsing an > array field which could lead to a double xfree. This applies to several > endpoints in data_parser v0.0.39, v0.0.40 and v0.0.41. > -- scancel - Fix a regression from 23.11.6 where using both the --ctld and > --sibling options would cancel the federated job on all clusters instead of > only the cluster(s) specified by --sibling. > -- accounting_storage/mysql - Fix bug when removing an association > specified with an empty partition. > -- Fix setting multiple partition state restore on a job correctly. > -- Fix difference in behavior when swapping partition order in job submission. > -- Fix security issue in stepmgr that could permit an attacker to execute > processes under other users' jobs. CVE-2024-48936.

1 0

HOST CPUs not used by jobs
by Bhaskar Chakraborty 21 Oct '24

21 Oct '24

I have a SLURM configuration of 2 hosts with 6 + 4 CPUs. I am submitting jobs with sbatch -n <CPU slots> <job script>. However, I see that even when I have exhausted all 10 CPU slots for the running jobs it's still allowing subsequent jobs to run ! The CPU slots availability is also show as full for the 2 hosts. No job is found pending. What could be problem? My Slurm.conf looks like (host names are changed to generic): ClusterName=MyClusterControlMachine=host1ControlAddr=<some address>SlurmUser=slurmsa#AuthType=auth/mungeStateSaveLocation=/var/spool/slurmdSlurmdSpoolDir=/var/spool/slurmdSlurmctldLogFile=/var/log/slurm/slurmctld.logSlurmdDebug=3SlurmctldDebug=6SlurmdLogFile=/var/log/slurm/slurmd.logAccountingStorageType=accounting_storage/slurmdbdAccountingStorageHost=host1#AccountingStoragePass=medslurmpass#AccountingStoragePass=/var/run/munge/munge.socket.2AccountingStorageUser=slurmsa#TaskPlugin=task/cgroupNodeName=host1 CPUs=6 SocketsPerBoard=3 CoresPerSocket=2 ThreadsPerCore=1 State=UNKNOWNNodeName=host2 CPUs=4 ThreadsPerCore=1 State=UNKNOWNPartitionName=debug Nodes=host1,host2 Default=YES MaxTime=INFINITE State=UPJobAcctGatherType=jobacct_gather/linuxJobAcctGatherFrequency=30 SelectType=select/cons_tresSelectTypeParameters=CR_CPUTaskPlugin=task/affinity Thanks in advance for any help! Regards,Bhaskar.

2 1

Customization of (error) messages after the job submission
by Sebastian Sitkiewicz 21 Oct '24

21 Oct '24

Dear SLUR Users and Administrators, I am interested in a way to customize the job submission exit statuses (mainly error codes) after the job has already been queued by the SLURM controller. We aim to provide more user-friendly messages and reminders in case of any errors or obstacles (also adjusted to our QoS/account system). For example, in the case of exceeding CPU minutes of given QoS (or account) and after the (successful) job submission, we would like to notify the user that his job has been queued (as it should) but won’t start until the CPU minutes limits are increased (and that he should contact the administrators to apply for more resources). Similarly, if the user queued a job that cannot be launched immediately because of exceeding the MaxJobs limit (per user), we would like to also give him some additional message after the srun/sbatch submission. We want to provide such information immediately after the job submission, without the need to check the status using `squeue` by the user. In the Job Launch Guide (https://slurm.schedmd.com/job_launch.html) there are distinguished following steps: 1. Call job_submit plugins to modify the request as appropriate 2. Validate that the options are valid for this user (e.g. valid partition name, valid limits, etc.) 3. Determine if this job is the highest priority runnable job, if so then really try to allocate resources for it now, otherwise only validate that it could run if no other jobs existed 4. Determine which nodes could be used for the job. If the feature specification uses an exclusive OR option, then multiple iterations of the selection process below will be required with disjoint sets of nodes 5. Call the select plugin to select the best resources for the request 6. The select plugin will consider network topology and the topology within a node (e.g. sockets, cores, and threads) to select the best resources for the job 7. If the job can not be initiated using available resources and preemption support is configured, the select plugin will also determine if the job can be initiated after preempting lower priority jobs. If so then initiate preemption as needed to start the job. From my understanding, to achieve our goal one would need to have access to source code or plugin related to point 2 (and some part of point 3). Unfortunately, the job_submit (lua) plugin from point 1 (and the cli_filter plugin as well) cannot be used because it only has access to the information on the parameters of the submitted job and the SLURM partitions (but not the QoS/account usage and their limits). Is there any way to extend the customization of job submission to include such features? Best regards, Sebastian -- dr inż. Sebastian Sitkiewicz Politechnika Wrocławska Wrocławskie Centrum Sieciowo-Superkomputerowe Dział Usług Obliczeniowych Wyb. Wyspiańskiego 27 50-370 Wrocław www.wcss.pl

1 0

Tracking costs - one single pool of credits, variable costs per partition
by John Snowdon 18 Oct '24

18 Oct '24

We are trying to design the charging and accounting system for our new institutional HPC facility and I'm having difficulty understanding exactly how we can use sacctmgr to achieve what we need. Until now, our previous HPC facilities have all operated as free delivery and we have not needed to track costs by user/group/project. Account codes have been purely optional. However, our new facility will be split into various resource types, with free partitions and paid/priority/reserved partitions across those resource types. All jobs will need to be submitted with an account code. For users submitting to 'free' partitions we don't need to track resource units against a balance, but the submitted account code would still be used for reporting purposes (i.e. "free resources accounted for % of all use by this project in August-September"). When submitting to a 'paid' partition, the account code needs to be checked to ensure it has a positive balance (or a balance that will not go past some negative threshold). Each of the 'paid' partitions may (will) have a different resource unit cost. A simple example: - Submit to a generic CPU paid partition -- 1 resource unit/token/credit/£/$ per allocated cpu, per hour of compute - Submit to a high-speed, non-blocking CPU paid partition -- 2 resource unit/token/credit/£/$ per allocated cpu, per hour of compute - Submit to a GPU paid partition -- 4 resource unit/token/credit/£/$ per allocated GPU card, per hour of compute We need to have *one* pool of resource units/tokens/credits per account - let's say 1000 credits, and a group of users may well decide to spend all of their credits on the generic CPU partition, all on the GPU partition, or some mixture of the two. So in the above examples, assuming one user (or group of users sharing the same account code) submit a 2 hour job to all three partitions, their one, single account code should be charged: - 2 units for the generic CPU partition - 4 units for the job on the low latency partition - 8 units for the gpu partition. - A total of 14 credits removed from their single account code Is this feasible to achieve without having to allocate credits to each of the partitions for an account, or creating a QOS variant for each and every combination of account and partition? John Snowdon Senior Research Infrastructure Engineer (HPC) Research Software Engineering Catalyst Building, Room 2.01 Newcastle University 3 Science Square Newcastle Helix Newcastle upon Tyne NE4 5TG https://rse.ncldata.dev/

2 1

How do you guys track which GPU is used by which job ?
by Sylvain MARET 18 Oct '24

18 Oct '24

Hey guys ! I'm looking to improve GPU monitoring on our cluster. I want to install this https://github.com/NVIDIA/dcgm-exporter and saw in the README that it can support tracking of job id : https://github.com/NVIDIA/dcgm-exporter?tab=readme-ov-file#enabling-hpc-job… However I haven't been able to see any examples on how to do it nor does slurm seem to expose this information by default. Does anyone do this here ? And if so do you have any examples I could try to follow ? If you have advise on best practices to monitor GPU I'd be happy to hear it out ! Regards, Sylvain Maret

5 6

Job information is not being added to accounting database on new setup
by Adrian Brady 17 Oct '24

17 Oct '24

Hi Everyone, I'm a new to slurm administration and looking for a bit of help! Just added Accounting to an existing cluster but job information is not being added to the Accounting Mariadb. When I submit a test job it gets scheduled fine and its visible with squeue, I get nothing returned from sacct! I have turned up the logging to debug5 on both slurmctld and slurmdbd logs and can't see any errors. I believe all the comms are ok between slurmctld and slurmdbd as when I enter the sacct command I can see the database is being queried but returning nothing, because nothing has been added to the tables. The cluster tables were created fine when I ran #sacctmgr add cluster ny5ktt $ sacct JobID JobName Partition Account AllocCPUS State ExitCode ------------ ---------- ---------- ---------- ---------- ---------- -------- # tail -f slurmdbd.log [2024-10-17T12:34:45.232] debug: REQUEST_PERSIST_INIT: CLUSTER:ny5ktt VERSION:9216 UID:10001 IP:10.202.233.117 CONN:10 [2024-10-17T12:34:45.232] debug2: accounting_storage/as_mysql: acct_storage_p_get_connection: acct_storage_p_get_connection: request new connection 1 [2024-10-17T12:34:45.233] debug2: Attempting to connect to localhost:3306 [2024-10-17T12:34:45.274] debug2: DBD_GET_JOBS_COND: called [2024-10-17T12:34:45.317] debug2: DBD_FINI: CLOSE:1 COMMIT:0 [2024-10-17T12:34:45.317] debug4: accounting_storage/as_mysql: acct_storage_p_commit: got 0 commits The Mariadb is running on it own node with slurmdbd and munged for authentication. I haven't setup any accounts, users, asssociations or enforcements yet. On my lab cluster, jobs were visible in the database without these being setup. I guess I must be missing something simple in the config that is stopping jobs being reported to slurmdbd. Master Node packages # rpm -qa |grep slurm slurm-slurmdbd-20.11.9-1.el8.x86_64 slurm-libs-20.11.9-1.el8.x86_64 slurm-20.11.9-1.el8.x86_64 slurm-slurmd-20.11.9-1.el8.x86_64 slurm-perlapi-20.11.9-1.el8.x86_64 slurm-doc-20.11.9-1.el8.x86_64 slurm-contribs-20.11.9-1.el8.x86_64 slurm-slurmctld-20.11.9-1.el8.x86_64 Database Node packages # rpm -qa |grep slurm slurm-slurmdbd-20.11.9-1.el8.x86_64 slurm-20.11.9-1.el8.x86_64 slurm-libs-20.11.9-1.el8.x86_64 slurm-devel-20.11.9-1.el8.x86_64 slurm.conf # # See the slurm.conf man page for more information. # ClusterName=ny5ktt ControlMachine=ny5-pr-kttslurm-01 ControlAddr=10.202.233.71 #BackupController= #BackupAddr= # AuthType=auth/munge #CheckpointType=checkpoint/none CryptoType=crypto/munge #DisableRootJobs=NO #EnforcePartLimits=NO #Epilog= #EpilogSlurmctld= #FirstJobId=1 #MaxJobId=999999 #GresTypes= #GroupUpdateForce=0 #GroupUpdateTime=600 #JobCheckpointDir=/var/slurm/checkpoint #JobCredentialPrivateKey= #JobCredentialPublicCertificate= #JobFileAppend=0 #JobRequeue=1 #JobSubmitPlugins= #KillOnBadExit=0 #LaunchType=launch/slurm #Licenses=foo*4,bar MailProg=/bin/true MaxJobCount=200000 #MaxStepCount=40000 #MaxTasksPerNode=128 MpiDefault=none #MpiParams=ports=#-# #PluginDir= #PlugStackConfig= #PrivateData=jobs ProctrackType=proctrack/cgroup #Prolog= #PrologFlags= #PrologSlurmctld= #PropagatePrioProcess=0 #PropagateResourceLimits= #PropagateResourceLimitsExcept= #RebootProgram= ReturnToService=1 #SallocDefaultCommand= SlurmctldPidFile=/var/run/slurm/slurmctld.pid SlurmctldPort=6817 SlurmdPidFile=/var/run/slurm/slurmd.pid SlurmdPort=6818 SlurmdSpoolDir=/var/spool/slurm/d SlurmUser=slurm #SlurmdUser=root #SrunEpilog= #SrunProlog= StateSaveLocation=/var/spool/slurm/ctld SwitchType=switch/none #TaskEpilog= TaskPlugin=task/none #TaskPluginParam= #TaskProlog= #TopologyPlugin=topology/tree #TmpFS=/tmp #TrackWCKey=no #TreeWidth= #UnkillableStepProgram= #UsePAM=0 # # # TIMERS #BatchStartTimeout=10 #CompleteWait=0 #EpilogMsgTime=2000 #GetEnvTimeout=2 #HealthCheckInterval=0 #HealthCheckProgram= InactiveLimit=0 KillWait=30 #MessageTimeout=10 #ResvOverRun=0 #MinJobAge=300 #MinJobAge=43200 # CHG0057915 MinJobAge=14400 # CHG0057915 #MaxJobCount=50000 #MaxJobCount=100000 #OverTimeLimit=0 SlurmctldTimeout=120 SlurmdTimeout=300 #UnkillableStepTimeout=60 #VSizeFactor=0 Waittime=0 # # # SCHEDULING DefMemPerCPU=3000 #FastSchedule=1 #MaxMemPerCPU=0 #SchedulerTimeSlice=30 SchedulerType=sched/backfill SelectType=select/cons_tres #SelectTypeParameters=CR_Core #SelectTypeParameters=CR_CPU SelectTypeParameters=CR_CPU_Memory # ECR CHG0056915 10/14/2023 MaxArraySize=5001 # # # JOB PRIORITY #PriorityFlags= #PriorityType=priority/basic #PriorityDecayHalfLife= #PriorityCalcPeriod= #PriorityFavorSmall= #PriorityMaxAge= #PriorityUsageResetPeriod= #PriorityWeightAge= #PriorityWeightFairshare= #PriorityWeightJobSize= #PriorityWeightPartition= #PriorityWeightQOS= # # # LOGGING AND ACCOUNTING #AccountingStorageEnforce=0 #AccountingStorageEnforce=limits AccountingStorageHost=ny5-pr-kttslurmdb-01.ktt.schonfeld.com #AccountingStorageLoc= #AccountingStoragePass= #AccountingStoragePort= #AccountingStorageType=accounting_storage/none AccountingStorageType=accounting_storage/slurmdbd #AccountingStorageUser= AccountingStoreJobComment=YES #DebugFlags= #JobCompHost= #JobCompLoc= #JobCompPass= #JobCompPort= JobCompType=jobcomp/none #JobCompUser= #JobContainerType=job_container/none JobAcctGatherFrequency=60 JobAcctGatherType=jobacct_gather/none SlurmctldDebug=info SlurmctldLogFile=/var/log/slurm/slurmctld.log SlurmdDebug=info SlurmdLogFile=/var/log/slurm/slurmd.log #SlurmdLogFile= #SlurmSchedLogFile= #SlurmSchedLogLevel= # # # POWER SAVE SUPPORT FOR IDLE NODES (optional) #SuspendProgram= #ResumeProgram= #SuspendTimeout= #ResumeTimeout= #ResumeRate= #SuspendExcNodes= #SuspendExcParts= #SuspendRate= #SuspendTime= # # # COMPUTE NODES ##using fqdn since the ctld domain is different. Can't use regex since it's not at the end ##save 17 and 18 as headnodes #NodeName=ny5-dv-kttres-17 Sockets=1 CoresPerSocket=18 ThreadsPerCore=2 Feature=HyperThread RealMemory=102400 #NodeName=ny5-dv-kttres-18 Sockets=1 CoresPerSocket=14 ThreadsPerCore=2 Feature=HyperThread RealMemory=102400 NodeName=ny5-dv-kttres-19 Sockets=1 CoresPerSocket=12 ThreadsPerCore=2 Feature=HyperThread RealMemory=102400 NodeName=ny5-dv-kttres-[20-21] Sockets=1 CoresPerSocket=18 ThreadsPerCore=2 Feature=HyperThread RealMemory=102400 NodeName=ny5-dv-kttres-[01-16] Sockets=2 CoresPerSocket=16 ThreadsPerCore=2 Feature=HyperThread RealMemory=233472 NodeName=ny5-dv-kttres-[22-35] Sockets=2 CoresPerSocket=32 ThreadsPerCore=2 Feature=HyperThread RealMemory=346884 PartitionName=ktt_slurm_light_1 Nodes=ny5-dv-kttres-[19-21] Default=NO MaxTime=INFINITE State=UP OverSubscribe=FORCE:2 PartitionName=ktt_slurm_medium_1 Nodes=ny5-dv-kttres-[01-08] Default=NO MaxTime=INFINITE State=UP OverSubscribe=FORCE:2 PartitionName=ktt_slurm_medium_2 Nodes=ny5-dv-kttres-[09-16] Default=NO MaxTime=INFINITE State=UP OverSubscribe=FORCE:2 PartitionName=ktt_slurm_medium_3 Nodes=ny5-dv-kttres-[22-28] Default=NO MaxTime=INFINITE State=UP OverSubscribe=FORCE:2 PartitionName=ktt_slurm_medium_4 Nodes=ny5-dv-kttres-[29-35] Default=NO MaxTime=INFINITE State=UP OverSubscribe=FORCE:2 PartitionName=ktt_slurm_large_1 Nodes=ny5-dv-kttres-[01-16] Default=YES MaxTime=INFINITE State=UP OverSubscribe=FORCE:2 PartitionName=ktt_slurm_large_2 Nodes=ny5-dv-kttres-[22-35] Default=NO MaxTime=INFINITE State=UP OverSubscribe=FORCE:2 Slurmdbd.conf AuthType=auth/munge DbdAddr=10.202.233.72 DbdHost=ny5-pr-kttslurmdb-01 DebugLevel=debug5 LogFile=/var/log/slurm/slurmdbd.log PidFile=/tmp/slurmdbd.pid StorageType=accounting_storage/mysql StorageHost=localhost #StorageHost=10.234.132.57 StorageUser=slurm SlurmUser=slurm StoragePass=xxxxxxx #StorageUser=slurm #StorageLoc=slurm_acct_db Database tables MariaDB [slurm_acct_db]> show tables; +--------------------------------+ | Tables_in_slurm_acct_db | +--------------------------------+ | acct_coord_table | | acct_table | | clus_res_table | | cluster_table | | convert_version_table | | federation_table | | ny5ktt_assoc_table | | ny5ktt_assoc_usage_day_table | | ny5ktt_assoc_usage_hour_table | | ny5ktt_assoc_usage_month_table | | ny5ktt_event_table | | ny5ktt_job_table | | ny5ktt_last_ran_table | | ny5ktt_resv_table | | ny5ktt_step_table | | ny5ktt_suspend_table | | ny5ktt_usage_day_table | | ny5ktt_usage_hour_table | | ny5ktt_usage_month_table | | ny5ktt_wckey_table | | ny5ktt_wckey_usage_day_table | | ny5ktt_wckey_usage_hour_table | | ny5ktt_wckey_usage_month_table | | qos_table | | res_table | | table_defs_table | | tres_table | | txn_table | | user_table | +--------------------------------+ Many Thanks Adrian Disclaimer Schonfeld Strategic Advisors (UK) LLP (“SSA UK”) is authorised and regulated by The Financial Conduct Authority. SSA UK is a limited liability partnership in England and Wales (No: OC420598) and its registered office is at 54 Jermyn Street, London, SW1Y 6LX. The contents of this message, including any attachments, are meant solely for the intended recipient and may be confidential, privileged, or otherwise protected from disclosure. If you receive this message in error, immediately alert the sender by reply e-mail, delete it and any attachments or copies from your systems, and do not read, disclose, distribute, or otherwise use the information contained herein. We do not waive any confidentiality or privilege if this message was misdirected. This e-mail does not constitute an offer to sell or a solicitation to buy any securities or an offer of any investment advisory services. If you reply to this email please note that we invest in securities and do not want to receive material, non-public information and you are instructed not to communicate any such information to us. We do not agree to keep confidential any information you provide nor restrict our trading activity, except as agreed pursuant to a written confidentiality agreement duly executed by us. We reserve the right to monitor and review the content of all messages sent to or from this e-mail address.

1 0

Issue with interactive jobs
by Nerjes, Onno 17 Oct '24

17 Oct '24

Dear all, we've set up SLURM 24.05.3 on our cluster and are experiencing an issue with interactive jobs. Before, we used 21.08 and pretty much the same settings, but without these issues. We've started with a fresh DB etc. The behavior of interactive jobs is very erratic. Sometimes they start absolutely fine, at other times they die silently in the background, while the user has to wait indefinitely. We have been unable to isolate certain users or nodes affected by this. On a given node, one user might be able to start an interactive job, while another user at the same time isn't able to. The day after, the situation might be the other way around. The exception are jobs that use a reservation. These start fine every time as far as we can tell. At the same time, the number of idle nodes does not seem to influence the behavior I described above. Failed allocation on the front end: [user1@login1 ~]$ salloc salloc: Pending job allocation 5052052 salloc: job 5052052 queued and waiting for resources The same job on the backend: 2024-10-14 11:41:57.680 slurmctld: _job_complete: JobId=5052052 done 2024-10-14 11:41:57.678 slurmctld: _job_complete: JobId=5052052 WEXITSTATUS 1 2024-10-14 11:41:57.678 slurmctld: Killing interactive JobId=5052052: Communication connection failure 2024-10-14 11:41:46.666 slurmctld: sched/backfill: _start_job: Started JobId=5052052 in devel on m02n01 2024-10-14 11:41:30.096 slurmctld: sched: _slurm_rpc_allocate_resources JobId=5052052 NodeList=(null) usec=6258 Raising the debug level has not brought additional information. We were hoping, that one of you might be able to provide some insight into what the next steps in troubleshooting might be. Best regards, Onno

1 0

Dependency jobs
by adam＠bramblecfd.com 17 Oct '24

17 Oct '24

Hi Slurm Users, I am trying to figure out if there is a way you can check if a running job has any jobs queued up after it that depend on the current running job, I know you can show job info and find what dependency a job is waiting for, But more after checking if there are jobs waiting on the current job to complete using the job ID, Many Thanks, Adam

3 2

AllowAccounts partition setting
by Marko Markoc 16 Oct '24

16 Oct '24

Hi All, At one point, when we were running slurm 22, we set up a few new partitions with `AllowAccounts` setting enabled. We limit access to these partitions only to a few accounts. We manually create these accounts and users using the `sacctmgr` command. At that time, everything was working. Only users in these accounts were able to run jobs in that partition. Few months ago we upgraded slurm to 23.02.7 but just a couple of days ago we noticed that anyone could submit jobs to these partitions. In addition to that, you can provide any value to the `--account` directive and slurm will accept and record it in the job accounting database. In our initial testing, you could only provide `--account` value that has been previously created. I'm still looking into this but I wanted to check if there was any change in version 23 that could have impacted this? I don't remember seeing anything in release notes. Thanks, Marko

6 8

Problem with nodes with 1 gpu
by Jörg Striewski 16 Oct '24

16 Oct '24

i cannot send jobs to nodes with one gpu, i don't find the bug in my configuration. can someone help me ? in slurm.conf GresTypes=gpu is set this are some nodes in slurm.conf NodeName=gpu-[001-003] CPUs=8 SocketsPerBoard=1 CoresPerSocket=4 RealMemory=31000 Gres=gpu:1080:1 NodeName=gpu-[010-019] CPUs=16 SocketsPerBoard=1 CoresPerSocket=8 RealMemory=64000 Gres=gpu:1080:2 the partition for this gpu nodes is # General GPU partitions PartitionName=GPU Nodes=gpu-[001-003,010-019] AllowAccounts=staff PreemptMode=REQUEUE PriorityTier=0 DefMemPerGPU=32000 DefCpuPerGPU=8 CpuBind=none TRESBillingWeights="GRES/gpu=1000" GraceTime=300 this are the entries for some nodes in gres.conf NodeName=gpu-[001-003] Name=gpu Type=1080 File=/dev/nvidia0 NodeName=gpu-[010-019] Name=gpu Type=1080 File=/dev/nvidia[0-1] when i send a job with sbatch to gpu-001 #SBATCH --job-name=hello #SBATCH --ntasks-per-node=1 #SBATCH --output=hello_%A.out #SBATCH --time=00:10:00 #SBATCH --mail-type=ALL #SBATCH --mail-user=striewski(a)ismll.de #SBATCH --partition=GPU #SBATCH --nodelist=gpu-001 #SBATCH --gres=gpu:1 [...] i get the error sbatch: error: Batch job submission failed: Requested node configuration is not available when i send the job to a node with 2 gpu's it runs with no error, just setting --nodelist=gpu-12 has someone a hint what i made wrong ? Mit freundlichen Grüßen / kind regards -- Jörg Striewski Information Systems and Machine Learning Lab (ISMLL) Institute of Computer Science University of Hildesheim Germany post address: Universitätsplatz 1, D-31141Hildesheim, Germany visitor address: Samelsonplatz 1, D-31141 Hildesheim,Germany Tel.(+49) 05121 / 883-40392 http://www.ismll.uni-hildesheim.de

2 2

unsuscribe
by LEROY Christine 208562 15 Oct '24

15 Oct '24

unsuscribe

1 0

How does --nodes=min[-max] determine number of nodes to allocate?
by Declan Valters 08 Oct '24

08 Oct '24

Hi, I am trying to understand how Slurm determines the actual number of nodes to allocate to a job specified with -nodes=min[-max] I've been trying to follow the source code through on Github - could anyone point me in the right area(s)/source files/functions to look at to understand the program logic behind this. Many thanks in advance, Declan The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

2 1

Jobs not getting scheduled, no priority calculation, but still in queue?
by Cutts, Tim 07 Oct '24

07 Oct '24

Something odd is going on on our cluster. User has a lot of pending jobs in a job array (a few thousand). squeue -u kmnx005 -r -t PD | head -5 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 3045324_875 core run_scp_ kmnx005 PD 0:00 1 (JobArrayTaskLimit) 3045324_876 core run_scp_ kmnx005 PD 0:00 1 (JobArrayTaskLimit) 3045324_877 core run_scp_ kmnx005 PD 0:00 1 (JobArrayTaskLimit) 3045324_878 core run_scp_ kmnx005 PD 0:00 1 (JobArrayTaskLimit) None are getting scheduled. But when I ask SLURM what that job’s priority is, it produces no output: $ sprio -j 3045324 JOBID PARTITION PRIORITY SITE AGE FAIRSHARE JOBSIZE PARTITION QOS TRES Any clues what’s going on here? -- 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>

2 3

SLURM GRES reservation not working properly on 24.05.1
by Minulakshmi S 07 Oct '24

07 Oct '24

Hello, *Issue 1:* I am using slurm version 24.05.1 , my slurmd has a single node where I connect multiple gres by enabling the overscribe feature. I am able to use the advance reservation of gres only using *gres** name* (tres=gres/gpu:*SYSTEM12*). i.e while in reservation period , if other users submits job with SYSTEM12 , then slurm places this job in queue *user1@host$ srun --gres=gpu:SYSTEM12:1 hostname* *srun: job 333 queued and waiting for resources * but when other users just submit a job without any system name , slurm jobs goes through on that gres immediately even though it is reserved. *user1@host$ srun --gres=gpu:1 hostname * *mylinux.wbi.com <http://mylinux.wbi.com/> * Also I can see GresUsed in busy mode using "*scontrol show node -d*" , this means the job is running on Gres/GPU and not on cpu etc. Same way , job submission based on Feature "rev1 in my case" is also going through even though it is reserved for other users in multiple partition slurm. *snippet of slurm.conf file* NodeName=cluster01 NodeAddr=cluster Port=6002CPUs=8 Boards=1 SocketsPerBoard=1 CoresPerSocket=8 ThreadsPerCore=2 Feature="rev1" Gres=gpu:SYSTEM12:1 RealMemory=64171 State=IDLE *Issue 2:* while execution , Slurm o/p's some extra prints in the srun output user1@host$ srun --gres=gpu:1 hostname srun: error: extract_net_cred: net_cred not provided srun: error: Malformed RPC of type RESPONSE_NODE_ALIAS_ADDRS(3017) received srun: error: slurm_unpack_received_msg: [mylinux.wbi.com]:41242] Header lengths are longer than data received *mylinux.wbi.com <http://mylinux.wbi.com/>* Regards, MS

1 1

Slurmctld process error 'double free or corruption' on RHEL 9 (Rocky Linux)
by William VINCENT 07 Oct '24

07 Oct '24

Hello I am writing to report an issue with the Slurmctld process on our RHEL 9 (Rocky Linux) . Twice in the past 5 days, the Slurmctld process has encountered an error that resulted in the service stopping. The error message displayed was "double free or corruption (out)". This error has caused significant disruption to our jobs, and we are concerned about its recurrence. We have tried troubleshooting the issue, but we have not been able to identify the root cause of the problem. We would appreciate any assistance or guidance you can provide to help us resolve this issue. Please let us know if you need any additional information or if there are any specific steps we should take to diagnose the problem further. Thank you for your attention to this matter. Best regards, _________________________ Jul 09 22:12:01 admin slurmctld[711010]: double free or corruption (fasttop) Jul 09 22:12:01 admin systemd[1]: slurmctld.service: Main process exited, code=killed, status=6/ABRT Jul 09 22:12:01 admin systemd[1]: slurmctld.service: Failed with result 'signal'. Jul 09 22:12:01 admin systemd[1]: slurmctld.service: Consumed 11min 26.451s CPU time. ..... Jul 14 10:15:01 admin slurmctld[1633720]: double free or corruption (out) Jul 14 10:15:02 admin systemd[1]: slurmctld.service: Main process exited, code=killed, status=6/ABRT Jul 14 10:15:02 admin systemd[1]: slurmctld.service: Failed with result 'signal'. Jul 14 10:15:02 admin systemd[1]: slurmctld.service: Consumed 7min 27.596s CPU time. _________________________ slurmctld -V slurm 22.05.9 ________________________ cat /etc/slurm/slurm.conf |grep -v '#' ClusterName=xxx SlurmctldHost=admin SlurmctldParameters=enable_configless SlurmUser=slurm AuthType=auth/munge CryptoType=crypto/munge SlurmctldPort=6817 StateSaveLocation=/var/spool/slurmctld SlurmctldLogFile=/var/log/slurm/slurmctld.log SlurmctldDebug=verbose DebugFlags=NO_CONF_HASH SlurmdPort=6818 SlurmdSpoolDir=/var/spool/slurmd SlurmdLogFile=/var/log/slurm/slurmd.log SlurmdDebug=verbose SchedulerType=sched/backfill SelectType=select/cons_tres SelectTypeParameters=CR_Core,CR_LLN DefMemPerCPU=1024 MaxMemPerCPU=4096 GresTypes=gpu ProctrackType=proctrack/cgroup JobAcctGatherType=jobacct_gather/cgroup JobAcctGatherFrequency=15 JobCompType=jobcomp/none TaskPlugin=task/cgroup LaunchParameters=use_interactive_step AccountingStorageType=accounting_storage/slurmdbd AccountingStorageHost=admin AccountingStoragePort=6819 AccountingStorageEnforce=associations AccountingStorageTRES=gres/gpu MailProg=/usr/bin/mailx EnforcePartLimits=YES MaxArraySize=200000 MaxJobCount=500000 MpiDefault=none ReturnToService=2 SwitchType=switch/none TmpFS=/tmpslurm/ UsePAM=1 InactiveLimit=0 KillWait=30 MessageTimeout=30 MinJobAge=300 SlurmctldTimeout=120 SlurmdTimeout=300 Waittime=0 PriorityType=priority/multifactor PriorityFlags=FAIR_TREE,MAX_TRES PriorityDecayHalfLife=1-0 PriorityWeightFairshare=10000 NodeName=xxx NodeHostname=xxx CPUs=4 Sockets=4 RealMemory=3500 TmpDisk=1 CoresPerSocket=1 ThreadsPerCore=1 State=DRAIN NodeName=xxx NodeHostname=xxx CPUs=2 Sockets=2 RealMemory=1700 TmpDisk=1 CoresPerSocket=1 ThreadsPerCore=1 State=DRAIN NodeName=xxx NodeHostname=xxx CPUs=4 Sockets=4 RealMemory=1700 TmpDisk=1 CoresPerSocket=1 ThreadsPerCore=1 State=DRAIN NodeName=xxx NodeHostname=xxx CPUs=4 Sockets=4 RealMemory=3500 TmpDisk=1 CoresPerSocket=1 ThreadsPerCore=1 State=DRAIN NodeName=r9nc-24-[1-12] NodeHostname=r9nc-24-[1-12] Sockets=2 CoresPerSocket=12 ThreadsPerCore=1 CPUs=24 RealMemory=180000 State=UNKNOWN NodeName=r9nc-48-[1-4] NodeHostname=r9nc-48-[1-4] Sockets=2 CoresPerSocket=24 ThreadsPerCore=1 CPUs=48 RealMemory=480000 State=UNKNOWN NodeName=r9ng-1080-[1-7] NodeHostname=r9ng-1080-[1-7] Sockets=2 CoresPerSocket=10 ThreadsPerCore=1 CPUs=20 RealMemory=180000 State=UNKNOWN Gres=gpu:1080ti:4 NodeName=r9ng-1080-8 NodeHostname=r9ng-1080-8 Sockets=2 CoresPerSocket=10 ThreadsPerCore=1 CPUs=20 RealMemory=176687 State=UNKNOWN Gres=gpu:1080ti:1 PartitionName=24CPUNodes Nodes=r9nc-24-[1-12] State=UP MaxTime=UNLIMITED OverSubscribe=NO MaxMemPerCPU=7500 DefMemPerCPU=7500 TRESBillingWeights="CPU=1.0,Mem=0.125G" Default=YES PartitionName=48CPUNodes Nodes=r9nc-48-[1-4] State=UP MaxTime=UNLIMITED OverSubscribe=NO MaxMemPerCPU=10000 DefMemPerCPU=8000 TRESBillingWeights="CPU=1.0,Mem=0.125G" PartitionName=GPUNodes Nodes=r9ng-1080-[1-7] State=UP MaxTime=UNLIMITED OverSubscribe=NO MaxMemPerCPU=9000 DefMemPerCPU=9000 PartitionName=GPUNodes1080-dev Nodes=r9ng-1080-8 State=UP MaxTime=UNLIMITED OverSubscribe=NO MaxMemPerCPU=9000 DefMemPerCPU=9000 Hidden=Yes _________________________ sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST 24CPUNodes* up infinite 12 idle r9nc-24-[1-12] 48CPUNodes up infinite 2 idle r9nc-48-[1-2] GPUNodes up infinite 4 idle r9ng-1080-[4-7] GPUNodes1080-dev up infinite 1 idle r9ng-1080-8 -- William VINCENT Administrateur systèmes et réseaux

4 15

license server redundancy
by Yves Kondoszek 03 Oct '24

03 Oct '24

Hello. I'm configuring a cluster that will run jobs that use FlexLM licenses. We have what I believe is a quite standard configuration of license servers - though I haven't found anything in the documentation or in the mailing list archives - that often provide the same features across several servers; for example, the license token "simulation" will be available at let's say 1717@server1, 1717@server2 and 4000@server3 . FlexLM clients support those through a path-style environment variable, typically LM_LICENSE_FILE=1717@server1:1717@server2:4000@server3 . Now, I have set up Slurm for remote dynamic licenses and update them live through "LastConsumed" from lmstat requests, so that Slurm is aware of some users checking them out externally (out of Slurm control). But my problem is that the documentation clearly states that: "When submitting jobs to remote licenses, the name and server must be used." So I have to specifically choose a server: $ sbatch -L simulation@server2 script.sh instead of telling Slurm to just use whatever license is available on any of the servers. Does any of you have any experience with redundant FlexLM licenses through several servers? Is there a way Slurm could support this?

1 0

GPU Accounting
by Emyr James 03 Oct '24

03 Oct '24

We have a node with 8 H100 GPUs that are split into MIG instances. We are using cgroups. This seems to work fine. Users can do something like sbatch --gres="gpu:1g.10gb:1"... and the job starts on the node with the gpus and cuda visible devices and the pytorch debug shows that the cgroup only gives them the gpu they asked for. In the accounting database, jobs in the job table always have the "gres_used" column be empty. I'd expect to see "gpu:1g.10gb:1" appearing for the job above. I have this set in slurm.conf AccountingStorageTRES=gres/gpu How can I see what gres was requested with the job ? At the moment I only see something like this in AllocTres billing=1,cpu=1,gres/gpu=1,mem=8G,node=1 and can't see any way to see what the specific MIG gpu asked for was. This is related to the email from Richard Lefebvre dated 7th June 2023 entitled "Billing/accounting for MIGs is not working". As far as I can see this got no replies. We are running slurm version 23.11.6. Regards, Emyr James Head of Scientific IT CRG - Centre for Genomic Regulation

2 1

SLUG Presentations Now Online!
by Victoria Hobson 01 Oct '24

01 Oct '24

Available presentations from this year's SLUG event are now online. They can be found at https://www.schedmd.com/publications/ We thank all those who presented and attended for a great event! -- Victoria Hobson SchedMD LLC Vice President of Marketing

1 0

Job Step State
by Emyr James 01 Oct '24

01 Oct '24

Dear all, I am working on a script to take completed job accounting data from the slurm accounting database and insert the equivalent data into a clickhouse table for fast reporting I can see that all the information is included in the cluster_job_table and cluster_job_step_table which seem to be joined on job_db_inx To get the cpu usage and peak memory usage etc. I can see that I need to parse the tres columns in the job steps. I couldn't find any column called MaxRSS in the database even though the sacct command prints this. I then found some data in tres_table and assume that sacct is using this. Please correct me if I'm wrong and if sacct is getting information from somwhere other than the accounting database? for the state column I get this... select state, count(*) as num from crg_step_table group by state order by num desc limit 10; +-------+--------+ | state | num | +-------+--------+ | 3 | 590635 | | 5 | 28345 | | 4 | 4401 | | 11 | 962 | | 1 | 8 | +-------+--------+ When I use sacct I see statuses seach as COMPLETED, OUT_OF_MEMORY etc. so there must be a mapping somewhere between these state ids and that text. Can someone prvide that mapping or point me to where it's defined in the database or in the code ? Many thanks, Emyr James Head of Scientific IT CRG - Centre for Genomic Regulation

2 2

Hardcoded CGroups v2 Slice
by Khalid Al-Hawaj 01 Oct '24

01 Oct '24

Hello, I am in the process of setting up SLURM to be used in a profiling cluster. The purpose of SLURM is to allow users to submit jobs to be profiled. The latency is a very important aspect of profiling the applications correctly. I was able to leverage cgroupsv2.0 to isolate user.slice from the cores that would be used by SLURM jobs. The issue is that slurmstepd shares the resources with system.slice; I was digging through the code, and I saw that the creation of the scope is here: https://github.com/SchedMD/slurm/blob/master/src/plugins/cgroup/v2/cgroup_v… And I noticed that the slice is hardcoded in the following line: https://github.com/SchedMD/slurm/blob/master/src/plugins/cgroup/v2/cgroup_v… So, my question, now, is about why is the slice hardcoded? What was the reason behind such a decision? I would have thought that the slice chosen would be set through cgroups.conf, instead. I would like to switch the slice for slurmstepd to a slice other than system.slice; by doing so, I would be able to isolate cores better by making sure that services' processes are isolated from the cores used for SLURM jobs. I can definitely change the defined value in the code and recompile. Are there anything to consider before doing so? Thanks, Khalid

1 0

Updated one compute node to Ubuntu 24.04 LTS, now it does not receive jobs
by Cristóbal Navarro 29 Sep '24

29 Sep '24

Dear community, I am having a strange issue I have been unable to find the cause. Last week I did a full update on the cluster, which is composed of the master node, and two compute nodes (nodeGPU01 -> DGXA100 and nodeGPU02 -> custom GPU server). After the update, I got - master node ended up with Ubuntu 24.04, - nodeGPU01 with latest DGX OS (still Ubuntu 22.04) - nodeGPU02 with Ubuntu 24.04 LTS. - Launching jobs from master choosing the partitions of nodeGPU01 works perfectly. - Launching jobs from master choosing the partition of nodeGPU02 stopped working (hangs). The nodeGPU02 (Ubuntu 24) is no longer processing jobs successfully, while the other nodeGPU01 works perfectly even when the master has Ubuntu 24. Any help is welcome, I have tried many things and had no success in finding the cause of this. Please let me know if you need more information. Many thanks in advance. This is the initial `slurmd` log of the problematic node (nodeGPU02), notice the messages in yellow ➜ ~ sudo systemctl status slurmd.service ● slurmd.service - Slurm node daemon Loaded: loaded (/etc/systemd/system/slurmd.service; enabled; preset: enabled) Active: active (running) since Sat 2024-09-28 14:00:22 -03; 4s ago Main PID: 4821 (slurmd) Tasks: 1 Memory: 17.0M (peak: 29.7M) CPU: 174ms CGroup: /system.slice/slurmd.service └─4821 /usr/sbin/slurmd -D -s Sep 28 14:00:25 nodeGPU02 slurmd[4821]: slurmd: debug: MPI: Loading all types Sep 28 14:00:25 nodeGPU02 slurmd[4821]: slurmd: debug: mpi/pmix_v5: init: PMIx plugin loaded Sep 28 14:00:25 nodeGPU02 slurmd[4821]: slurmd: debug: mpi/pmix_v5: init: PMIx plugin loaded Sep 28 14:00:25 nodeGPU02 slurmd[4821]: slurmd: debug2: No mpi.conf file (/etc/slurm/mpi.conf) Sep 28 14:00:25 nodeGPU02 slurmd[4821]: slurmd: slurmd started on Sat, 28 Sep 2024 14:00:25 -0300 Sep 28 14:00:25 nodeGPU02 slurmd[4821]: slurmd: debug: _step_connect: connect() failed for /var/spool/slurmd/slurmd/nodeGPU02_57436.0: Connection refused Sep 28 14:00:25 nodeGPU02 slurmd[4821]: slurmd: debug2: health_check success rc:0 output: Sep 28 14:00:25 nodeGPU02 slurmd[4821]: slurmd: CPUs=128 Boards=1 Sockets=2 Cores=64 Threads=1 Memory=773744 TmpDisk=899181 Uptime=2829 CPUSpecList=(null) FeaturesAvail=(nu> Sep 28 14:00:25 nodeGPU02 slurmd[4821]: slurmd: debug: _step_connect: connect() failed for /var/spool/slurmd/slurmd/nodeGPU02_57436.0: Connection refused Sep 28 14:00:25 nodeGPU02 slurmd[4821]: slurmd: debug: _handle_node_reg_resp: slurmctld sent back 11 TRES This is the verbose output of the srun command (notice yellow messages). ➜ ~ srun -vvvp rtx hostname srun: defined options srun: -------------------- -------------------- srun: partition : rtx srun: verbose : 3 srun: -------------------- -------------------- srun: end of defined options srun: debug: propagating RLIMIT_CPU=18446744073709551615 srun: debug: propagating RLIMIT_FSIZE=18446744073709551615 srun: debug: propagating RLIMIT_DATA=18446744073709551615 srun: debug: propagating RLIMIT_STACK=8388608 srun: debug: propagating RLIMIT_CORE=0 srun: debug: propagating RLIMIT_RSS=18446744073709551615 srun: debug: propagating RLIMIT_NPROC=3090276 srun: debug: propagating RLIMIT_NOFILE=1024 srun: debug: propagating RLIMIT_MEMLOCK=18446744073709551615 srun: debug: propagating RLIMIT_AS=18446744073709551615 srun: debug: propagating SLURM_PRIO_PROCESS=0 srun: debug: propagating UMASK=0002 srun: debug: Entering slurm_allocation_msg_thr_create() srun: debug: port from net_stream_listen is 34081 srun: debug: Entering _msg_thr_internal srun: Waiting for resource configuration srun: Nodes nodeGPU02 are ready for job srun: jobid 57463: nodes(1):`nodeGPU02', cpu counts: 1(x1) srun: debug2: creating job with 1 tasks srun: debug2: cpu:1 is not a gres: srun: debug: requesting job 57463, user 99, nodes 1 including ((null)) srun: debug: cpus 1, tasks 1, name hostname, relative 65534 srun: CpuBindType=(null type) srun: debug: Entering slurm_step_launch srun: debug: mpi/pmix_v4: pmixp_abort_agent_start: (null) [0]: pmixp_agent.c:382: Abort agent port: 41393 srun: debug: mpi/pmix_v4: mpi_p_client_prelaunch: (null) [0]: mpi_pmix.c:285: setup process mapping in srun srun: debug: Entering _msg_thr_create() srun: debug: mpi/pmix_v4: _pmix_abort_thread: (null) [0]: pmixp_agent.c:353: Start abort thread srun: debug: initialized stdio listening socket, port 33223 srun: debug: Started IO server thread (140079189182144) srun: debug: Entering _launch_tasks srun: launching StepId=57463.0 on host nodeGPU02, 1 tasks: 0 srun: debug2: Called _file_readable srun: debug2: Called _file_writable srun: route/default: init: route default plugin loaded srun: debug2: Called _file_writable srun: topology/none: init: topology NONE plugin loaded srun: debug2: Tree head got back 0 looking for 1 srun: debug: slurm_recv_timeout at 0 of 4, timeout srun: error: slurm_receive_msgs: [[nodeGPU02]:6818] failed: Socket timed out on send/recv operation srun: debug2: Tree head got back 1 srun: debug: launch returned msg_rc=1001 err=5004 type=9001 srun: debug2: marking task 0 done on failed node 0 srun: error: Task launch for StepId=57463.0 failed on node nodeGPU02: Socket timed out on send/recv operation srun: error: Application launch failed: Socket timed out on send/recv operation srun: Job step aborted srun: debug2: false, shutdown srun: debug2: false, shutdown srun: debug2: Called _file_readable srun: debug2: Called _file_writable srun: debug2: Called _file_writable srun: debug2: false, shutdown srun: debug: IO thread exiting srun: debug: mpi/pmix_v4: _conn_readable: (null) [0]: pmixp_agent.c:105: false, shutdown srun: debug: mpi/pmix_v4: _pmix_abort_thread: (null) [0]: pmixp_agent.c:355: Abort thread exit srun: debug2: slurm_allocation_msg_thr_destroy: clearing up message thread srun: debug2: false, shutdown srun: debug: Leaving _msg_thr_internal srun: debug2: spank: spank_pyxis.so: exit = 0 This is the `tail -f` log of slurmctld when launching a simple `srun hostname` [2024-09-28T14:08:10.264] ==================== [2024-09-28T14:08:10.264] JobId=57463 nhosts:1 ncpus:1 node_req:1 nodes=nodeGPU02 [2024-09-28T14:08:10.264] Node[0]: [2024-09-28T14:08:10.264] Mem(MB):65536:0 Sockets:2 Cores:64 CPUs:1:0 [2024-09-28T14:08:10.264] Socket[0] Core[0] is allocated [2024-09-28T14:08:10.264] -------------------- [2024-09-28T14:08:10.264] cpu_array_value[0]:1 reps:1 [2024-09-28T14:08:10.264] ==================== [2024-09-28T14:08:10.264] gres/gpu: state for nodeGPU02 [2024-09-28T14:08:10.264] gres_cnt found:3 configured:3 avail:3 alloc:0 [2024-09-28T14:08:10.264] gres_bit_alloc: of 3 [2024-09-28T14:08:10.264] gres_used:(null) [2024-09-28T14:08:10.264] topo[0]:(null)(0) [2024-09-28T14:08:10.264] topo_core_bitmap[0]:0-63 of 128 [2024-09-28T14:08:10.264] topo_gres_bitmap[0]:0 of 3 [2024-09-28T14:08:10.264] topo_gres_cnt_alloc[0]:0 [2024-09-28T14:08:10.264] topo_gres_cnt_avail[0]:1 [2024-09-28T14:08:10.264] topo[1]:(null)(0) [2024-09-28T14:08:10.264] topo_core_bitmap[1]:0-63 of 128 [2024-09-28T14:08:10.264] topo_gres_bitmap[1]:1 of 3 [2024-09-28T14:08:10.264] topo_gres_cnt_alloc[1]:0 [2024-09-28T14:08:10.264] topo_gres_cnt_avail[1]:1 [2024-09-28T14:08:10.264] topo[2]:(null)(0) [2024-09-28T14:08:10.264] topo_core_bitmap[2]:0-63 of 128 [2024-09-28T14:08:10.264] topo_gres_bitmap[2]:2 of 3 [2024-09-28T14:08:10.264] topo_gres_cnt_alloc[2]:0 [2024-09-28T14:08:10.264] topo_gres_cnt_avail[2]:1 [2024-09-28T14:08:10.265] sched: _slurm_rpc_allocate_resources JobId=57463 NodeList=nodeGPU02 usec=1339 [2024-09-28T14:08:10.368] ==================== [2024-09-28T14:08:10.368] JobId=57463 StepId=0 [2024-09-28T14:08:10.368] JobNode[0] Socket[0] Core[0] is allocated [2024-09-28T14:08:10.368] ==================== [2024-09-28T14:08:30.409] _job_complete: JobId=57463 WTERMSIG 12 [2024-09-28T14:08:30.410] gres/gpu: state for nodeGPU02 [2024-09-28T14:08:30.410] gres_cnt found:3 configured:3 avail:3 alloc:0 [2024-09-28T14:08:30.410] gres_bit_alloc: of 3 [2024-09-28T14:08:30.410] gres_used:(null) [2024-09-28T14:08:30.410] topo[0]:(null)(0) [2024-09-28T14:08:30.410] topo_core_bitmap[0]:0-63 of 128 [2024-09-28T14:08:30.410] topo_gres_bitmap[0]:0 of 3 [2024-09-28T14:08:30.410] topo_gres_cnt_alloc[0]:0 [2024-09-28T14:08:30.410] topo_gres_cnt_avail[0]:1 [2024-09-28T14:08:30.410] topo[1]:(null)(0) [2024-09-28T14:08:30.410] topo_core_bitmap[1]:0-63 of 128 [2024-09-28T14:08:30.410] topo_gres_bitmap[1]:1 of 3 [2024-09-28T14:08:30.410] topo_gres_cnt_alloc[1]:0 [2024-09-28T14:08:30.410] topo_gres_cnt_avail[1]:1 [2024-09-28T14:08:30.410] topo[2]:(null)(0) [2024-09-28T14:08:30.410] topo_core_bitmap[2]:0-63 of 128 [2024-09-28T14:08:30.410] topo_gres_bitmap[2]:2 of 3 [2024-09-28T14:08:30.410] topo_gres_cnt_alloc[2]:0 [2024-09-28T14:08:30.410] topo_gres_cnt_avail[2]:1 [2024-09-28T14:08:30.410] _job_complete: JobId=57463 done [2024-09-28T14:08:58.687] gres/gpu: state for nodeGPU01 [2024-09-28T14:08:58.687] gres_cnt found:8 configured:8 avail:8 alloc:0 [2024-09-28T14:08:58.687] gres_bit_alloc: of 8 [2024-09-28T14:08:58.687] gres_used:(null) [2024-09-28T14:08:58.687] topo[0]:A100(808464705) [2024-09-28T14:08:58.687] topo_core_bitmap[0]:48-63 of 128 [2024-09-28T14:08:58.687] topo_gres_bitmap[0]:0 of 8 [2024-09-28T14:08:58.687] topo_gres_cnt_alloc[0]:0 [2024-09-28T14:08:58.687] topo_gres_cnt_avail[0]:1 [2024-09-28T14:08:58.687] topo[1]:A100(808464705) [2024-09-28T14:08:58.687] topo_core_bitmap[1]:48-63 of 128 [2024-09-28T14:08:58.687] topo_gres_bitmap[1]:1 of 8 [2024-09-28T14:08:58.687] topo_gres_cnt_alloc[1]:0 [2024-09-28T14:08:58.687] topo_gres_cnt_avail[1]:1 [2024-09-28T14:08:58.687] topo[2]:A100(808464705) [2024-09-28T14:08:58.687] topo_core_bitmap[2]:16-31 of 128 [2024-09-28T14:08:58.687] topo_gres_bitmap[2]:2 of 8 [2024-09-28T14:08:58.687] topo_gres_cnt_alloc[2]:0 [2024-09-28T14:08:58.687] topo_gres_cnt_avail[2]:1 [2024-09-28T14:08:58.687] topo[3]:A100(808464705) [2024-09-28T14:08:58.687] topo_core_bitmap[3]:16-31 of 128 [2024-09-28T14:08:58.688] topo_gres_bitmap[3]:3 of 8 [2024-09-28T14:08:58.688] topo_gres_cnt_alloc[3]:0 [2024-09-28T14:08:58.688] topo_gres_cnt_avail[3]:1 [2024-09-28T14:08:58.688] topo[4]:A100(808464705) [2024-09-28T14:08:58.688] topo_core_bitmap[4]:112-127 of 128 [2024-09-28T14:08:58.688] topo_gres_bitmap[4]:4 of 8 [2024-09-28T14:08:58.688] topo_gres_cnt_alloc[4]:0 [2024-09-28T14:08:58.688] topo_gres_cnt_avail[4]:1 [2024-09-28T14:08:58.688] topo[5]:A100(808464705) [2024-09-28T14:08:58.688] topo_core_bitmap[5]:112-127 of 128 [2024-09-28T14:08:58.688] topo_gres_bitmap[5]:5 of 8 [2024-09-28T14:08:58.688] topo_gres_cnt_alloc[5]:0 [2024-09-28T14:08:58.688] topo_gres_cnt_avail[5]:1 [2024-09-28T14:08:58.688] topo[6]:A100(808464705) [2024-09-28T14:08:58.688] topo_core_bitmap[6]:80-95 of 128 [2024-09-28T14:08:58.688] topo_gres_bitmap[6]:6 of 8 [2024-09-28T14:08:58.688] topo_gres_cnt_alloc[6]:0 [2024-09-28T14:08:58.688] topo_gres_cnt_avail[6]:1 [2024-09-28T14:08:58.688] topo[7]:A100(808464705) [2024-09-28T14:08:58.688] topo_core_bitmap[7]:80-95 of 128 [2024-09-28T14:08:58.688] topo_gres_bitmap[7]:7 of 8 [2024-09-28T14:08:58.688] topo_gres_cnt_alloc[7]:0 [2024-09-28T14:08:58.688] topo_gres_cnt_avail[7]:1 [2024-09-28T14:08:58.688] type[0]:A100(808464705) [2024-09-28T14:08:58.688] type_cnt_alloc[0]:0 [2024-09-28T14:08:58.688] type_cnt_avail[0]:8 [2024-09-28T14:08:58.690] gres/gpu: state for nodeGPU02 [2024-09-28T14:08:58.690] gres_cnt found:3 configured:3 avail:3 alloc:0 [2024-09-28T14:08:58.690] gres_bit_alloc: of 3 [2024-09-28T14:08:58.690] gres_used:(null) [2024-09-28T14:08:58.690] topo[0]:(null)(0) [2024-09-28T14:08:58.690] topo_core_bitmap[0]:0-63 of 128 [2024-09-28T14:08:58.690] topo_gres_bitmap[0]:0 of 3 [2024-09-28T14:08:58.690] topo_gres_cnt_alloc[0]:0 [2024-09-28T14:08:58.690] topo_gres_cnt_avail[0]:1 [2024-09-28T14:08:58.690] topo[1]:(null)(0) [2024-09-28T14:08:58.690] topo_core_bitmap[1]:0-63 of 128 [2024-09-28T14:08:58.690] topo_gres_bitmap[1]:1 of 3 [2024-09-28T14:08:58.690] topo_gres_cnt_alloc[1]:0 [2024-09-28T14:08:58.690] topo_gres_cnt_avail[1]:1 [2024-09-28T14:08:58.690] topo[2]:(null)(0) [2024-09-28T14:08:58.690] topo_core_bitmap[2]:0-63 of 128 [2024-09-28T14:08:58.690] topo_gres_bitmap[2]:2 of 3 [2024-09-28T14:08:58.690] topo_gres_cnt_alloc[2]:0 [2024-09-28T14:08:58.690] topo_gres_cnt_avail[2]:1 [2024-09-28T14:09:49.763] Resending TERMINATE_JOB request JobId=57463 Nodelist=nodeGPU02 This is the `tail -f` log of slurmd when launching the job from master, notice the messages in yellow [2024-09-28T14:08:10.270] debug2: Processing RPC: REQUEST_LAUNCH_PROLOG [2024-09-28T14:08:10.321] debug2: prep/script: _run_subpath_command: prolog success rc:0 output: [2024-09-28T14:08:10.323] debug2: Finish processing RPC: REQUEST_LAUNCH_PROLOG [2024-09-28T14:08:10.377] debug: Checking credential with 720 bytes of sig data [2024-09-28T14:08:10.377] debug2: Start processing RPC: REQUEST_LAUNCH_TASKS [2024-09-28T14:08:10.377] debug2: Processing RPC: REQUEST_LAUNCH_TASKS [2024-09-28T14:08:10.377] launch task StepId=57463.0 request from UID:10082 GID:10088 HOST:10.10.0.1 PORT:36478 [2024-09-28T14:08:10.377] CPU_BIND: JobNode[0] CPU[0] Step alloc [2024-09-28T14:08:10.377] CPU_BIND: ==================== [2024-09-28T14:08:10.377] CPU_BIND: Memory extracted from credential for StepId=57463.0 job_mem_limit=65536 step_mem_limit=65536 [2024-09-28T14:08:10.377] debug: Waiting for job 57463's prolog to complete [2024-09-28T14:08:10.377] debug: Finished wait for job 57463's prolog to complete [2024-09-28T14:08:10.378] error: _send_slurmstepd_init failed [2024-09-28T14:08:10.384] debug2: debug level read from slurmd is 'debug2'. [2024-09-28T14:08:10.385] debug2: _read_slurmd_conf_lite: slurmd sent 11 TRES. [2024-09-28T14:08:10.385] debug2: Received CPU frequency information for 128 CPUs [2024-09-28T14:08:10.385] select/cons_tres: common_init: select/cons_tres loaded [2024-09-28T14:08:10.385] debug: switch/none: init: switch NONE plugin loaded [2024-09-28T14:08:10.385] [57463.0] debug: auth/munge: init: loaded [2024-09-28T14:08:10.385] [57463.0] debug: Reading cgroup.conf file /etc/slurm/cgroup.conf [2024-09-28T14:08:10.395] [57463.0] debug: cgroup/v2: init: Cgroup v2 plugin loaded [2024-09-28T14:08:10.396] [57463.0] debug: hash/k12: init: init: KangarooTwelve hash plugin loaded [2024-09-28T14:08:10.396] [57463.0] debug: acct_gather_energy/none: init: AcctGatherEnergy NONE plugin loaded [2024-09-28T14:08:10.396] [57463.0] debug: acct_gather_profile/none: init: AcctGatherProfile NONE plugin loaded [2024-09-28T14:08:10.396] [57463.0] debug: acct_gather_interconnect/none: init: AcctGatherInterconnect NONE plugin loaded [2024-09-28T14:08:10.396] [57463.0] debug: acct_gather_filesystem/none: init: AcctGatherFilesystem NONE plugin loaded [2024-09-28T14:08:10.396] [57463.0] debug2: Reading acct_gather.conf file /etc/slurm/acct_gather.conf [2024-09-28T14:08:10.396] [57463.0] debug2: hwloc_topology_init [2024-09-28T14:08:10.399] [57463.0] debug2: xcpuinfo_hwloc_topo_load: xml file (/var/spool/slurmd/slurmd/hwloc_topo_whole.xml) found [2024-09-28T14:08:10.400] [57463.0] debug: CPUs:128 Boards:1 Sockets:2 CoresPerSocket:64 ThreadsPerCore:1 [2024-09-28T14:08:10.401] [57463.0] debug: task/cgroup: init: core enforcement enabled [2024-09-28T14:08:10.401] [57463.0] debug: task/cgroup: task_cgroup_memory_init: task/cgroup/memory: TotCfgRealMem:773744M allowed:100%(enforced), swap:0%(enforced), max:100%(773744M) max+swap:0%(773744M) min:30M kmem:100%(773744M permissive) min:30M [2024-09-28T14:08:10.401] [57463.0] debug: task/cgroup: init: memory enforcement enabled [2024-09-28T14:08:10.401] [57463.0] debug: task/cgroup: init: device enforcement enabled [2024-09-28T14:08:10.401] [57463.0] debug: task/cgroup: init: Tasks containment cgroup plugin loaded [2024-09-28T14:08:10.401] [57463.0] debug: jobacct_gather/linux: init: Job accounting gather LINUX plugin loaded [2024-09-28T14:08:10.401] [57463.0] cred/munge: init: Munge credential signature plugin loaded [2024-09-28T14:08:10.401] [57463.0] debug: job_container/none: init: job_container none plugin loaded [2024-09-28T14:08:10.401] [57463.0] debug: gres/gpu: init: loaded [2024-09-28T14:08:10.401] [57463.0] debug: gpu/generic: init: init: GPU Generic plugin loaded [2024-09-28T14:08:30.415] debug2: Start processing RPC: REQUEST_TERMINATE_JOB [2024-09-28T14:08:30.415] debug2: Processing RPC: REQUEST_TERMINATE_JOB [2024-09-28T14:08:30.415] debug: _rpc_terminate_job: uid = 777 JobId=57463 [2024-09-28T14:08:30.415] debug: credential for job 57463 revoked [2024-09-28T14:08:30.415] debug: sent SUCCESS, waiting for step to start [2024-09-28T14:08:30.415] debug: Blocked waiting for JobId=57463, all steps [2024-09-28T14:08:58.688] debug2: Start processing RPC: REQUEST_NODE_REGISTRATION_STATUS [2024-09-28T14:08:58.689] debug2: Processing RPC: REQUEST_NODE_REGISTRATION_STATUS [2024-09-28T14:08:58.689] debug: _step_connect: connect() failed for /var/spool/slurmd/slurmd/nodeGPU02_57436.0: Connection refused [2024-09-28T14:08:58.692] debug: _handle_node_reg_resp: slurmctld sent back 11 TRES. [2024-09-28T14:08:58.692] debug2: Finish processing RPC: REQUEST_NODE_REGISTRATION_STATUS -- Cristóbal A. Navarro

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errors compiling Slurm 18 on RHEL 9: [Makefile:577: scancel] Error 1 & It's not recommended to have unversioned Obsoletes
by Robert Kudyba 27 Sep '24

27 Sep '24

We're in the process of upgrading but first we're moving to RHEL 9. My attempt to compile using rpmbuild -v -ta --define "_lto_cflags %{nil}" slurm-18.08.9.tar.bz2 (H/T to Brian for this flag <https://groups.google.com/g/slurm-users/c/W8YfGIn1rDI/m/4bsSAoqZAAAJ>). I've stumped Google and the Slurm mailing list with the scancel error so hoping someone here knows of a work around. /bin/ld: opt.o:/root/rpmbuild/BUILD/slurm-18.08.9/src/scancel/../../src/scancel/scancel.h:78: multiple definition of `opt'; scancel.o:/root/rpmbuild/BUILD/slurm-18.08.9/src/scancel/../../src/scancel/scancel.h:78: first defined here collect2: error: ld returned 1 exit status make[3]: *** [Makefile:577: scancel] Error 1 make[3]: Leaving directory '/root/rpmbuild/BUILD/slurm-18.08.9/src/scancel' make[2]: *** [Makefile:563: all-recursive] Error 1 make[2]: Leaving directory '/root/rpmbuild/BUILD/slurm-18.08.9/src' make[1]: *** [Makefile:690: all-recursive] Error 1 make[1]: Leaving directory '/root/rpmbuild/BUILD/slurm-18.08.9' make: *** [Makefile:589: all] Error 2 error: Bad exit status from /var/tmp/rpm-tmp.jhiGyR (%build) RPM build errors: Macro expanded in comment on line 22: %_prefix path install path for commands, libraries, etc. line 70: It's not recommended to have unversioned Obsoletes: Obsoletes: slurm-lua slurm-munge slurm-plugins Macro expanded in comment on line 158: %define _unpackaged_files_terminate_build 0 line 224: It's not recommended to have unversioned Obsoletes: Obsoletes: slurm-sql line 256: It's not recommended to have unversioned Obsoletes: Obsoletes: slurm-sjobexit slurm-sjstat slurm-seff line 275: It's not recommended to have unversioned Obsoletes: Obsoletes: pam_slurm Bad exit status from /var/tmp/rpm-tmp.jhiGyR (%build) #!/bin/sh RPM_SOURCE_DIR="/root" RPM_BUILD_DIR="/root/rpmbuild/BUILD" RPM_OPT_FLAGS="-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS "-Wl,-z,lazy" -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection" RPM_LD_FLAGS="-Wl,-z,relro -Wl,--as-needed "-Wl,-z,lazy" -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 " RPM_ARCH="x86_64" RPM_OS="linux" RPM_BUILD_NCPUS="48" export RPM_SOURCE_DIR RPM_BUILD_DIR RPM_OPT_FLAGS RPM_LD_FLAGS RPM_ARCH RPM_OS RPM_BUILD_NCPUS RPM_LD_FLAGS RPM_DOC_DIR="/usr/share/doc" export RPM_DOC_DIR RPM_PACKAGE_NAME="slurm" RPM_PACKAGE_VERSION="18.08.9" RPM_PACKAGE_RELEASE="1.el9" export RPM_PACKAGE_NAME RPM_PACKAGE_VERSION RPM_PACKAGE_RELEASE LANG=C export LANG unset CDPATH DISPLAY ||: RPM_BUILD_ROOT="/root/rpmbuild/BUILDROOT/slurm-18.08.9-1.el9.x86_64" export RPM_BUILD_ROOT PKG_CONFIG_PATH="${PKG_CONFIG_PATH}:/usr/lib64/pkgconfig:/usr/share/pkgconfig" export PKG_CONFIG_PATH CONFIG_SITE=${CONFIG_SITE:-NONE} export CONFIG_SITE set -x umask 022 cd "/root/rpmbuild/BUILD" cd 'slurm-18.08.9' CFLAGS="${CFLAGS:--O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS "-Wl,-z,lazy" -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection}" ; export CFLAGS ; CXXFLAGS="${CXXFLAGS:--O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS "-Wl,-z,lazy" -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection}" ; export CXXFLAGS ; FFLAGS="${FFLAGS:--O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS "-Wl,-z,lazy" -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules}" ; export FFLAGS ; FCFLAGS="${FCFLAGS:--O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS "-Wl,-z,lazy" -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules}" ; export FCFLAGS ; LDFLAGS="${LDFLAGS:--Wl,-z,relro -Wl,--as-needed "-Wl,-z,lazy" -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 }" ; export LDFLAGS ; LT_SYS_LIBRARY_PATH="${LT_SYS_LIBRARY_PATH:-/usr/lib64:}" ; export LT_SYS_LIBRARY_PATH ; CC="${CC:-gcc}" ; export CC ; CXX="${CXX:-g++}" ; export CXX; [ ""x != x ] && for file in $(find . -type f -name configure -print); do /usr/bin/sed -r --in-place=.backup 's/^char $\*f$  = /__attribute__ ((used)) char (*f) () = /g' $file; diff -u $file.backup $file && mv $file.backup $file /usr/bin/sed -r --in-place=.backup 's/^char $\*f$ ;/__attribute__ ((used)) char (*f) ();/g' $file; diff -u $file.backup $file && mv $file.backup $file /usr/bin/sed -r --in-place=.backup 's/^char \$2 ;/__attribute__ ((used)) char \$2 ();/g' $file; diff -u $file.backup $file && mv $file.backup $file /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' $file; diff -u $file.backup $file && mv $file.backup $file /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '"'"'s/^T .* \$.*\$$/extern int \\1();/p'"'"' -e '"'"'s/^$symcode* .* \$.*\$$/extern char \\1;/p'"'"'"#' $file; diff -u $file.backup $file && mv $file.backup $file done; [ "1" = 1 ] && for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ; do [ -f /usr/lib/rpm/redhat/$(basename $i) ] && /usr/bin/rm -f $i && /usr/bin/cp -fv /usr/lib/rpm/redhat/$(basename $i) $i ; done ; [ "1" = 1 ] && [ x != "x"-Wl,-z,lazy"" ] && for i in $(find . -name ltmain.sh) ; do /usr/bin/sed -i.backup -e 's~compiler_flags=$~compiler_flags=""-Wl,-z,lazy""~' $i done ; ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu \ --program-prefix= \ --disable-dependency-tracking \ \ --prefix=/usr \ --exec-prefix=/usr \ --bindir=/usr/bin \ --sbindir=/usr/sbin \ --sysconfdir=/etc/slurm \ --datadir=/usr/share \ --includedir=/usr/include \ --libdir=/usr/lib64 \ --libexecdir=/usr/libexec \ --localstatedir=/var \ --sharedstatedir=/var/lib \ --mandir=/usr/share/man \ --infodir=/usr/share/info \ \ make -j48 RPM_EC=$? for pid in $(jobs -p); do kill -9 ${pid} || continue; done exit ${RPM_EC}

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