September 2024 - slurm-users - lists.schedmd.com

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

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

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

1 1

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}

2 2

Re: SLUG'24 presentation slides?
by Kilian Cavalotti 27 Sep '24

27 Sep '24

Awesome, thanks Victoria! Cheers, -- Kilian On Thu, Sep 26, 2024 at 11:17 AM Victoria Hobson <victoria(a)schedmd.com> wrote: > Hi Kilian, > > We're getting these posted now and an email will go out when they are > available! > > Thanks, > > > Victoria Hobson > > *Vice President of Marketing * > > 909.609.8889 > > www.schedmd.com > > > On Mon, Sep 23, 2024 at 10:49 AM Kilian Cavalotti via slurm-users < > slurm-users(a)lists.schedmd.com> wrote: > >> Hi SchedMD, >> >> I'm sure they will eventually, but do you know when the slides of the >> SLUG'24 presentation will be available online at >> https://slurm.schedmd.com/publications.html, like previous editions'? >> >> Thanks! >> -- >> Kilian >> >> -- >> slurm-users mailing list -- slurm-users(a)lists.schedmd.com >> To unsubscribe send an email to slurm-users-leave(a)lists.schedmd.com >> > -- Kilian

1 0

A note on updating Slurm from 23.02 to 24.05 & multi-cluster
by Ward Poelmans 26 Sep '24

26 Sep '24

Hi all, We hit a snag when updating our clusters from Slurm 23.02 to 24.05. After updating the slurmdbd, our multi cluster setup was broken until everything was updated to 24.05. We had not anticipated this. SchedMD says that fixing it would be a very complex operation. Hence, this warning to everybody on planning to update: make sure to quickly updating everything once you've updated the slurmdbd daemon. Reference: https://support.schedmd.com/show_bug.cgi?id=20931 Ward

3 3

Jobs pending with reason "priority" but nodes are idle
by Long, Daniel S. 25 Sep '24

25 Sep '24

Hi, On our cluster we have some jobs that are queued even though there are available nodes to run on. The listed reason is "priority" but that doesn't really make sense to me. Slurm isn't picking another job to run on those nodes; it's just not running anything at all. We do have a quite heterogeneous cluster, but as far as I can tell the queued jobs aren't requesting anything that would preclude them from running on the idle nodes. They are array jobs, if that makes a difference. Thanks for any help you all can provide.

3 6

Max TRES per user and node
by Guillaume COCHARD 25 Sep '24

25 Sep '24

Hello, We are looking for a method to limit the TRES used by each user on a per-node basis. For example, we would like to limit the total memory allocation of jobs from a user to 200G per node. There is MaxTRESperNode (https://slurm.schedmd.com/sacctmgr.html#OPT_MaxTRESPerNode), but unfortunately, this is a per-job limit, not per user. Ideally, we would like to apply this limit on partitions and/or QoS. Does anyone know if this is possible and how to achieve it? Thank you,

4 9

SLURM Telegraf Plugin
by Pablo Collado Soto 25 Sep '24

25 Sep '24

Hi all, I recently wrote an SLURM input plugin [0] for Telegraf [1]. I just wanted to let the community know so that you can use it if you'd find that useful. Maybe its existence can also be included in the documentation somewhere? Anyway, thanks a ton for your time, Pablo Collado Soto References: 0: https://github.com/influxdata/telegraf/tree/master/plugins/inputs/slurm 1: https://www.influxdata.com/time-series-platform/telegraf/ + -------------------------------------- + | Never let your sense of morals prevent | | you from doing what is right. | | -- Salvor Hardin, "Foundation" | + -------------------------------------- +

2 1

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