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Interfaces of topology/tree and Topology Awareness
by nico.derl＠tutanota.com 15 Apr '24

15 Apr '24

Hello everyone, I'm trying to improve topology awareness in a local Slurm-managed HPC system. It's using the default hierarchical 3-level topology with the tree-plugin. It however does not always confine jobs to the most tightly packed group of nodes, seems to over-provision switches for smaller jobs, and gets slow or overwhelmed with jobs that have a high node count. I'd like to implement something more literally aligned with best-fit, but I'm having trouble understanding the relevant interfaces to hook into the topology model of Slurm. I would like a high-level explanation of how the tree- and common topology components work, how they integrate into the higher scheduling logic and what the internal topology model looks like. Or some pointers to relevant docs discussing this. I have read the topology guide and its dev-doc, which does note some of the caveats I mentioned. It however only talks about providing a set of weights to the upper logic levels in the form of a node ranking. I can't see how this ranking resembles the topology and how it's being used. From looking at the signatures and C-code I can tell this much: topology-tree consumes the topology.conf and generates a ranking of some kind that is passed to topology-common. topology-common consumes a ranking and uses its own gres-sched to figure out what nodes can fit a job (possibly pulling info from the gres-select-plugin to determine node capabilities). It's then supposed to apply a best-fit algorithm to efficiently fill up vacant cluster-capacity, but I can't manage to follow this part in the code as everything crumbles into separate files that I can't link correctly in my head. Thanks in advance. referenced docs: <https://slurm.schedmd.com/topology.html> <https://hpc.rz.rptu.de/documentation/topology_plugin.html> <https://github.com/SchedMD/slurm/tree/master/src/plugins/topology/common>

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Re: slurmrestd connect to 192.168.87.113:6819 Connection refused
by shaobo liu 14 Apr '24

14 Apr '24

Thanks, The reason was found. It was caused by the expiration of the rest api token. <nico.derl(a)tutanota.com> 于2024年4月12日周五 22:56写道： > If you say DBd isn't using 6819, in the sense that you selected a > different port, make sure the dbdport directive reflects that in both > slurmdbd.conf and AccountingStoragePort in slurm.conf. > It must be getting the 6819 from somewhere. > > > 12. Apr. 2024, 16:05 von dspam.liu(a)gmail.com: > > slurmctrld and rest are on the same machine, No firewall. secondary > slurmdbd is background mode, slurmdbd does not listen on port 6819. > > OS: ubuntu 20.04 > SLURM: 23.11.0 > > <nico.derl(a)tutanota.com> 于2024年4月12日周五 20:18写道： > > Hey, > Are slurmctrld and restd on separate machines? Can you manually reach > them? Could there be a firewall/closed port in the way? > > > 12. Apr. 2024, 11:36 von slurm-users(a)lists.schedmd.com: > > hi，slurm configured primary and secondary，The error when requesting > slurmrest api is as follows, may I ask what is the reason? > > # scontrol ping > Slurmctld(primary) at node003 is UP > Slurmctld(backup) at node113 is UP > > > # systemctl status slurmrestd.service > ● slurmrestd.service - Slurm REST daemon > Loaded: loaded (/lib/systemd/system/slurmrestd.service; enabled; > vendor preset: enabled) > Active: active (running) since Fri 2024-04-12 17:07:08 CST; 21min ago > Main PID: 705425 (slurmrestd) > Tasks: 21 (limit: 629145) > Memory: 20.3M > CGroup: /system.slice/slurmrestd.service > └─705425 /usr/sbin/slurmrestd -f /etc/slurm/slurm.conf > unix:/var/spool/slurm/slurmrestd.socket 0.0.0.0:6820 -vvv > > Apr 12 17:08:46 node003 slurmrestd[705425]: debug2: _slurm_connect: failed > to connect to 192.168.87.113:6819: Connection refused > Apr 12 17:08:46 node003 slurmrestd[705425]: debug2: Error connecting slurm > stream socket at 192.168.87.113:6819: Connection refused > Apr 12 17:08:46 node003 slurmrestd[705425]: slurmrestd: error: > slurm_persist_conn_open_without_init: failed to open persistent connection > to host:node113:6819: Connection refused > Apr 12 17:08:46 node003 slurmrestd[705425]: slurmrestd: error: Sending > PersistInit msg: Connection refused > Apr 12 17:08:46 node003 slurmrestd[705425]: slurmrestd: error: > slurm_rest_auth_p_get_db_conn: unable to connect to slurmdbd: Connection > refused > Apr 12 17:08:46 node003 slurmrestd[705425]: slurmrestd: error: > init_connection[v0.0.39]:[[2.0.1.191]:50652] rc[7000]=Unable to connect to > database -> openapi_get_db_conn() failed to open slurmdb connecti> > Apr 12 17:08:46 node003 slurmrestd[705425]: error: > slurm_persist_conn_open_without_init: failed to open persistent connection > to host:node113:6819: Connection refused > Apr 12 17:08:46 node003 slurmrestd[705425]: error: Sending PersistInit > msg: Connection refused > Apr 12 17:08:46 node003 slurmrestd[705425]: error: > slurm_rest_auth_p_get_db_conn: unable to connect to slurmdbd: Connection > refused > Apr 12 17:08:46 node003 slurmrestd[705425]: error: > init_connection[v0.0.39]:[[2.0.1.191]:50652] rc[7000]=Unable to connect to > database -> openapi_get_db_conn() failed to open slurmdb connection > > > >

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slurmrestd connect to 192.168.87.113:6819 Connection refused
by shaobo liu 12 Apr '24

12 Apr '24

hi，slurm configured primary and secondary，The error when requesting slurmrest api is as follows, may I ask what is the reason? # scontrol ping Slurmctld(primary) at node003 is UP Slurmctld(backup) at node113 is UP # systemctl status slurmrestd.service ● slurmrestd.service - Slurm REST daemon Loaded: loaded (/lib/systemd/system/slurmrestd.service; enabled; vendor preset: enabled) Active: active (running) since Fri 2024-04-12 17:07:08 CST; 21min ago Main PID: 705425 (slurmrestd) Tasks: 21 (limit: 629145) Memory: 20.3M CGroup: /system.slice/slurmrestd.service └─705425 /usr/sbin/slurmrestd -f /etc/slurm/slurm.conf unix:/var/spool/slurm/slurmrestd.socket 0.0.0.0:6820 -vvv Apr 12 17:08:46 node003 slurmrestd[705425]: debug2: _slurm_connect: failed to connect to 192.168.87.113:6819: Connection refused Apr 12 17:08:46 node003 slurmrestd[705425]: debug2: Error connecting slurm stream socket at 192.168.87.113:6819: Connection refused Apr 12 17:08:46 node003 slurmrestd[705425]: slurmrestd: error: slurm_persist_conn_open_without_init: failed to open persistent connection to host:node113:6819: Connection refused Apr 12 17:08:46 node003 slurmrestd[705425]: slurmrestd: error: Sending PersistInit msg: Connection refused Apr 12 17:08:46 node003 slurmrestd[705425]: slurmrestd: error: slurm_rest_auth_p_get_db_conn: unable to connect to slurmdbd: Connection refused Apr 12 17:08:46 node003 slurmrestd[705425]: slurmrestd: error: init_connection[v0.0.39]:[[2.0.1.191]:50652] rc[7000]=Unable to connect to database -> openapi_get_db_conn() failed to open slurmdb connecti> Apr 12 17:08:46 node003 slurmrestd[705425]: error: slurm_persist_conn_open_without_init: failed to open persistent connection to host:node113:6819: Connection refused Apr 12 17:08:46 node003 slurmrestd[705425]: error: Sending PersistInit msg: Connection refused Apr 12 17:08:46 node003 slurmrestd[705425]: error: slurm_rest_auth_p_get_db_conn: unable to connect to slurmdbd: Connection refused Apr 12 17:08:46 node003 slurmrestd[705425]: error: init_connection[v0.0.39]:[[2.0.1.191]:50652] rc[7000]=Unable to connect to database -> openapi_get_db_conn() failed to open slurmdb connection

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visualisation of JobComp and JobacctGather data with Grafana - screenshots, ideas?
by Josef Dvoracek 12 Apr '24

12 Apr '24

Is here anybody having nice visualization of JobComp and JobacctGather data in Grafana? I save JobComp data in Elasticsearch, JobacctGather data in influxDB, and thinking about how to provide meaningful insights to $users. Things I'd like to show..: especially memory & cpu utilization, job result, possible malicious effects like OOMs... Any screenshots, ideas, experience welcomed! cheers Josef

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Re: Slurmd enabled crash with CgroupV2
by Josef Dvoracek 11 Apr '24

11 Apr '24

I observe same behavior on slurm 23.11.5 Rocky Linux8.9.. > [root@compute ~]# cat /sys/fs/cgroup/cgroup.subtree_control > memory pids > [root@compute ~]# systemctl disable slurmd > Removed /etc/systemd/system/multi-user.target.wants/slurmd.service. > [root@compute ~]# cat /sys/fs/cgroup/cgroup.subtree_control > cpuset cpu io memory pids > [root@compute ~]# systemctl enable slurmd > Created symlink /etc/systemd/system/multi-user.target.wants/slurmd.service → /usr/lib/systemd/system/slurmd.service. > [root@compute ~]# cat /sys/fs/cgroup/cgroup.subtree_control > cpuset cpu io memory pids over time (i see this thread is ~1 year old, is here better / new understanding of this? cheers josef On 23. 05. 23 12:46, Alan Orth wrote: > I notice the exact same behavior as Tristan. My CentOS Stream 8 system > is in full unified cgroupv2 mode, the slurmd.service has a > "Delegate=Yes" override added to it, and all cgroup stuff is added to > slurm.conf and cgroup.conf, yet slurmd does not start after reboot. I > don't understand what is happening, but I see the exact same behavior > regarding the cgroup subtree_control with disabling / re-enabling slurmd. >

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Jobs of a user are stuck in Completing stage for a long time and cannot cancel them
by archisman.pathak＠nksecurities.com 11 Apr '24

11 Apr '24

We are running a slurm cluster with version `slurm 22.05.8`. One of our users has reported that their jobs have been stuck at the completion stage for a long time. Referring to Slurm Workload Manager - Slurm Troubleshooting Guide we found that indeed the batchhost for the job was removed from the cluster, perhaps without draining it first. How do we cancel/delete the jobs ? * We tried scancel on the batch and individual job ids from both the user and from SlurmUser

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Upgrading nodes
by Steve Berg 10 Apr '24

10 Apr '24

I just finished migrating a few dozen blade servers from torque to slurm. They're all running Alma 8 currently with the slurm that is available from epel. I do want to get it all upgraded to running Alma 9 and the current version of slurm. Got one system set up as the slurmctld system running Alma 9. I grabbed the tar ball and built RPMs for 9.x. Got a few questions about the best path to proceed. Can I use the Alma 9 system to build rpms for Alma 8? I'm sure I can rig up an 8 system to build rpms on but thought I'd see if there was a way to do it on the one 9 system. My plan will be to get the rpms built for 8 and 9, update the slurmctld system to the latest version of slurm, then update all the nodes to the current slurmd version. Once that's done I should be able to reinstall individual nodes to Alma 9 and the same version of slurmd. Am I missing anything in that sequence? I'm fairly confident that the users aren't running any code that will notice the difference between a node running 8 or 9, that should be transparent to them. -- //- Fixer of that which is broke -// //- Home = sberg(a)mississippi.com -// //- Sinners can repent, but stupid is forever. -//

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single node configuration
by Alison Peterson 10 Apr '24

10 Apr '24

Hi everyone, I'm conducting some tests. I've just set up SLURM on the head node and haven't added any compute nodes yet. I'm trying to test it to ensure it's working, but I'm encountering an error: 'Nodes required for the job are DOWN, DRAINED, or reserved for jobs in higher priority partitions. *[stsadmin@head ~]$ squeue* JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 6 lab test_slu stsadmin PD 0:00 1 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions) *[stsadmin@head ~]$ scontrol show job 6* JobId=6 JobName=test_slurm UserId=stsadmin(1000) GroupId=stsadmin(1000) MCS_label=N/A Priority=1 Nice=0 Account=(null) QOS=normal JobState=PENDING Reason=Nodes_required_for_job_are_DOWN,_DRAINED_or_reserved_for_jobs_in_higher_priority_partitions Dependency=(null) Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0 RunTime=00:00:00 TimeLimit=01:00:00 TimeMin=N/A SubmitTime=2024-04-09T10:43:14 EligibleTime=2024-04-09T10:43:14 AccrueTime=2024-04-09T10:43:14 StartTime=Unknown EndTime=Unknown Deadline=N/A SuspendTime=None SecsPreSuspend=0 LastSchedEval=2024-04-09T10:43:23 Scheduler=Backfill:* Partition=lab AllocNode:Sid=head:5147 ReqNodeList=(null) ExcNodeList=(null) NodeList= NumNodes=1-1 NumCPUs=1 NumTasks=1 CPUs/Task=1 ReqB:S:C:T=0:0:*:* ReqTRES=cpu=1,mem=1G,node=1,billing=1 AllocTRES=(null) Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=* MinCPUsNode=1 MinMemoryCPU=1G MinTmpDiskNode=0 Features=(null) DelayBoot=00:00:00 OverSubscribe=YES Contiguous=0 Licenses=(null) Network=(null) Command=/home/stsadmin/Downloads/test.sh WorkDir=/home/stsadmin StdErr=/home/stsadmin/test_slurm_output.txt StdIn=/dev/null StdOut=/home/stsadmin/test_slurm_output.txt Power= *[stsadmin@head ~]$ scontrol show node head* NodeName=head CoresPerSocket=6 CPUAlloc=0 CPUEfctv=24 CPUTot=24 CPULoad=0.00 AvailableFeatures=(null) ActiveFeatures=(null) Gres=(null) NodeAddr=head NodeHostName=head RealMemory=184000 AllocMem=0 FreeMem=N/A Sockets=2 Boards=1 State=DOWN+NOT_RESPONDING ThreadsPerCore=2 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A Partitions=lab BootTime=None SlurmdStartTime=None LastBusyTime=2024-04-09T10:42:53 ResumeAfterTime=None CfgTRES=cpu=24,mem=184000M,billing=24 AllocTRES= CapWatts=n/a CurrentWatts=0 AveWatts=0 ExtSensorsJoules=n/a ExtSensorsWatts=0 ExtSensorsTemp=n/a Reason=Not responding [slurm@2024-04-09T10:14:10] I will take any advice to guide me in the proper direction, thank you! -- *Alison Peterson* IT Research Support Analyst *Information Technology* apeterson5(a)sdsu.edu <mfarley(a)sdsu.edu> O: 619-594-3364 *San Diego State University | SDSU.edu <http://sdsu.edu/>* 5500 Campanile Drive | San Diego, CA 92182-8080

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Avoiding fragmentation
by Gerhard Strangar 10 Apr '24

10 Apr '24

Hi, I'm trying to figure out how to deal with a mix of few- and many-cpu jobs. By that I mean most jobs use 128 cpus, but sometimes there are jobs with only 16. As soon as that job with only 16 is running, the scheduler splits the next 128 cpu jobs into 96+16 each, instead of assigning a full 128 cpu node to them. Is there a way for the administrator to achieve preferring full nodes? The existence of pack_serial_at_end makes me believe there is not, because that basically is what I needed, apart from my serial jobs using 16 cpus instead of 1. Gerhard

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Nodes required for job are down, drained or reserved
by Alison Peterson 09 Apr '24

09 Apr '24

Hi everyone, I'm conducting some tests. I've just set up SLURM on the head node and haven't added any compute nodes yet. I'm trying to test it to ensure it's working, but I'm encountering an error: 'Nodes required for the job are DOWN, DRAINED, or reserved for jobs in higher priority partitions. Any guidance will be appreciated thank you! -- *Alison Peterson* IT Research Support Analyst *Information Technology* apeterson5(a)sdsu.edu <mfarley(a)sdsu.edu> O: 619-594-3364 *San Diego State University | SDSU.edu <http://sdsu.edu/>* 5500 Campanile Drive | San Diego, CA 92182-8080

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