[slurm-users] job is pending but resources are available

[Adam Xu]

在 2021/10/13 9:22, Brian Andrus 写道:
>
> Something is very odd when you have the node reporting:
>
> RealMemory=1 AllocMem=0 FreeMem=47563 Sockets=2 Boards=1
>
> What do you get when you run ‘slurmd -C’ on the node?
>
# slurmd -C
NodeName=apollo CPUs=36 Boards=1 SocketsPerBoard=2 CoresPerSocket=18 
ThreadsPerCore=1 RealMemory=128306
UpTime=22-16:14:48
>
> Brian Andrus
>
> *From: *Adam Xu <mailto:adam_xu at adagene.com.cn>
> *Sent: *Tuesday, October 12, 2021 6:07 PM
> *To: *slurm-users at lists.schedmd.com
> *Subject: *Re: [slurm-users] job is pending but resources are available
>
> 在 2021/10/12 21:21, Adam Xu 写道:
>
>     Hi All,
>
>     OS: Rocky Linux 8.4
>
>     slurm version: 20.11.7
>
>     the partition's name is apollo. the node's name is apollo too. the
>     node has 36 cpu cores and 8GPUs in it.
>
>     partition info
>
>     $ scontrol show partition apollo
>     PartitionName=apollo
>        AllowGroups=ALL AllowAccounts=ALL AllowQos=ALL
>        AllocNodes=ALL Default=NO QoS=N/A
>        DefaultTime=NONE DisableRootJobs=NO ExclusiveUser=NO
>     GraceTime=0 Hidden=NO
>        MaxNodes=UNLIMITED MaxTime=UNLIMITED MinNodes=0 LLN=NO
>     MaxCPUsPerNode=UNLIMITED
>        Nodes=apollo
>        PriorityJobFactor=1 PriorityTier=1 RootOnly=NO ReqResv=NO
>     OverSubscribe=YES:36
>        OverTimeLimit=NONE PreemptMode=OFF
>        State=UP TotalCPUs=36 TotalNodes=1 SelectTypeParameters=NONE
>        JobDefaults=(null)
>        DefMemPerNode=UNLIMITED MaxMemPerNode=UNLIMITED
>
>     node info
>
>     $ scontrol show node apollo
>     NodeName=apollo Arch=x86_64 CoresPerSocket=18
>        CPUAlloc=28 CPUTot=36 CPULoad=7.02
>        AvailableFeatures=(null)
>        ActiveFeatures=(null)
>        Gres=gpu:v100:8,mps:v100:800
>        NodeAddr=apollo NodeHostName=apollo Version=20.11.7
>        OS=Linux 4.18.0-305.19.1.el8_4.x86_64 #1 SMP Wed Sep 15
>     19:12:32 UTC 2021
>        RealMemory=1 AllocMem=0 FreeMem=47563 Sockets=2 Boards=1
>        State=MIXED ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A
>     MCS_label=N/A
>        Partitions=apollo
>        BootTime=2021-09-20T23:43:49 SlurmdStartTime=2021-10-12T16:55:44
>        CfgTRES=cpu=36,mem=1M,billing=36
>        AllocTRES=cpu=28
>        CapWatts=n/a
>        CurrentWatts=0 AveWatts=0
>        ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s
>        Comment=(null)
>
>     Now I have 7 jobs running but when I submit 8th job, the status of
>     the job is pending beacuse Resources.
>
>     $ squeue
>                  JOBID PARTITION     NAME     USER ST       TIME NODES
>     NODELIST(REASON)
>                    879    apollo    do.sh zhining_ PD       0:00 1
>     (Resources)
>                    489    apollo    do.sh zhining_  R 13-12:50:45 1
>     apollo
>                    490    apollo    do.sh zhining_  R 13-12:41:00 1
>     apollo
>                    592    apollo runme-gp junwen_f  R 4-12:42:31 1 apollo
>                    751    apollo runme-gp junwen_f  R 1-12:48:20 1 apollo
>                    752    apollo runme-gp junwen_f  R 1-12:48:10 1 apollo
>                    871    apollo runme-gp junwen_f  R    7:13:45 1 apollo
>                    872    apollo runme-gp junwen_f  R    7:12:42 1 apollo
>
>     $ scontrol show job 879
>     JobId=879 JobName=do.sh
>        UserId=zhining_wan(1001) GroupId=zhining_wan(1001) MCS_label=N/A
>        Priority=4294900882 Nice=0 Account=(null) QOS=(null)
>        JobState=PENDING Reason=Resources Dependency=(null)
>        Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0
>        RunTime=00:00:00 TimeLimit=UNLIMITED TimeMin=N/A
>        SubmitTime=2021-10-12T16:29:29 EligibleTime=2021-10-12T16:29:29
>        AccrueTime=2021-10-12T16:29:29
>        StartTime=2021-10-12T21:17:41 EndTime=Unknown Deadline=N/A
>        SuspendTime=None SecsPreSuspend=0
>     LastSchedEval=2021-10-12T21:17:39
>        Partition=apollo AllocNode:Sid=sms:1281191
>        ReqNodeList=(null) ExcNodeList=(null)
>        NodeList=(null) SchedNodeList=apollo
>        NumNodes=1-1 NumCPUs=4 NumTasks=4 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
>        TRES=cpu=4,node=1,billing=4
>        Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=*
>        MinCPUsNode=1 MinMemoryNode=0 MinTmpDiskNode=0
>        Features=(null) DelayBoot=00:00:00
>        OverSubscribe=YES Contiguous=0 Licenses=(null) Network=(null)
>     Command=/home/zhining_wan/job/2021/20210603_ctla4_double_bilayer/final_pdb_minimize/amber/nolipid/test/do.sh
>
>     WorkDir=/home/zhining_wan/job/2021/20210603_ctla4_double_bilayer/final_pdb_minimize/amber/nolipid/test
>
>     StdErr=/home/zhining_wan/job/2021/20210603_ctla4_double_bilayer/final_pdb_minimize/amber/nolipid/test/slurm-879.out
>
>        StdIn=/dev/null
>     StdOut=/home/zhining_wan/job/2021/20210603_ctla4_double_bilayer/final_pdb_minimize/amber/nolipid/test/slurm-879.out
>
>        Power=
>        TresPerNode=gpu:1
>        NtasksPerTRES:0
>
>     After running 7 jobs, the node has 8 cpu cores and 1 gpu left, so
>     I can be sure that the remaining resources are sufficient. but why
>     the job is pending with reason "Resources"?
>
> Some information to add：
>
> I have killed some jobs with kill instead of scancle, Could this be 
> the cause of this result?
>
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