Show pageOld revisionsBack to top This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong. <booktoc/> ====== Managing Jobs on DARWIN ====== Once a user has been able to submit jobs to the cluster -- interactive or batch -- the user will from time to time want to know what those jobs are doing. Is the job waiting in a queue for resources to become available, or is it executing? How long has the job been executing? How much CPU time or memory has the job consumed? Users can query Slurm for job information using the ''squeue'' command while the job is still active in the Slurm. The ''squeue'' command has a variety of command line options available to customize and filter what information it displays; discussing all of them is beyond the scope of this document. Use ''squeue %%-%%-help'' or ''man squeue'' commands on the login node to view a complete description of available options. With no options provided, ''squeue'' defaults to displaying a list of all jobs submitted by all the users on the cluster currently active in Slurm. This includes jobs that are waiting in a queue, jobs that are executing, and jobs that are in an error state. The list below is presented in a tabular format, with the following columns: ^Column^Description^ |JOBID|Numerical identifier assigned when the job was submitted| |PARTITION|The partition to which the job is assigned| |NAME|The name assigned to the job| |USER|The owner of the job| |ST|Current state of the job (see next table)| |TIME|Either the time the job was submitted or the time the job began execution, depending on its state| |NODES|The number of nodes assigned to the job| |NODELIST(Reason)|The list of nodes on which the job is running or the reason for which the job is in its current state(other than running)| The different states in which a job may exist are enumerated by the following codes: ^State Code^Description^ |''CA''|Job was explicitly cancelled by the user or system administrator. The job may or may not have been initiated| |''CG''|Job is in the process of completing. Some processes on some nodes may still be active| |''F''|Job terminated with non-zero exit code or other failure condition| |''PD''|Job is awaiting resource allocation| |''PR''|Job terminated due to preemption| |''R''|Job currently has an allocation and is running| |''RD''|Job is held| |''RQ''|Completing job is being requeued| |''RS''|Job is about to change size| |''S''|Job has an allocation, but execution has been suspended and CPUs have been released for other jobs| |''TO''|Job terminated upon reaching its time limit| There are many other possible [[https://slurm.schedmd.com/squeue.html#lbAG|job states codes]] which can be found in the official Slurm documentation. ===== Checking job status ===== ==== squeue or ssqueue ==== Use the ''squeue'' command to check the status of queued jobs. The ''ssqueue'' version is a UD IT version of ''squeue'' that provides output as an interactive spreadsheet using the curses display library such that each column in the spreadsheet is sized to match the longest string present, rather than truncating at a fixed width as the Slurm commands do. Use ''squeue %%-%%-help'' or ''man squeue'' commands on the login node to view a complete description of available options. The same options work with ''ssqueue'' too. Some of the most often-used options are summarized here: ^ Option ^ Result ^ | ''-j'' <<//job_id_list//>> | Displays information for specified job(s) | | ''-u'' <<//user_list//>> | Displays information for jobs associated with the specified user(s) | | ''%%-%%-start'' | List estimated start time for queued jobs | | ''-t'' | Can be used to List the jobs that are in particular state(passed as argument) | | ''%%-%%-Format'' | Customize output of squeue | With no options provided, ''squeue'' defaults to displaying a list of all jobs submitted by all the users on the cluster currently active in Slurm. This includes jobs that are waiting in a queue, jobs that are executing, and jobs that are in an error state. <code bash> [(it_css:traine)@login00 it_css]$ squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 488072 ccei_biom P-irc rameswar CG 3-23:26:11 1 r01n41 496264 clj NOVA_Hcs delgorio PD 0:00 4 (QOSGrpCpuLimit) 496312 clj NOVA_Hcs delgorio PD 0:00 4 (QOSGrpCpuLimit) 502942 standard run.a8.p heil PD 0:00 4 (Resources) 502954 standard run.s8.p heil PD 0:00 3 (Priority) 502970 standard PEG44_EQ utkarsk PD 0:00 2 (Priority) 502821 standard R3_FineM yashar PD 0:00 2 (Priority) 502822 standard B9_ResCo yashar PD 0:00 2 (Priority) 502823 standard R3_ResCo yashar PD 0:00 2 (Priority) 502979 standard MOH_2Pro utkarsk PD 0:00 2 (Priority) 502967 standard run_442c heil PD 0:00 1 (Dependency) 502975 standard run.s10. heil PD 0:00 1 (Dependency) 496263 clj NOVA_Hcs delgorio R 2:33:10 4 r00n[25-26,36-37] 501784 elliottla fluidvis safa R 1-02:51:00 1 r01n53 498144 kukulka_l ph005crc txthoman R 2-21:01:27 1 r00n17 498436 biophysic CdI cyxu R 1-21:29:05 1 r01g04 . . . </code> The ''squeue'' command can also be used to see the job status information of all the current jobs for a particular user by using ''-u'' flag followed by the ''USER''. For example, <code bash> [(it_css:traine)@login00 ~]$ squeue -u traine JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 913 standard date traine PD 0:00 1 (QOSMaxJobsPerUserLimit) 912 standard openmp_j traine R 0:23 1 r00n45 911 standard sh traine R 1:14 1 r00n56 910 standard sh traine R 3:30 1 r00n56 </code> shows only the jobs currently in Slurm for user ''traine''. Jobs 910, 911, and 912 are currently running. Job 913 is pending due to a "MaxJobsPerUser" limit enforced by the quality-of-service (QOS) level associated with the devel partition (see the section on [[abstract:darwin:runjobs:queues|Partitions]] for discussion of these limits). Notably absent from both the standard and long format for ''squeue'' are the resources (CPU cores, memory, GPUs) allocated to the job. Historically, Slurm was heavily focused on scheduling nodes themselves and not the component resources on those nodes, and this is reflected in the data it tends to display by default. The ''%%--%%Format'' flag must be used to augment the displayed information: <code bash> [(it_css:traine)@login00 ~]$ squeue --Format="jobid,name,state,partition,account,username,numnodes,numtasks,numcpus,gres" JOBID NAME STATE PARTITION ACCOUNT USER NODES TASKS CPUS GRES 922 date PENDING devel it_nss frey 1 1 1 (null) 921 sh RUNNING devel it_nss frey 1 2 2 gpu:p100 918 openmp_job RUNNING standard it_nss frey 1 1 4 (null) 915 sh RUNNING devel it_nss frey 1 4 4 (null) </code> === Job status is PD === When your job status is ''PD'' it means your job is queued and waiting to execute. When you check with ''squeue'' you might see something like this <code base> [(it_css:traine)@traine it_css]$ squeue -u traine JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 1354 standard A3WF traine PD 0.00 1 (Priority) </code> Sometimes your job is stuck and remains in the ''PD'' state and never starts running. You can use ''squeue'' in combination with ''-j'' and ''%%-%%-start'' to see the estimated start time of your pending job. <code bash> [(it_css:traine)@traine it_css]$ squeue -j 91487 --start JOBID PARTITION NAME USER ST START_TIME NODES NODELIST(REASON) 91487 standard hello_te traine PD 2018-07-09T13:09:40 2 (Priority) </code> ==== sstat or ssstat ==== To check the status information of a running job/step, use the ''sstat'' command with appropriate options. The ''ssstat'' version is a UD IT version of ''sstat'' that provides output as an interactive spreadsheet using the curses display library such that each column in the spreadsheet is sized to match the longest string present, rather than truncating at a fixed width as the Slurm commands do. Some of the useful options are mentioned below, but keep in mind you can only use this command for jobs you own. The same options work with ''ssstat'' too. A detailed list and explanation of options and column values results are explained in the man page,''man sstat''. ^ Option ^ Result ^ | ''-a'' <<//job_id_list//>> | Print all steps for the given job(s) when no step is specified | | ''-u'' <<//user_list//>> | Displays information for jobs associated with the specified user(s) | | ''-i'' | Predefined format to list the pids running for each job step. (JobId,Nodes,Pids) | | ''-p'' | output will be ''|'' delimited with a ''|'' at the end | | ''%%-%%-format'' | Customize output of sstat | <code base> [(it_css:traine)@login00 it_css]$ sstat -p --format=AveCPU,AvePages,AveRSS,AveVMSize,JobID -j 1354 25:02.000|0K|1.37M|5.93M|9.0| </code> ==== scontrol ==== ''scontrol'' is used for monitoring and modifying queued jobs, as well as holding and releasing jobs. One of its most powerful options is the ''scontrol show job'' option with the ''JobID''. Also, by default the per-job output has been limited to a name, submit/run time, and some state flags. Slurm maintains a far more extensive set of parameters for each job which can be viewed using the command ''scontrol''. For example, <code bash> [(it_css:traine)@login00 it_css]$ scontrol show job 1354 JobId=1354 JobName=A33_6_WF.qs UserId=traine(1111) GroupId=xxxx(10111) MCS_label=N/A Priority=2181 Nice=0 Account=thsu QOS=normal JobState=RUNNING Reason=None Dependency=(null) Requeue=0 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0 RunTime=05:04:27 TimeLimit=1-00:00:00 TimeMin=N/A SubmitTime=2018-08-14T09:56:15 EligibleTime=2018-08-14T09:56:15 StartTime=2018-08-14T09:56:16 EndTime=2018-08-15T09:56:16 Deadline=N/A PreemptTime=None SuspendTime=None SecsPreSuspend=0 LastSchedEval=2018-08-14T09:56:16 Partition=standard AllocNode:Sid=login01:19458 ReqNodeList=(null) ExcNodeList=(null) NodeList=r00n16 BatchHost=r00n16 NumNodes=1 NumCPUs=20 NumTasks=20 CPUs/Task=1 ReqB:S:C:T=0:0:*:* TRES=cpu=20,mem=60G,node=1,billing=49168 Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=* MinCPUsNode=1 MinMemoryCPU=3G MinTmpDiskNode=0 Features=(null) DelayBoot=00:00:00 Gres=(null) Reservation=(null) OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null) Command=/lustre/scratch/traine/AAd3F.qs WorkDir=/lustre/scratch/traine/ StdErr=/lustre/scratch/traine/ler/%x.o1354 StdIn=/dev/null StdOut=/lustre/scratch/traine/ler/%x.o1354 Power= </code> ==== sacct or ssacct ==== To check the information about a job from history (i.e. a job that has already completed), ''sacct'' can be used to fetch various details as long as you know the ''JobID''. The ''ssacct'' version is a UD IT version of ''sacct'' that provides output as an interactive spreadsheet using the curses display library such that each column in the spreadsheet is sized to match the longest string present, rather than truncating at a fixed width as the Slurm commands do. <code bash> [(it_css:traine)@login01 ~]$ sacct -j 10544 JobID JobName Partition Account AllocCPUS State ExitCode ------------ ---------- ---------- ---------- ---------- ---------- -------- 10544 Mg_FFS standard afwallace 10 PREEMPTED 0:0 10544.batch batch afwallace 10 CANCELLED 0:15 10544.extern extern afwallace 10 COMPLETED 0:0 </code> In the above example, it indcates the job was preempted from the standard partition. Remember jobs in the standard partition are preempted to make way for workgroup specific jobs. If we want to check how much time a job was given to run, we can use the ''--format'' option to display the ''TimeLimit'' for the ''JobID 10544''. <code bash> [(it_css:traine)@login01 ~]$ sacct -j 10544 --format=TimeLimit Timelimit ---------- 7-00:00:00 </code> From this we can see this job had 7 days to complete, the maximum time limit on Caviness, however because the job was running in the standard partition it was preempted after running 21 hours, 5 minutes and 10 seconds. Below is an example requesting additional information such as memory, number of nodes, list of nodes, etc. <code bash> [(it_css:traine)@login01 ~]$ sacct -j 10544 --format=user,jobid,jobname,partition,state,time,start,end,elapsed,MaxRss,MaxVMSize,nnodes,ncpus,nodelist abrarq 10544 Mg_FFS standard PREEMPTED 7-00:00:00 2018-10-29T19:23:54 2018-10-30T16:29:04 21:05:10 1 10 r00n25 10544.batch batch CANCELLED 2018-10-29T19:23:54 2018-10-30T16:29:05 21:05:11 219520K 182124K 1 10 r00n25 10544.extern extern COMPLETED 2018-10-29T19:23:54 2018-10-30T16:23:50 20:59:56 4K 107904K 1 10 r00n25 </code> Here is another example showing a job exited because enough memory was not specified for the job, so it indicates ''OUT_OF_ME+'' which means OUT OF MEMORY. <code bash> [traine@login00 ~]$ sacct -j 9176640 JobID JobName Partition Account AllocCPUS State ExitCode ------------ ---------- ---------- ---------- ---------- ---------- -------- 9176640 FVM standard zurakowski 1 OUT_OF_ME+ 0:125 9176640.bat+ batch zurakowski 1 OUT_OF_ME+ 0:125 9176640.ext+ extern zurakowski 1 COMPLETED 0:0 9176640.0 date zurakowski 1 COMPLETED 0:0 </code> Using ''ssacct -j 17035767'' instead is an example displaying the full text and clearly seeing ''OUT_OF_MEMORY'' as follows <code bash> ┌──────────────────────────────────────────────────────────────────────────────┐ │JobID │ JobName │ Partition │ Account │ AllocCPUS │ State │ │ │────────────────┼─────────┼───────────┼─────────┼───────────┼───────────────┼─│ │17035767 │ sbatch │ devel │ it_nss │ 1 │ OUT_OF_MEMORY │ │ │17035767.batch │ batch │ │ it_nss │ 1 │ OUT_OF_MEMORY │ │ │17035767.extern │ extern │ │ it_nss │ 1 │ COMPLETED │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │──────────────────────────────────────────────────────────────────────────────│ │ [Q]uit [P]rev/[N]ext page Page [L]eft/[R]ight [E]nd/[B]eginning of list│ └──────────────────────────────────────────────────────────────────────────────┘ </code> and pressing ''R'' to move right to see more, you see the following <code bash> ┌──────────────────────────────────────────────────────────────────────────────┐ │ │ JobName │ Partition │ Account │ AllocCPUS │ State │ ExitCode│ │────────┼─────────┼───────────┼─────────┼───────────┼───────────────┼─────────│ │ │ sbatch │ devel │ it_nss │ 1 │ OUT_OF_MEMORY │ 0:125 │ │.batch │ batch │ │ it_nss │ 1 │ OUT_OF_MEMORY │ 0:125 │ │.extern │ extern │ │ it_nss │ 1 │ COMPLETED │ 0:0 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │──────────────────────────────────────────────────────────────────────────────│ │ [Q]uit [P]rev/[N]ext page Page [L]eft/[R]ight [E]nd/[B]eginning of list│ └──────────────────────────────────────────────────────────────────────────────┘ </code> ===== Deleting a job ====== Use the **scancel** <<//job_id//>> command to remove pending and running jobs from the queue. For example, to delete job 28000 <code bash> scancel 28000 </code> ===== Available Resources ===== DARWIN utilizes a fair share policy implemented based on allocations and using the quality-of-service (QOS) concept of Slurm. These allocations are represented per-workgroup/per-partition limits via Slurm QOS facility. Each QOS has its own set of aggregate limits that apply to the workgroup involved with jobs. Each QOS is **usable only on those partitions that explicitly allow it.** Each allocation group (workgroup) allocation has access to certain [[abstract:darwin:runjobs:queues|partitions]] (CPU and/or GPU) and is [[abstract:darwin:runjobs:accounting|charged]] based on the compute node resources used against the allocation request. See [[abstract:darwin:runjobs:accounting|Job Accounting on DARWIN]] for complete details regarding available resources and usage. One can determine the nodes available in a particular partition by using the ''scontrol'' command. The command to check the nodes for the ''standard'' partition would look like this show ''Nodes=r1n[00-47]]'' which means nodes ''r1n00'', ''r1n01'', ... , ''r1n47'' are available in the ''standard'' partition. <code bash> $ scontrol show partition standard PartitionName=standard AllowGroups=ALL AllowAccounts=ALL AllowQos=wg-cpu-1001,wg-cpu-1002 AllocNodes=ALL Default=YES QoS=part-standard DefaultTime=00:30:00 DisableRootJobs=NO ExclusiveUser=NO GraceTime=0 Hidden=NO MaxNodes=UNLIMITED MaxTime=2-00:00:00 MinNodes=0 LLN=NO MaxCPUsPerNode=UNLIMITED Nodes=r1n[00-47] PriorityJobFactor=32768 PriorityTier=32768 RootOnly=NO ReqResv=NO OverSubscribe=NO OverTimeLimit=NONE PreemptMode=OFF State=UP TotalCPUs=3072 TotalNodes=48 SelectTypeParameters=NONE JobDefaults=(null) DefMemPerNode=UNLIMITED MaxMemPerNode=UNLIMITED TRESBillingWeights=cpu=1.0,mem=0.125G </code> Now to check the usable memory on each accessible node of a given //investing-entity// (workgroup), please use the [[abstract:darwin:runjobs:job_status#qhost|qhost]] command. ==== sworkgroup and sproject ==== One can use ''sworkgroup'' (UD IT customized utility) command to see the limits for the idle partition only. All other available resources for an allocation are tracked via the ''sproject'' command (UD IT customized utility). See [[abstract:darwin:runjobs:accounting|Job Accounting on DARWIN]] for complete details regarding available resources and usage for your allocation. <code bash> [(it_css:traine)@login01 ~]$ sworkgroup --help usage: sworkgroup [-h] [--workgroup group] [--limits] [--noheader] [--human-readable] [--parseable] Show Slurm partitions and limits for a workgroup optional arguments: -h, --help show this help message and exit --workgroup group, -g group display partitions available to a specific workgroup --limits, -l show TRES limits for each partition --noheader, -N do not display column headers on output --human-readable, -H show TRES in a more human-readable format --parseable show as parseable lines rather than a tabular format </code> <code bash> [(it_css:anita)@login01.darwin ~]$ sworkgroup -g it_css --limits Partition Per user Per job Per workgroup ---------+--------+-------+------------- idle cpu=640 [(it_css:anita)@login01.darwin ~]$ sworkgroup -g it_css --human-readable --limits Partition Per user Per job Per workgroup ---------+---------+-------+------------- idle 640 cores </code> ==== Host Status, Literally (sinfo or ssinfo) ==== Slurm also features a ''sinfo'' command that can be used to report status of all the nodes of cluster, period, no job information or information will be displayed. The ''ssinfo'' version is a UD IT version of ''sinfo'' that provides output as an interactive spreadsheet using the curses display library such that each column in the spreadsheet is sized to match the longest string present, rather than truncating at a fixed width as the Slurm commands do. The same options for ''sinfo'' work with ''sssinfo'' too. <code bash> [(it_css:traine)@login00.darwin ~]$ sinfo --long --Node Mon Apr 26 11:38:42 2021 NODELIST NODES PARTITION STATE CPUS S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON r1n00 1 standard* idle 64 2:32:1 499712 1800000 1 standard none r1n01 1 standard* idle 64 2:32:1 499712 1800000 1 standard none r1n02 1 standard* idle 64 2:32:1 499712 1800000 1 standard none . . . r1n46 1 standard* idle 64 2:32:1 499712 1800000 1 standard none r1n47 1 standard* idle 64 2:32:1 499712 1800000 1 standard none r1t00 1 gpu-t4 idle 64 2:32:1 491520 1800000 1000 nvidia-g none r1t01 1 gpu-t4 idle 64 2:32:1 491520 1800000 1000 nvidia-g none r1t02 1 gpu-t4 idle 64 2:32:1 491520 1800000 1000 nvidia-g none . . . r1t06 1 gpu-t4 idle 64 2:32:1 491520 1800000 1000 nvidia-g none r1t07 1 gpu-t4 idle 64 2:32:1 491520 1800000 1000 nvidia-g none r2e00 1 extended-mem idle 64 2:32:1 999424 1800000 100000 Optane-N none r2l00 1 large-mem idle 64 2:32:1 999424 1800000 10 large-me none r2l01 1 large-mem idle 64 2:32:1 999424 1800000 10 large-me none . . . r2l31 1 large-mem idle 64 2:32:1 999424 1800000 10 large-me none r2m00 1 gpu-mi50 idle 64 2:32:1 491520 1800000 100000 amd-gpu, none r2t08 1 gpu-t4 idle 64 2:32:1 491520 1800000 1000 nvidia-g none r2v00 1 gpu-v100 idle 48 2:24:1 737280 1800000 10000 nvidia-g none r2v01 1 gpu-v100 idle 48 2:24:1 737280 1800000 10000 nvidia-g none r2v02 1 gpu-v100 idle 48 2:24:1 737280 1800000 10000 nvidia-g none r2x00 1 xlarge-mem idle 64 2:32:1 203161 1800000 100 xlarge-m none r2x01 1 xlarge-mem idle 64 2:32:1 203161 1800000 100 xlarge-m none r2x02 1 xlarge-mem idle 64 2:32:1 203161 1800000 100 xlarge-m none . . . r2x09 1 xlarge-mem idle 64 2:32:1 203161 1800000 100 xlarge-m none r2x10 1 xlarge-mem idle 64 2:32:1 203161 1800000 100 xlarge-m none </code> The command has other options that will be discussed elsewhere; view the ''sinfo'' man page for a description of all options available. Memory refers to the size of memory for each node in MB.The column S:C:T refers to the extended processor information: number of sockets, cores, threads (S:C:T) per node, whereas TMP_DISK refers to the size of temporary disk space per node in megabytes. WEIGHT column refers to scheduling weight of the nodes. To fetch the information of all the nodes for a particular partition, use the ''-p'' argument followed the partition. Here is the output from ''ssinfo --long --Node -p large-mem'' to see the full text especially in the ''AVAIL_FEATURES'' column <code bash> ┌─────────────────────────────────────────────────────────────────────────┐ │Wed Apr 19 11:18:52 2023 │ │──────────────────────── │ │NODELIST │ NODES │ PARTITION │ STATE │ CPUS │ S:C:T │ │r2l00 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l01 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l02 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l03 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l04 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l05 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l06 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l07 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l08 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l09 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l10 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l11 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l12 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l13 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l14 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l15 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l16 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │r2l17 │ 1 │ large-mem │ allocated │ 64 │ 2:32:1 │ │─────────────────────────────────────────────────────────────────────────│ │ [Q]uit [P]rev/[N]ext page Page [L]eft/[R]ight [E]nd/[B]eginning of│ └─────────────────────────────────────────────────────────────────────────┘ </code> and pressing ''R'' to move right to see more, you see the following <code bash> ┌─────────────────────────────────────────────────────────────────────────┐ │ │ │ │ │ S:C:T │ MEMORY │ TMP_DISK │ WEIGHT │ AVAIL_FEATURES │ REASON│ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │ 2:32:1 │ 999424 │ 1800000 │ 10 │ large-memory,1024GiB,1TiB │ none │ │─────────────────────────────────────────────────────────────────────────│ │ [Q]uit [P]rev/[N]ext page Page [L]eft/[R]ight [E]nd/[B]eginning of│ └─────────────────────────────────────────────────────────────────────────┘ </code> ===== UD IT Status Commands ===== UD IT has created additional status summary commands that build on the ''squeue'' and ''sacct'' commands provided by Slurm. In most cases these commands are conveniences that fill-in some of the options that were summarized above for the user. All commands display a terse summary of their options if the ''-h'' or ''--help'' option is provided with the command. <note warning>These commands are not part of the Slurm job scheduling software. They are made available on clusters maintained by UD IT that use the Slurm job scheduler and are not likely to be available on other clusters to which a user has access.</note> ==== sjobs ==== The ''sjobs'' command displays job status in a more compact format: <code bash> [traine@login01 ~]$ sjobs -h usage: sjobs [-h] [-a] [-G] [-g <workgroup>] [-u <username>] [-t] [-H] [--parseable] [-d <string>] Display information for running and queued jobs optional arguments: -h, --help show this help message and exit job selection options: -a, --all show all users (not just yourself) -G, --current-group show jobs for users in your current workgroup -g <workgroup>, --group <workgroup> show jobs for users in the given workgroup (can be used multiple times) -u <username>, --user <username> show jobs for the given user (can be used multiple times) output options: -t, --totals show total jobs, users, groups, cpus, nodes, and tasks -H, --no-header do not show column headers --parseable do not display in a tabular format -d <string>, --delimiter <string> when --parseable is selected, separate columns with this string If no job selection options are provided then jobs for the current user will be displayed. </code> <code bash> [(it_css:traine)@login01.darwin ~]$ sjobs JOBID USER STATE JOBNAME GROUP NCPUS NNODES NTASKS ----- -------- ------- ---------- ------ ----- ------ ------ 1904 traine RUNNING arrayJob it_css 1 1 1 1903 traine RUNNING openmp_job it_css 8 1 1 </code> By default, only jobs owned by the user issuing the command are displayed. The ''-g'' option followed by the group name displays jobs for users who are members of that specific group: <code bash> [traine@login01.darwin ~]$ sjobs -g arce JOBID USER STATE JOBNAME GROUP NCPUS NNODES NTASKS --------- ----- ------- ---------- ----- ----- ------ ------ 771536_6 xmdrm RUNNING STAC_train arce 4 1 1 771536_8 xmdrm RUNNING STAC_train arce 4 1 1 771536_9 xmdrm RUNNING STAC_train arce 4 1 1 771536_10 xmdrm RUNNING STAC_train arce 4 1 1 </code> The ''-a'' option displays jobs for all cluster users. ==== qhost ==== ''qhost'' is a wrapper written for DARWIN to consolidate the information collected from Slurm commands and joined together to display the host/node information in a similar fashion to that of ''qhost'' on Farber. <code bash> [traine@login01 ~]$ qhost --help usage: qhost [-help] [-h <hostlist>] [-ncb] [-j] [-u <username>] [--help] [--hosts <hostlist>] [--jobs] [--users <userlist>] [--no-node-sort] [--std-host-topo] Display host information akin to Grid Engine qhost original options: options inherited from Grid Engine qhost -help print this help -h <hostlist> display only selected hosts -ncb suppress host topology based information -j display jobs running on the host(s) -u <username> show only jobs for user extended options: additional options not present in Grid Engine qhost --help alternate to -help --hosts <hostlist> alternate to -h --jobs alternate to -j --users <userlist> alternate to -u --no-node-sort, -S do not sort the list of nodes by name before displaying --std-host-topo, -T show host topology as sockets, cores-per-socket, and threads-per-core A <hostlist> is one or more node names or name patterns (e.g. r00n[00-24]) separated by commas. A <userlist> is one or more user names separated by commas </code> The following example shows the specifications for node ''r1n03'' and this is helpful to understand that the actual **usable** memory on ''r1n03'' is 480G versus the physical memory which is 488G. This is important when specifying the amount of memory as a option especially when using a workgroup partition. See details about managing jobs using command options for sbatch: [[abstract:darwin:runjobs:schedule_jobs#memory | Memory ]] <code bash> [(it_css:traine)@login01.darwin ~]$ qhost -h r1n03 HOSTNAME ARCH NCPU NSOC NCOR NTHR NLOAD MEMTOT MEMUSE SWAPTO SWAPUS ---------------------------------------------------------------------------------------------- r1n03 standard 64 2 64 64 0.63 488.0G 480.0G 0.0 0.0 </code> Adding option ''-j'' will now show the jobs running on node ''r1n03'' in this example. <code bash> [(it_css:traine)@login01.darwin ~]$ qhost -h r1n03 -j HOSTNAME ARCH NCPU NSOC NCOR NTHR NLOAD MEMTOT MEMUSE SWAPTO SWAPUS ---------------------------------------------------------------------------------------------- r1n03 standard 64 2 64 64 0.63 488.0G 480.0G 0.0 0.0 job-ID prior name user state submit/start at queue master ja-task-ID ----------------------------------------------------------------------------------------------------------------- 771529 176093110 conf msafrono R 2021-09-28T16:00:57 idle SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE 771455 17179808 27476_SAPT allinson R 2021-09-28T06:52:57 idle MASTER SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE SLAVE </code> ==== qstatgrp ==== ''qstatgrp'' makes use of the Slurm commands ''squeue'' and ''sacctmgr'' to display the current utilization of resources within a workgroup. Using the ''-h'' or ''--help'' argument will display the list of operations and options that can be used with qstatgrp. <code bash> [(it_css:traine)@login00 ~]$ qstatgrp --help usage: qstatgrp [-h] [-g <gid>] [-o] [-j] Display per-workgroup job information akin to Grid Engine qstatgrp optional arguments: -h, --help show this help message and exit -g <gid>, --group <gid> restrict to jobs running under the given workgroup (can be specified multiple times) -o, --group-only display for the workgroup partition only -j, --jobs show all jobs, not an aggregate summary of them </code> With no options specified ''qstatgrp'' will list a summary of current utilization of resources for the current workgroup. To see the current utilization for a particular workgroup use the ''-g '' option. <code bash> [(it_css:traine)@login01.darwin ~]$ qstatgrp -g jayaraman_lab PARTITION NODES CPUS MAX MEM MAX CPUS ------------------------------------------------------------------------ idle 20 650 - TOTAL 20 650 </code> And to see the individual jobs and resources being used for the default workgroup, use the ''-j'' option or add the workgroup to see for a particular workgroup. <code bash> [(it_css:traine)@login01.darwin ~]$ qstatgrp -g jayaraman_lab -j PARTITION JOBID OWNER PRIORITY STATE NODES CPUS MEM GRES -------------------------------------------------------------------------------------------------------------------------------------- idle 771468 heil 64424266 PD 1 1 1G N/A idle 771414 heil 64424266 PD 1 1 1G N/A idle 771412 heil 64424266 PD 1 1 1G N/A idle 771134 heil 64424266 PD 1 1 1G N/A idle 771127 heil 64424266 PD 1 1 1G N/A idle 771123 heil 64424266 PD 1 1 1G N/A idle 771116 heil 64424266 PD 1 1 1G N/A idle 771059 heil 64424266 PD 1 1 1G N/A idle 771051 heil 64424266 PD 1 1 1G N/A idle 770960 heil 64424266 PD 1 1 1G N/A idle 771467 heil 64424272 R 1 64 3G N/A idle 771413 heil 42949518 R 1 64 3G N/A idle 771411 heil 42949518 R 1 64 3G N/A idle 771133 heil 42949518 R 1 64 3G N/A idle 771126 heil 42949518 R 1 64 3G N/A idle 771122 heil 42949518 R 1 64 3G N/A idle 771115 heil 42949518 R 1 64 3G N/A idle 771058 heil 38654567 R 1 64 3G N/A idle 771050 heil 38654567 R 1 64 3G N/A idle 770959 heil 64424272 R 1 64 3G N/A </code> ==== spreempted ==== Due to a certain level of inconsistency in Slurm's error logging, preempted jobs are notified as ''FAILED'' due to improper handling of SIGCONT/SIGTERM signals which leads to default behavior of SIGTERM that makes jobs to immediately exit rather than waiting for a grace period of 5 minutes (technically should happen when job is preempted). Therefore to really determine if a job has been preempted or not, UD IT has developed a command which tests various conditions and concludes on preemption. Also please note that, preemption occurs only to the jobs are being submitted to the ''idle'' partition. <code bash> [traine@login01.darwin ~]$ spreempted -h usage: spreempted [-h] [--verbose] [--quiet] [--show-jobid] [--sort-properties] [--jobid <job-id>{,<job-id>..}] Determine if jobs were preempted optional arguments: -h, --help show this help message and exit --verbose, -v Emit additional information --quiet, -q Do not summarize preemptions, just return non-zero result code if any were preempted --show-jobid, -s Always prefix output lines with job id --sort-properties For verbose output, show properties in alphabetized order --jobid <job-id>{,<job-id>..}, -j <job-id>{,<job-id>..} Slurm job id to check; can be used multiple times to check more than one job. For array jobs, use the syntax #_# for individual array indices </code> <code bash> [traine@login01.darwin ~]$ spreempted -j 410289 preempted, did not reach grace period limit </code> abstract/darwin/runjobs/job_status.txt Last modified: 2023-04-19 11:46by anita