Tmp

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Pending or Running Jobs

The easiest way to monitor pending or running jobs is with the Slurm squeue command. Like most Slurm commands, you are able to control the columns displayed in the output of this command (see man squeue for more information). To save you that trouble and to make things more convenient, we've created the sq command, which is squeue but pre-formatted and with some additional options for convenience. The key thing to remember about squeue/sq is that without any options, it shows ALL currently running and pending jobs on the cluster. In order to show only your currently running and pending jobs, you will want to use the --me option.

The default squeue columns are as follows: 

JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

Using sq runs the squeue command but provides the following columns: 

JOBID      TIME            TIME_LIMIT      NAME            PARTITION        USER       NODES  CPUS   MIN_MEMORY   PRIORITY   STATE      NODELIST(REASON)

As you can see, you're able to get much more useful information with sq than with just the default squeue formatting.


Output Columns Explained

  • JOBID: The unique ID of the job.
  • TIME: How much (wall) time has elapsed since the job started, in the format DAYS-HOURS:MINUTES:SECONDS
  • TIME_LIMIT: The maximum time given for the job to run, in the format DAYS-HOURS:MINUTES:SECONDS.
  • NAME: The name of the job. If not specified in one's submission script, it will default to the name of the submission script (e.g. "sub.sh").
  • PARTITION: The partition to which the job was sent (e.g. batch, highmem_p, gpu_p, etc...).
  • USER: The user who submitted the job.
  • NODES: The number of nodes allocated to the job.
  • CPUS: The number of CPU cores allocated to the job.
  • MIN_MEMORY: The amount of memory allocated to the job.
  • PRIORITY: The job's priority per Slurm's Multifactor Priority Plugin
  • STATE: The job's state (e.g. Running, Pending, etc...)
  • NODELIST(REASON): The name of the node(s) on which the job is running or the reason the job has not started yet, if it is pending.


sq also has a -h/--help option: 

bc06026@ss-sub3 ~$ sq --help

Usage: sq [OPTIONS]

Descriptions: sq - preformatted wrapper for squeue.  See man squeue for more information.

    --me                        Displays squeue output for the user executing this command
    -p                          Displays squeue output for a given partition
    -u                          Displays squeue output for a given user
    -T                          Displays submit and start time columns
    -h, --help                  Displays this help output


Examples

  • See all pending and running jobs: sq
  • See all of your pending and running jobs: sq --me
  • See all pending and running jobs in the highmem_p: sq -p highmem_p
  • See all of your pending and running jobs in the batch partition: sq --me -p batch
  • See all of your pending and running jobs including submit time and start time columns: sq --me -T (Note, this will require a wide monitor or small font to display without columns wrapping around)


Example sq output: 

bc06026@ss-sub3 ~$ sq
JOBID      TIME            TIME_LIMIT      NAME            PARTITION        USER       NODES  CPUS   MIN_MEMORY   PRIORITY   STATE      NODELIST(REASON)    
4581410    2:10:56         10:00:00        Bowtie2-test    batch            zp21982    1      1      12G          6003       RUNNING    c5-4               
4584815    1:51:03         2:00:00         test-job        highmem_p        rt12352    1      12     300G         5473       RUNNING    d3-9               
4578428    4:57:15         1-2:00:00       PR6_Cd3         batch            un12354    1      1      40G          5449       RUNNING    c4-16               
4583491    1:57:38         12:00:00        interact        inter_p          ai38821    1      4      2G           5428       RUNNING    d5-21               
4580374    2:54:41         12:00:00        BLAST           batch            gh98762    1      1      10G          5397       RUNNING    b1-9

...

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Previously Ran Jobs

The easiest way to monitor previously ran jobs is with the Slurm sacct command. Like most Slurm commands, you are able to control the columns displayed in the output of this command (see man sacct for more information). To save you that trouble and to make things more convenient, we've created the sacct-gacrc command, which is sacct but pre-formatted and with some additional options for convenience. A big difference between squeue/sq and sacct/sacct-gacrc is that by default, sacct/sacct-gacrc without any options only shows you YOUR Jobs.

The default sacct columns are as follows: 

JobID    JobName  Partition    Account  AllocCPUS      State ExitCode

Using sacct-gacrc runs the sacct command but provides the following columns: 

JobID         JobName      User  Partition NNode NCPUS   ReqMem    CPUTime    Elapsed  Timelimit      State ExitCode   NodeList

As you can see, you're able to get much more useful information with sacct-gacrc than with just the default sacct formatting.


Output Columns Explained

  • JobID: The unique ID of the job.
  • JobName: The name of the job. If not specified in one's submission script, it will default to the name of the submission script (e.g. "sub.sh").
  • User: The user who submitted the job.
  • Partition: The partition to which the job was sent (e.g. batch, highmem_p, gpu_p, etc...).
  • NNode: The number of nodes allocated to the job.
  • NCPUS: The number of CPU cores allocated to the job.
  • ReqMem: The amount of memory allocated to the job.
  • Elapsed: How much (wall) time has elapsed since the job started, in the format DAYS-HOURS:MINUTES:SECONDS
  • Timelimit: The maximum time given for the job to run, in the format DAYS-HOURS:MINUTES:SECONDS.
  • State: The job's state (e.g. Running, Pending, etc...).
  • ExitCode: The job's exit code.
  • Nodelist: The name of the node(s) on which the job is running or ran.


sacct-gacrc also has a -h/--help option: 

bc06026@ss-sub3 ~$ sacct-gacrc --help

Usage: sacct-gacrc [OPTIONS]

Description: preformatted wrapper for sacct.  See man sacct for more information. 

    -E, --endtime               Display information about jobs up to a date, in the format of yyyy-mm-dd (default: now)
    -j, --jobs                  Display information about a particular job or jobs
    -r, --partition             Display information about jobs from a particular partition
    -S, --starttime             Display information about jobs starting from a date in the format of yyyy-mm-dd (default: Midnight of today)
    -u, --user                  Display information about a particular user's job(s) (default: current user)
    -X, --allocations           Only show one line per job (do not display job steps)
    --debug                     Display the sacct command being executed
    -h, --help                  Display this help output


Examples

  • See information about all of your jobs that started from midnight up to now: sacct-gacrc
  • See information about a particular job: sacct-gacrc -j JOBID (replacing JOBID with a particular job ID)
  • See information about all of your jobs that started from midnight up to now in the highmem_p: sacct-gacrc -r highmem_p
  • See information about your jobs that from a particular date up to now: sacct-gacrc -S YYYY-MM-DD (replacing YYYY-MM-DD with a date, e.g. 2021-09-01)


Example sq output: 

bc06026@ss-sub3 ~$ sq
JOBID      TIME            TIME_LIMIT      NAME            PARTITION        USER       NODES  CPUS   MIN_MEMORY   PRIORITY   STATE      NODELIST(REASON)    
4581410    2:10:56         10:00:00        Bowtie2-test    batch            zp21982    1      1      12G          6003       RUNNING    c5-4               
4584815    1:51:03         2:00:00         test-job        highmem_p        rt12352    1      12     300G         5473       RUNNING    d3-9               
4578428    4:57:15         1-2:00:00       PR6_Cd3         batch            un12354    1      1      40G          5449       RUNNING    c4-16               
4583491    1:57:38         12:00:00        interact        inter_p          ai38821    1      4      2G           5428       RUNNING    d5-21               
4580374    2:54:41         12:00:00        BLAST           batch            gh98762    1      1      10G          5397       RUNNING    b1-9

...

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