Tmp
Pending or Running Jobs
squeue and sq
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 NAME PARTITION USER NODES CPUS MIN_MEMORY PRIORITY TIME TIME_LIMIT 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.
- 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
- 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.
- 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.
-j Displays squeue output for a given job
--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 NAME PARTITION USER NODES CPUS MIN_MEMORY PRIORITY TIME TIME_LIMIT STATE NODELIST(REASON) 4581410 Bowtie2-test batch zp21982 1 1 12G 6003 2:10:56 10:00:00 RUNNING c5-4 4584815 test-job highmem_p rt12352 1 12 300G 5473 1:51:03 2:00:00 RUNNING d3-9 4578428 PR6_Cd3 batch un12354 1 1 40G 5449 4:57:15 1-2:00:00 RUNNING c4-16 4583491 interact inter_p ai38821 1 4 2G 5428 1:57:38 12:00:00 RUNNING d5-21 4580374 BLAST batch gh98762 1 1 10G 5397 2:54:41 12:00:00 RUNNING b1-9 ...
scontrol show job
insert info/examples here
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. Another important note about sacct/sacct-gacrc is that by default it will display Slurm job steps. Unless you're dividing your job into steps with srun, you probably will want sacct/sacct-gacrc to display one line per job (hide job steps, only show job allocation). To do this, use the -X option. For more information on Slurm job allocation, please see the Slurm documentation.
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 (comma-separated list if more than one job)
-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 sacct-gacrc output:
bc06026@b1-24 ~$ sacct-gacrc -X -S 2021-09-14
JobID JobName User Partition NodeList AllocNodes NTask NCPUS ReqMem MaxVMSize State CPUTime Elapsed Timelimit ExitCode
------------ ---------- --------- ---------- ---------- ---------- ----- ----- ------- ---------- ---------- ---------- ---------- ---------- --------
4580375 interact bc06026 highmem_p ra4-22 1 1 200Gn FAILED 00:00:07 00:00:07 12:00:00 1:0
4580382 interact bc06026 highmem_p d1-22 1 28 200Gn COMPLETED 00:03:16 00:00:07 12:00:00 0:0
4584992 interact bc06026 inter_p c4-16 1 1 2Gn COMPLETED 00:00:18 00:00:18 12:00:00 0:0
...