Quest and Kellogg Linux Cluster Downtime, June 8th-14th, 2024.
Quest, including the Quest Analytics Nodes, the Genomics Compute Cluster (GCC), the Kellogg Linux Cluster (KLC), and Quest OnDemand, will be unavailable for scheduled maintenance starting at 7 A.M. on Saturday, June 8, and ending approximately at 5 P.M. on Friday, June 14. During the maintenance window, you will not be able to login to Quest, Quest Analytics Nodes, the GCC, KLC, or Quest OnDemand submit new jobs, run jobs, or access files stored on Quest in any way including Globus. For details on this maintenance, please see the Status of University IT Services page.
For more detailed information, see Slurm sbatch documentation.
Job Submission Options
| Option |
Slurm (sbatch) |
| Script directive |
#SBATCH |
| Job name |
--job-name=<name>
-J <name> |
| Account |
--account=<account>
-A <account> |
| Queue |
--partition=<queue> |
| Wall time limit |
--time=<hh:mm:ss>
-t<hh:mm:ss> |
| Node count |
--nodes=<count>
-N <count> |
| Core count |
-n <count> |
| Process count per node |
--ntasks-per-node=<count> |
| Core count (per process) |
--cpus-per-task=<cores> |
| Memory limit |
--mem=<limit> (Memory per node in MB) |
| Minimum memory per processor |
--mem-per-cpu=<memory> |
| Request GPUs |
--gres=gpu:<count> |
| Request specific nodes |
-w, --nodelist=<node>[,node2[,...]]>
-F, --nodefile=<node file> |
| Job array |
-a <array indices> |
| Standard output file |
--output=<file path> (path must exist) |
| Standard error file |
--error=<file path> (path must exist) |
| Combine stdout/stderr to stdout |
--output=<combined out and err file path> |
| Architecture constraint |
--constraint=<architecture>
-C <architecture> |
| Copy environment |
--export=ALL (default)
--export=NONE to not export environment |
| Copy environment variable |
--export=<variable[=value][,variable2=value2[,...]]> |
| Job dependency |
--dependency=after:jobID[:jobID...]
--dependency=afterok:jobID[:jobID...]
--dependency=afternotok:jobID[:jobID...]
--dependency=afterany:jobID[:jobID...] |
| Request event notification |
--mail-type=<events>
Note: multiple mail-type requests may be specified in a comma separated list:
--mail-type=BEGIN,END,FAIL |
| Email address |
--mail-user=<email address> |
| Defer job until the specified time |
--begin=<date/time> |
| Node exclusive job |
--exclusive |
Common Job Commands
| Option |
Slurm (sbatch) |
| Submit a job |
sbatch <job script> |
| Delete a job |
scancel <job ID> |
| Job status (all) |
squeue |
| Job status (by job) |
squeue -j <job ID> |
| Job status (by user) |
squeue -u <netID> |
| Job status (detailed) |
scontrol show job -dd <job ID>
checkjob <job ID> |
| Show expected start time |
squeue -j <job ID> --start |
| Queue list / info |
scontrol show partition [queue] |
| Hold a job |
scontrol hold <job ID> |
| Release a job |
scontrol release <job ID> |
| Start an interactive job |
salloc <args>
srun --pty <args> |
| X forwarding |
srun --pty <args> --x11 |
| Monitor or review a job's resource usage |
sacct -j <job_num> --format JobID,jobname,NTasks,nodelist,CPUTime,ReqMem,Elapsed
(see sacct for all format options) |
| View job batch script |
scontrol write batch_script <jobID> [filename] |
Script Variables
| Info |
Slurm |
Notes |
| Version |
– |
Can extract from sbatch --version |
| Job name |
$SLURM_JOB_NAME |
|
| Job ID |
$SLURM_JOB_ID |
|
| Submit directory |
$SLURM_SUBMIT_DIR |
Slurm jobs starts from the submit directory by default |
| Node list |
$SLURM_JOB_NODELIST |
The Slurm variable has a different format to the PBS one.
To get a list of nodes use:
scontrol show hostnames $SLURM_JOB_NODELIST |
| Job array index |
$SLURM_ARRAY_TASK_ID |
|
| Queue name |
$SLURM_JOB_PARTITION |
|
| Number of nodes allocated |
$SLURM_JOB_NUM_NODES
$SLURM_NNODES |
|
| Number of processes |
$SLURM_NTASKS |
|
| Number of processes per node |
$SLURM_TASKS_PER_NODE |
|
| Requested tasks per node |
$SLURM_NTASKS_PER_NODE |
|
| Requested CPUs per task |
$SLURM_CPUS_PER_TASK |
|
| Scheduling priority |
$SLURM_PRIO_PROCESS |
|
| Job user |
$SLURM_JOB_USER |
|
| Hostname |
$HOSTNAME == $SLURM_SUBMIT_HOST |
Unless a shell is invoked on an allocated resource, the $HOSTNAME variable is propagated (copied) from the submit machine environment to all allocated nodes. |