Difference between revisions of "General/Slurm"
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Revision as of 16:17, 2 February 2017
Contents
Application Details
- Version: 15.08.8
- Further information: https://slurm.schedmd.com/
- Slurm Rosetta (Useful for converting submission scripts from other formats)
Introduction
The SLURM (Simple Linux Utility for Resource Management workload manager is a free and open-source job scheduler for the Linux kernel. It is used by Viper and many of the world's supercomputers (and clusters).
Common Slurm Commands
| Command | Description |
| sbatch | Submits a batch script to SLURM. The batch script may be given to sbatch through a file name on the command line, or if no file name is specified, sbatch will read in a script from standard input. |
| squeue | Used to view job and job step information for jobs managed by SLURM. |
| scancel | Used to signal or cancel jobs, job arrays or job steps. |
| sinfo | Used to view partition and node information for a system running SLURM. |
sbatch
[username@login01 ~]$ sbatch jobfile.job Submitted batch job 289535
squeue
squeue shows information about jobs in the scheduling queue
[username@login01 ~]$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
306414 compute clasDFT 495711 R 16:36 1 c006
306413 compute mpi_benc 535286 R 31:02 2 c[005,007]
306411 compute orca_1n 442104 R 1:00:32 1 c004
306410 compute orca_1n 442104 R 1:04:17 1 c003
306409 highmem cnv_obit 524274 R 11:37:17 1 c232
306407 compute 20M4_20 535822 R 11:45:54 1 c012
306406 compute 20_ML_20 535822 R 11:55:40 1 c012
scancel
Note: No output is given by the command.
[username@login01 ~]$ scancel 289535
sinfo
[username@login01 ~]$ sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST compute* up 2-00:00:00 9 mix c[006,012,014,016,018-020,022,170] compute* up 2-00:00:00 11 alloc c[003-004,008,015,046,086,093,098,138,167-168] compute* up 2-00:00:00 156 idle c[001-002,005,007,009-011,013,017,021,023-045,047-085,087-092,094-097,099-137,139-166,169,171-176] highmem up 4-00:00:00 1 mix c230 highmem up 4-00:00:00 2 alloc c[231-232] highmem up 4-00:00:00 1 idle c233 gpu up 5-00:00:00 4 idle gpu[01-04]
Common Submission Flags
| Flag | Description |
| -J / --job-name | Specify a name for the job |
| -N / --nodes | Specifies the number of nodes to be allocated to a job |
| -n / --ntasks | Specifies the allocation of resources e.g. for 1 Compute Node the maximum would be 28 |
| -o / --output | Specifies the name of the output file |
| -e / --error | Specifies the name of the error file |
| -p / --partition | Specifies the specific partition for the job e.g. compute, highmem, gpu |
| --exclusive | Requests exclusive access to nodes preventing other jobs from running |
Example Job Submission Script
#!/bin/bash #SBATCH -J Example_Slurm_Job #SBATCH -N 1 #SBATCH -n 28 #SBATCH -o %N.%j.%a.out #SBATCH -e %N.%j.%a.err #SBATCH -p compute #SBATCH --exclusive echo $SLURM_JOB_NODELIST module purge module load gcc/4.9.3 export I_MPI_DEBUG=5 export I_MPI_FABRICS=shm:tmi export I_MPI_FALLBACK=no /home/user/slurmexample