SLURM is a resource manager and job scheduler for high-performance computing clusters. We use a job scheduler to ensure fair usage of the research-computing resources by all users, with hopes that no one user can monopolize the computing resources. Users who wish to use the cluster must "request" CPU time and possibly "queue" for resources.

Our SLURM is configured with the following job queues (also called "partitions" in SLURM):

• debug
• batch
• highmem

"debug" is the default queue, which is useful for testing job parameters, program paths, etc. The runtime limit of the "debug" partition is 5 minutes, after which jobs are killed.

To see more information about the queue configuration, use sinfo -lNe.

How to get an interactive session, ie when you want to interact with a program (like R, etc):

[aorth@hpc: ~]$ interactive 
salloc: Granted job allocation 1080
[aorth@taurus: ~]$

Request 4 CPUs for a NCBI BLAST+ job in the batch partition. Create a file blast.sbatch:

#!/bin/bash
#SBATCH -p batch
#SBATCH -J blastn
#SBATCH -n 4

export BLASTDB=/export/data/bio/ncbi/blast/db

module load blast/2.2.28+

blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4

Submit the script with sbatch:

$ sbatch blastn_test.sh 
Submitted batch job 1082

squeue