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. At ILRI our SLURM is configured with two main job queues (also called "partitions" in SLURM):

• batch
• highmem

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 -n 4

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

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