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--- usingslurm [2013/05/27 15:17] – [Using SLURM] aorth
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-====== Using SLURM ======
-[[http://slurm.schedmd.com/|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 the following job queues (also called "partitions" in SLURM):
-  * test
-  * batch
-  * highmem
-"test" is the default queue, which is useful for testing job parameters, program paths, etc. The runtime limite of the "test" partition is 5 minutes, after which jobs are killed.
-To see more information about the queue configuration, use ''sinfo -lNe''.
-===== Submitting jobs =====
-==== Interactive jobs ====
-How to get an interactive session, ie when you want to interact with a program (like R, etc):
-<code>[aorth@hpc: ~]$ interactive
-salloc: Granted job allocation 1080
-[aorth@taurus: ~]$</code>
-==== Batch jobs ====
-Request 4 CPUs for a NCBI BLAST+ job in the ''batch'' partition.  Create a file //blast.sbatch//:
-<code>#!/bin/bash
-#SBATCH -p batch
-#SBATCH -n 4
-export BLASTDB=/export/data/bio/ncbi/blast/db
-blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4</code>
-Submit the script with ''sbatch'':
-<code>$ sbatch blastn_test.sh
-Submitted batch job 1082</code>
-==== Check SLURM queue ====
-<code>squeue</code>