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using-slurm [2013/12/02 14:21] – aorthusing-slurm [2019/02/01 12:20] – [Check queue status] jean-baka
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 salloc: Granted job allocation 1080 salloc: Granted job allocation 1080
 [aorth@taurus: ~]$</code> [aorth@taurus: ~]$</code>
 +
 +**NB:** interactive jobs have a time limit of 8 hours: if you need more, then you should write a batch script.
 +
 +You can also open an interactive session on a specific node of the cluster by specifying it through the ''-w'' commandline argument:
 +<code>[jbaka@hpc ~]$ interactive -w compute03
 +salloc: Granted job allocation 16349
 +[jbaka@compute03 ~]$</code>
  
 ==== Batch jobs ==== ==== Batch jobs ====
 Request 4 CPUs for a NCBI BLAST+ job in the ''batch'' partition.  Create a file //blast.sbatch//: Request 4 CPUs for a NCBI BLAST+ job in the ''batch'' partition.  Create a file //blast.sbatch//:
-<code>#!/bin/bash+<code>#!/usr/bin/env bash
 #SBATCH -p batch #SBATCH -p batch
 #SBATCH -J blastn #SBATCH -J blastn
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 # load the blast module # load the blast module
-module load blast/2.2.28++module load blast/2.6.0+
  
 # run the blast with 4 CPU threads (cores) # run the blast with 4 CPU threads (cores)
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 Submit the script with ''sbatch'': Submit the script with ''sbatch'':
-<code>$ sbatch blastn_test.sh +<code>$ sbatch blast.sbatch 
 Submitted batch job 1082</code> Submitted batch job 1082</code>
  
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 Instead, you can use a local "scratch" folder on the compute nodes to alleviate this burden, for example: Instead, you can use a local "scratch" folder on the compute nodes to alleviate this burden, for example:
  
-<code>#!/bin/env bash+<code>#!/usr/bin/env bash
 #SBATCH -p batch #SBATCH -p batch
 #SBATCH -n 4 #SBATCH -n 4
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 # load the blast module # load the blast module
-module load blast/2.2.28++module load blast/2.2.30+
  
-WORKDIR=/var/scratch/$SLURM_JOBID+WORKDIR=/var/scratch/$USER/$SLURM_JOBID
 mkdir -p $WORKDIR mkdir -p $WORKDIR
  
 echo "Using $WORKDIR on $SLURMD_NODENAME" echo "Using $WORKDIR on $SLURMD_NODENAME"
 echo echo
 +
 +# change to working directory on compute node
 +cd $WORKDIR
  
 # run the blast with 4 CPU threads (cores) # run the blast with 4 CPU threads (cores)
-blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4 -out $WORKDIR/output</code>+blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4 -out blast.out</code>
  
-All output is directed to ''$WORKDIR/'', which is the temporary folder on the compute node.  See these slides from [[http://alanorth.github.io/hpc-users-group3/#/2|HPC Users Group #3]] for more info.+All output is directed to ''$WORKDIR/'', which is the temporary folder on the compute node. See these slides from [[https://alanorth.github.io/hpc-users-group3/#/2|HPC Users Group #3]] for more info.
  
 ==== Check queue status ==== ==== Check queue status ====
-<code>squeue</code>+''squeue'' is the command to use to get more information about the different jobs that are running on the cluster, waiting in a queue for resources to become available, or halted for some reason: 
 +<code>[jbaka@compute03 ~]$ squeue 
 +             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON) 
 +             16330     batch interact  pyumbya  R    6:33:26      1 taurus 
 +             16339     batch interact ckeambou  R    5:19:07      1 compute04 
 +             16340     batch interact ckeambou  R    5:12:52      1 compute04 
 +             16346     batch velvet_o  dkiambi  R    1:39:09      1 compute04 
 +             16348     batch interact fkibegwa  R      22:38      1 taurus 
 +             16349     batch interact    jbaka  R       3:27      1 compute03 
 +</code>
using-slurm.txt · Last modified: 2022/11/03 11:38 by jean-baka