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using-slurm [2013/12/02 14:21] – aorthusing-slurm [2016/03/08 08:42] – [Receive mail notifications] joguya
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 [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.
 ==== 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>#!/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/2.2.30+
  
 # 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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 # 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 [[http://alanorth.github.io/hpc-users-group3/#/2|HPC Users Group #3]] for more info.
  
 ==== Check queue status ==== ==== Check queue status ====
 <code>squeue</code> <code>squeue</code>
 +
 +==== Receive mail notifications ====
 +To receive mail notifications about the state of your job, add the following lines to your sbatch script: whereby <EMAIL_ADDRESS> is your email address<code>
 +#SBATCH --mail-user <EMAIL_ADDRESS>
 +#SBATCH --mail-type ALL</code>
 +
 +Notification mail types(--mail-type) can be BEGIN, END, FAIL, REQUEUE and ALL(any state change).
 +
 +Example:
 +<code>
 +#SBATCH --mail-user J.Doe@cgiar.org
 +#SBATCH --mail-type ALL</code>
 +
using-slurm.txt · Last modified: 2022/11/03 11:38 by jean-baka