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using-slurm

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using-slurm [2015/03/26 10:16] – aorthusing-slurm [2017/06/07 06:28] – aorth
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 ==== 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/env 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/2.2.30++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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 ==== 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