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using-slurm [2022/08/04 12:10] – aorthusing-slurm [2022/11/03 11:38] (current) – jean-baka
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 ==== Batch jobs ==== ==== Batch jobs ====
 We are writing a SLURM script below. The parameters in its header request 4 CPUs for in the ''batch'' partition, and name our job "blastn". This name is only used internally by SLURM for reporting purposes. So let's go ahead and ceate a file //blast.sbatch//: We are writing a SLURM script below. The parameters in its header request 4 CPUs for in the ''batch'' partition, and name our job "blastn". This name is only used internally by SLURM for reporting purposes. So let's go ahead and ceate a file //blast.sbatch//:
-<code>#!/usr/bin/bash -l # <--- DO NOT FORGET '-l', it enables the module command+<code>#!/usr/bin/bash -l
 #SBATCH -p batch #SBATCH -p batch
 #SBATCH -J blastn #SBATCH -J blastn
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 # 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</code> blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4</code>
 +
 +In the above, please **DO NOT FORGET the '-l' option** on the first ("sha-bang") line, as it is compulsory for correct interpretation of the ''module load'' commands.
  
 We then submit the script with the ''sbatch'' command: We then submit the script with the ''sbatch'' command:
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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>#!/usr/bin/bash -l # <--- DO NOT FORGET '-l', it enables the module command+<code>#!/usr/bin/bash -l
 #SBATCH -p batch #SBATCH -p batch
 #SBATCH -J blastn #SBATCH -J blastn
using-slurm.1659615029.txt.gz · Last modified: 2022/08/04 12:10 by aorth