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using-slurm [2015/05/11 06:33] – joguyausing-slurm [2019/02/01 12:17] – jean-baka
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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.+**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/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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 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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 blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4 -out blast.out</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> <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). 
- 
- 
using-slurm.txt · Last modified: 2022/11/03 11:38 by jean-baka