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using-slurm [2017/06/07 06:28] – aorthusing-slurm [2019/02/01 12:20] – [Check queue status] 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//:
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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> +''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 
-==== Receive mail notifications ==== +             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON) 
-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> +             16330     batch interact  pyumbya  R    6:33:26      1 taurus 
-#SBATCH --mail-user <EMAIL_ADDRESS> +             16339     batch interact ckeambou  R    5:19:07      1 compute04 
-#SBATCH --mail-type ALL</code> +             16340     batch interact ckeambou  R    5:12:52      1 compute04 
- +             16346     batch velvet_o  dkiambi  R    1:39:09      1 compute04 
-Notification mail types(--mail-type) can be BEGIN, END, FAIL, REQUEUE and ALL(any state change). +             16348     batch interact fkibegwa  R      22:38      1 taurus 
- +             16349     batch interact    jbaka  R       3:27      1 compute03 
-Example: +</code>
-<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