ILRI Research Computing

User Tools

Site Tools

You are here: start » using-slurm
using-slurm

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
Next revisionBoth sides next revision
using-slurm [2015/03/26 10:16] – aorthusing-slurm [2018/11/29 09:25] – [Batch job using local storage] aorth
Line 22: Line 22:
 ==== 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
Line 28: Line 28:
  
 # 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)
Line 42: Line 42:
 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
Line 62: Line 62:
 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>
using-slurm.txt · Last modified: 2022/11/03 11:38 by jean-baka