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 [2014/08/29 06:29] – [Interactive jobs] aorthusing-slurm [2015/03/18 15:43] – aorth
Line 28: Line 28:
  
 # load the blast module # load the blast module
-module load blast/2.2.28++module load blast/2.2.30+
  
 # run the blast with 4 CPU threads (cores) # run the blast with 4 CPU threads (cores)
Line 48: Line 48:
  
 # load the blast module # load the blast module
-module load blast/2.2.28++module load blast/2.2.30+
  
 WORKDIR=/var/scratch/$SLURM_JOBID WORKDIR=/var/scratch/$SLURM_JOBID
Line 55: Line 55:
 echo "Using $WORKDIR on $SLURMD_NODENAME" echo "Using $WORKDIR on $SLURMD_NODENAME"
 echo echo
 +
 +# change to working directory on compute node
 +cd $WORKDIR
  
 # 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 -out $WORKDIR/output</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 [[http://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