using-slurm
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using-slurm [2013/12/02 14:21] – aorth | using-slurm [2019/02/01 12:17] – jean-baka | ||
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salloc: Granted job allocation 1080 | salloc: Granted job allocation 1080 | ||
[aorth@taurus: | [aorth@taurus: | ||
+ | |||
+ | **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 '' | ||
+ | < | ||
+ | salloc: Granted job allocation 16349 | ||
+ | [jbaka@compute03 ~]$</ | ||
==== Batch jobs ==== | ==== Batch jobs ==== | ||
Request 4 CPUs for a NCBI BLAST+ job in the '' | Request 4 CPUs for a NCBI BLAST+ job in the '' | ||
- | < | + | < |
#SBATCH -p batch | #SBATCH -p batch | ||
#SBATCH -J blastn | #SBATCH -J blastn | ||
Line 27: | Line 34: | ||
# load the blast module | # load the blast module | ||
- | module load blast/2.2.28+ | + | module load blast/2.6.0+ |
# run the blast with 4 CPU threads (cores) | # run the blast with 4 CPU threads (cores) | ||
Line 33: | Line 40: | ||
Submit the script with '' | Submit the script with '' | ||
- | < | + | < |
Submitted batch job 1082</ | Submitted batch job 1082</ | ||
Line 41: | Line 48: | ||
Instead, you can use a local " | Instead, you can use a local " | ||
- | < | + | < |
#SBATCH -p batch | #SBATCH -p batch | ||
#SBATCH -n 4 | #SBATCH -n 4 | ||
Line 47: | Line 54: | ||
# load the blast module | # load the blast module | ||
- | module load blast/2.2.28+ | + | module load blast/2.2.30+ |
- | WORKDIR=/ | + | WORKDIR=/ |
mkdir -p $WORKDIR | mkdir -p $WORKDIR | ||
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 ~/ | + | blastn -query ~/ |
- | All output is directed to '' | + | All output is directed to '' |
==== Check queue status ==== | ==== Check queue status ==== | ||
< | < |
using-slurm.txt · Last modified: 2022/11/03 11:38 by jean-baka