using-slurm
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using-slurm [2015/03/18 15:42] – [Batch job using local storage] aorth | using-slurm [2017/06/07 06:29] – aorth | ||
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==== 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 28: | Line 28: | ||
# 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 42: | Line 42: | ||
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 50: | Line 50: | ||
module load blast/ | module load blast/ | ||
- | WORKDIR=/ | + | WORKDIR=/ |
mkdir -p $WORKDIR | mkdir -p $WORKDIR | ||
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==== Check queue status ==== | ==== Check queue status ==== | ||
< | < | ||
+ | |||
+ | ==== Receive mail notifications ==== | ||
+ | To receive mail notifications about the state of your job, add the following lines to your sbatch script: whereby < | ||
+ | #SBATCH --mail-user < | ||
+ | #SBATCH --mail-type ALL</ | ||
+ | |||
+ | Notification mail types(--mail-type) can be BEGIN, END, FAIL, REQUEUE and ALL(any state change). | ||
+ | |||
+ | Example: | ||
+ | < | ||
+ | #SBATCH --mail-user J.Doe@cgiar.org | ||
+ | #SBATCH --mail-type ALL</ | ||
+ |
using-slurm.txt · Last modified: 2022/11/03 11:38 by jean-baka