using-slurm
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using-slurm [2017/06/07 06:29] – aorth | using-slurm [2019/02/01 12:17] – jean-baka | ||
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[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. | + | **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 '' | ||
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blastn -query ~/ | blastn -query ~/ | ||
- | All output is directed to '' | + | All output is directed to '' |
==== 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