using-slurm
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using-slurm [2019/11/11 13:20] – aorth | using-slurm [2022/08/04 12:08] – aorth | ||
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==== Batch jobs ==== | ==== Batch jobs ==== | ||
- | Request | + | We are writing a SLURM script below. The parameters in its header request |
- | < | + | < |
#SBATCH -p batch | #SBATCH -p batch | ||
#SBATCH -J blastn | #SBATCH -J blastn | ||
Line 53: | Line 53: | ||
blastn -query ~/ | blastn -query ~/ | ||
- | Submit | + | We then submit |
< | < | ||
Submitted batch job 1082</ | Submitted batch job 1082</ | ||
Line 62: | Line 62: | ||
Instead, you can use a local " | Instead, you can use a local " | ||
- | < | + | < |
#SBATCH -p batch | #SBATCH -p batch | ||
- | #SBATCH -n 4 | ||
#SBATCH -J blastn | #SBATCH -J blastn | ||
+ | #SBATCH -n 4 | ||
# load the blast module | # load the blast module | ||
Line 86: | Line 86: | ||
==== Check queue status ==== | ==== Check queue status ==== | ||
'' | '' | ||
- | < | + | < |
- | | + | JOBID PARTITION |
- | 16330 batch interact | + | 746596 |
- | 16339 batch interact ckeambou | + | 746597 |
- | 16340 batch interact ckeambou | + | 746885 |
- | 16346 batch velvet_o | + | 746998 |
- | 16348 batch interact fkibegwa | + | 746999 |
- | | + | |
</ | </ | ||
- | |||
- | In addition to the information above, it is sometimes useful to know what is the number of CPUs (computing cores) allocated to each job: the scheduler will queue jobs asking for resources that aren't available, most often because the other jobs are eating up all the CPUs available on the host. To get the number of CPUs for each job and display the whole thing nicely, the command is slightly more involved: | ||
- | |||
- | < | ||
- | JOBID PARTITION | ||
- | 16330 | ||
- | 16339 | ||
- | 16340 | ||
- | 16346 batch velvet_out_ra_10 | ||
- | 16348 | ||
- | 16349 | ||
- | </ | ||
- | |||
- | or, alternatively: | ||
- | |||
- | < | ||
- | USER JOBID | ||
- | pyumbya | ||
- | ckeambou | ||
- | ckeambou | ||
- | dkiambi | ||
- | fkibegwa | ||
- | jbaka | ||
- | </ | ||
- |
using-slurm.txt · Last modified: 2022/11/03 11:38 by jean-baka