slurm_basics
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slurm_basics [2018/12/06 14:51] xteng created |
slurm_basics [2019/02/12 15:06] xteng |
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| **Example Scripts** | **Example Scripts** | ||
| - | * Script 1 | + | * Script 1 |
| The following snippet runs a program asking for four (4) tasks. | The following snippet runs a program asking for four (4) tasks. | ||
| + | http://osirim.irit.fr/site/en/articles/sbatch-options | ||
| + | <code> | ||
| #!/bin/bash | #!/bin/bash | ||
| srun -n 4 my_program | srun -n 4 my_program | ||
| + | </code> | ||
| + | * Script 2 | ||
| - | * Script 2 | ||
| This script is the same as Script 1 except it uses slurm directives instead of passing the arguments as part of the srun command. | This script is the same as Script 1 except it uses slurm directives instead of passing the arguments as part of the srun command. | ||
| + | <code> | ||
| #!/bin/bash | #!/bin/bash | ||
| #SBATCH -n 4 | #SBATCH -n 4 | ||
| #SBATCH --ntasks-per-node=2 | #SBATCH --ntasks-per-node=2 | ||
| #SBATCH --time=00:30:00 | #SBATCH --time=00:30:00 | ||
| - | |||
| srun ./my_program | srun ./my_program | ||
| + | </code> | ||
| To submit the script, just run | To submit the script, just run | ||
| + | <code> | ||
| $> sbatch jobscript | $> sbatch jobscript | ||
| - | + | </code> | |
| - | * Script 3 | + | * Script 3 |
| Running two jobs per node: | Running two jobs per node: | ||
| + | <code> | ||
| #!/bin/bash | #!/bin/bash | ||
| #SBATCH -N 1 | #SBATCH -N 1 | ||
| #SBATCH -n 2 | #SBATCH -n 2 | ||
| #SBATCH --time=00:30:00 | #SBATCH --time=00:30:00 | ||
| + | </code> | ||
| # Use '&' to move the first job to the background | # Use '&' to move the first job to the background | ||
| + | <code> | ||
| srun -n 1 ./job1.batch & | srun -n 1 ./job1.batch & | ||
| srun -n 1 ./job2.batch | srun -n 1 ./job2.batch | ||
| + | </code> | ||
| # Use 'wait' as a barrier to collect both executables when they are done. | # Use 'wait' as a barrier to collect both executables when they are done. | ||
| wait | wait | ||
| To submit the script, just run | To submit the script, just run | ||
| + | <code> | ||
| $> sbatch jobscript | $> sbatch jobscript | ||
| - | + | </code> | |
| - | * Script 4 | + | * Script 4 |
| Naming output and error files: | Naming output and error files: | ||
| + | <code> | ||
| #!/bin/bash | #!/bin/bash | ||
| #SBATCH -n 2 | #SBATCH -n 2 | ||
| Line 67: | Line 69: | ||
| #SBATCH --error=job.%J.err | #SBATCH --error=job.%J.err | ||
| #SBATCH --output=job.%J.out | #SBATCH --output=job.%J.out | ||
| + | </code> | ||
| + | <code> | ||
| srun ./my_program | srun ./my_program | ||
| + | </code> | ||
| To submit the script, just run | To submit the script, just run | ||
| $> sbatch jobscript | $> sbatch jobscript | ||
| - | * Script 5 | + | * Script 5 |
| + | <code> | ||
| #!/bin/bash | #!/bin/bash | ||
| #SBATCH --nodes=1 #request one node | #SBATCH --nodes=1 #request one node | ||
| - | #SBATCH --cpus-per-task=8 #ask for 8 cpus | + | #SBATCH --cpus-per-task=2 #e .g. ask for 2 cpus |
| #SBATCH --time=02:00:00 #ask that the job be allowed to run for 2 hours. | #SBATCH --time=02:00:00 #ask that the job be allowed to run for 2 hours. | ||
| - | #SBATCH --error=job.%J.err # tell it to store the output console text to a file | + | #SBATCH --error=/PATH/<NAME>.%J.err # tell it to store the output console text to a file |
| - | #SBATCH --output=job.%J.out #tell it to store the error messages to a file | + | #SBATCH --output=/PATH/<NAME>.%J.out #tell it to store the error messages to a file |
| module load R #load the most recent version of R available | module load R #load the most recent version of R available | ||
| Rscript --vanilla myRscript.R #run an R script using R | Rscript --vanilla myRscript.R #run an R script using R | ||
| + | </code> | ||
| To submit the script, just run | To submit the script, just run | ||
| + | <code> | ||
| $> sbatch jobscript | $> sbatch jobscript | ||
| - | + | </code> | |
| - | * Script 6 | + | * Script 6 |
| Running a job that needs a GPU | Running a job that needs a GPU | ||
| + | <code> | ||
| #!/bin/bash | #!/bin/bash | ||
| Line 115: | Line 120: | ||
| Rscript--vanilla myRScript.R #run an R script using R | Rscript--vanilla myRScript.R #run an R script using R | ||
| + | </code> | ||
| To submit the script, just run | To submit the script, just run | ||
| + | <code> | ||
| $> sbatch jobscript | $> sbatch jobscript | ||
| + | </code> | ||
| Interactive session example | Interactive session example | ||
| To get an interactive session for an hour | To get an interactive session for an hour | ||
| + | <code> | ||
| + | salloc --time=01:00:00 --nodes=1 | ||
| + | </code> | ||
| - | salloc --time=01:00:00 --nodes=1 | + | back to [[ace-gpu-1_slurm|ace-gpu-1 slurm]] |
slurm_basics.txt · Last modified: 2019/02/12 15:08 by xteng
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