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Both sides previous revision Previous revision Next revision | Previous revision | ||
guides:slurm:using-r [23.09.2019 11:06] Teemu Kuulasmaa |
guides:slurm:using-r [18.10.2024 14:10] (current) Administrator |
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- | # Using R with SLURM | + | # Using R with Slurm |
Example script (**hello.R**): | Example script (**hello.R**): | ||
Line 14: | Line 14: | ||
2. Rscript script.R | 2. Rscript script.R | ||
- | Note: With the **R CMD BATCH** command the output of the R script is redirected to file instead of the screen | + | **Note**: With the **R CMD BATCH** command the output of the R script is redirected to file instead of the screen. |
- | Next user must embed the script | + | Next user must embed the script |
``` | ``` | ||
- | |||
#!/bin/bash | #!/bin/bash | ||
- | #SBATCH --job-name helloworld # Name for your job | + | #SBATCH --job-name helloworld # |
- | #SBATCH --ntasks 1 # Number of task | + | #SBATCH --ntasks 1 # Number of task |
- | #SBATCH --time 5 # Runtime in minutes. | + | #SBATCH --time 5 # Runtime in minutes. |
- | #SBATCH --mem=2000 # Reserve 2 GB RAM for the job | + | #SBATCH --mem=2000 # Reserve 2 GB RAM for the job |
- | #SBATCH --partition | + | #SBATCH --partition |
- | #SBATCH --output hello.out # Standard out goes to this file | + | #SBATCH --output hello.out # Standard out goes to this file |
- | #SBATCH --error hello.err # Standard err goes to this file | + | #SBATCH --error hello.err # Standard err goes to this file |
- | #SBATCH --mail-user username@uef.fi # this is the email you wish to be notified at | + | #SBATCH --mail-user username@uef.fi # |
- | #SBATCH --mail-type ALL # ALL will alert you of job beginning, completion, failure etc | + | #SBATCH --mail-type ALL # ALL will alert you of job beginning, completion, failure etc |
- | module load r # load modules | + | module load r/ |
Rscript hello.R # Execute the script | Rscript hello.R # Execute the script | ||
- | sbatch | ||
``` | ``` | ||
- | User can submit the job to the compute queue with the **[sbatch](https:// | + | The last step is to submit the job to the compute queue with the **[sbatch](https:// |
``` | ``` | ||
- | sbatch | + | sbatch |
``` | ``` |