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guides:slurm:using-r

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guides:slurm:using-r [23.09.2019 11:06]
Teemu Kuulasmaa 		guides:slurm:using-r [23.09.2019 11:15]
Teemu Kuulasmaa
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-# Using R with SLURM+# Using R with Slurm
  
 Example script (**hello.R**): Example script (**hello.R**):
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 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 to the **SLURM batch job file/control file** (**submit.sbatch**):+Next user must embed the script into the SLURM batch job file/control file (e.g. scriptR.sbatch):
  
 ``` ```
- 
 #!/bin/bash #!/bin/bash
-#SBATCH --job-name helloworld # Name for your job +#SBATCH --job-name helloworld # Name for your job 
-#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 serial # Partition to submit +#SBATCH --partition serial # Partition to submit 
-#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 # this is the email you wish to be notified at 
-#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 # load modules
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 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://slurm.schedmd.com/sbatch.html)** command. Note that the batch file (and R script and data) must be located at the /home/ disk.+The last step is to submit the job to the compute queue with the **[sbatch](https://slurm.schedmd.com/sbatch.html)** command. Note that the batch file (and R script and data) must be located at local file system of login node, e.g. /home/users/ disk.
  
 ``` ```
-sbatch submit.sbatch+sbatch scriptR.sbatch
 ``` ```
guides/slurm/using-r.txt · Last modified: 18.11.2021 11:19 by Administrator

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