Example 1This tutorial will cover how to submit an R batch job to the Aloe supercomputer. A batch job. This is a job that is submitted as a complete script and runs unattended. This is done through a SBATCH script.

Submitting a Batch Job

Follow these steps to submit an R batch job:

1. Create the SBATCH script. You can create this script on your workstation and then upload it to the Aloe supercomputer. You can also create this script through the shell. To do this:

   1. Connect to the web portal and log on with your credentials.

   2. Select “System“ in the navigation bar then select “Aloe Shell Access“. You will be prompted for your credentials and a DUO push will be sent to you.

   3. In the command prompt, use the following commands to create a SBATCH script called “R_test_script.sh“.

      Code Block
      nano R_test_script.sh

   4. In the file editor, specify the resources, R version, and the Rscript file needed for your computation. Here is an example of a R SBATCH script:

      Code Block
      #!/bin/bash #SBATCH -c 1 # number of TASKS #SBATCH -

...

1. 1. N 1 # keep all tasks on the same node #SBATCH -

...

1. 1. -mem=120G # request

...

1. 1. 120 GB of memory #SBATCH -t 0-1

...

1. 1. # request 1 hour

...

1. 1. of walltime module load r-4.3.0-gcc-11.2.0-6t5 # load in R version 4.3.0 # Use one of the following commands to run R: R --no-save --quiet < regression.r

...

Example: Submitting the job

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1. 1. # OR Rscript regression.r # OR Rscript regression.r <arguments to be passed into R>

      1. This job will allocate one core and 120 GB of memory on one node for one hour. It will also execute the “regression.r“ file with R version 4.3.0.

   2. Save the SBATCH script and exit the file editor.

   3. In the command prompt, use the following commands to submit the batch job:

      Code Block
      sbatch MATLAB_test_script.sh

   4. Done. Your job has been submitted. Here are some helpful commands to manage your job:

      Code Block

...

#!/bin/bash
#SBATCH -c 1
#SBATCH -o %j.out      ## stdout
#SBATCH -e %j.err      ## stderr
#SBATCH -t 0-1         ## 1 hour runtime

module load r-4.3.0-gcc-11.2.0-6t5
Rscript regression.r 20000

1. 1. myjobs # This will show the status for all of your jobs.

      Code Block
      scancel JOBID # This will cancel one job by using its JOBID.

      Code Block
      scancel –u $USER # This will cancel all of your jobs.

      Code Block
      seff JOBID # This will give the efficiency report for one job by using its JOBID.