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Basic R jobs

Multiple R versions exist in HPC environment. To check what are available, on Prince:

Suppose we want to use 3.3.2, run these commands:

We first clean up the environment by doing 'module purge'. Then we load the R version selected, check what are available in current environment. We can see that R 3.3.2 is indeed loaded along with its dependency modules. Let's try this basic R example. We name it "example.R":

Below is the screen scene while running it on Prince:

What is shown above is a simple demo case on login nodes. For real interactive analysis scenario, users are encouraged to run on compute nodes using the 'srun' command to request dedicated resources, e.g.:

Besides running our analysis interactively, long running and big data crunching jobs ought to be submitted to the batch system slurm. The "example.R" can be submitted to slurm to run in batch mode.

Copy example files to your newly created directory.

example

Below is how the example looks like:

example

Then create a sbatch job script as:

Once the sbatch script file is ready, it can be submitted to the job scheduler using sbatch. After successful completion of job, verify output log file for detail output information.

sbatch

 

 

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