Computational Cluster Programs

R Libraries

R includes a base package and additional add-on libraries. At ATS we have installed the base package and more than 25 libraries. To see a list of the installed libraries, at the R command prompt, enter:

> library()

Additional libraries can be installed upon request. To have additional libraries installed send an email to atshpc@ucla.edu.

How to Run R on ATS-Hosted Clusters

You can use any text editor to make the appropriate input files for R.

How to Run R in Batch

To Run R from the UCLA Grid Portal

To run PGM in batch from the UCLA Grid Portal click on the Job Services tab. Then click on Applications. If you have access to a cluster that has R installed, you can run it on that cluster. In the form that you have to fill out to run an R job in the field labeled Arguments enter:

CMD BATCH filename

where filename is the name of your R input file.

To Run R from the Cluster Head Node using the Queue Scripts

The easiest way to run R in batch from the head node is to use the queue scripts. See Running a Batch Job on an ATS-Hosted Cluster for a discussion of the queue scripts and how they are used.

The following queue scripts are available for R:

R.q

Asks you for the name of your input file.

To Run R from the Cluster Head Node Using SGE Comands

See Running a Batch Job on an ATS-Hosted Cluster for guidelines to follow to create the required SGE command file. Alternatively, you could create an SGE command file with R.q. After saving the command file, you can modify it if necessary. See Commonly-Used SGE Commands for a list of the most commonly used SGE commands.

How to Run R Interactively

To Run R Interactively from the UCLA Grid Portal

R is not available interactively from the UCLA Grid Portal.

To Run PGM Interactively from a Cluster Interactive Node

To run an interactive program on one of the ATS-hosted clusters you must follow the rules that require you to run interactive programs on specific nodes and which limit how long they can run. For example, here are the rules for the Hoffman2 cluster. Rules for other ATS-hosted clusters are linked from their home pages.

To run R interactively, enter:

R