Munich Usage

How to use BatchJobs on snickers and bounty

• Login to snickers or bounty per SSH.
• Create a valid config file called .BatchJobs.R in your home directory. Here is a template:

cluster.functions = makeClusterFunctionsSSH(
  makeSSHWorker(nodename = "bounty", max.jobs = 20, max.load = 63, ncpus = 64),
  makeSSHWorker(nodename = "snickers", max.jobs = 20, max.load = 63, ncpus = 64)
)
staged.queries = TRUE

• The only argument that you may want to change is max.jobs. It gives the maximal number of jobs that can run concurrently for the current registry, for the correspondent node.
• Now you can either work interactively with R or run batch jobs using the BatchJobs package.

The jobs will be submitted to the specified nodes. Helpful commands to check the status of your jobs and more can be found in the Reference Manual of BatchJobs and the links on the README of the project.

As you are working on a makeshift SSH cluster, you should also read the SSH wiki page (e.g. you have to configure the machines so that passwordless SSH authentication works).