SSH to a compute node

Log in via SSH to a compute node to submit work

Sometimes you may want to log in to a compute node via SSH to run a job (e.g., R script) while keeping your master node free.

For example, say my R script uses parallel::mclapply. This function forks processes without using the grid, so it's typically used to parallelize work on the master node. However, you may want to run this work on a compute node to leave your master node free to do other work.

  1. SSH in to your master node
  2. If you do not have any compute nodes active, bring one up:
echo "sleep 10" | qsub
  1. Find the IP address of the compute node when it comes up:
sudo su - -c "qconf -sh"
  1. SSH in to that compute node
ssh <one of the IP addresses>
  1. Navigate to /data, start a screen session, and run your script
cd /data/<projDir>
R CMD BATCH <file.R>

Because you started a screen session, feel free to close the terminal as the job will run in the background.