Relion

General Environment Setup to Work with SCU Resources

Setup Slurm

In order to use SCU resources, you'll first need to setup your environment to work properly with our implementation of the job scheduler, Slurm. This is described here: Using Slurm

Setup Spack

Once this is done, you'll need to setup your environment to use Spack, our cluster-wide package manager. This is described here: Spack

Relion-specific Environment Setup

In order to use the Relion graphical user interface (GUI), you'll need to do log on to curie, the Slurm submission node (see Using Slurm for more details), and add this to your ~/.bashrc:

export RELION_QSUB_EXTRA_COUNT=2
export RELION_QSUB_EXTRA1="Number of nodes:"
export RELION_QSUB_EXTRA1_DEFAULT="1"
export RELION_QSUB_EXTRA2="Number of GPUs:"
export RELION_QSUB_EXTRA2_DEFAULT="0"

After editing your ~/.bashrc, log out of curie.

Launching the Relion GUI

Log on to curie, with X11

ssh -Y pascal # if off campus, use ssh -Y pascal.med.cornell.edu
ssh -Y curie

The -Y enables the use of the GUI