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Open OnDemand - A Graphical Application (RELION)

Open OnDemand is a suite of software that provides a graphical web interface to HPC resources and other interactive research computing applications. RELION is a software package for analyzing Cryo Electron Microscopy (Cryo-EM) data. The purpose of this document is to demonstrate how to run the RELION software in an interactive desktop in Open OnDemand.

Lines beginning with $ indicate shell commands. You may type these manually, or copy/paste them from this document. Either way, do not include the $ when executing commands. Text below commands indicates expected output.

1.    Login to the Open OnDemand portal and launch an interactive desktop session on Thunder. Once the session is running, open the graphical desktop window.

2.    Working in the virtual desktop, open the terminal application by clicking the icon on the dock at the bottom of the screen.

3.    Using the terminal, navigate to the directory that will store your RELION project. You should use a location in your project or scratch directory. For example:

$ cd /gpfs1/scratch/first.lastname
$ mkdir relion-test
$ cd relion-test

Load the necessary software modules. In addition to RELION, you will need the Intel compiler and MPI runtime libraries. Then launch the RELION software. When asked if you want to start a new project in the current directory, answer “y” and hit Enter.

$ module load intel impi relion
$ relion
Only run the relion GUI from your ProjectDirectory. Do you want to start a new project here [y/n]? y

4.    The RELION software should start and a graphical window will be opened.

For documentation on using RELION, refer to the RELION website:

Keywords:CCAST Open-OnDemand   Doc ID:107831
Owner:Conner R.Group:IT Knowledge Base
Created:2020-12-14 16:15 CSTUpdated:2020-12-30 10:15 CST
Sites:IT Knowledge Base
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