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Using RELION via OnDemand

RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. Using RELION on Apocrita via OnDemand allows you to run GUI interface. Please refer to the overview section for instructions on how to login to OnDemand.

Starting a RELION session

Select RELION (GPU) from the GUIs list of the Interactive Apps drop-down menu, or from the My Interactive Sessions page to launch the RELION GUI on a GPU node.

RELION 5 has a regular option (5.0.0-gpu) and a new subtomo-gram averaging pipeline (5.0.0-gpu (with tomo)) option. The Graphical User Interface (GUI) for each option is different, so please select carefully:

RELION tomo

Choose the resources your job will need. Choosing a 1 hour maximum running time is the best option for getting a session quickly, unless you have access to owned nodes which may offer sessions immediately for up to 240hrs if resources are available.

Project directory

You need to enter a path to your project directory (where project files are located) or your session will be started in your home directory by default.

RELION resources

Once clicking Launch, the request will be queued, and when resources have been allocated, you will be presented with the option to connect to the session by clicking on the blue Launch RELION button.

Once connected, the familiar RELION interface is presented, and you will be able to use the allocated resources, and access your research data located on Apocrita.

RELION session

Selection the correct CPU and GPU count

WARNING

By default, many of the RELION jobs in the GUI will make poor choices regarding CPU threading, MPI processes and GPU counts. Please ensure you set these to match the session - 8 CPU cores, 1 MPI proc and a single GPU defined as 0, as pictured below:

RELION CPU threads

RELION GPU

Exiting the session

If a session exceeds the requested running time, it will be killed. You can finish your session using one of the following methods:

  • clicking [x] in the upper right corner of the RELION application
  • selecting File -> Quit from the application menus
  • clicking the red Delete button for the relevant session on the My Interactive Sessions page.

After a session ends, the resources will be returned to the cluster queues.