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 (CPU) or RELION (GPU) from the GUIs list of the Interactive Apps drop-down menu, or from the My Interactive Sessions page. If your code does not specifically use GPU acceleration and/or you do not have access to GPU-enabled nodes, then choose "RELION (CPU)" from the Interactive Apps list.
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.
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.
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.
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.