RELION

RELION (REgularised LIkelihood OptimisatioN) is a stand-alone computer program for the refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy. 

We have identified some issues with the RELION installations. For more details, please refere the "Known Issues" section below.

To address the issues, we have decided to deprecate affected versions, including: relion/3.1, relion/3.1-gpu, relion/3.1.3, relion/4.0.0, and relion/4.0b on both Owens and Pitzer. Additionally, we will deprecate other versions that are rarely used to improve maintenance. These versions include relion2/2.0 and relion/3.0.4.

The deprecation action was done on January 23, 2024. To migrate your jobs, please refer to the "Versions" table below for available versions. If you require any assistance, please contact OSC help.

Availability and Restrictions

Versions

RELION is available on the Owens cluster. The versions currently available at OSC are:

Version Owens Pitzer Ascend Note
3.1-cuda10.1   X   Built with CUDA 10.1
4.0-cuda10.1   X   RELION 4.0 beta2
Built with CUDA 10.1
4.0.1 X X X Built with CUDA 10.2 (11.8 for Ascend)
5.0b   X   Built with CUDA 11.8
* Current Default Version

You can use module spider relion  to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Available third-party packages

Cluster RELION CTFFIND MotionCor2 GCTF ResMap Unblur & Summovie
Pitzer 4.0.1, 5.0b 4.1.14 1.4.4 1.18 1.1.4 1.0.2
Ascend 4.0.1 4.1.14 1.4.5 1.18 1.1.4 1.0.2

Access

RELION is available to all OSC users.

Publisher/Vendor/Repository and License Type

MRC Lab of Molecular Biology, Open source

Usage

Usage on Owens

Set-up

To set up the environment for RELION on the Owens cluster, use the command:

module load relion/version

where version is chosen from the available versions (omitting the version will load the default version).

Usage on Pitzer

Set-up

To set up the environment for RELION on the Pitzer cluster, use the command:

module load relion/version

where version is chosen from the available versions (omitting the version will load the default version).

Known issues

Hybrid MPI+OpenMP job Hangs on multiple nodes

Update: January 2024
Version: All Intel+MVAPICH2 versions

Hybrid MPI+OpenMP jobs utilizing programs built with the Intel compiler and MVAPICH2 may experience hangs when running on multiple nodes. This issue is attributed to a known problem in MVAPICH2 built with the Intel compiler stack.

Resolution

All versions of Intel+MVAPICH2 have been removed to address this issue.

Poor performance with hybrid MPI+OpenMPI jobs and more than 4 MPI Tasks on multiple nodes

Update: January 2024
Version: Prior to 5

RELION versions prior to 5 may exhibit poor performance in hybrid MPI+OpenMP jobs when the number of MPI tasks exceeds 4 on multiple nodes.

Resolution

If possible, limit the number of MPI tasks to 4 or less for optimal performance. Consider using RELION version 5 or later, as newer versions may include optimizations and improvements that address this performance issue.

Further Reading

Supercomputer: