RELION (REgularised LIkelihood OptimisatioN) is a stand-alone computer program for the refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy.
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 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 OSC clusters. The versions currently available at OSC are:
| Version | 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 | Built with CUDA 10.2 (11.8 for Ascend) | |
| 5.0b | X | Built with CUDA 11.8 | |
| 5.0 | X | Built with CUDA 11.8 and OpenMPI |
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 | 5.0 | 4.1.14 | 1.4.5 |
Access
RELION is available to all OSC users.
Publisher/Vendor/Repository and License Type
MRC Lab of Molecular Biology, Open source
Usage
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
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
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.
