(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
SBGrid Usage Info
RELION versions > 2.0 are GPU-accelerated using Nvidia CUDA on Linux. For general information on running GPU accelerated applications from SBGrid, please see here : https://sbgrid.org/wiki/gpu
CUDA builds of RELION are designated by a '_cu' suffix in the version of the application. For example, 3.1.0_cu9.2 is linked against CUDA v9.2 libraries. All builds are single precision on the GPU and can be run on 'consumer-grade' GPU hardware.
RELION builds without CUDA support are compiled with Intel 2019.5 with accelation options and Intel math libraries.
RELION and MPI versions
RELION uses the 'mpirun' executable to manage MPI "ranks" for parallel processing. SBGrid includes several OpenMPI versions which are matched to specific RELION versions. When called from the SBGrid capsule environment, the relion GUI is configured to use the correct version of OpenMPI to manage parallel processing. When calling RELION binaries from the command line, the
mpirun.relionexecutable can be used.
mpirun.relionis configured to used the correct version of OpenMPI for each version of RELION.
The 3.1.* versions for RELION use the default configuration of OpenMPI (3.1.6 on Linux, 2.1.3 on macOS) and do not require the version to be defined. Older releases use OpenMPI 2.1.2 which should be specified in $HOME/.sbgrid.conf. To set the OpenMPI version, add :
to $HOME/.sbgrid.conf and open a new terminal to use the correct mpirun. As noted above, you can also use the
mpirun.relionexecutable in place of
mpirunto use the MPI that matches the currently configured version of RELION. In this case, no other configuration is needed.
Version 3.1.0_cu8.0 is compiled to support legacy CPUs (pre-Haswell). OpenMPI 3.1.6_compat is also needed for this version.
Versions 3.1.0_cu8.0_slurm20 3.1-beta_cu8.0_slurm20 and 3.0.8_cu8.0_slurm20 support Slurm v20 PMI library.
20201111 : Add 3.1.1 RELION versions 20200703 : Add 3.1.0 release version 20200629 : reconfigure RELION gui to automatically use correct 'mpirun' in capsules. 20200610 : rebuild of 3.1-beta releases with OpenMPI 3.1.6 from commit 5997001
20200610 : Empty values in GUI during autopicking can be interpreted as Text instead of Float values.
The following verions are deprecated and will be removed in a future SBGrid update.
20200706: 3.0.8_cu10.1 3.0.8_cu9.2 3.0.8_avx2 3.1-beta_cu9.2 3.1-beta_cu10.1
(c) Copyright 2008, Structural Biology Grid (www.sbgrid.org)
Last Update to this document
Jason Key 0a6b896 2020-11-15 18:39:38 -0500
InstallationUse the following command to install this title with the CLI client:
$ sbgrid-cli install relion
S. H. W. Scheres. 2012. A Bayesian View on Cryo-EM Structure Determination. J Mol Biol. 415(2): 406-418.
S. H. W. Scheres. 2012. RELION: Implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol. 180(3): 519-530.
*Full citation information available through
Citation NoteIf RELION is useful in your work, please use at least one of the primary citations listed. Additional citations can be found here: https://www2.mrc-lmb.cam.ac.uk/groups/scheres/publications.html
OS X INTEL:3.1.1, 3.1.0, 3.0.8, 2.1, 1.4, 1.3