Skip to content

RELION

REgularised LIkelihood OptimisatioN (RELION) employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryomicroscopy.

RELION is available as a module on Apocrita.

Usage

To run the default installed version of RELION, simply load the relion module:

module load relion

For usage documentation, pass the -h switch to any of the RELION commands, for example: relion_refine -h.

No GUI support for RELION

RELION has been compiled without support for the GUI so the binary relion is not available on Apocrita; Please use the command line binaries instead.

Example jobs

Serial job

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load relion

relion_refine --angpix 1 \
              --i example.mrcs \
              --iter 5 \
              --j ${NSLOTS} \
              --o output

Parallel job

Here is an example job running on 48 cores across 2 sdv nodes using MPI:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe parallel 48
#$ -l infiniband=sdv-i
#$ -l h_rt=240:0:0

module load relion

mpirun -np ${NSLOTS} relion_refine_mpi \
  -x LD_LIBRARY_PATH \
  --angpix 1 \
  --i preprocessed.mrcs \
  --iter 2 \
  --o test

GPU serial job

Here is an example job running on 1 GPU:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 8
#$ -l h_rt=240:0:0
#$ -l h_vmem=7.5G
#$ -l gpu=1

module load relion
relion_refine --angpix 1 \
              --gpu \
              --i example.mrcs \
              --iter 5 \
              --j ${NSLOTS} \
              --o output

GPU parallel job

Here is an example job running on 4 GPUs across 2 nxg nodes using MPI:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe parallel 64
#$ -l infiniband_direct=nxg3-4
#$ -l h_rt=240:0:0
#$ -l gpu=2

module load relion

mpirun -np ${NSLOTS} relion_refine_mpi \
  -x LD_LIBRARY_PATH \
  --angpix 1 \
  --gpu \
  --i example.mrcs \
  --iter 5 \
  --o output

References