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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

RELION 4

To specifically load RELION 4:

module load relion/4

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

RELION 5

To specifically load RELION 5:

module load relion/5

Since RELION 5 runs from a container, you need to run relion and then the command you wish to run, e.g.:

relion relion_refine -h

GUI support for RELION

RELION has been compiled with support for the GUI and the binary relion is available on Apocrita, however we strongly suggest to use our OnDemand service for GUI jobs.

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

# If using RELION 4
module load relion/4
relion_refine --angpix 1 \
              --i example.mrcs \
              --iter 5 \
              --j ${NSLOTS} \
              --o output

# If using RELION 5
module load relion/5
relion relion_refine --angpix 1 \
              --i example.mrcs \
              --iter 5 \
              --j ${NSLOTS} \
              --o output

Parallel job (RELION 4 only)

Parallel jobs are only supported by RELION 4

RELION 4 supports parallel jobs but RELION 5 currently runs from a container and has no support for multi-node Open MPI or Infiniband.

Here is an example RELION 4 job running on 96 cores across 2 ddy nodes using MPI:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe parallel 96
#$ -l infiniband=ddy-i
#$ -l h_rt=240:0:0

module load relion/4

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=11G
#$ -l gpu=1

# If using RELION 4
module load relion/4
relion_refine --angpix 1 \
              --gpu \
              --i example.mrcs \
              --iter 5 \
              --j ${NSLOTS} \
              --o output

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

References