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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 latest 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 cores and 1GB total 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 2 whole nxv nodes:

#!/bin/sh
#$ -cwd
#$ -j y
#$ -pe parallel 64
#$ -l infiniband=nxv
#$ -l h_rt=1:0:0

module load relion

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

GPU Serial Job

Here is an example job running on half of 1 GPU node (1 GPU):

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 16
#$ -l h_rt=1:0:0
#$ -l h_vmem=7.5G
#$ -l gpu=1

module load relion
export CUDA_VISIBLE_DEVICES=${SGE_HGR_gpu// /,}

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

GPU Parallel Job

Here is an example job running on 2 whole GPU nodes (4 GPUs):

#!/bin/sh
#$ -cwd
#$ -j y
#$ -pe parallel 64
#$ -l h_rt=1:0:0
#$ -l gpu=2

module load relion
export CUDA_VISIBLE_DEVICES=${SGE_HGR_gpu// /,}

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

References