gitea-pages/docs/cls/software/EM/relion.md

RELION

RELION (for REgularised LIkelihood OptimisatioN, pronounced rely-on) is a software package for structure determination using electron cryo-microscopy (cryo-EM). It employs an empirical Bayesian approach to perform image processing and 3D reconstruction.

RELION is developed by the group of Sjors Scheres at the MRC Laboratory of Molecular Biology.

For more information, see the official RELION documentation.

Package availability

Compute node type	Available	Notes
CPU	✓
NVIDIA A100 GPU	✓
NVIDIA Grace Hopper GPU	✓	IMOD is not available

Run RELION

Load the RELION module

Load the RELION module before starting the application:

module load relion/5.0.1

Launch the RELION GUI

To start the RELION GUI in either a new project directory or an existing RELION project directory, run:

relion &

For tomographic processing, use:

relion --tomo &

Batch submission

RELION can submit jobs to the cluster's batch system using sbatch. The following settings are recommended.

Compute tab settings

Keep the following default values:

Setting	Value
Use parallel disk I/O?	Yes
Pre-read all particles into RAM?	No
Copy particles to scratch directory	/scratch
Combine iterations through disk?	No

CPU jobs

For CPU-only jobs:

Setting	Value
Use GPU acceleration?	No

GPU jobs

For GPU-accelerated jobs:

Setting	Value
Use GPU acceleration?	Yes
Which GPUs to use	Leave blank
ModelAngelo	$CUDA_VISIBLE_DEVICES

Running tab settings

Configure the following settings:

Setting	Value
Number of MPI procs	1–16
Number of threads	1–36
Submit to queue?	Yes
Queue submit command	sbatch
Time limit	dd-hh:mm:ss
Additional sbatch arguments	Leave blank or specify additional arguments
Number of nodes	1
Total memory per node	0–818 GB
Number of GPUs per node	0–4
Minimum dedicated cores per node	1
Additional arguments	Leave blank

!!! warning "Additional sbatch arguments" Additional sbatch arguments override the corresponding settings above. If there is a conflict, the values specified in the additional arguments take precedence.

Queue names

For CPU jobs, use one of the following queues:

hourly
daily
general

For GPU jobs, use one of the following queues:

a100-hourly
a100-daily
a100-general

gh-hourly
gh-daily
gh-general

Standard submission scripts

For CPU jobs:

/opt/psi/overlays/Alps/EM/relion/5.0.1/scripts/CPU.sh

For GPU jobs:

/opt/psi/overlays/Alps/EM/relion/5.0.1/scripts/GPU.sh

CPU jobs

The following settings illustrate a typical CPU job configuration:

GPU jobs

The following settings illustrate a typical GPU job configuration:

The main differences from a CPU job are:

• Queue name: a100-daily
• Standard submission script: /opt/psi/overlays/Alps/EM/relion/5.0.1/scripts/GPU.sh
• Use GPU acceleration: Yes

By default, the GPU.sh submission script requests one GPU per job. To request additional GPUs, specify the desired number in Number of GPUs per node.

!!! tip "Resource allocation" Request resources according to the requirements of your job. Requesting more resources than necessary may increase queue wait times and reduce cluster efficiency.