Gautomatch

Gautomatch is a GPU-accelerated program that provides functionality to pick particles from cryo-EM micrographs.

Gautomatch is available as a module on Apocrita.

Gautomatch will only run on GPU nodes

Gautomatch will produce a CUDA error if the application is ran on a non-gpu node because the CUDA driver and runtime library are required. Researchers need to request permission to be added to the list of GPU node users.

Usage

To run the default version of Gautomatch, simply load the gautomatch module:

$ module load gautomatch
$ gautomatch --help
Usage:
         gautomatch [options] <micrographs>
...

Example job

GPU job

Here is an example job running on 1 GPU:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 12
#$ -l h_rt=240:0:0
#$ -l h_vmem=7.5G
#$ -l gpu=1

module load gautomatch/0.56-gpu

gautomatch DATA.mrc