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Introduction to GPU accelerated jobs

Currently we have 31 nodes in the yoshi cluster (ygpu01-ygpu31) equipped with GPU boards. The exact hardware config is:

2x NVidia Tesla M2070
2x Xeon X5570
24GB RAM
QDR Infiniband between all GPU nodes

In oder to use the GPU cards, you need to allocate them through the queuing system using the –gres=gpu:2 option. You could also just use one card if you submit with –gres=gpu:1. You also have to explicitly state the partition to run in using –partition=gpu-main (or gpu-test for the GPU test queue).

GROMACS example using GPU acceleration

Here I give a simple example using GROMACS. First I'll use an interactive session to explore the GPU feature, in the end I'll supply a complete batch script for use with sbatch.