Software

What software is available on Bridges; common errors with a given package.

To run Gromacs on both GPUs and CPUs, use the same number of CPU tasks as GPUs. Thus, no matter how many nodes you use, set the value of the SBATCH option ntasks-per-node to 4 if you are using the K80 GPU nodes and to 2 if you are using the P100 GPU nodes.

You must also use the correct GROMACS module to insure that your compilation will work.

To use GPUs and CPUs, load a gromacs module with "gpu" in its name, similar to

module load gromacs/2018_gpu

To use just CPUs, load a gromacs module with "cpu" in its name, similar to

module load gromacs/2018_cpu

There are complete sample scripts for both cases in directory /opt/packages/examples/gromacs on Bridges.

on May 17, 2019