HDF5 is a general purpose library and file format for storing scientific data. HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file. Using these two basic objects, one can create and store almost any kind of scientific data structure, such as images, arrays of vectors, and structured and unstructured grids.


GROMACS is a versatile package of molecular dynamics simulation programs. It is primarily designed for biochemical molecules, but it has also been used on non-biological systems.  GROMACS generally scales well on OSC platforms. Starting with version 4.6 GROMACS includes GPU acceleration.


FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. It is portable and performs well on a wide variety of platforms.


The Assisted Model Building with Energy Refinement (AMBER) package contains many molecular simulation programs targeted at biomolecular systems. A wide variety of modelling techniques are available. It generally scales well on modest numbers of processors, and the GPU enabled CUDA programs are very efficient.


CUDA™ (Compute Unified Device Architecture) is a parallel computing platform and programming model developed by Nvidia that enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU).

Job Submission

Job scripts are submitted to the batch system using the sbatch command.  Be sure to submit your job on the system you want your job to run on, or use the --cluster=<system> option to specify one.

Standard batch job

Most jobs on our system are submitted as scripts with no command-line options. If your script is in a file named myscript:

sbatch myscript

In response to this command you’ll see a line with your job ID: