Please revew the OSC Home storage policy in our Policy page.
Each user ID has a home directory on the NetApp WAFL service. You have the same home directory regardless of what system you’re on, including all login nodes and all compute nodes, so your files are accessible everywhere. Most of your work in the login environment will be done in your home directory.
The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a classical molecular dynamics code designed for high-performance simulation of large atomistic systems. LAMMPS generally scales well on OSC platforms, provides a variety of modeling techniques, and offers GPU accelerated computation.
The Intel compilers for both C/C++ and FORTRAN.
The versions currently available at OSC are:
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.
The only access to significant resources on the HPC machines is through the batch process.
Access to the OSC clusters is through a system of login nodes. These nodes are reserved solely for the purpose of managing your files and submitting jobs to the batch system. Acceptable activities include editing/creating files, uploading and downloading files of moderate size, and managing your batch jobs. You may also compile and link small-to-moderate size programs on the login nodes.
This section summarizes two groups of batch-related commands: commands that are run on the login nodes to manage your jobs and commands that are run only inside a batch script. Only the most common options are described here.
Many of these commands are discussed in more detail elsewhere in this document. All have online manual pages (example: man sbatch ) unless otherwise noted.
In describing the usage of the commands we use square brackets [like this] to indicate optional arguments. The brackets are not part of the command.
Slurm directives may appear as header lines in a batch script or as options on the sbatch command line. They specify the resource requirements of your job and various other attributes. Many of the directives are discussed in more detail elsewhere in this document. The online manual page for sbatch (man sbatch) describes many of them.
