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OSC has several different file systems where you can create files and directories. The characteristics of those systems and the policies associated with them determine their suitability for any particular purpose. This section describes the characteristics and policies that you should take into consideration in selecting a file system to use.
The various file systems are described in subsequent sections.
The storage at OSC consists of servers, data storage subsystems, and networks providing a number of storage services to OSC HPC systems. The current configuration consists of:
LS-DYNA is a general purpose finite element code for simulating complex structural problems, specializing in nonlinear, transient dynamic problems using explicit integration. LS-DYNA is one of the codes developed at Livermore Software Technology Corporation (LSTC).
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.
Availability and Restrictions
The versions currently available at OSC are:
A job script, or PBS batch script, is a text file containing job setup information for the batch system followed by commands to be executed. It can be created using any text editor and may be given any name. Some people like to name their scripts something like myscript.job or myscript.pbs, but myscript works just as well.
The only access to significant resources on the HPC machines is through the batch process. This guide will provide an overview of OSC's computing environment, and provide some instruction for how to use the batch system to accomplish your computing goals. The menu at the right provides links to all the pages in the guide, or you can use the navigation links at the bottom of the page to step through the guide one page at a time.
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.