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Python is a high-level, multi-paradigm programming language that is both easy to learn and useful in a wide variety of applications. Python has a large standard library as well as a large number of third-party extensions, most of which are completely free and open source.
The Vienna Ab initio Simulation Package, VASP, is a suite for ab-initio quantum-mechanical molecular dynamics (MD) simulations and electronic structure calculations.
Stata is a complete, integrated statistical package that provides everything needed for data analysis, data management, and graphics. 32-processor MP version is currently available at OSC.
ScaLAPACK is a library of high-performance linear algebra routines for clusters supporting MPI. It contains routines for solving systems of linear equations, least squares problems, and eigenvalue problems.
This page documents usage of the ScaLAPACK library installed by OSC from source. An optimized implementation of ScaLAPACK is included in MKL; see the software documentation page for Intel Math Kernel Library for usage information.
Fortran, C, and C++ compilers exist from the Portland Group.
OpenFOAM is a suite of computational fluid dynamics applications. It contains myriad solvers, both compressible and incompressible, as well as many utilities and libraries.
Availability and Restrictions
The following versions of OpenFOAM are available on OSC clusters:
MATLAB is a technical computing environment for high-performance numeric computation and visualization. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an easy-to-use environment where problems and solutions are expressed just as they are written mathematically--without traditional programming.
NetCDF (Network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netcdf library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD generally scales well on OSC platforms and offers a variety of modelling techniques. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR.