Using application software and libraries

CITI offers a number of popular application software packages and libraries for your use. We will add things over time, so please check back often and refer to the

module avail

for additions and current version numbers. If particular software is of interest to you, please let us know and we will investigate installation on palmetto.

Some software has been purchased by certain faculty and research groups and is available only to them via a license service. We currently do not have plans to list those here.

GROMACS

GROMACS is a package to perform molecular dynamics, to simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions. Since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

MATLAB

MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.

Intel® Math Kernel Library (MKL)

The Intel Math Kernel Library (MKL) offers highly optimized, extensively threaded math routines for scientific, engineering, and financial applications that require maximum performance. MKL includes

• Basic Linear Algebra Subprograms (BLAS)
• Linear Algebra Package (LAPACK)
• Scalable LAPACK (ScaLAPACK)
• Vector Statistical Library
• Vector Math Library
• Fast Fourier Transforms

PETSc

PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for all message-passing communication.

FFTW

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 (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.

gsl - GNU Scientific Library

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.