Alphabetical list of software installed on PSC machines

If you are unfamiliar with the formatting of this list, take a look at this description.

ABINIT, finds the total energy, charge density and electronic structure of systems of electrons and nuclei within DFT using pseudopotentials and a planewave basis.

(Warhol)

ADINA, a general linear and nonlinear finite element analysis system.

(Blacklight)

ALLPATHS-LG, a whole-genome shotgun assembler.

(Blacklight)

AMBER, uses classical mechanics to study large molecules.

(Blacklight, Salk)

BLAS, routines for performing vector and matrix operations.

( Salk)

CHARMM, mechanics and dynamics of macromolecular systems. Academic and industrial users must make special arrangements for use. See the documentation for details.

(Blacklight, Salk)

CPMD, a parallelized, plane wave/pseudo-potential DFT package, designed for ab-inito molecular mechanics.

(Blacklight)

DESMOND, a molecular dynamics package.

(Blacklight)

DMOL3, an ab initito quantum chemistry software package.

(Blacklight)

DRAWP3D, a PSC developed 3D graphics library.

Source code is available.

DReAMM, PSC developed visualization package for MCell models.

FFTW, a C subroutine library for computing Discrete Fourier Transforms.

(Blacklight, Salk, Warhol)

FLUENT, a fluid dynamics solver which can model fluid flow and heat transfer in complex geometries.

(Blacklight, Warhol)

GAMESS, an ab initio molecular quantum chemistry program.

(Blacklight)

GAUSSIAN, an ab initio quantum chemistry program. Academic and industrial users must make special arrangements for use. See the documentation for details.

(Blacklight, Salk, Warhol)

GNUPLOT, an interactive 2-and 3-D function and data plotting program.

(Blacklight, Salk)

GROMACS, molecular dynamics package.

( Salk)

HDF (Hierarchical Data Format), a multi-object file format that facilitates the transfer of various types of scientific data between machines and operating systems.

(Blacklight, Warhol)

IPM, performance profiling tool for parallel MPI applications.

(Blacklight)

LAMMPS, a classical molecular dynamics code.

(Blacklight)

LS-DYNA, a general purpose transient dynamic finite element program.

(Blacklight, Warhol)

LSMS, uses the locally self-consistent multiple scattering method to calculate the electronic structure of large systems within the local density approximation.

m2e, a tool to translate MFIX data files to Ensight 6 data files.

Source code is available.

m2t, a tool to print information from MFIX data files.

Source code is available.

MATLAB, a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages.

(Blacklight)

MCELL, (Monte Carlo Cell), simulates the movements and reaction of molecules within and between cells.

(Salk)

MESA, an open source implementation of the OpenGL library.

(Blacklight)

MFIX, a general program describing hydrodynamics, heat transfer, and chemical reactions in fluid-solids systems. (See also MFIXReader, m2e, m2t, and py2dx.)

(License restictions apply; see documentation)

MFIXReader, a library of routines that can read MFIX data files.

Source code is available.

MKL, Math Kernel Library, highly optimized and threaded routines for linear algebra, FFTs, vector math and random number generators.

(Blacklight, Salk, Warhol)

MODULE, a package which provides for the dynamic modification of a user environment.

(Blacklight, Salk, Warhol)

MOLPRO, MOLPRO is a complete system of ab initio programs for molecular electronic structure calculations.

(Blacklight)

MPFR, a C library for multiple-precision floating-point computations with correct rounding.

(Blacklight, Warhol)

MPI/ MPICH, Message Passing Interface, a communications substrate for scientific computing. MPICH, an implementation of MPI, was a joint-effort project between Argonne National Laboratories and Mississippi State University.

(Blacklight, Salk)

NAMD, a parallel, object-oriented molecular dynamics code for the simulation of large biomolecular systems.

(Blacklight, Salk, Warhol)

NETCDF, an interface for array-oriented data access and a library that provides an implementation of the interface.

(Blacklight)

NETLIB, an electronic repository, available through email and the WWW, of mathematical software, data, documents, address lists, and other useful items. In particular, take a look at toms and quadpack.

NWCHEM, uses quantum mechanical descriptions of electronic wavefunctions or density to compute the properties of molecular or periodic systems.

(Blacklight)

OpenFOAM, an open source finite volume CFD package.

(Blacklight, Warhol)

PAPI, an API for accessing hardware performance counters.

(Blacklight)

PARAVIEW, open source program for the visualization of scientific, engineering, and analytical data.

(Blacklight)

PETSC, a suite of routines for the solution of large scale scientific applications modeled by partial differential equations.

(Blacklight, Warhol)

PYTHON, a powerful, object-oriented programming language.

(Blacklight)

PY2DX, Python extensions for the OpenDX visualization package.

Source code is available.

Quantum Espresso, an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale.

(Blacklight)

R, a language and environment for statistical computing and graphs.

(Blacklight)

SIESTA, electronic structure calculation and ab initio molecular dynamics simulation software.

(Blacklight)

StarSplatter, a tool to create images and animations from astrophysical particle simulation data.

TAU, Tuning and Analysis Utility.

(Blacklight)

TRINITY, a package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data.

(Blacklight)

UPC, Unified Parallel C.

(Blacklight, Salk)