Gordon Software Packages

Software Package	Compiler Suites	Parallel Interface
AMBER: Assisted Model Building with Energy Refinement	intel	mvapich2_ib
APBS: Adaptive Poisson-Boltzmann Solver	intel	mvapich2_ib
Car-Parrinello 2000 (CP2K)	intel	mvapich2_ib
DDT
FFTW: Fastest Fourier Transform in the West	intel,pgi,gnu	mvapich2_ib
GAMESS: General Atomic Molecular Electronic Structure System	intel	native: sockets, ip over ib vsmp: scalemp mpich2
GAUSSIAN	pgi	Single node, shared memory
GROMACS: GROningen MAchine for Chemical Simulations	intel	mvapich2_ib
HDF4/HDF5: Hierarchical Data Format	intel,pgi,gnu	mvapich2_ib for hdf5
Lammps:Large-scale Atomic/Molecular Massively Parallel Simulator.	intel	mvapich2_ib
NAMD: NAnoscale Molecular Dynamics	intel	mvapich2_ib
NCO: NetCDF Operators	intel,pgi,gnu	none
NetCDF: Network Common Data Format	Intel,pgi,gnu	none
Python modules (scipy etc)	gnu:ipython,nose,pytz intel:matplotlib,numpy,scipy,pyfits,	None
VisIt Visualization Package	intel	openmpi
Software Package Descriptions
AMBER AMBER is package of molecular simulation programs including SANDER (Simulated Annealing with NMR-Derived Energy Restraints) and a modified version PMEME (Particle Mesh Ewald Molecular Dynamics) that is faster and more scalable.
top APBS APBS evaluates the electrostatic properties of solvated biomolecular systems.
CP2K CP2K is a program to perform simulations of molecular systems. It provides a general framework for different methods such as e.g., density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials. CP2K documentation.
top DDT DDT is a debugging tool for scalar, multithreaded and parallel applications. DDT Debugging Guide from TACC.
FFTW FFTW is a library for computing the discrete Fourier transform in one or more dimensions, of arbitrary input size, and of both real and complex data. FFTW documentation.
top GAMESS GAMESS is a program for ab initio quantum chemistry. GAMESS can compute SCF wavefunctions, and correlation corrections to these wavefunctions as well as Density Functional Theory. GAMESS documentation, examples, etc.
Gaussian 09 Gaussian 09 provides state-of-the-art capabilities for electronic structure modeling.
top GROMACS GROMACS is a versatile package to perform molecular dynamics, It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids. GROMACS Online Manual.
HDF HDF is a collection of utilities, applications and libraries for manipulating, viewing, and analyzing data in HDF format. HDF 5 Resources.
top LAMMPS LAMMPS is a classical molecular dynamics simulation code.
NAMD NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD User's Guide.
top NCO NCO takes NetCDF files as input, then operates (e.g., derive new data, average, print, hyperslab, manipulate metadata) and outputs the results to screen or files in text, binary, or netCDF formats. Visit the NCO site on Source Forge.
NetCDF NetCDF is a set of libraries that support the creation, access, and sharing of array-oriented scientific data using machine-independent data formats. Learn more about NetCDF at UCAR's Unidata site.
top Python Modules (scipy etc.) The modules under /opt/scipy consist of: node,numpy,scipy,matplotlib,pyfits,ipython,and pytz. View an online video tutorial from a TACC workshop on Python. Khan Academy has several videos on Python. The HPC University includes a few resources for Python.
VisIt Visualization Package The VisIt visualization package supports remote submission of parallel jobs and includes a Python (see above) interface that provides bindings to all of its plots and operators so they may be controlled by scripting. View the "Getting Started With VisIt on Gordon" tutorial.

Gordon Software Packages

Software Package

Compiler Suites

Parallel Interface

Software Package Descriptions