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SDSC > User Support > Compute and Data Resource Guides > Gordon > Gordon Software Packages

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.



















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