HPC/Applications

This is the catalog for HPC applications on Carbon. Applications are often referred to as modules because they are managed using the Environment Modules package.

Index

General modeling, analysis, and visualization

mathematica
matlab
comsol
povray

Molecular Visualization

jmol
rasmol
vmd
xcrysden
GaussView
rings
atomeye

Quantum/DFT

libxc
atk
abinit
cp2k
dacapo

dacapo-python

g03
g09
gpaw

gpaw-setups

molpro
nwchem
octopus
phonopy
q-chem
quantum-espresso

wannier90

pwgui

siesta
vasp

vasp-vtst

vasp-vtstscripts

vasp5
wien2k

Classical MD

amber
lammps
namd
asap
asap3
packmol

Nanophotonics and fabrication

lumerical
meep
ddscat
layout-beamer

Toolkits

Numeric
ScientificPython
ase2
ase3
campos
campos-ase3
vtk

Libraries

atlas
GotoBLAS
fftw3
harminv
hdf5

h5utils

libctl
libint
libint2
libmatheval
netcdf
numpy
scipy
openmpi
charm
boost
cuda
fox

Development

python
icc

icc/10

icc/11

icc/12

ifort

ifort/10

ifort/11

ifort/12

idb

idb/10

idb/11

idb/12

impi
mkl
intel-licenses

Deprecated

intel

intel/10

intel/11

System

moab
gold

Modules

embody
dot
null
use.own

• See also: System packages, in particular:
  • Applications/Engineering
  • Applications/Multimedia
  • Development/Languages
• Packages supporting GPUs:
  • lammps
  • namd
  • q-chem (to be confirmed)

Summaries

Query date: 2013-06-25, 10:25.

Name	Date	Summary	Versions
comsol	2013-01-14	COMSOL Multiphysics simulation software	4.1-1 4.2-1 4.2a-1 4.3-1 4.3a-1 4.3b-1 4.3b-2
mathematica	2012-04-06	Computing environment for modeling, simulation, visualization	7.0.1-1 8.0.4-1
matlab	2013-02-11	Language and interactive environment for numerical computation	R2012b-1 R2013a-2
povray	2011-08-09	Persistence of Vision Ray-Tracer	3.7.0.RC3-1 3.7.0.RC3-2
atomeye	2012-10-31	Atomistic configuration viewer	kermode-2010-1
GaussView	2012-01-16	GaussView - graphical user interface for Gaussian09	5.0-1 5.0.9-1
jmol	2011-03-08	Molecule viewer for chemical structures in 3D	11.8.24-1 12.0.24-1 12.0.34-1 12.1.25-1 12.1.37-1 12.1.6-1
rasmol	2010-05-19	Fast molecular graphics program	2.6.4-foc-1 2.7.5-1
rings	2013-03-26	Rigorous Investigation of Networks Generated using Simulations	1.2.1-1 1.2.3-1
vmd	2010-05-18	Mol-Vis for biomolecular systems, with 3-D graphics, built-in scripting	1.8.6 1.8.7-1
xcrysden	2011-02-24	Simple molecular viewer with isosurfaces and contours	1.5.21-1
abinit	2013-05-07	Electronic structure modeling package	6.12.3-3 7.0.5-1 7.0.5-2 7.2.1-2
atk	2013-03-01	Atomistix ToolKit (ATK) from QuantumWise	10.8.0-1 10.8.1-1 10.8.2-1 10.8.2-2 10.8.2-3 11.2.0-1 11.2.1-1 11.2.3-1 11.8.2-1 12.2.0-1 12.2.2-1 12.8.0-1 12.8.1-1 12.8.2-1
cp2k	2012-05-15	Classical and DFT-based atomistic simulations	2.2-2 2.2-3 2.2-4
dacapo	2010-02-23	Dacapo - a total energy program based on density functional theory	2.7.15-ifort-2 2.7.15-ifort-3 2.7.15-ifort-5 2.7.7
dacapo-python	2010-03-09	ASE calculator for Dacapo (python interface)	0.9.4-1 0.9.4-5 0.9.4-5b
g03	2011-02-24	Gaussian 03 - an electronic structure program	C.02.i386-2 C.02.i386-3
g09	2012-01-16	Gaussian 09 - an electronic structure program	A.02.x86_64-1 A.02.x86_64-2 C.01.x86_64-1
gpaw	2012-09-11	GPAW - a grid-based density-functional theory (DFT) Python code	0.4-gcc-4 0.4-gcc-5 0.4-gcc-6 0.4.1762-1 0.6-gcc-1 0.6-gcc-2 0.6-gcc-3 0.8.0-gcc-1 0.8.0-gcc-2 0.8.0-gcc-3 0.9.0-gcc-1 0.9.0-gcc-3
gpaw-setups	2011-09-21	Pseudopotential data for GPAW (see module gpaw)	0.4.2039 0.5.3574 0.6.6300 0.8.7929
libxc	2011-11-11	Exchange-correlation functionals for density-functional theory	1.1.0-1
molpro	2010-06-25	Quantum chemistry package	2009.1-1 2009.1-2
nwchem	2013-01-24	Computational chemistry tool from PNNL	6.1-1 6.1.1-1
octopus	2013-01-29	Octopus - time-dependent Density-Functional Theory (DFT)	3.0.1-intel10-mkl10.0.2.018-openmpi13-4 3.1.0-intel10-mkl10.1.1.019-1 3.1.0-intel10-mkl10.1.1.019-openmpi13-1 4.0.0-4 4.0.1-1 4.0.1-3 4.0.1-4 4.0.1-5 4.0.1-6 4.0.1-7 4.0.1-8
phonopy	2013-02-25	Phonon analyzer interfacing to various calculators	1.2.1-1 1.6.3-1
pwgui	2011-02-24	Quantum ESPRESSO GUI	4.2-1
q-chem	2012-10-24	Q-Chem - ab initio quantum chemistry package	3.2.0.1-1 3.2.0.2-1 4.0.0.1-1 4.0.0.2-1 4.0.1-2
quantum-espresso	2013-01-18	Quantum ESPRESSO suite, with plugins	4.2.1-2 4.3.2-1 4.3.2-2
siesta	2010-06-16	Spanish Initiative for Electronic Simulations with Thousands of Atoms	3.0-rc1-3
vasp	2012-11-12	VASP - Vienna Ab-initio Simulation Package	4.6.35-mkl-10 4.6.35-mkl-11 4.6.35-mkl-12 4.6.35-mkl-13 4.6.35-mkl-7 4.6.35-mkl-8 4.6.35-mkl-nozheevx-8 4.6.36-mkl-1
vasp-vtst	2011-03-01	VASP - Vienna Ab-initio Simulation Package	4.6.35-mkl-10 4.6.35-mkl-11 4.6.35-mkl-12 4.6.35-mkl-7 4.6.35-mkl-8
vasp-vtstscripts	2012-03-19	Vasp TST Tools - scripts to help with VASP calculations	2.03d-1 2009-06-12-1 2011-08-24-1 2012-11-11-1
vasp5	2013-05-02	VASP - Vienna Ab-initio Simulation Package	5.2.11-mkl-3 5.2.12-mkl-3 5.2.12a-mkl-1 5.2.12a-mkl-4 5.2.12a-mkl-5 5.2.12a-mkl-7 5.2.8-mkl-2 5.3.2-mkl-1 5.3.2-mkl-2 5.3.3-mkl-1 5.3.3-mkl-2 5.3.3p1-mkl-1 5.3.3p3-mkl-1 5.3.3p3-mkl-2
wannier90	2011-02-24	Maximally-Localised Generalised Wannier Functions Code	1.2-1
wien2k	2010-01-17	WIEN2k - electronic structure calculations of solids; all-electron DFT LAPW	09.2-1
amber	2013-02-13	Molecular mechanical force fields and simulation programs	11.0-6 12.0-1
asap	2009-10-27	ASE calculator for Dacapo (python interface)	3.2.0-1
asap3	2009-10-27	ASE calculator for Dacapo (python interface)	3.2.0-1
lammps	2012-11-02	LAMMPS - Sandia's Large-scale Atomic/Molecular Massively Parallel Simulator	2010-09-09-parallel-1 2010-12-05-parallel-3 2012-02-12-parallel-1 2012-02-12-parallel-jr-10 2012-02-12-parallel-jr-11 2012-10-10-3
namd	2012-11-05	NAMD - parallel, object-oriented molecular dynamics	2.6.2009-02-11-Linux-x86_64-MPI-icc-1 2.7b1-MPI-icc-1 2.9-MPI-icc-4 2.9plus-MPI-icc-3
packmol	2013-05-03	Pack molecules in space as starting points for molecular dynamics	13.112-1 13.112-2
ddscat	2013-01-31	Scattering and absorption of light on irregular particles	7.2.2-3
layout-beamer	2009-03-25	LayoutBEAMER - layout preparation for e-beam lithography devices	3.2.0beta 3.3.0beta2_64 3.3.0beta_64 3.3.0beta_64-1
lumerical	2013-05-17	Lumerical FDTD Solutions - microscale optics simulation	6.5.5-1 7.5.4-1 7.5.7-1 8.0.5-1 8.0.7-1 8.5.4-1 8.6.2-1
meep	2011-07-26	finite-difference time-domain (FDTD) simulation software from MIT	1.0-parallel-4 1.0-parallel-5 1.0-serial-4 1.0-serial-5 1.1.1-parallel-1 1.1.1-parallel-2 1.1.1-serial-1
ase2	2009-01-19	ASE is an Atomistic Simulation Environment in Python.	2.3.13-1 2.3.13-2 2.3.13-3
ase3	2012-11-10	ASE is an Atomistic Simulation Environment in Python.	3.0.0-3 3.2.0-1 3.2.0-3 3.4.1-1 3.5.1-1 3.6.0-1
campos	2009-02-20	Compound: The CAMPOS modelling suite	stable
campos-ase3	2009-04-04	ASE is an Atomistic Simulation Environment in Python.	3.1.0-2
Numeric	2009-06-18	Numeric was the first arrayobject built for Python.	24.2-1 24.2-3
ScientificPython	2009-01-19	ScientificPython is a Python library for scientific computing.	2.4.11-1 2.4.11-3 2.8-1 2.8-2
vtk	2011-05-22	VTK - a system for 3D graphics, image processing, and visualization	5.0.4-icc-3
atlas	2009-01-30	ATLAS - Automatically Tuned Linear Algebra Software (BLAS and a subset of LAPACK)	3.8.0-4
boost	2011-08-09	Portable C++ source libraries	1.47.0-1
charm	2009-02-13	Charm++ - message-passing parallel language and runtime system	6.0-mpi-linux-x86_64-ifort-mpicxx-1 6.0-mpi-linux-x86_64-ifort-smp-mpicxx-1 6.1b-2009-04-02-mpi-linux-x86_64-ifort-mpicxx-1 6.4.0-mpi-linux-x86_64-ifort-mpicxx-1 6.4.0-mpi-linux-x86_64-ifort-smp-mpicxx-1
cuda	2012-09-25	Development environment for GPU-accelerated applications	4.2.9-1 5.0-1
fftw3	2012-07-30	library for computing the discrete Fourier transform (DFT)	3.2.1-1 3.2.2-1 3.3-1 3.3.2-1 3.3.2-4
fox	2013-05-07	A Fortran library for XML	4.1.2-1
GotoBLAS	2009-02-09	Goto BLAS - fast implementation of the Basic Linear Algebra Subroutines	1.26-gfortran-1 1.26-gfortran-smp-1 1.26-intel-1 1.26-intel-smp-1
h5utils	2009-09-10	utilities for visualization and conversion of scientific data in HDF5 format	1.12.1-1 1.12.1-2 1.12.1-3
harminv	2011-07-26	Harminv - program and library to solve harmonic inversion problems	1.3.1-mkl-4 1.3.1-netlib-4
hdf5	2011-07-26	HDF5 - management of extremely large and complex data collections	1.8.3-parallel-4 1.8.3-serial-4
libctl	2013-02-04	Guile-based library for control files for scientific simulations	3.0.3-4 3.0.3-5
libint	2012-05-14	library for two-body integrals over Gaussian functions	1.1.4-1
libint2	2012-05-22	library for two-body integrals over Gaussian functions	2.0.0-2
libmatheval	2009-09-10	library to parse and evaluate symbolic expressions	1.1.7-2 1.1.7-3
netcdf	2009-02-22	NetCDF - network Common Data Form libraries	3.6.3-gfortran-4 3.6.3-gfortran-5 3.6.3-intel10-4 3.6.3-intel10-5 3.6.3-intel11-4 3.6.3-intel11-5
numpy	2011-11-21	Numerical computing with Python	1.0.4-mkl-1 1.6.1-4 1.6.1-5
openmpi	2013-01-14	Open MPI - A High Performance Message Passing Library	1.2.7-gcc 1.3-gcc-4 1.3-gcc-4.orig 1.3-intel10-4 1.3-intel11-4 1.3.2-gcc-1 1.3.2-gcc-1.orig 1.3.2-intel10-1 1.3.2-intel10-2 1.3.2-intel11-1 1.4.1-gcc-2 1.4.1-intel10-2 1.4.1-intel11-1 1.4.1-intel11-2 1.4.1-intel11-3 1.4.1-intel11-4 1.4.1-intel11-5 1.4.2-intel10-1 1.4.2-intel11-1 1.4.2-intel12-1 1.4.3-gcc-1 1.4.3-intel10-1 1.4.3-intel11-1 1.4.3-intel12-1 1.4.4-gcc-1 1.4.4-intel10-1 1.4.4-intel11-1 1.4.4-intel12-1 1.4.4-intel12-2 1.4.5-gcc-1 1.4.5-intel11-1 1.4.5-intel12-1
scipy	2011-11-22	Scientific computing with Python	0.10.0-1 0.9.0-1
icc	2013-02-07	The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025 11.0.074 11.0.081 11.0.083 11.1.056 11.1.059 11.1.064 11.1.072 11.1.073
icc/10	2013-02-07	The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025
icc/11	2013-02-07	The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture	11.0.074 11.0.081 11.0.083 11.1.056 11.1.059 11.1.064 11.1.072 11.1.073
icc/12	2013-02-07	The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture	12.0.2 12.0.4 12.1.0 12.1.0.7 12.1.2 12.1.4 12.1.6
idb	2013-02-07	The Intel debugger for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025 11.0.074 11.0.081 11.0.083 11.1.059 11.1.064 11.1.072 11.1.073
idb/10	2013-02-07	The Intel debugger for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025
idb/11	2013-02-07	The Intel debugger for the x86_64/EM64T/Intel64 architecture	11.0.074 11.0.081 11.0.083 11.1.059 11.1.064 11.1.072 11.1.073
idb/12	2013-02-07	The Intel debugger for the x86_64/EM64T/Intel64 architecture	12.0.2 12.0.4 12.1.0 12.1.0.7 12.1.2 12.1.4 12.1.6
ifort	2013-02-07	The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025 11.0.074 11.0.081 11.0.083 11.1.056 11.1.059 11.1.064 11.1.072 11.1.073
ifort/10	2013-02-07	The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture	10.0.023 10.1.013 10.1.015 10.1.017 10.1.022 10.1.025
ifort/11	2013-02-07	The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture	11.0.074 11.0.081 11.0.083 11.1.056 11.1.059 11.1.064 11.1.072 11.1.073
ifort/12	2013-02-07	The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture	12.0.2 12.0.4 12.1.0 12.1.0.7 12.1.2 12.1.4 12.1.6
impi	2013-02-07	The Intel MPI implementation for the x86_64/EM64T/Intel64 architecture	3.0 3.1 3.2.0.011 3.2.2.006 4.0.0.025 4.0.0.028 4.0.1.007 4.0.2.003 4.0.3.008 4.1.0.024 4.1.0.030
intel-licenses	2010-05-23	Enable non-version-specific licenses for the Intel compilers and libraries
mkl	2013-02-07	The Intel Math Kernel Library for the x86_64/EM64T/Intel64 architecture	09.1.023 10.0.005 10.0.2.018 10.0.3.020 10.0.4.023 10.1.0.015 10.1.1.019 10.1.2.024 10.2.2.025 10.2.3.029 10.2.4.032 10.2.5.035 10.2.6.038 10.3.10 10.3.12 10.3.2 10.3.4 10.3.6 10.3.7 10.3.8
python	2012-07-12	An interpreted, interactive, object-oriented programming language.	2.7.3-1
intel	2009-02-21	Compound: Intel compilers and MKL version 11	10.1.015 10.1.022 11.0.074 11.0.081
intel/10	2009-10-20	Compound: Intel compilers version 10	10.1.015 10.1.022 10.1.025
intel/11	2011-02-24	Compound: Intel compilers and MKL version 11	11.0.074 11.0.081 11.0.083 11.1.056 11.1.064 11.1.073
gold	2012-06-10	Open source accounting system for High Performance Computers	2.1.11.0-4 2.1.11.0-5 2.1.8.1-1 2.2.0.4-1 2.2.0.4-2 2.2.0.5-1 2.2.0.5-2
moab	2013-05-30	Moab Workload Manager - a policy-based job scheduler and event engine	5.4.4-1 6.0.3-1 6.0.6-2 6.1.10-1 6.1.11-1 6.1.3-1 6.1.3-2 6.1.3-3 6.1.8-1 6.1.9-1
dot	2008-03-05	adds `.' to your PATH environment variable	3.2.6
embody	2013-05-07	EMBODY - Environment Modules Build system	0.9.26 1.0.0 1.0.2
null	2008-03-05	does absolutely nothing	3.2.6
use.own	2008-03-05	adds your own modulefiles directory to MODULEPATH	3.2.6
epics	2013-06-18	EPCIS	3.15.0.1-1
idl	2013-06-05	Scientific programming language	8.2.2-1
module-cvs	2008-03-05	get most recent module sources from CVS or ftp	3.2.6
module-info	2008-03-05	returns all various module-info values	3.2.6
modules	2008-03-05	loads the modules environment	3.2.6
p4vasp	2013-05-21	Tools for processing xml-formatted VASP output	0.3.26-1
readline	2013-06-18	Library for editing typed command lines	6.2-1
test	2012-07-18	Python path testing	0.1-1

Key to columns

• Name: Leads to the package descriptions below.
• Date: Modification date of the the default version's modulefile (not necessarily of the package itself).
• Summary: A one-line description.
• Versions: The version shown in bold is the default.

Descriptions

General modeling, analysis, and visualization

comsol

• 4.1-1, 4.2-1, 4.2a-1, 4.3-1, 4.3a-1, 4.3b-1, 4.3b-2

Continuum-level simulation software including modeler and visualization.

• fluid flow (CFD)
• heat transfer
• structural mechanics
• electromagnetics

Material properties, source terms and boundary conditions can be arbitrary functions of the dependent variables.

http://www.comsol.com/products/multiphysics/

mathematica

• 8.0.4-1

Mathematica is an extensive computer algebra system. Features include:

• Elementary mathematical function library
• Special mathematical function library
• Matrix and data manipulation tools including support for sparse arrays
• Support for complex number, arbitrary precision, interval arithmetic and symbolic computation
• 2D and 3D data and function visualization and animation tools
• Solvers for systems of equations, diophantine equations, ODEs, PDEs, DAEs, DDEs and recurrence relations
• Numeric and symbolic tools for discrete and continuous calculus
• Multivariate statistics libraries
• Constrained and unconstrained local and global optimization
• Programming language supporting procedural, functional and object oriented constructs
• Toolkit for adding user interfaces to calculations and applications
• Tools for image processing and morphological image processing
• Tools for visualizing and analysing graphs
• Tools for combinatoric problems
• Data mining tools such as cluster analysis, sequence alignment and pattern matching
• Number theory function library
• Continuous and discrete integral transforms
• Import and export filters for data, images, video, sound, CAD, GIS, document and biomedical formats
• Database collection for mathematical, scientific, and socio-economic information
• Notebook interface for review and re-use of previous inputs and outputs including graphics and text annotations
• Technical word processing including formula editing and automated report generating
• Tools for connecting to SQL, Java, .NET, C++, FORTRAN and http based systems
• Tools for parallel programing

Start the kernel (text UI): math Start the GUI frontend: mathematica

http://www.wolfram.com/

• 7.0.1-1

Mathematica is an extensive computer algebra system. Features include:

• Elementary mathematical function library
• Special mathematical function library
• Matrix and data manipulation tools including support for sparse arrays
• Support for complex number, arbitrary precision, interval arithmetic and symbolic computation
• 2D and 3D data and function visualization and animation tools
• Solvers for systems of equations, diophantine equations, ODEs, PDEs, DAEs, DDEs and recurrence relations
• Numeric and symbolic tools for discrete and continuous calculus
• Multivariate statistics libraries
• Constrained and unconstrained local and global optimization
• Programming language supporting procedural, functional and object oriented constructs
• Toolkit for adding user interfaces to calculations and applications
• Tools for image processing and morphological image processing
• Tools for visualizing and analysing graphs
• Tools for combinatoric problems
• Data mining tools such as cluster analysis, sequence alignment and pattern matching
• Number theory function library
• Continuous and discrete integral transforms
• Import and export filters for data, images, video, sound, CAD, GIS, document and biomedical formats
• Database collection for mathematical, scientific, and socio-economic information
• Notebook interface for review and re-use of previous inputs and outputs including graphics and text annotations
• Technical word processing including formula editing and automated report generating
• Tools for connecting to SQL, Java, .NET, C++, FORTRAN and http based systems
• Tools for parallel programing

http://www.wolfram.com/

matlab

• R2012b-1, R2013a-2

MATLAB is a high-level language and interactive environment for numerical computation, visualization, and programming. You can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java.

To run the GUI remotely, VNC is recommended instead of X11.

Licensed to run on login5, by Argonne employees only.

http://www.mathworks.com/

povray

• 3.7.0.RC3-1, 3.7.0.RC3-2

POVRay - The Persistence of Vision Ray-Tracer creates three-dimensional, photo-realistic images using a rendering technique called ray-tracing. It reads in a text file containing information describing the objects and lighting in a scene and generates an image of that scene from the view point of a camera also described in the text file. Ray-tracing is not a fast process by any means, but it produces very high quality images with realistic reflections, shading, perspective and other effects.

Renderings of the scene samples and the include portfolio are located in $POVRAY_HOME/share/rendered/.

Requires: module load boost

http://www.povray.org/

Molecular Visualization

atomeye

• kermode-2010-1

AtomEye is a molecular visualization tool with these key features:

• XYZ, PDB, and native CFG formats
• periodic boundary conditions
• high-resolution bitmap PNG/JPEG/EPS screenshots (bitmap only)
• handles gzip- or bzip2-compressed input
• order-N in execution time and memory; supports more than 1 million atoms
• coordination number color-encoding with customizable cutoff radii and invisibility controls
• local atomic von Mises shear strain invariant color-encoding
• up to 16 arbitrary cutting planes with advancing / rotation / flipping controls
• animation script for making movies
• interactive command line

AtomEye (c) Ju Li. http://mt.seas.upenn.edu/Archive/Graphics/A

Modifications to read XYZ and NetCDF files and Python interface (c) James Kermode 2008-2010 <[email protected]>

http://www.jrkermode.co.uk/AtomEye

GaussView

• 5.0.9-1

GaussView is a graphical user interface designed to help you prepare input for submission to Gaussian and to examine graphically the output that Gaussian produces. GaussView is not integrated with the computational module of Gaussian, but rather is a front-end/back-end processor to aid in the use of Gaussian.

To start: gview (NOT: gv)

http://gaussian.com/g_tech/gv5ref/gv5ref_toc.htm

• 5.0-1

GaussView is a graphical user interface designed to help you prepare input for submission to Gaussian and to examine graphically the output that Gaussian produces. GaussView is not integrated with the computational module of Gaussian, but rather is a front-end/back-end processor to aid in the use of Gaussian.

http://gaussian.com/g_tech/gv5ref/gv5ref_toc.htm

jmol

• 11.8.24-1, 12.0.24-1, 12.0.34-1, 12.1.25-1, 12.1.37-1, 12.1.6-1

Jmol is a molecule viewer platform for researchers in chemistry and biochemistry, implemented in Java for multi-platform use. This is the standalone application. It offers high-performance 3D rendering with no hardware requirements and supports many popular file formats.

http://jmol.sourceforge.net/

http://wiki.jmol.org/

rasmol

• 2.6.4-foc-1, 2.7.5-1

RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The program reads in a molecule co-ordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.

http://www.openrasmol.org/

rings

• 1.2.1-1, 1.2.3-1

The R.I.N.G.S. code (Rigorous Investigation of Networks Generated using Simulations) analyzes the results of molecular dynamics simulations. Its main feature connectivity analysis using ring statistics.

Installed in $RINGS_HOME .

http://rings-code.sourceforge.net/

vmd

• 1.8.7-1

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

http://www.ks.uiuc.edu/Research/vmd/

• 1.8.6

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Copyright © 1995-2006 Board of Trustees of the nUiv. of Illinois and others

http://www.ks.uiuc.edu/Research/vmd/

xcrysden

• 1.5.21-1

XCrySDen (Crystalline Structures and Densities and X) is a crystalline and molecular visualisation program with support for superimposed isosurfaces and contours.

See also: module help quantum-espresso

Installed in $XCRYSDEN_HOME .

http://www.xcrysden.org/

Quantum/DFT

abinit

• 7.2.1-2

ABINIT is an electronic structure modeling package to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

ABINIT can optimize geometries and perform molecular dynamics, generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory (for molecules). Different utility programs are provided.

ABINIT is distributed under the GNU General Public Licence.

This module version supports netcdf+etsf_io+fox and libxc+wannier90 .

http://www.abinit.org/

• 6.12.3-3, 7.0.5-1, 7.0.5-2

ABINIT is an electronic structure modeling package to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

ABINIT can optimize geometries and perform molecular dynamics, generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory (for molecules). Different utility programs are provided.

ABINIT is distributed under the GNU General Public Licence.

http://www.abinit.org/

atk

• 10.8.0-1, 10.8.1-1, 10.8.2-1, 10.8.2-2

Atomistix ToolKit - a quantum-mechanical modeling package

• atomic-scale electrical transport properties of nanodevices
• open architecture
• scripting language and graphical user interface
• accurate first-principles and fast semi-empirical methods.
• handles large-scale systems with upwards of 1,000 atoms
• advanced electrostatic model
• geometry optimization of molecules and periodic structures

http://www.quantumwise.com/

• 10.8.2-3, 11.2.0-1, 11.2.1-1, 11.2.3-1, 11.8.2-1, 12.2.0-1, 12.2.2-1, 12.8.0-1, 12.8.1-1, 12.8.2-1

Atomistix ToolKit - a quantum-mechanical modeling package

• atomic-scale electrical transport properties of nanodevices
• open architecture
• scripting language and graphical user interface
• accurate first-principles and fast semi-empirical methods.
• handles large-scale systems with upwards of 1,000 atoms
• advanced electrostatic model
• geometry optimization of molecules and periodic structures

Note: This module should be loaded BEFORE vasp.

http://www.quantumwise.com/

cp2k

• 2.2-2, 2.2-3, 2.2-4

CP2K performs atomistic and molecular simulations of solid state, liquid, molecular, and biological 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.

Warning: There is little documentation, no warranty, no official release. Using the code for production quality simulations is possible but requires detailed knowledge about the active development.

Freely available under the GPL.

http://www.cp2k.org/

dacapo

• 2.7.15-ifort-2, 2.7.15-ifort-3, 2.7.15-ifort-5

Dacapo is a total energy program based on density functional theory. It uses a plane wave basis for the valence electronic states and describes the core-electron interactions with Vanderbilt ultrasoft pseudo-potentials.

The program performs self-consistent calculations for both Local Density Approximation (LDA) and various Generalized Gradient Approximation (GGA) exchange-correlations potentials, using state-of-art iterative algorithms. The code may perform molecular dynamics / structural relaxation simultaneous with solving the Schroedinger equations within density functional theory.

https://wiki.fysik.dtu.dk/dacapo/Dacapo

• 2.7.7

Dacapo is a total energy program based on density functional theory. It uses a plane wave basis for the valence electronic states and describes the core-electron interactions with Vanderbilt ultrasoft pseudo-potentials.

The program performs self-consistent calculations for both Local Density Approximation (LDA) and various Generalized Gradient Approximation (GGA) exchange-correlations potentials, using state-of-art iterative algorithms. The code may perform molecular dynamics / structural relaxation simultaneous with solving the Schroedinger equations within density functional theory.

This is a fairly old build from Jan. 2008.

https://wiki.fysik.dtu.dk/dacapo/Dacapo

dacapo-python

• 0.9.4-1, 0.9.4-5, 0.9.4-5b

This is the ASE calculator interface for Dacapo.

https://wiki.fysik.dtu.dk/dacapo/Installation#dacapo-python-interface

g03

• C.02.i386-2, C.02.i386-3

Gaussian 03 is the latest in the Gaussian series of electronic structure programs. Gaussian 03 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.

Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures. This article introduces several of its new and enhanced features.

Available to Argonne users only.

http://gaussian.com/

g09

• A.02.x86_64-1, A.02.x86_64-2, C.01.x86_64-1

Gaussian 09 is the latest in the Gaussian series of electronic structure programs. Gaussian 09 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.

Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures. This article introduces several of its new and enhanced features.

Available only to Argonne employees and students under confidentiality.

http://gaussian.com/ Help on running with Linda: http://gaussian.com/g_tech/g_ur/m_linda.htm

gpaw

• 0.4-gcc-4, 0.4-gcc-5, 0.4-gcc-6, 0.6-gcc-1, 0.6-gcc-2, 0.6-gcc-3, 0.8.0-gcc-1, 0.8.0-gcc-2, 0.8.0-gcc-3, 0.9.0-gcc-1, 0.9.0-gcc-3

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method. It uses real-space uniform grids and multigrid methods or atom-centered basis-functions. It features flexible boundary conditions, k-points and gradient corrected exchange-correlation functionals.

https://wiki.fysik.dtu.dk/gpaw/

• 0.4.1762-1

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method. It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.

https://wiki.fysik.dtu.dk/gpaw/

gpaw-setups

• 0.4.2039, 0.5.3574, 0.6.6300, 0.8.7929

Pseudopotential data for GPAW (see module gpaw).

https://wiki.fysik.dtu.dk/gpaw/

libxc

• 1.1.0-1

Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals that can be used by all the ETSF codes and also other codes. In libxc you can find different types of functionals: LDA, GGA, hybrids, mGGA (experimental) and LCA (not working). This functionals depend on local information, in the sense that the value of the potential at a given point depends only on the values of the density - and the gradient of the density and the kinetic energy density, for the GGA and mGGA cases, or the vorticity for LCA - at a given point.

It can calculate the functional itself and its derivative, for some functionals higher order derivatives are available. Libxc is written in C and has Fortran bindings. It is released under the LGPL license (v. 3.0). Contributions are welcome.

http://www.tddft.org/programs/octopus/wiki/index.php/Libxc

molpro

• 2009.1-1, 2009.1-2

Molpro is a system of ab initio programs for molecular electronic structure calculations. The emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods. Integral-direct local electron correlation methods reduce computational scaling.

Available for Argonne users.

http://www.molpro.net/

nwchem

• 6.1-1, 6.1.1-1

NWChem provides computational chemistry tools scalable to large problems and parallel computing. It can handle:

• Biomolecules, nanostructures, and solid-state
• From quantum to classical, and all combinations
• Gaussian basis functions or plane-waves
• Scaling from one to thousands of processors
• Properties and relativity

NWChem is developed and maintained by EMSL at Pacific Northwest National Laboratory (PNNL).

Distributed as open-source under the terms of the Educational Community License version 2.0 (ECL 2.0).

Please cite the following reference when publishing results obtained with NWChem:

M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha, E. Apra, T.L. Windus, W.A. de Jong, 'NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations' Comput. Phys. Commun. 181, 1477 (2010)

http://www.nwchem-sw.org/

octopus

• 3.0.1-intel10-mkl10.0.2.018-openmpi13-4

Octopus is an ab initio virtual experimentation program for a range of systems. Electrons are described quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.

This version was built with:

• intel/10.1.02210.1.022 mkl/10.0.2.018
• openmpi/1.3-intel10-4
• netcdf/3.6.3-intel10-4

Octopus is free software, released under the GPL license, so you are free to use it and modify it.

http://www.tddft.org/programs/octopus/

• 3.1.0-intel10-mkl10.1.1.019-1

Octopus is an ab initio virtual experimentation program for a range of systems. Electrons are described quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.

This version was built with:

• intel/10/10.1.02210/10.1.022 mkl/10.1.1.019
• without MPI
• netcdf/3.6.3-intel10-4

Octopus is free software, released under the GPL license, so you are free to use it and modify it.

http://www.tddft.org/programs/octopus/

• 3.1.0-intel10-mkl10.1.1.019-openmpi13-1

Octopus is an ab initio virtual experimentation program for a range of systems. Electrons are described quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.

This version was built with:

• intel/10/10.1.02210/10.1.022 mkl/10.1.1.019
• openmpi/1.3.2-intel10-1
• netcdf/3.6.3-intel10-4

Octopus is free software, released under the GPL license, so you are free to use it and modify it.

http://www.tddft.org/programs/octopus/

• 4.0.0-4, 4.0.1-1, 4.0.1-3, 4.0.1-4, 4.0.1-5, 4.0.1-6, 4.0.1-7, 4.0.1-8

Octopus is an ab initio virtual experimentation program for a range of systems. Electrons are described quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.

This version contains both the serial and parallel executables.

Octopus is free software, released under the GPL license, so you are free to use it and modify it.

http://www.tddft.org/programs/octopus/

phonopy

• 1.2.1-1, 1.6.3-1

Phonopy is a phonon analyzer based on the supercell approach and using:

• force constants from forces on atoms with finite displacements (Parlinski-Li-Kawazoe method)
• non-analytical-term correction (LO-TO splitting)

Selected features:

• Phonon dispersion relation (band structure)
• Phonon DOS and partial-DOS
• Phonon thermal properties, free energy, heat capacity, and entropy
• Thermal expansion and heat capacity at constant pressure within quasi-harmonic approximation (phonopy-qha)

Provides built-in interfaces for: VASP, VASP DFPT, Wien2k, FHI-aims; extensible for the other calculators via formatted files or a Python module.

License: LGPL after ver. 0.9.3 and GPL before 0.9.2.

http://phonopy.sourceforge.net/

pwgui

• 4.2-1

PWgui - a GUI for the PWscf subset of the Quantum ESPRESSO suite, supporting creation and editing of input files, and support for interactive runs of the PWscf programs.

The GUI can also use the XCRYSDEN program (http://www.xcrysden.org/) for the visualization of atomic structures from the pw.x input/output files, or for the visualization of properties calculated via the sequence: pw.x-->pp.x (when the property was saved into an XSF file).

The following PWscf programs are supported:

• pw.x
• ph.x
• pp.x
• projwfc.x
• d3.x
• ld1.x (atomic)

See also: module help quantum-espresso

Installed in $QUANTUM_ESPRESSO_GUI_HOME .

http://www.quantum-espresso.org/

q-chem

• 3.2.0.1-1, 3.2.0.2-1, 4.0.0.1-1, 4.0.0.2-1, 4.0.1-2

Q-Chem is a comprehensive ab initio quantum chemistry package. Its capabilities range from the highest performance DFT/HF calculations to high level post-HF correlation methods. Q-Chem tackles a wide range of problems including:

• Molecular Structures
• Chemical Reactions
• Molecular Vibrations
• Electronic Spectra
• NMR Spectra
• Solvation Effects

Q-Chem offers Fast DFT calculations with accurate linear scaling algorithms A wide range of post-HF correlation methods that are efficient and unique Quantum calculations extended with QM/MM and molecular dynamics Detailed description in Q-Chem paper

http://www.q-chem.com/

quantum-espresso

• 4.2.1-2, 4.3.2-1, 4.3.2-2

Quantum ESPRESSO (opEn Source Package for Research in Electronic Structure, Simulation, and Optimization) is a suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

Quantum ESPRESSO builds onto newly-restructured electronic-structure codes (PWscf, PHONON, CP90, FPMD, Wannier) that have been developed and tested by some of the original authors of novel electronic-structure algorithms - from Car-Parrinello molecular dynamics to density-functional perturbation theory - and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency is still our main focus.

This build contains the 'historical' QE core set, plus the WanT (Wannier transport) plugin. GPL-licensed.

See also: module help wannier90 module help pwgui module help xcrysden

Installed in $QUANTUM_ESPRESSO_HOME .

http://www.quantum-espresso.org/

http://www.wannier-transport.org/

siesta

• 3.0-rc1-3

SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Its main characteristics are:

• Kohn-Sham self-consistent density functional method in the local density (LDA-LSD) or generalized gradient (GGA) approximations.
• norm-conserving pseudopotentials in their fully nonlocal (Kleinman-Bylander) form.
• numeric finite-range atomic orbital basis, unlimited multiple-zeta and angular momenta, polarization and off-site orbitals.
• Projects the electron wavefunctions and density onto a real-space grid in order to calculate the Hartree and exchange-correlation potentials and their matrix elements.
• localized linear combinations of the occupied orbitals (valence-bond or Wannier-like functions), for O(N) time and memory scaling.
• dynamic memory allocation
• serial or parallel execution

Available for users with confirmed licenses.

http://www.icmab.es/siesta/

vasp

• 4.6.35-mkl-13, 4.6.36-mkl-1

VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.

This version provides a full set of binaries resulting from various compile-time configuration options, plus the VTST patch by Graeme Henkelman, http://theory.cm.utexas.edu/vtsttools/downloads/ .

Likewise, there are binaries to calculate the DOS projected in Bader Volumes, http://theory.cm.utexas.edu/bader/ .

Available to licensed users only.

http://cms.mpi.univie.ac.at/vasp/

• 4.6.35-mkl-10, 4.6.35-mkl-11, 4.6.35-mkl-12, 4.6.35-mkl-7, 4.6.35-mkl-8, 4.6.35-mkl-nozheevx-8

VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.

Available to licensed users only.

http://cms.mpi.univie.ac.at/vasp/

vasp-vtst

• 4.6.35-mkl-10, 4.6.35-mkl-11, 4.6.35-mkl-12, 4.6.35-mkl-7, 4.6.35-mkl-8

VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.

This version contains the VTST patch by Graeme Henkelman,

http://theory.cm.utexas.edu/vtsttools/downloads/

Available to licensed users only.

http://cms.mpi.univie.ac.at/vasp/

vasp-vtstscripts

• 2.03d-1, 2009-06-12-1, 2011-08-24-1, 2012-11-11-1

Vasp TST Tools - a set of scripts to perform common tasks to help with VASP calculations, and particularly with transition state finding. The included Vasp.pm perl module contains several simple routines that are used by many of the scripts.

http://theory.cm.utexas.edu/vtsttools/scripts/

vasp5

• 5.2.11-mkl-3, 5.2.12-mkl-3, 5.2.12a-mkl-1, 5.2.12a-mkl-4, 5.2.8-mkl-2

VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.

Available to licensed users only.

http://cms.mpi.univie.ac.at/vasp/

• 5.2.12a-mkl-5

VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.

This version provides a full set of binaries resulting from various compile-time configuration options, plus the VTST patch by Graeme Henkelman, http://theory.cm.utexas.edu/vtsttools/downloads/ .

Available to licensed users only.

http://cms.mpi.univie.ac.at/vasp/

• 5.2.12a-mkl-7, 5.3.2-mkl-1, 5.3.2-mkl-2, 5.3.3-mkl-1, 5.3.3-mkl-2, 5.3.3p1-mkl-1, 5.3.3p3-mkl-1, 5.3.3p3-mkl-2

VASP (Vienna Ab-initio Simulation Package) performs quantum-mechanical molecular dynamics (MD) using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Forces and stress can be used to relax atoms into their instantaneous groundstate.

This version provides a full set of binaries resulting from various compile-time configuration options, plus the VTST patch by Graeme Henkelman, http://theory.cm.utexas.edu/vtsttools/downloads/ .

Likewise, there are binaries to calculate the DOS projected in Bader Volumes, http://theory.cm.utexas.edu/bader/ .

Available to licensed users only.

http://cms.mpi.univie.ac.at/vasp/

wannier90

• 1.2-1

The wannier90 code obtains maximally-localised generalised Wannier functions, using them to calculate bandstructures, Fermi surfaces, dielectric properties, sparse Hamiltonians and many things besides.

The method is those of Marzari and Vanderbilt, except for entangled energy bands, where the method of Souza, Marzari and Vanderbilt is used.

See also: module help quantum-espresso

Installed in $WANNIER90_HOME .

http://www.wannier.org/

wien2k

• 09.2-1

WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. WIEN2k is an all-electron scheme including relativistic effects and has many features.

Available to registered users only.

http://www.wien2k.at/

Classical MD

amber

• 12.0-1

AMBER refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

This is the AMBER code, version 12.0, which is distributed by UCSF subject to a licensing agreement.

This module includes binary flavors for serial, parallel, and single-GPU.

http://ambermd.org/

• 11.0-6

AMBER refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

This is the AMBER code, version 11.0, which is distributed by UCSF subject to a licensing agreement.

http://ambermd.org/

asap

• 3.2.0-1

ASAP (As Soon As Possible) is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE). ASAP currently implements the Effective Medium Potential (EMT) for the elements Ni, Cu, Pd, Ag, Pt and Au (and their alloys). There is also experimental support for Mg and Mo. ASAP supports simulations on parallel clusters.

https://wiki.fysik.dtu.dk/asap/

asap3

• 3.2.0-1

ASAP (As Soon As Possible) is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE). ASAP currently implements the Effective Medium Potential (EMT) for the elements Ni, Cu, Pd, Ag, Pt and Au (and their alloys). There is also experimental support for Mg and Mo. ASAP supports simulations on parallel clusters.

https://wiki.fysik.dtu.dk/asap/

lammps

• 2012-10-10-3

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator)

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

This version has been compiled with the following packages: class2, colloid, kspace, manybody, mc, meam, molecule, poems, reax, replica, user-atc, user-misc, user-omp, user-reaxc.

LAMMPS is open source, distributed by Sandia National Laboratories.

http://lammps.sandia.gov/

http://lammps.sandia.gov/doc/Manual.html

• 2010-09-09-parallel-1

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator)

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

This version has been compiled with support for the following modules: kspace manybody meam molecule poems reax atc

LAMMPS is open source, distributed by Sandia National Laboratories.

http://lammps.sandia.gov/

• 2010-12-05-parallel-3

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator)

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

This version has been compiled with support for the following modules: class2 colloid kspace manybody meam molecule poems reax atc

LAMMPS is open source, distributed by Sandia National Laboratories.

http://lammps.sandia.gov/

• 2012-02-12-parallel-1, 2012-02-12-parallel-jr-10, 2012-02-12-parallel-jr-11

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator)

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

This version has been compiled with support for the following modules: class2 colloid kspace manybody mc meam molecule poems reax replica user-atc user-misc user-reaxc user-omp

LAMMPS is open source, distributed by Sandia National Laboratories.

http://lammps.sandia.gov/

http://lammps.sandia.gov/doc/Manual.html

namd

• 2.6.2009-02-11-Linux-x86_64-MPI-icc-1, 2.7b1-MPI-icc-1, 2.9-MPI-icc-4, 2.9plus-MPI-icc-3

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.

Subject to Univ. of Illinois Non-Exclusive, Non-Commercial Use License.

The NAMD project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969).

http://www.ks.uiuc.edu/Research/namd/

packmol

• 13.112-1, 13.112-2

Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.

The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.

The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy.

The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats.

http://www.ime.unicamp.br/~martinez/packmol/

Nanophotonics and fabrication

ddscat

• 7.2.2-3

Discrete Dipole Scattering (DDSCAT) calculates scattering and absorption of light by irregular particles and periodic arrangement of irregular particles.

• scattering and absorption by isolated particles (e.g., dust grains, ice crystals).
• scattering and absorption by periodic structures
• very fast near field calculation
• display scattering targets, their composition with support for 3D graphics
• conversion code between DDSCAT shape file format and VTK format.
• single and double precision options.

The binaries were compiled with Intel's MKL and OpenMP, but not MPI. Performance gains under OpenMP are modest.

License: GNU GPL v3

http://code.google.com/p/ddscat/

layout-beamer

• 3.2.0beta, 3.3.0beta2_64, 3.3.0beta_64, 3.3.0beta_64-1

LayoutBEAMER is a tool for the preparation of layout data for e-beam lithography devices.

http://www.genisys-gmbh.com/

lumerical

• 6.5.5-1, 7.5.4-1, 7.5.7-1, 8.0.5-1, 8.0.7-1, 8.5.4-1, 8.6.2-1

Lumerical FDTD Solutions is a high performance microscale optics simulation software. Employing a finite-difference time-domain (FDTD) algorithm, FDTD Solutions allows study of light propagation on the nanoscale.

http://www.lumerical.com/fdtd.php

meep

• 1.0-parallel-4, 1.0-parallel-5, 1.0-serial-4, 1.0-serial-5, 1.1.1-parallel-1, 1.1.1-parallel-2, 1.1.1-serial-1

MEEP (MIT Electromagnetic Equation Propagation) is a finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems, along with the MPB eigenmode package.

http://ab-initio.mit.edu/meep/meep-1.0.tar.gz

Toolkits

ase2

• 2.3.13-1, 2.3.13-2, 2.3.13-3

The Atomic Simulation Environment (ASE) is the common part of the simulation tools developed at CAMd. ASE provides Python modules for manipulating atoms, analyzing simulations, visualization etc.

The CAMPOS Atomic Simulation Environment is released under GPL2.

NOTE: ASE-2.x is no longer maintained but required for Dacapo.

https://wiki.fysik.dtu.dk/ase2/

ase3

• 3.0.0-3, 3.2.0-1, 3.2.0-3, 3.4.1-1, 3.5.1-1, 3.6.0-1

The Atomic Simulation Environment (ASE) is the common part of the simulation tools developed at CAMd. ASE provides Python modules for manipulating atoms, analyzing simulations, visualization etc.

The CAMPOS Atomic Simulation Environment is released under GPL2.

https://wiki.fysik.dtu.dk/ase/

campos

• stable

Compound: The CAMPOS modelling suite

vtk Numeric ScientificPython ase2 ase3 dacapo dacapo-python gpaw-setups gpaw

Details at the individual modules

campos-ase3

• 3.1.0-2

The Atomic Simulation Environment (ASE) is the common part of the simulation tools developed at CAMd. ASE provides Python modules for manipulating atoms, analyzing simulations, visualization etc.

The CAMPOS Atomic Simulation Environment is released under GPL2.

https://wiki.fysik.dtu.dk/ase/

Numeric

• 24.2-1

Numeric was the first arrayobject built for Python. It has been quite successful and is used in a wide variety of settings and applications. Maintenance has ceased for Numeric, and users should transisition to NumPy as quickly as possible.

This package is needed for Dacapo.

http://numpy.scipy.org/#older_array

• 24.2-3

Numeric is a Python module for high-performance, numeric computing. It provides much of the functionality and performance of commercial numeric software such as Matlab; in some cases, it provides more functionality than commercial software.

ScientificPython

• 2.4.11-1

ScientificPython is a collection of Python modules that are useful for scientific computing. In this collection you will find modules that cover basic geometry (vectors, tensors, transformations, vector and tensor fields), quaternions, automatic derivatives, (linear) interpolation, polynomials, elementary statistics, nonlinear least-squares fits, unit calculations, Fortran-compatible text formatting, 3D visualization via VRML, and two Tk widgets for simple line plots and 3D wireframe models. There are also interfaces to the netCDF library (portable structured binary files), to MPI (Message Passing Interface, message-based parallel programming), and to BSPlib (Bulk Synchronous Parallel programming).

http://dirac.cnrs-orleans.fr/plone/software/scientificpython/

• 2.4.11-3, 2.8-1, 2.8-2

ScientificPython is a collection of Python modules useful for scientific computing. Modules cover basic geometry (vectors, tensors, transformations, vector and tensor fields), quaternions, automatic derivatives, (linear) interpolation, polynomials, elementary statistics, nonlinear least-squares fits, unit calculations, Fortran-compatible text formatting, 3D visualization via VRML, and two Tk widgets for simple line plots and 3D wireframe models. There are also interfaces to the netCDF library (portable structured binary files), to MPI (Message Passing Interface, message-based parallel programming), and to BSPlib (Bulk Synchronous Parallel programming).

http://dirac.cnrs-orleans.fr/plone/software/scientificpython/

vtk

• 5.0.4-icc-3

The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python. Professional support and products for VTK are provided by Kitware, Inc. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as implicit modelling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. In addition, dozens of imaging algorithms have been directly integrated to allow the user to mix 2D imaging / 3D graphics algorithms and data. The design and implementation of the library has been strongly influenced by object-oriented principles.

http://www.vtk.org/

https://visualization.hpc.mil/wiki/VTK

https://visualization.hpc.mil/wiki/Getting_Started_with_VTK

Libraries

atlas

• 3.8.0-4

The ATLAS (Automatically Tuned Linear Algebra Software) project is an ongoing research effort focusing on applying empirical techniques in order to provide portable performance. At present, it provides C and Fortran77 interfaces to a portably efficient BLAS implementation, as well as a few routines from LAPACK.

http://math-atlas.sourceforge.net/

boost

• 1.47.0-1

Boost provides free peer-reviewed portable C++ source libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.

Boost libraries are intended to be suitable for eventual standardization. Ten Boost libraries are already included in the C++ Standards Committee's Library Technical Report (TR1) and will be in the new C++0x Standard now being finalized. C++0x will also include several more Boost libraries in addition to those from TR1. More Boost libraries are proposed for TR2.

To use Boost, supply in your Makefile:

CPPFLAGS += -I$BOOST_HOME LDFLAGS += -L$BOOST_HOME/lib -lboost_<component>

http://www.boost.org/

charm

• 6.0-mpi-linux-x86_64-ifort-mpicxx-1, 6.1b-2009-04-02-mpi-linux-x86_64-ifort-mpicxx-1

Charm++ is a message-passing parallel language and runtime system. It is implemented as a set of libraries for C++, is efficient, and is portable to a wide variety of parallel machines. Source code is provided, and non-commercial use is free.

This version was compiled for mpi-linux-x86_64-ifort-mpicxx

Copyright (C) 1989-2000 Regents of the University of Illinois

http://charm.cs.uiuc.edu/

• 6.0-mpi-linux-x86_64-ifort-smp-mpicxx-1

Charm++ is a message-passing parallel language and runtime system. It is implemented as a set of libraries for C++, is efficient, and is portable to a wide variety of parallel machines. Source code is provided, and non-commercial use is free.

This version was compiled for mpi-linux-x86_64-ifort-smp-mpicxx

Copyright (C) 1989-2000 Regents of the University of Illinois

http://charm.cs.uiuc.edu/

• 6.4.0-mpi-linux-x86_64-ifort-mpicxx-1

Charm++ is a message-passing parallel language and runtime system. It is implemented as a set of libraries for C++, is efficient, and is portable to a wide variety of parallel machines. Source code is provided, and non-commercial use is free.

This version was compiled for mpi-linux-x86_64-ifort-mpicxx

Subject to the University of Illinois Charm++/Converse License Copyright (C) 1989-2012 Regents of the University of Illinois

http://charm.cs.uiuc.edu/

• 6.4.0-mpi-linux-x86_64-ifort-smp-mpicxx-1

Charm++ is a message-passing parallel language and runtime system. It is implemented as a set of libraries for C++, is efficient, and is portable to a wide variety of parallel machines. Source code is provided, and non-commercial use is free.

This version was compiled for mpi-linux-x86_64-ifort-smp-mpicxx

Subject to the University of Illinois Charm++/Converse License Copyright (C) 1989-2012 Regents of the University of Illinois

http://charm.cs.uiuc.edu/

cuda

• 4.2.9-1, 5.0-1

The NVIDIA CUDA Toolkit provides a comprehensive development environment for C and C++ developers building GPU-accelerated applications. The CUDA Toolkit includes a compiler for NVIDIA GPUs, math libraries, and tools for debugging and optimizing the performance of your applications. You’ll also find programming guides, user manuals, API reference, and other documentation to help you get started quickly accelerating your application with GPUs.

http://developer.nvidia.com/cuda/cuda-toolkit

fftw3

• 3.2.1-1, 3.2.2-1, 3.3-1, 3.3.2-1, 3.3.2-4

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). FFTW is free software and is highly recommended as FFT library of choice for most applications.

http://www.fftw.org/

fox

• 4.1.2-1

FoX is an XML library written in Fortran 95. It allows software developers to read, write and modify XML documents from Fortran applications without the complications of dealing with multi-language development.

FoX can be freely redistributed as part of open source and commercial software packages.

http://www1.gly.bris.ac.uk/~walker/FoX/

GotoBLAS

• 1.26-intel-1

The GotoBLAS codes are fast implementations of the Basic Linear Algebra Subroutines, written by Kazushige Goto /goat-toe/.

The performance depends in part on the code from which you call the GotoBLAS subroutine(s) and on the combination of architecture and operating system under which you are running. Your own tuning here can make a big difference.

This version was compiled using: COMPILER_OPTION='BINARY64=1 F_COMPILER=INTEL'

http://www.tacc.utexas.edu/resources/software/software.php

• 1.26-gfortran-1

The GotoBLAS codes are fast implementations of the Basic Linear Algebra Subroutines, written by Kazushige Goto /goat-toe/.

The performance depends in part on the code from which you call the GotoBLAS subroutine(s) and on the combination of architecture and operating system under which you are running. Your own tuning here can make a big difference.

This version was compiled using: COMPILER_OPTION='BINARY64=1 F_COMPILER=GFORTRAN'

http://www.tacc.utexas.edu/resources/software/software.php

• 1.26-gfortran-smp-1

The GotoBLAS codes are fast implementations of the Basic Linear Algebra Subroutines, written by Kazushige Goto /goat-toe/.

The performance depends in part on the code from which you call the GotoBLAS subroutine(s) and on the combination of architecture and operating system under which you are running. Your own tuning here can make a big difference.

This version was compiled using: COMPILER_OPTION='BINARY64=1 F_COMPILER=GFORTRAN SMP=1'

http://www.tacc.utexas.edu/resources/software/software.php

• 1.26-intel-smp-1

The GotoBLAS codes are fast implementations of the Basic Linear Algebra Subroutines, written by Kazushige Goto /goat-toe/.

The performance depends in part on the code from which you call the GotoBLAS subroutine(s) and on the combination of architecture and operating system under which you are running. Your own tuning here can make a big difference.

This version was compiled using: COMPILER_OPTION='BINARY64=1 F_COMPILER=INTEL SMP=1'

http://www.tacc.utexas.edu/resources/software/software.php

h5utils

• 1.12.1-1, 1.12.1-2, 1.12.1-3

h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format. Besides providing a simple tool for batch visualization as PNG images, h5utils also includes programs to convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, Vis5d, and VTK).

http://ab-initio.mit.edu/wiki/index.php/H5utils

harminv

• 1.3.1-mkl-4, 1.3.1-netlib-4

Harminv is a program and accompanying library to solve the problem of harmonic inversion -- given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.

http://ab-initio.mit.edu/wiki/index.php/Harminv

hdf5

• 1.8.3-parallel-4, 1.8.3-serial-4

The HDF5 suite includes:

• A data model that can represent complex data objects and metadata.
• A portable file format with no limit on the number or size of data objects.
• A portable library with high-level APIs for C, C++, Fortran 90, and Java.
• Tools and applications.

The HDF5 data model, file format, API, library, and tools are open and distributed without charge.

http://www.hdfgroup.org/HDF5/

libctl

• 3.0.3-4, 3.0.3-5

libctl is a Guile-based library implementing flexible control files for scientific simulations. It was written to support the MIT Photonic Bands and Meep software, but has proven useful in other programs too.

http://ab-initio.mit.edu/wiki/index.php/Libctl

libint

• 1.1.4-1

A library of C/C++ functions for efficient evaluation of several kinds of two-body molecular integrals over Gaussian functions.

http://libint.valeyev.net/

libint2

• 2.0.0-2

A library of C/C++ functions for efficient evaluation of several kinds of two-body molecular integrals over Gaussian functions.

http://libint.valeyev.net/

libmatheval

• 1.1.7-2, 1.1.7-3

GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. It supports expressions in any number of variables of arbitrary names, decimal and symbolic constants, basic unary and binary operators, and elementary mathematical functions. In addition to parsing and evaluation, libmatheval can also compute symbolic derivatives and output expressions to strings.

http://www.gnu.org/software/libmatheval/

netcdf

• 3.6.3-intel11-4

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

This version uses the intel/11.0.081 compilers.

http://www.unidata.ucar.edu/software/netcdf/

• 3.6.3-gfortran-4, 3.6.3-gfortran-5

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

This version uses the GNU compilers.

http://www.unidata.ucar.edu/software/netcdf/

• 3.6.3-intel10-4

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

This version uses the intel/10.1.022 compilers.

http://www.unidata.ucar.edu/software/netcdf/

• 3.6.3-intel10-5

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

This version uses the icc/10.1.025 ifort/10.1.025 compilers.

http://www.unidata.ucar.edu/software/netcdf/

• 3.6.3-intel11-5

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

This version uses the icc/11.1.064 ifort/11.1.064 compilers.

http://www.unidata.ucar.edu/software/netcdf/

numpy

• 1.6.1-5

NumPy is a fundamental package for scientific computing in Python. It is a Python library that provides a multidimensional array object, various derived objects (such as masked arrays and matrices), and an assortment of routines for fast operations on arrays, including mathematical, logical, shape manipulation, sorting, selecting, I/O, discrete Fourier transforms, basic linear algebra, basic statistical operations, random simulation and much more.

NumPy also contains tools for integrating C/C++ and Fortran code.

Besides numeric applications, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to interface with databases.

Numpy is licensed under the BSD license, enabling reuse with few restrictions.

http://numpy.org/

• 1.0.4-mkl-1

NumPy is a fundamental package needed for scientific computing with Python. It contains:

• a powerful N-dimensional array object
• sophisticated broadcasting functions
• basic linear algebra functions
• basic Fourier transforms
• sophisticated random number capabilities
• tools for integrating Fortran code.
• tools for integrating C/C++ code.

This version uses the Intel MKL libraries. There is also an OS version which uses the OS versions of blas and lapack.

WARNING: This package is currently unstable and may lead to MPI errors and segfaults.

http://numpy.scipy.org/

• 1.6.1-4

NumPy is a base package for scientific computing with Python. It contains:

• a powerful N-dimensional array object
• sophisticated (broadcasting) functions
• tools for integrating C/C++ and Fortran code
• useful linear algebra, Fourier transform, and random number capabilities.

Besides numeric applications, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to integrate with databases.

Numpy is licensed under the BSD license, enabling reuse with few restrictions.

http://numpy.org/

openmpi

• 1.2.7-gcc

The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

This version uses the Intel compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.3-gcc-4, 1.3-gcc-4.orig, 1.3.2-gcc-1, 1.3.2-gcc-1.orig, 1.4.1-gcc-2, 1.4.3-gcc-1, 1.4.4-gcc-1, 1.4.5-gcc-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the GNU compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.3-intel10-4

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/10.1.022 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.3-intel11-4

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/11.0.081 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.3.2-intel10-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/10/10.1.022 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.3.2-intel10-2

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/10/10.1.025 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.3.2-intel11-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/11/11.0.083 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.4.1-intel10-2

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/10.1.025 ifort/10.1.025 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.4.1-intel11-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the intel/11/11.1.056 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.4.1-intel11-2

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/11.1.064 ifort/11.1.064 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.4.1-intel11-3, 1.4.1-intel11-4, 1.4.1-intel11-5

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/11/11.1.072 ifort/11/11.1.072 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.4.2-intel10-1, 1.4.3-intel10-1, 1.4.4-intel10-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/10 ifort/10 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.4.2-intel11-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/11/11.1.073 ifort/11/11.1.073 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.4.2-intel12-1, 1.4.3-intel12-1, 1.4.4-intel12-1, 1.4.4-intel12-2, 1.4.5-intel12-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/12 ifort/12 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

• 1.4.3-intel11-1, 1.4.4-intel11-1, 1.4.5-intel11-1

Open MPI is an open source, freely available implementation of both the MPI-1 and MPI-2 standards, combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation, Open MPI offers advantages for system and software vendors, application developers, and computer science researchers.

This version uses the icc/11 ifort/11 compilers for mpicc, mpif90, etc.

http://www.open-mpi.org/

scipy

• 0.10.0-1, 0.9.0-1

SciPy (pronounced 'Sigh Pie') is a library for mathematics, science, and engineering, named after a popular conference on scientific programming with Python

SciPy depends on NumPy, which provides convenient and fast N-dimensional array manipulation. SciPy works with NumPy arrays, and provides user-friendly and efficient numerical routines e.g. for integration and optimization.

Open-Source, free of charge.

http://www.scipy.org/

Intel development tools

Note on binary architectures

CPU architecture labels used by Intel and others can be confusing and have changed over time. Here's a summary of the labels and directory names commonly used:

32, ia32, x86

legacy 32-bit x86 generations up to Pentium 4 and Intel Core.

em64t, intel64, Intel-64, x86_64, AMD-64

64-bit generations of the Xeon branded CPUs, and the Core 2 generation, mostly compatible with AMD's Opteron and later.

64, ia64, Itanium

Itanium – limited ia32 support, but none for x86_64; not used on Carbon.

icc

• 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025, 11.0.074, 11.0.081, 11.0.083, 11.1.056, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture

icc/10

• 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025

The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture

icc/11

• 11.0.074, 11.0.081, 11.0.083, 11.1.056, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture

icc/12

• 12.0.2, 12.0.4, 12.1.0, 12.1.0.7, 12.1.2, 12.1.4, 12.1.6

The Intel C/C++ Compiler for the x86_64/EM64T/Intel64 architecture

idb

• 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025, 11.0.074, 11.0.081, 11.0.083, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel debugger for the x86_64/EM64T/Intel64 architecture

idb/10

• 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025

The Intel debugger for the x86_64/EM64T/Intel64 architecture

idb/11

• 11.0.074, 11.0.081, 11.0.083, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel debugger for the x86_64/EM64T/Intel64 architecture

idb/12

• 12.0.2, 12.0.4, 12.1.0, 12.1.0.7, 12.1.2, 12.1.4, 12.1.6

The Intel debugger for the x86_64/EM64T/Intel64 architecture

ifort

• 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025, 11.0.074, 11.0.081, 11.0.083, 11.1.056, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture

ifort/10

• 10.0.023, 10.1.013, 10.1.015, 10.1.017, 10.1.022, 10.1.025

The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture

ifort/11

• 11.0.074, 11.0.081, 11.0.083, 11.1.056, 11.1.059, 11.1.064, 11.1.072, 11.1.073

The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture

ifort/12

• 12.0.2, 12.0.4, 12.1.0, 12.1.0.7, 12.1.2, 12.1.4, 12.1.6

The Intel Fortran Compiler for the x86_64/EM64T/Intel64 architecture

impi

• 3.0, 3.1, 3.2.0.011, 3.2.2.006, 4.0.0.025, 4.0.0.028, 4.0.1.007, 4.0.2.003, 4.0.3.008, 4.1.0.024, 4.1.0.030

The Intel MPI implementation for the x86_64/EM64T/Intel64 architecture

intel-licenses

(No Module Specific Help for intel-licenses)

mkl

• 09.1.023, 10.0.005, 10.0.2.018, 10.0.3.020, 10.0.4.023, 10.1.0.015, 10.1.1.019, 10.1.2.024, 10.2.2.025, 10.2.3.029, 10.2.4.032, 10.2.5.035, 10.2.6.038, 10.3.10, 10.3.12, 10.3.2, 10.3.4, 10.3.6, 10.3.7, 10.3.8

The Intel Math Kernel Library for the x86_64/EM64T/Intel64 architecture

python

• 2.7.3-1

Python is an interpreted, interactive, object-oriented programming language often compared to Tcl, Perl, Scheme or Java. Python includes modules, classes, exceptions, very high level dynamic data types and dynamic typing. Python supports interfaces to many system calls and libraries, as well as to various windowing systems (X11, Motif, Tk, Mac and MFC).

Programmers can write new built-in modules for Python in C or C++. Python can be used as an extension language for applications that need a programmable interface. This package contains most of the standard Python modules, as well as modules for interfacing to the Tix widget set for Tk and RPM.

http://www.python.org/

Deprecated

intel

• 11.0.081

Compound: Intel compilers and MKL version 11

icc/11.0.081 ifort/11.0.081 mkl/10.1.1.019 idb/11.0.081

Details at the individual modules

• 10.1.015

Compound: Intel compilers version 10

icc/10.1.015 ifort/10.1.015 idb/10.0.023

Details at the individual modules

• 10.1.022

Compound: Intel compilers version 10

icc/10.1.022 ifort/10.1.022 idb/10.1.022

Details at the individual modules

• 11.0.074

Compound: Intel compilers version 11 and the MKL 10.1

icc/11.0.074 ifort/11.0.074 mkl/10.1.1.019 idb/11.0.074

Details at the individual modules

intel/10

• 10.1.025

Compound: Intel compilers version 10

icc/10.1.025 ifort/10.1.025 idb/10.1.025

Details at the individual modules

• 10.1.015

Compound: Intel compilers version 10

icc/10.1.015 ifort/10.1.015 idb/10.0.023

Details at the individual modules

• 10.1.022

Compound: Intel compilers version 10

icc/10.1.022 ifort/10.1.022 idb/10.1.022

Details at the individual modules

intel/11

• 11.1.073

Compound: Intel compilers and MKL version 11

icc/11.1.073 ifort/11.1.073

Details at the individual modules

• 11.0.074

Compound: Intel compilers version 11 and the MKL 10.1

icc/11.0.074 ifort/11.0.074 mkl/10.1.1.019 idb/11.0.074

Details at the individual modules

• 11.0.081

Compound: Intel compilers and MKL version 11

icc/11.0.081 ifort/11.0.081 mkl/10.1.1.019 idb/11.0.081

Details at the individual modules

• 11.0.083

Compound: Intel compilers and MKL version 11

icc/11.0.083 ifort/11.0.083 mkl/10.1.2.024 idb/11.0.083

Details at the individual modules

• 11.1.056

Compound: Intel compilers and MKL version 11

icc/11.1.056 ifort/11.1.056

Details at the individual modules

• 11.1.064

Compound: Intel compilers and MKL version 11

icc/11.1.064 ifort/11.1.064

Details at the individual modules

System

gold

• 2.1.11.0-4, 2.1.11.0-5, 2.1.8.1-1, 2.2.0.4-1, 2.2.0.4-2, 2.2.0.5-1, 2.2.0.5-2

Gold is an open source accounting system developed by Pacific Northwest National Laboratory (PNNL) as part of the Department of Energy (DOE) Scalable Systems Software Project (SSS). It tracks resource usage on High Performance Computers and acts much like a bank, establishing accounts in order to pre-allocate user and project resource usage over specific nodes and timeframe. Gold provides balance and usage feedback to users, managers, and system administrators.

http://www.clusterresources.com/pages/products/gold-allocation-manager.php

moab

• 5.4.4-1, 6.0.3-1, 6.0.6-2, 6.1.3-1, 6.1.3-2

Moab Workload Manager is a policy-based job scheduler and event engine that enables utility-based computing for clusters. It simplifies management across one or multiple hardware, operating system, storage, network, license and resource manager environments to increase the ROI of clustered resources, improve system utilization to run between 90-99 percent, and allow for expansion.

Moab Workload Manager combines intelligent scheduling of resources with advanced reservations to process jobs on the right resources at the right time. It also provides flexible policy and event engines that process workloads faster and in line with set business requirements and priorities.

http://www.clusterresources.com/pages/products/moab-cluster-suite/

• 6.1.10-1, 6.1.11-1, 6.1.3-3, 6.1.8-1, 6.1.9-1

Moab Workload Manager is a policy-based job scheduler and event engine that enables utility-based computing for clusters. It simplifies management across one or multiple hardware, operating system, storage, network, license and resource manager environments to increase the ROI of clustered resources, improve system utilization to run between 90-99 percent, and allow for expansion.

Moab Workload Manager combines intelligent scheduling of resources with advanced reservations to process jobs on the right resources at the right time. It also provides flexible policy and event engines that process workloads faster and in line with set business requirements and priorities.

http://www.adaptivecomputing.com/products/moab-hpc-suite-basic.php

Modules

dot

• 3.2.6

Adds `.' to your PATH environment variable

This makes it easy to add the current working directory to your PATH environment variable. This allows you to run executables in your current working directory without prepending ./ to the excutable name

Version 3.2.6

embody

• 0.9.26

EMBODY (Environment Modules Build) is a build tool with support for the environment-modules package at http://modules.sourceforge.net/.

The tool eases and automates the task of building and installing software from source or binary packages, and integrated the management of associated modulefiles.

Copyright (C) 2009, UChicago Argonne, LLC; All Rights Reserved.

• 1.0.0, 1.0.2

EMBODY (Environment Modules Build) is a build tool with support for the environment-modules package at http://modules.sourceforge.net/.

The tool eases and automates the task of building and installing software from source or binary packages, and integrated the management of associated modulefiles.

Copyright (C) 2012, UChicago Argonne, LLC; All Rights Reserved.

null

• 3.2.6

This module does absolutely nothing. It's meant simply as a place holder in your dot file initialization.

Version 3.2.6

use.own

• 3.2.6

This module file will add $HOME/privatemodules to the list of directories that the module command will search for modules. Place your own module files here. This module, when loaded, will create this directory if necessary.

Version 3.2.6

Uncategorized

epics

• 3.15.0.1-1

The Experimental Physics and Industrial Control Systems (EPICS) is an extensible set of software components and tools with which application developers can create a control system. This control system can be used to control accelerators, detectors, telescopes, or other scientific experimental equipment. EPICS base is the set of core software, i.e. the components of EPICS without which EPICS would not function. EPICS base allows an arbitrary number of target systems, IOCs (input/output controllers), and host systems, OPIs (operator interfaces) of various types.

Distributed under ...

http://www.aps.anl.gov/epics/

idl

• 8.2.2-1

IDL is a cross-platform scientific programming language to extract visualizations from complex numerical data. IDL interprets data and the IDL Development Environment may be used to build applications.

http://www.exelisvis.com/ProductsServices/IDL.aspx

module-cvs

• 3.2.6

This module will set up aliases and environment variables for easy check-out of the most recent version of the environment modules package.

For CVS access - do the 'login' first then the 'get' when prompted for a password - just hit return

• modules-login - login into the modules CVS repository anonymously
• modules-get - retrieve modules sources

For anonymous ftp access cd to /pub/modules once logged in when prompted for a username/password - give it anonymous and your email address

• modules-ftp - ftp into the modules tar ball directory anonymously. Go to /pub/sourceforge/m/mo/modules

Version 3.2.6

module-info

• 3.2.6

This module returns all the various module-info values in whatever mode you use (except in `whatis' mode)

Version 3.2.6

modules

• 3.2.6

modules - loads the modules software & application environment

This adds /usr/share/Modules/* to several of the environment variables.

Version 3.2.6

p4vasp

• 0.3.26-1

p4vasp is a set of tools for processing xml-formatted VASP output (vasprun.xml). A GUI is included.

It is based on python; applets run off the GUI. At startup p4v loads vasprun.xml from the directory where it was started. Parsing of the desired information is performed only when it is required and it is cached for later use.

http://www.p4vasp.at/

readline

• 6.2-1

The Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

The history facilites are also placed into a separate library, the History library, as part of the build process. The History library may be used without Readline in applications which desire its capabilities.

(No Module Specific Help for readline/6.2-1)

test

• 0.1-1

Set PYTHONPATH based on Python's major version.