Open-Source Software Installed on ARCHIE-WeSt

 

Package Version Application Area Official Website
ASE 3.6.0 Atomistic Simulation Environment https://wiki.fysik.dtu.dk/ase/overview.html
Autodock 4.2.3 Molecular Dynamics http://autodock.scripps.edu
Autodock Vina 1.1.2 Molecular Dynamics http://vina.scripps.edu
BLAST 2.2.24 Genomics, Bioinformatics http://blast.ncbi.nlm.nih.gov
CAESES-FFW 3.0.19 CFD Analysis https://www.caeses.com/products/caeses-free/
CMake 2.8.9 Testing Tool http://www.cmake.org
CP2K 2.3 Molecular Dynamics http://www.cp2k.org/about
CPLEX 12.6.0 Optimization http://www-03.ibm.com/software/products/en/ibmilogcpleoptistud
Dakota 6.1 Analysis and Optimization https://dakota.sandia.gov/
EPOCH 4.2.13 Plasma Physics  http://www.ccpp.ac.uk/codes.html
FEBio 2.4.2 Finite Element Analysis http://febio.org/
FLUKA 2011.2c-0 MonteCarlo http://www.fluka.org/fluka.php
fpocket 2.0 Protein Cavity Detection http://fpocket.sourceforge.net/
GAMESS  2013125 Quantum Chemistry http://www.msg.chem.iastate.edu/gamess
GEANT4 4.9.6 Particle Simulations http://geant4.web.cern.ch/geant4/support/gettingstarted.shtml
GROMACS 4.5.5 Molecular Dynamics http://www.gromacs.org
GPAW 0.9.0 Electronic Structure http://wiki.fysik.dtu.dk/gpaw
HDF5 1.8.7 Portable Data Format http://www.hdfgroup.org/HDF5
IOzone 3.397 Benchmark Tool http://www.iozone.org
KlustaKwik 3.0 Quantum Chemistry http://sourceforge.net/projects/klustakwik/
LAMMPS 16thFeb2016 Solid State Molecular Dynamics http://lammps.sandia.gov/
Molden 5.2 Quantum Chemistry Visualization http://www.cmbi.ru.nl/molden/
MrBayes 3.2.1 Phylogenetic and Evolutionary Models http://mrbayes.sourceforge.net/
NAMD 2.8 Molecular Dynamics http://www.ks.uiuc.edu/Research/namd
netCDF 4.3.2 Data Manipulation  http://www.unidata.ucar.edu/software/netcdf/
NEURON 7.3 Neuron Networks http://www.neuron.yale.edu/neuron/
ns-3 3.24 Network Simulator https://www.nsnam.org/
NWChem 6.1 Computational Chemistry http://www.nwchem-sw.org/index.php/Main_Page
Octave 3.6.1 Data Analysis & Visualization http://www.gnu.org/software/octave
Open Babel 2.3.1 Chemical Data Toolbox http://sourceforge.net/projects/openbabel
OpenFOAM 2.1.0 Computational Fluid Dynamics http://www.openfoam.com
OpenMD 2.0 Molecular Dynamics http://openmd.org/
Paraview 3.12 Visualization http://www.paraview.org
Perl 5.12.3 General purpose programming language http://www.perl.org
Placevent 0.2 Molecular Dynamics http://sites.google.com/site/dansindhikara/Home/software/placement
Python 2.7.1 General purpose programming language http://www.python.org
Qhull 2012.1 Computational Geometry http://www.qhull.org
QIIME 1.8.0 Bioinformatics http://www.qiime.org
QUANTUM ESPRESSO 5.4.0 Quantum Chemistry http://www.quantum-espresso.org/
R 2.12.1 Statistical Computing Language http://www.r-project.org
Root 5.34 Data Processing http://root.cern.ch/drupal/
Su-2 4.2.0 Computational Fluid Dynamics http://su2.stanford.edu/
Trinity 2.0.6 RNA Sequencing https://github.com/trinityrnaseq/trinityrnaseq/wiki
VisIt 2.10.2 Visualization and Analysis https://wci.llnl.gov/simulation/computer-codes/visit/
VMD 1.9.1 Molecular Dynamics Visualization http://www.ks.uiuc.edu/Research/vmd

Compilers and Libraries Installed on ARCHIE-WeSt

 

Package Version Application Area Official Website
ACML 5.1.0 Numerical Libraries http://developer.amd.com/tools/cpu-development/amd-core-math-library-acml
arpack-ng 3.1.0 Linear Algebra http://forge.scilab.org/index.php/p/arpack-ng
atlas 3.10.0 Linear Algebra http://math-atlas.sourceforge.net
blacs 3.0 Linear Algebra http://www.netlib.org/blacs
blas 1 Linear Algebra http://www.netlib.org/blas
boost  1.47  C++ Library  http://www.boost.org/
clapack 3.2.1 Linear Algebra http://www.netlib.org/clapack
cuda 4.2.9 GPU Computing https://developer.nvidia.com/category/zone/cuda-zone
fftw 3.2.2 Fourier Transforms http://www.fftw.org
fftw 2.1.5 Fourier Transforms http://www.fftw.org
fltk 1.3 GUI Toolkit http://www.fltk.org
GCC 4.6.2 Compiler Suite http://gcc.gnu.org
impi 4.03 MPI (Intel) http://software.intel.com/en-us/intel-mpi-library
intel Compiler Suite  http://software.intel.com/en-us/intel-compilers
lapack 3.31 Linear Algebra http://www.netlib.org/lapack
metis 5.0.2 Linear Algebra http://glaros.dtc.umn.edu/gkhome/views/metis
netcdf 4.3.2 Libraries http://www.unidata.ucar.edu/downloads/netcdf/index.jsp
Open64 4.2.4 Compiler Suite http://www.open64.net
OpenMM  4.4.1 Molecular Dynamics https://simtk.org/home/openmm
openmpi 1.6.2 MPI http://www.open-mpi.org
parmetis 4.0.2 Linear Algebra http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview
qrupdate 1.1.2 Linear Algebra http://qrupdate.sourceforge.net
scalapack 2.0.2 Linear Algebra http://www.netlib.org/scalapack
scotch 5.1.12 Mesh Partitioning http://www.labri.fr/perso/pelegrin/scotch/

 

 

 
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