Software

Biology and Bioinformatics
Names and Offical Hompeages Main
Applications
License Types Parallelization
Methods 
Versions Installed
Fuji Aurora Cirrus Stratus 
AByss homepage
homepage


Sequence Assembler Non-Commercial MPI Not installed 1.2.4 Not installed  
AMBER homepage
homepage


MD Commercial MPI, CUDA 11 Not installed To Be Installed  
AutoDock homepage
homepage


Docking GPL ver. 3   Not installed 4.2.3 Not installed  
CHARMM homepage
homepage


MD Commercial MPI Not installed To Be Installed Not installed  
Desmond homepage
homepage
MD Non-Commercial MPI Not installed To Be installed Not installed  
GROMACS homepage
homepage
MD GPL ver. 3 MPI, CUDA 4.0.7 4.5.1 To Be Installed  
IMPUTE homepage
homepage
Genotype Imputation and Phasing Non-Commercial   Not installed 2.1.0 Not installed  
NAMD homepage
homepage
MD Non-Commercial Charm++, CUDA 2.7b3, 2.7c 2.7, 2.8 Not installed  
Velvet  homepage
homepage
Sequence Assembler  GPL ver. 3 OpenMP Not installed 1.0.13 Not installed  
 SOAPdenovo  homepage
homepage
Generation Sequencing Data Analysis GPL ver. 3   Not installed 1.04 Not installed 2.1.2

 

Chemistry and Molecular Modeling
Names and Offical Hompeages Main
Applications
License Types Parallelization
Methods 
Versions Installed
Fuji Aurora
Cirrus Stratus 
ABINIT homepage
homepage
QM GPL ver. 3 MPI, CUDA 6.8.1 6.6.2 To Be Installed  
ACES III homepage
homepage
QM GPL ver. 3 MPI To Be Installed To Be Installed To Be Installed  
 AMBER homepage
homepage
MD Commercial MPI, CUDA 11 Not installed To Be Installed  
 CHARMM homepage
homepage
MD Commercial MPI Not installed Not Installed Not installed  
 CPMD homepage
homepage
QMMD CPMD Free License   To Be Installed To Be Installed To Be Installed  
 DESMOND
homepage
MD Non-Commercial  MPI Not Installed To Be installed Not installed  
GAUSSIAN homepage
homepage
QM Commercial Linda 09 09 Not installed  
GROMACS homepage
homepage
MD GPL ver. 3 MPI, CUDA 4.0.7 4.5.1 To Be Installed  
JMol homepage
homepage
Graphical GPL ver. 3
To Be Installed To Be Installed To Be Installed  
LAMMPS homepage
homepage
MD GPL ver. 3   To Be Installed To Be Installed 27Oct11  
Materials Studio homepage
homepage
QM Commercial MPI 5.5.3 Not Installed Not Installed  
NAMD homepage
homepage
MD Non-Commercial Charm++, CUDA 2.7b3, 2.7c 2.7, 2.8b1 Not Installed  
NWChem homepage
homepage
QM, QMMD ECL ver. 2.0 MPI 6.1 6.1 To Be Installed  
Open Babel homepage
homepage
Chemistry File Format Converter GPL ver. 2   Not installed To Be Installed Not Installed  
Quantum Espresso homepage
homepage
QM GPL ver. 3 MPI 4.1.1, 4.1.2, 4.1.3, 4.2, 4.2.1, 4.3 4.2.1 4.3.2  
VASP homepage
homepage
QMMD Commercial MPI 4.6, 5.2 5.2 To Be Installed  
XCrySDen homepage
homepage
Molecular Visialization GPL ver. 3   Not installed Not installed Not installed  
CP2K  

homepage
homepage


Ab-initio atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems  GNU General Public License
multi-threading, MPI, and CUDA



4.1

Physics and Material Science
Names and Offical Hompeages Main
Applications
License Types Parallelization
Methods 
Versions Installed
Fuji Aurora
Cirrus
Stratus
Abaqus homepage
homepage
Coupled Physical Phenomena Commercial MPI 2.9-2, 2.10-2 2.10-2 Not Installed  
COMSOL Myltiphysics homepage
homepage
Coupled Physical Phenomena Commercial MPI Not Intalled 3.5, 4.0.0.993 Not Installed  
CST homepage
homepage
EM Field Simulation Commercial MPI, OpenMP Not Installed Not Installed Not Installed  
LAMMPS homepage
homepage
MD  GPL ver. 3  MPI To Be Installed To Be Installed 27Oct11  
Materials Studio homepage
homepage
QM Commercial  MPI 5.5.3 Not Intalled Not Intalled  
MEEP homepage
homepage
Electromagnetic System Modeling GPL ver. 3 MPI Not Intalled 1.1.1 Not Intalled  
NWChem homepage
homepage
QM, QMMD  ECL ver. 2.0  MPI 6.1 6.1 To Be Installed  
OpenFOAM homepage
homepage
Fluid Dynamics GPL ver. 3 MPI Not Installed 1.7.1 Not Installed  
Quantum Espresso homepage
homepage
QM   GPL ver. 3 MPI 4.1.1, 4.1.2, 4.1.3, 4.2, 4.2.1, 4.3 4.2.1 4.3.2  
VASP homepage
homepage
 QMMD Commercial  MPI 4.6, 5.2 5.2 To Be Installed  
VORPAL homepage
homepage
Plasma and EM Model Commercial MPI 4.2 Not Installed Not Installed  
XCrySDen   homepage
homepage
Molecular Visialization GPL ver. 3   Not Installed Not Installed Not Installed  
Quantumn Expresso homepage
homepage
Electronic-structure calculations and materials modelling at the nanoscale GNU General Public License MPI and OpenMP       6.1

 Mathematical, Statistical and Other Utilities
Names and Offical Hompeages Main Applications License Types Parallelization
Methods 
Versions Installed
Fuji Aurora Cirrus
Stratus
FFTW homepage
homepage
Fast Fourier Transform Library GPL ver. 2 MPI, Pthreads To Be Installed To Be Installed To Be Installed  
gnuplot homepage
homepage
Data Visualization gnuplot License   4.4.2 To Be Installed Not Installed  
GotoBLAS2 homepage
homepage
Basic Linear Algebra Subroutines BSD License OpenMP 1.13 1.13 To Be Installed  
ImageMagick homepage
homepage
Image Editor ImageMagick License   6.6.6-5 Not Installed Not Installed  
Intel Maths Kernel Library homepage
homepage
Maths Library Commercial OpenMP 10.1.0.015, 11.1.028, 11.1.072, 2011 10.1.0,015, 11.1.038, 11.1.072, 2011 Not Installed  
MATLAB homepage
homepage
Numerical Computation and Visualization Commercial MATLAB Parallel Computing Toolbox (PCT), MATLAB Distributed Computing Server (MDCS)


 
 Octave  homepage
homepage
Numerical Computation GPL ver.3   To Be Installed To Be Installed To Be Installed  
R homepage
homepage
Statistical Computating GNU R Licenses   To Be Installed To Be Installed To Be Installed  
Hypre homepage

homepage
Scalable algorithms for solving linear systems of equations GNU General Public License MPI and OpenMP


2.11.2
Metis homepage

homepage
Serial Graph Partitioning and Fill-reducing Matrix Ordering Apache License, Version 2.0 ParMetis will come later.


5.1.0
Mumps homepage

homepage
MUltifrontal Massively Parallel Sparse direct Solver CeCILL-C license MPI and OpenMP


5.0.2
Netcdf homepage

homepage
C Libraries for the Unidata network Common Data Form Copyright 1993-2015 University Corporation for Atmospheric Research/Unidata N.A.


4.4.1.1
Netcdf-cxx homepage

homepage
C++ Libraries for the Unidata network Common Data Form Copyright 1993-2015 University Corporation for Atmospheric Research/Unidata N.A.


4.3.0
netcdf-fortran homepage

homepage
Fortran Libraries for the Unidata network Common Data Form Copyright 1993-2015 University Corporation for Atmospheric Research/Unidata N.A.


4.4.4
Numpy homepage

homepage
NumPy array processing for numbers, strings, records and objects Copyright © 2005-2017, NumPy Developers Multiprocessing and multithreading


1.11.2
pHDF5 homepage

homepage
A general purpose library and file format for storing scientific data BSD-style open source MPI


1.8.17
SuperLu homepage

homepage
A general purpose library for the direct solution of linear equations




5.2.1
Superlu_dis homepage

homepage
Distributed SuperLu Copyright (c) 2003, The Regents of the University of California, through Lawrence Berkeley National Laboratory MPI and OpenMP


5.2.1
Trilinos homepage

homepage
A collection of libraries of numerical algorithms LGPL or BSD MPI


12.10.1

 

 

 

 

 

Software Development
Names and Offical Hompeages Main
Applications
License Types Parallelization
Methods 
Versions Installed
Fuji Aurora Cirrus Stratus 
GNU GDB homepage
homepage
Debugger GPL ver. 3    6.8-27.el5  7.0-0.4.16   Not Installed  
GNU Compilers homepage
homepage
Compilers GPL ver. 3  MPI, OpenMP 3.4.6, 4.1.2, 4.3.2 3.3.3, 4.3.4, 4.5.0 Not Installed   
GNU gprof homepage
homepage
Profiling Tools GPL ver. 3  MPi, OpenMP 2.17.50.0.6-9.el5 2.20.0.20100122-0.7.9  Not Installed  
Intel Compilers homepage
homepage
Compilers Commercial MPI, OpenMP 11.0.074, 11.1.038, 11.1.072, 12.1.1.072
11.1.038, 11.1.072, 12.1.1.038 Not Installed  
PGI Compilers homepage
homepage
Compilers Commercial MPI, OpenMP 10.9-0 Not Installed Not Installed  
LF Compilers homepage
homepage
Compilers Commercial MPI, OpenMP   Not Installed Not Installed  
nVidia nvcc homepage
homepage
Compiler, Maths Libraries
CUDA Not Installed Not Installed Not Installed  
PerfSuite homepage
homepage
Profiling Tools UI/NCSA Open Source   Not Installed 1.0.0 To Be Installed  
IBM Compilers         homepage
homepage
Compilers Commercial MPI, OpenMP Not Instaledl Not Installed 2010  
EasyBuild homepage
homepage
A software build and installation framework for managing (scientific) software on HPC systems GNU GPLv2 N.A.


3.1.2
Adios homepage
homepage

? MPI


1.11.0
Autotools homepage
homepage
Software packages Autoconf, Automake, and Libtool GNU Free Documentation License N.A.



boost homepage
homepage
Boost free peer-reviewed portable C++ source libraries Boost Software License



1.63.0
Papi homepage
homepage
Performance Application Programming Interface




5.5.1
Pdtoolkit homepage
homepage
PDT is a framework for analyzing source code




5.5.1
PETSc homepage
homepage
Portable Extensible Toolkit for Scientific Computation




3.7.5
Scalasca homepage
homepage
Toolset for performance analysis of large-scale parallel applications




2.3.1
Scalasca homepage
homepage
Scientific Tools for Python




0.19.0
Scorep homepage
homepage
Scalable Performance Measurement Infrastructure for Parallel Codes




3.0
IONlib homepage
homepage
Scalable I/O library for parallel access to task-local files




1.7.1
Tau homepage
homepage
Tuning and Analysis Utilities Profiling Package




2.26.1

System Software
Names and Offical Hompeages Main Applications License Types Versions Installed
Fuji Aurora Cirrus Stratus
Intel MPI homepage
homepage
Message Passing Interface Commercial 3.2.0, 4.0.0, 4.0.1 3.2.1, 4.0.0, 4.0.1 Not Installed
MPICH2 homepage
homepage
Message Passing Interface MPICH License To Be Installed To Be Installed To Be Installed
MVAPICH2 homepage
homepage
Message Passing Interface BSD License To Be Installed To Be Installed To Be Installed
OpenMPI homepage
homepage
Message Passing Interface BSD License To Be Installed To Be Installed To Be Installed
Platform LSF homepage
homepage
Job Scheduler Commercial 7.0 7.0 8.0
SGI MPT homepage
homepage
Message Passing Interface Commercial Not Installed 2.01, 2.02, 2.04 Not Installed
Hdf5 homepage
homepage
A general purpose library and file format for storing scientific data



1.8.17
Intel mkl-dnn homepage
homepage
Optimized MKL for Machine Learning



0.9
mpiP

homepage
homepage


lightweight profiling library for MPI applications



3.4.1
SGI mpt homepage
homepage
SGI Message Passing Toolkit



2.15
Perfboost

homepage
homepage


SGI MPI PerfBoost



1.15
Perfcatcher

homepage
homepage


A pro ling tool for SGI MPI and OpenSHMEM



26
Prun

homepage
homepage


Job launch utility for multiple MPI families



1.1
Intel Python

homepage
homepage


Intel Distribution for Python



intel-2.7u3, intel-3.5u3
Valgrind

homepage
homepage


Memory debugging utilities



3.12.0