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Scientific Software and Programming Tools

The following scientific computing software is available on our cluster systems under directory /share1/

  1. Licensed/Open Source Software Applications

  2. Utilities and Libraries


Licensed/Open Source Software Applications

Software Description HPCPOWER2 GRIDPOINT HPC2015
Bioinformatics and Genomics
Bowtie2 An ultrafast and meory0efficient tools for aligning sequencing reads to long reference sequences   2.2.9 2.2.9
GARLI A program that performs phylogenetic inference using the maximum-likelihood criterion. Several sequence types are supported, including nucleotide, amino acid and codon. 0.96b8 2.1 2.1
Mrbayes A program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters 3.1.2    
HyPhy An open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning 2.1020120113    
PHYML A software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences     2.4.5
MEME A software package to discover motifs (highly conserved regions) in groups of related DNA or protein sequences and, search sequence databases using motifs   4.6.1, 4.9.0* 4.11.2
MEGAHIT An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph     1.1.1
mpiBLAST A freely available, open-source, parallel implementation of NCBI BLAST. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors 1.6.0 1.6.0 1.6.0
(Please refer to this page for mpiBLAST and other BLAST on hpc2015)
SAMtools A software suite for interacting with high-throuhput sequencing data   1.3.1 1.3.1, 1.4*
Chemistry and Molecular Modeling
ADF An accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT)   2012, 2014.10 2014.10
AMBER A package of programs for molecular dynamics simulations of proteins and nucleic acids 8, 10 10, 16* 16
CPMD A parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics, or the underlying theory known as the Car–Parrinello method 3.11.1 4.1 4.1
Gaussian It provides state-of-the-art capabilities for electronic structure modeling g03, g09 g03, g09, g16 g09, g16
GAMESS A program for ab initio molecular quantum chemistry 20090112R3, 20130501R1* 20090112R3, 20130501R1* 20141205R1, 20170420R1*
GROMACS A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids 4.0.3 4.0.7, 4.5.5* 5.1.1
LAMMPS A classical molecular dynamics code. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale 19 Dec 2011, 24 Apr 2013* 24 Apr 2013 16 Feb 2016
NAMD A parallel molecular dynamics simulation package with Charm++ for high-performance simulation of large biomolecular systems. 2.9, 2.10 2.9, 2.10 2.10
NWChem High performance computational chemistry tools for kinetics and dynamics of chemical transformations, chemistry at interfaces and in the condensed phase,   6.6 6.6
ORCA A flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.   3.0.1, 3.0.3 3.0.3, 4.0.0
SIESTA A software perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids   2.0.1, 3.2 3.2
Physics and Materials Science
Abaqus A finite element solver used for stress, heat transfer, modeling and other types of analysis in mechanical, structural, civil, biomedical, and related engineering applications. 6.8-1, 6.11-1, 6.13-3*   6.13-4, 6.14-1, 2016, 2017*
ParaDiS The Parallel Dislocation Simulator is a large scale dislocation dynamics simulation code to study the fundamental mechanisms of plasticity on massively parallel computers 2.3.5.1   2.3.5.1
Quantum ESPRESSO Software suite for electronic-structure calculations and materials modeling at tje nanoscale     6.1
VASP A package for atomic scale materials modeling, e.g. electronic structure calculations and quantum-machanical molecular dynamics, from first principles   4.6, 5.3 4.6, 5.3, 5.4.1, 5.4.4
Mathematics and Statistics
MATLAB A programming environment for algorithm development, data analysis, visualization, and numerical computation R2009a, R2012a, R2013a* R2009a, R2012a, R2013a* R2015a, R2015b, R2016b, R2017b*
R A free software environment for statistical computing and graphics 2.15, 3.0.0*, 3.2.2 2.15.1, 3.0.0, 3.2.2, 3.2.5* 3.2.2, 3.2.5, 3.4.1*
Octave Open source numerical computing program compatible with MATLAB 2009 3.8.1, 4.0.0* 3.4.3, 4.0.0*
Mathematica An interactive system which handles numerical, grahpic and symbolic calculations with its algorithmic, visualization, and user interface capabilities within a document-like user interface paradigm      
Deep Learning
Caffe A fast, open framework for deep learning     1.0.0
TensorFlow Software library for numerical computation using data flow graphs     1.3.0
Theano A numerical computation library for Python   Available Available

* Several versions are installed; listed is the default version.

Utilities and Libraries

Type Description GRIDPOINT HPC2015
Compilers and programming languages
GNU Compiler GNU Compiler Collection compilers and libraries (gcc, gfortran, g++) 4.1.2*, 4.4.2, 4.6.2, 4.7.1, 4.9.0, 5.1.0 4.4.7*, 4.9.3, 5.2.0, 6.3.0
Intel Compilers Intel compilers and libraries for C/C++ and Fortran (icc, icpc, ifort) 2013, 2015, 2016 2013, 2015, 2016, 2017*
PGI Compilers Portland Group compilers and libraries (pgcc, pgf90, pgCC, etc) 7.2, 12.4, 14.2, 15.7, 17.7* 15.7, 16.10, 17.7*
Python Tool for analyzng Python source code and generating Python bytecode. 2.4.3*, 2.7.5, 2.7.11, 3.4.2 2.6.6*, 2.7.11, 3.4.3
Julia High-Performance numerical computing environment and language 0.5.2 0.5.2
Ruby A dynamics, object-oriented programming language 2.3 2.4
Parallel Libraries
MPICH A freely available, portable implementation of MPI, the standard for message-passing libraries. Available Available
MVAPICH MPI over InfiniBand, 10GigE/iWARP and RoCE Available Available
Intel MPI A multi-fabric message passing library that implements MPI-3.0. It provides a standard library across Intel platforms 5.0.3, 5.1.3 4.1.3, 5.0.3, 5.1.1, 5.1.3, 2017.4*
Open MPI A High Performance Message Passing Library for parallel computing Available Available
MPI for Python Package enabling applications to exploit multiple processors using standard MPI in Python scripts 1.3.1 2.0.0
Math Libraries
ACML The AMD Core Math Library (ACML) contains the complete set of LAPACK routines, the complete set of functions from the Basic Linear Algebra Subprograms (BLAS) and the extended BLAS (sparse) Available Available
FFTW A highly optimized 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) 2.1.5, 3.2.2, 3.3.3 3.3.4
GMP A free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers 4.3.1, 5.0.1 6.1.0
GSL GNU Scientific Library is a numerical library for C and C++ programmers 1.9 2.1
IMSL The IMSL Numerical analysis libraries are comprehensive set of mathematical and statistical functions for C, C# for .NET, Java, Fortran and Python fnl700 fnl710, cnl860
Intel MKL Intel Math Kernel Library is an optimized math library that contains BLACS, LAPACK, FFTs, and other functions. Available Available
BLAS, LAPACK, ScaLAPACK Basic Linear Algebra Subprograms (BLAS) is a de facto application programming interface standard for publishing libraries to perform basic linear algebra operations such as vector and matrix multiplication.
LAPACK extends BLAS to provide higher level linear algebra routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines.
Available Available
NAG A collection of hundreds of complex and highly sophisticated user callable routines for mathematical and statistical computation NPL6A60NA, FSL6A23DF, FSL6I24DD, CLL6I25DC, MBL6I24DM NPL6A60NA, FSL6A23DF, FSL6I24DD, CLL6I25DC, MBL6A24DN, FSLM626DC
SPRNG A scalable package for parallel pseudo random number generation which will be easy to use on a variety of architectures, especially in large-scale parallel Monte Carlo applications. 2.0b  
SuperLU_DIST A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance distributed memory machines. 2.5  
Programming Utilities
HDF5 A data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data 1.8.4 1.8.16, 1.10.1*
MPC A C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result 0.8.1, 0.9, 1.0.2 1.0.3
MPFR A C library for multiple-precision floating-point computations with correct rounding 2.4.2, 3.0.0, 3.1.2 3.1.3
NETCDF A set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data 4.0.4, 4.3.0 4.3.3.1
Visualization and Plotting
Gnuplot A portable command-line driven graphing utility 4.0.0 4.2.6
Grace/Xmgr A WYSIWYG 2D plotting tool for the X Window System and M*tif 5.1.22 5.1.25
GrADS A tool for easy access, manipulation, and visualization of earth science data. 2.0.2 2.0.2
Molden A package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format 4.8, 5.0* 5.4
ParaView An interactive parallel visualization platform for data analysis.   5.2.0
VMD A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. 1.9.2 1.9.2
VisIt An interactive parallel visualization and graphical analysis tool for viewing scientific data 2.12.1 2.12.1

* Several versions are installed; listed is the default version.

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