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

### Licensed/Open Source Software Applications

Software | Description | HPC2015 |
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Bioinformatics and Genomics |
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Bowtie2 | An ultrafast and memory-efficient tools for aligning sequencing reads to long reference sequences | 2.2.9 |

CD-HIT | A program for clustering and comparing protein or nucleotide sequences | 4.6.8 |

GARLI | A program that performs phylogenetic inference using the maximum-likelihood criterion. Several sequence types are supported, including nucleotide, amino acid and codon. | 2.1 |

HyPhy | An open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning | 2.2.7 |

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 | 4.11.2 |

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 (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, 1.4* |

Chemistry and Molecular Modeling |
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ADF | An accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT) | 2014, 2019* |

AMBER | A package of programs for molecular dynamics simulations of proteins and nucleic acids | 16, 18, 20 |

CFOUR | A program package for performing high-level qauntum chemical calculations on atoms and molecules. | 1.0 |

CP2K | A quantum chemistry and solid state physics software package | 6.1 |

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 | 4.1 |

Gaussian | It provides state-of-the-art capabilities for electronic structure modeling | g09, g16 |

GAMESS |
A program for ab initio molecular quantum chemistry |
20141205R1, 20170420R1, 20180214R1* |

GROMACS | A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids | 5.1.1, 2018.2* |

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 | 16 Feb 2016 |

NAMD | A parallel molecular dynamics simulation package with Charm++ for high-performance simulation of large biomolecular systems. | 2.12 |

NWChem | High performance computational chemistry tools for kinetics and dynamics of chemical transformations, chemistry at interfaces and in the condensed phase, | 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. | 3.0.3, 4.0.0 |

SIESTA | A software perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids | 3.2 |

Physics and Materials Science |
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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. | 6.13-4, 6.14-1, 2016, 2017, 2018* |

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 |

Quantum ESPRESSO | Software suite for electronic-structure calculations and materials modeling at tje nanoscale | 6.1, 6.3* |

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, 5.4.1, 5.4.4, 6.1.2 |

Mathematics and Statistics |
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MATLAB | A programming environment for algorithm development, data analysis, visualization, and numerical computation | R2015a, R2015b, R2016b, R2017b, R2018b* |

R | A free software environment for statistical computing and graphics | 3.2.2, 3.2.5, 3.4.1, 3.5.1, 3.6.1, 4.0.1* |

Octave | Open source numerical computing program compatible with MATLAB | 3.4.3, 4.0.0* |

Data Analysis and Machine Learning |
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Anaconda | An open source distrubution of Python & R programming languages for data science and machine learning related applications | 5.2 |

Caffe | A fast, open framework for deep learning | 1.0.0 |

TensorFlow | Software library for numerical computation using data flow graphs | 2.3.1 |

Theano | A numerical computation library for Python | 1.0.2 |

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

### Utilities and Libraries

Type | Description | HPC2015 | |
---|---|---|---|

Compilers and programming languages |
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GNU Compiler | GNU Compiler Collection compilers and libraries (gcc, gfortran, g++) | 4.4.7*, 4.9.3, 5.2.0, 6.3.0, 8.2.0 | |

Intel Compiler | Intel compilers and libraries for C/C++ and Fortran (icc, icpc, ifort) | 2013, 2015, 2016, 2017, 2018*, 2019 | |

PGI Compiler | Portland Group compilers and libraries (pgcc, pgf90, pgCC, etc) | 15.7, 16.10, 17.7, 18.5, 19.7* | |

CUDA | CUDA Toolkit for programming nVidia GPUs | 7.0, 7.5, 8.0, 9.0, 10.0* | |

Python | Ab interpreted high-level programming language for general-purpose programming. | 2.6.6*, 2.7.11, 3.6.3, 3.7.3, 3.8.3 | |

Julia | High-Performance numerical computing environment and language | 0.5.2, 0.6.2*, 0.7.0, 1.0.2 | |

Ruby | A dynamics, object-oriented programming language | 2.4 | |

Parallel Libraries |
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MPICH | A freely available, portable implementation of MPI, the standard for message-passing libraries. | Available | |

MVAPICH | MPI over InfiniBand, 10GigE/iWARP and RoCE | Available | |

Intel MPI | A multi-fabric message passing library that implements MPI-3.0. It provides a standard library across Intel platforms | 4.1.3, 5.0.3, 5.1.1, 5.1.3, 2017.7, 2018.4* | |

Open MPI | A High Performance Message Passing Library for parallel computing | Available | |

MPI for Python (mpi4py) | Package enabling applications to exploit multiple processors using standard MPI in Python scripts | 2.0.0 | |

Math Libraries |
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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 | |

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) | 3.3.4, 3.3.7 | |

GMP | A free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers | 6.1.0 | |

GSL | GNU Scientific Library is a numerical library for C and C++ programmers | 2.1, 2.5 | |

IMSL | The IMSL Numerical analysis libraries are comprehensive set of mathematical and statistical functions for C, C# for .NET, Java, Fortran and Python | fnl710, cnl860 | |

Intel MKL | Intel Math Kernel Library is an optimized math library that contains BLACS, LAPACK, FFTs, and other functions. | Available | |

BLAS, LAPACK and 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 | |

NAG | A collection of hundreds of complex and highly sophisticated user callable routines for mathematical and statistical computation | NPL6A62NA, FSL6I26DC, FSL6I24DD, FSLM626DC, CSL6I26DD, CSLM626DD, CLL6I262C, CLL6I262D, MBL6I25DN | |

Programming Utilities |
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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 | 1.8.16, 1.10.1* | |

MPC | A C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result | 1.0.3 | |

MPFR |
A C library for multiple-precision floating-point computations with correct rounding |
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 | 4.3.3.1 | |

Visualization and Plotting |
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Gnuplot | A portable command-line driven graphing utility | 4.2.6 | |

Grace/Xmgr | A WYSIWYG 2D plotting tool for the X Window System and M*tif | 5.1.25 | |

GrADS | A tool for easy access, manipulation, and visualization of earth science data. | 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 | 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 | |

VisIt | An interactive parallel visualization and graphical analysis tool for viewing scientific data | 2.12.1 |

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

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