**EXAMPLES_ARC** is a directory of examples for various software
packages installed on the computer clusters of Virginia Tech's
Advanced Research Computing (ARC) center.

The ARC software list appears at: https://secure.hosting.vt.edu/www.arc.vt.edu/software/ .

One of my projects was to extend the set of brief introductory articles about software installed on the ARC clusters.

- abaqus, a finite element program;
- abinit, an ab-initio Density Functional Theory program;
- abyss, de novo short sequence assembler program;
- allinea-forge, ALLINEA-DDT for debugging, and ALLINEA-MAP for program performance monitoring;.
- amber, molecular simulation programs;
- anaconda, an extensive collection of Python libraries;
- anaconda2, an extensive collection of Python libraries;
- ansys, finite element programs for fluids, structures, electronics, semiconductors, systems, and multiphysics;
- apache-ant, a Java-based build tool;
- apbs-static, adaptive Poisson-Boltzmann solver;
- archive, the archive storage system;
- aspect, a program which simulates convection within the mantle of the earth;
- atlas, automatically tuned Basic Linear Algebra Subprograms library;
- autodocksuite, predict how small molecules bind to a receptor;
- automake, automatic generation of GNU style makefiles;
- bamtools, tools for BAM files;
- bcftools, manipulate variant calls in Variant Call Format (VCF) and its binary counterpart BCF;
- beagle-lib, estimate likelihood of sequence evolution on trees;
- bedtools, a toolkit for genome arithmetic;
- blas_atlas, use the BLAS library available through ATLAS;
- blas_mkl, use the BLAS library available through MKL;
- boost, a C++ library of high-quality functions;
- boost-mpi, a C++ library of high-quality functions for MPI applications;
- boost-ucs2, a C++ library of high-quality functions;
- bowtie, a tool for fast, efficient short sequencing read alignment;
- bowtie2, a tool for fast and sensitive sequencing read alignment;
- bwa, Burrows-Wheeler alignment;
- bzip2, compression program;
- caelus, a computational fluid dynamics package;
- cddlib, analysis of polygon, polyhedron, or polytope in higher dimensions;
- cgal, computational geometry library;
- citcoms, a finite element code which solves compressible thermochemical convection problems posed in the Earth's mantel;
- clapack, a C translation of the BLAS and LAPACK libraries;
- cmake, automatic compilation, loading, and maintenance of software;
- comsol, multiphysics modeling and simulation;
- cora, time-signal correlation;
- cplex, a program for linear programming, network flow, quadratic programming, and mixed integer programming;
- cuda, GPU programming language;
- cuda_fortran, GPU programming language;
- cufflinks assembles RNA-Seq read alignments into transcripts;
- dcw, the Digital Chart of the World;
- dealii, a C++ finite element library;
- dev_q, a queue available on all ARC systems, requiring an allocation, and intended for "program development", that is, short testing, debugging, and interactive sessions.
- ea-utils, commandline tools for biological sequencing data;
- eigen, a C++ template library for linear algebra;
- ensight, a visualization program for fluid dynammics data;
- espresso, electronic-structure calculations and materials modeling at the nanoscale;
- examl, maximum-likelihood inference of phylogenetic trees;
- expat, a library which can process XML files, including files which are too large to reside in memory;
- fastqc, fast quality checks of sequence data;
- fastx_toolkit, short-reads FASTA/FASTQ preprocessing;
- fdk-aac, AAC sound file encoder and decoder;
- ffmpeg, a program which converts a sequence of still images into a movie;
- fftw, a library for Fast Fourier Transforms;
- fieldview, a visualization program for fluid dynammics data;
- flann, fast library for approximate nearest neighbors;
- flint, fast library for number theory;
- fluent, computational fluid dynamics package in ANSYS suite;
- fortran_realsize, examples for requesting that FORTRAN "REAL" variables be treated by the compiler as "DOUBLE PRECISION".
- ga, a library for global arrays;
- gatb, a genome analysis toolbox;
- gatk, a genome analysis toolkit;
- gaussian, an ab initio quantum chemistry program;
- gcc, the Gnu Compiler Collection, whose main component is the Gnu C Compiler gcc;
- gdal, Geospatial Data Abstraction Library;
- geos, geometry engine, open source;
- gfortran, the Gnu Fortran Compiler;
- glm, OpenGL mathematical library;
- glog, Google error logging facility;
- gmsh, a mesh generator and manipulator for 1D/2D/3D discretized geometries;
- gmt, a generic mapping tool library;
- gnuplot, an interactive graphics program;
- gromacs, programs for molecular dynamics simulation and energy minimization;
- grouper, BASH scripts to assist research groups who wish to allow group members to share files;
- gshhg, a geographic database used by GMT.
- gsl, the Gnu Scientific Library, a library of general purpose numerical software;
- guile, GNU programming and extension language;
- harfbuzz, a text shaping engine;
- harminv, harmonic inversion;
- hdf5, a portable scientific dataset formatting library;
- hmmer, hidden Markov model sequence homology search;
- hpl, an implementation of the High Performance Linpack benchmark;
- ifort, the Intel Fortran compiler;
- imagemagick, programs which create, edit, compose, convert graphics images;
- impi, the Intel implementation of the MPI interface for distributed parallel programming;
- intel, the Intel C/C++/Fortran compilers;
- iozone, file system benchmark;
- ipm, integrated performance monitor for MPI programs;
- ipp, Intel integrated performance primitives;
- ipython, a command shell for interactive computing, particularly for Python;
- jags, Markov Chain Monte Carlo analysis of Bayesian graphical models;
- jdk, the Java Development Kit;
- julia, a numerical programming language for high performance computers;
- lame, a program which encodes audo information as an MP3 file;
- lammps, a parallel, classical molecular dynamics code;
- lapack_atlas, use the LAPACK library available through ATLAS;
- lapack_mkl, use the LAPACK library available through MKL;
- largemem_q, the large memory queue, available only on the Cascades cluster.
- libgtextutils, a text utility library;
- libjpeg-turbo, an accelerated version of the libjpeg graphics library;
- licensed_software, a list of software installed on ARC systems which are controlled by some kind of license;
- lordec, correct sequencing errors in long reads;
- ls-dyna, a finite element program for highly nonlinear transient dynamic problems;
- lsopt, optimization of models constructed with LS-DYNA;
- lua, a lightweight scripting language;
- luajit, a Just-In-Time compiler for LUA;
- m4, the Gnu macro editor;
- mathematica, a programming language for symbolic computing;
- matlab, a programming language for numerical computing;
- matlab_parallel, how a MATLAB computation can be submitted to the batch system for parallel execution;
- matplotlib, a graphics library for Python;
- meep, a finite-difference time-domain (FDTD) software package for simulating electromagnetic systems.
- metis, partition graphs and meshes, reorder sparse matrices;
- minia, ultra-low memory DNA sequence assembly;
- mkl, the Intel Math Kernel Library;
- mkl_ifort, the Intel Math Kernel Library, used with the Intel Fortran compiler ifort;
- mothur, a Python-based bioinformatics tool for analyzing 16S rRNA gene sequences and is focussed on the microbial ecology community.
- mpe2, MPI performance visualization tools;
- mpi4py, allows Python programs to run in parallel under MPI.
- mpich, an implementation of the MPI interface for distributed parallel programming;
- mpip, a utility for monitoring MPI program performance;
- mrbayes, Bayesian inference for evolutionary and phylogenetic models;
- mvapich2, an implementation of the MPI interface for distributed parallel programming;
- mvapich2-test, an implementation of the MPI interface for distributed parallel programming (a variant test version);
- namd, a parallel, object-oriented molecular dynamics code;
- namd-gpu, a GPU version of the NAMD code;
- nastran, finite element structural analysis program;
- ncbi-blast+, basic local alignment search tool;
- ncl, NCAR Command Language for graphics;
- nco, NETCDF Operators to manipulate data in NETCDF files;
- ncview, reads and displays the data in a NETCDF file;
- netcdf, NETCDF portable datafile library;
- netcdf-c, C interface to the NETCDF portable datafile library;
- netcdf-c-par, C interface to the NETCDF portable datafile library including parallelism;
- netcdf-cxx, C++ interface to the NETCDF portable datafile library;
- netcdf-fortran, FORTRAN interface to the NETCDF portable datafile library;
- netcdf-fortran-par, FORTRAN interface to the parallel NETCDF portable datafile library;
- netcdf-par, interface to the NETCDF portable datafile library including parallelism;
- normal_q, the "normal_q".
- nose, automatic unit-testing facility for Python;
- numpy, a numerical library for Python;
- octave, an interactive program for scientific and numerical calculation;
- open_q, a queue available on all systems, to all users, but with limited resources; access to this queue does not require an allocation;
- openacc, a parallel programming system;
- openblas, an optimized version of the Basic Linear Algebra Subprogram (BLAS) package;
- opencv, a C++ library for real-time applications involving computer vision;
- openfoam, a computational fluid dynamics package;
- openmp, a set of directives and functions for shared memory parallel programming;
- openmpi, an implementation of the MPI interface for distributed parallel programming;
- openmpi-test, an implementation of the MPI interface for distributed parallel programming (Test Version);
- opensees, an earthquake engineering simulation program;
- p100, the P100 GPU nodes;
- p100_dev_q, the "development" queue for the P100 GPU's, available only on the NewRiver cluster.
- p100_normal_q, the "normal" queue for the P100 GPU's, available only on the NewRiver cluster.
- p2fa, Penn Phonetics Lab Forced Aligner;
- p4est, dynamically manage a collection of octrees;
- p7zip, lossless compression program;
- pango, a library for text layout and rendering;
- papi, performance application programming interface;
- parallel, GNU Parallel scripting command;
- parallel-netcdf, parallel version of NETCDF;
- parmetis, parallel program to partition nodes in a sparse graph or matrix;
- pbdr, highly scalable R packages for distributed computing and profiling in data science;
- pbs, a job scheduler.
- pbs_nodefile, how the PBS scheduler creates a list of nodes to be used cooperatively as part of the execution of a parallel MPI job.
- pcl, the Point Cloud Library;
- perl, a high level dynamic programming language;
- pgf90, Portland Group Fortran90 compiler;
- pgi, Portland Group Fortran, C, and C++ compilers;
- phdf5, Parallel HDF5 library, for large, complex data files with MPI;
- picard, tools for manipulating high throughput sequencing data;
- pigz, a parallel data compression program;
- proj, a program to poject geographic longitude/latitude to various cartesian coordinate systems;
- pycuda, a Python interface for CUDA programming;
- python, a high-level programming language;
- python-ucs2, the Python programming language;
- python3gdal, Geospatial Data Abstraction Library;
- r, a programming language for statistical applications;
- r-parallel, parallel R libraries pbdr, rmpi, snow, snowfall;
- rutils, the R utils package;
- sac, seismic analysis program;
- samtools, tools for high throughput sequencing data;
- scalapack, distributed parallel linear algebra algorithms;
- scipy, a Python library for scientific computing;
- scons, a software construction tool;
- seqtk, a toolkit for FASTA and FASTQ sequence data files;
- singular, a computer algebra system for polynomial computations;
- slurm, a job scheduler.
- sox, a program for the manipulation of sound data;
- spades, St Petersburg genome assembler;
- sparsehash, a space-efficient hash-table utility;
- sprai, correct sequencing errors in single-pass reads;
- stata, an interactive statistical analysis package;
- swig, call C and C++ functions from other languages;
- szip, a lossless compression algorithm for HDF5;
- tbb, threading building blocks for C++;
- tecplot, interactive scientific illustration, animation and visualization program;
- tensorflow, an interface for expressing machine learning algorithms on heterogeneous systems;
- test_suite_blueridge, runs the BlueRidge test codes;
- test_suite_cascades_broadwell, runs the Cascades Broadwell test codes;
- test_suite_cascades_skylake, runs the Cascades Skylake test codes;
- test_suite_dragonstooth, runs the DragonsTooth test codes;
- test_suite_huckleberry, runs the Huckleberry test codes;
- test_suite_newriver_broadwell, runs the NewRiver/Broadwell test codes;
- test_suite_newriver_haswell, runs the NewRiver/Haswell test codes;
- test_suite_newriver_ivybridge, runs the NewRiver/Ivybridge test codes;
- theano, a deep learning package written in Python;
- tophat, a spliced read mapper for RNA-Seq;
- torch, a scientific computing framework for LUAJIT;
- trilinos, an extensive library for multiphysics problems;
- trimmomatic, a read trimming tool for Illumina NGS data;
- trinityrnaseq, RNA-Seq de novo assembly;
- uuid, generate universally unique identifiers;
- v100_dev_q the "development" queue for the V100 GPU's, available only on the Cascades cluster.
- v100_large_q a large memory queue for the V100 GPU's, available only on the Cascades cluster.
- v100_normal_q, the research and production queue for the V100 GPU's, available only on the Cascades cluster.
- valgrind, checks programs for illegal memory references, uninitialized variable use, and memory leaks;
- vasp, ab-initio quantum-mechanical molecular dynamics (MD) simulations;
- vasp-gpu, GPU version of VASP;
- velvet, genomic assembler;
- viennacl, scientific library for CUDA/OpenCL/OpenMP;
- vis_q, a queue available on the ARC BlueRidge and NewRiver clusters, requiring an allocation, and intended for jobs involving visualization tasks, such as rendering.
- wannier90, maximally localized Wannier functions;
- x264, a library for converting video formats;
- yasm, an assembler with multiple output formats;
- zip, lossless compression program;
- zlib, lossless compression and uncompression;

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