EXAMPLES_ARC


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.

  1. abaqus, a finite element program;
  2. abinit, an ab-initio Density Functional Theory program;
  3. abyss, de novo short sequence assembler program;
  4. allinea-forge, ALLINEA-DDT for debugging, and ALLINEA-MAP for program performance monitoring;.
  5. amber, molecular simulation programs;
  6. anaconda, an extensive collection of Python libraries;
  7. anaconda2, an extensive collection of Python libraries;
  8. ansys, finite element programs for fluids, structures, electronics, semiconductors, systems, and multiphysics;
  9. apache-ant, a Java-based build tool;
  10. apbs-static, adaptive Poisson-Boltzmann solver;
  11. archive, the archive storage system;
  12. aspect, a program which simulates convection within the mantle of the earth;
  13. atlas, automatically tuned Basic Linear Algebra Subprograms library;
  14. autodocksuite, predict how small molecules bind to a receptor;
  15. automake, automatic generation of GNU style makefiles;
  16. bamtools, tools for BAM files;
  17. bcftools, manipulate variant calls in Variant Call Format (VCF) and its binary counterpart BCF;
  18. beagle-lib, estimate likelihood of sequence evolution on trees;
  19. bedtools, a toolkit for genome arithmetic;
  20. blas_atlas, use the BLAS library available through ATLAS;
  21. blas_mkl, use the BLAS library available through MKL;
  22. boost, a C++ library of high-quality functions;
  23. boost-mpi, a C++ library of high-quality functions for MPI applications;
  24. boost-ucs2, a C++ library of high-quality functions;
  25. bowtie, a tool for fast, efficient short sequencing read alignment;
  26. bowtie2, a tool for fast and sensitive sequencing read alignment;
  27. bwa, Burrows-Wheeler alignment;
  28. bzip2, compression program;
  29. caelus, a computational fluid dynamics package;
  30. cddlib, analysis of polygon, polyhedron, or polytope in higher dimensions;
  31. cgal, computational geometry library;
  32. citcoms, a finite element code which solves compressible thermochemical convection problems posed in the Earth's mantel;
  33. clapack, a C translation of the BLAS and LAPACK libraries;
  34. cmake, automatic compilation, loading, and maintenance of software;
  35. comsol, multiphysics modeling and simulation;
  36. cora, time-signal correlation;
  37. cplex, a program for linear programming, network flow, quadratic programming, and mixed integer programming;
  38. cuda, GPU programming language;
  39. cuda_fortran, GPU programming language;
  40. cufflinks assembles RNA-Seq read alignments into transcripts;
  41. dcw, the Digital Chart of the World;
  42. dealii, a C++ finite element library;
  43. 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.
  44. ea-utils, commandline tools for biological sequencing data;
  45. eigen, a C++ template library for linear algebra;
  46. ensight, a visualization program for fluid dynammics data;
  47. espresso, electronic-structure calculations and materials modeling at the nanoscale;
  48. examl, maximum-likelihood inference of phylogenetic trees;
  49. expat, a library which can process XML files, including files which are too large to reside in memory;
  50. fastqc, fast quality checks of sequence data;
  51. fastx_toolkit, short-reads FASTA/FASTQ preprocessing;
  52. fdk-aac, AAC sound file encoder and decoder;
  53. ffmpeg, a program which converts a sequence of still images into a movie;
  54. fftw, a library for Fast Fourier Transforms;
  55. fieldview, a visualization program for fluid dynammics data;
  56. flann, fast library for approximate nearest neighbors;
  57. flint, fast library for number theory;
  58. fluent, computational fluid dynamics package in ANSYS suite;
  59. fortran_realsize, examples for requesting that FORTRAN "REAL" variables be treated by the compiler as "DOUBLE PRECISION".
  60. ga, a library for global arrays;
  61. gatb, a genome analysis toolbox;
  62. gatk, a genome analysis toolkit;
  63. gaussian, an ab initio quantum chemistry program;
  64. gcc, the Gnu Compiler Collection, whose main component is the Gnu C Compiler gcc;
  65. gdal, Geospatial Data Abstraction Library;
  66. geos, geometry engine, open source;
  67. gfortran, the Gnu Fortran Compiler;
  68. glm, OpenGL mathematical library;
  69. glog, Google error logging facility;
  70. gmsh, a mesh generator and manipulator for 1D/2D/3D discretized geometries;
  71. gmt, a generic mapping tool library;
  72. gnuplot, an interactive graphics program;
  73. gromacs, programs for molecular dynamics simulation and energy minimization;
  74. grouper, BASH scripts to assist research groups who wish to allow group members to share files;
  75. gshhg, a geographic database used by GMT.
  76. gsl, the Gnu Scientific Library, a library of general purpose numerical software;
  77. guile, GNU programming and extension language;
  78. harfbuzz, a text shaping engine;
  79. harminv, harmonic inversion;
  80. hdf5, a portable scientific dataset formatting library;
  81. hmmer, hidden Markov model sequence homology search;
  82. hpl, an implementation of the High Performance Linpack benchmark;
  83. ifort, the Intel Fortran compiler;
  84. imagemagick, programs which create, edit, compose, convert graphics images;
  85. impi, the Intel implementation of the MPI interface for distributed parallel programming;
  86. intel, the Intel C/C++/Fortran compilers;
  87. iozone, file system benchmark;
  88. ipm, integrated performance monitor for MPI programs;
  89. ipp, Intel integrated performance primitives;
  90. ipython, a command shell for interactive computing, particularly for Python;
  91. jags, Markov Chain Monte Carlo analysis of Bayesian graphical models;
  92. jdk, the Java Development Kit;
  93. julia, a numerical programming language for high performance computers;
  94. lame, a program which encodes audo information as an MP3 file;
  95. lammps, a parallel, classical molecular dynamics code;
  96. lapack_atlas, use the LAPACK library available through ATLAS;
  97. lapack_mkl, use the LAPACK library available through MKL;
  98. largemem_q, the large memory queue, available only on the Cascades cluster.
  99. libgtextutils, a text utility library;
  100. libjpeg-turbo, an accelerated version of the libjpeg graphics library;
  101. licensed_software, a list of software installed on ARC systems which are controlled by some kind of license;
  102. lordec, correct sequencing errors in long reads;
  103. ls-dyna, a finite element program for highly nonlinear transient dynamic problems;
  104. lsopt, optimization of models constructed with LS-DYNA;
  105. lua, a lightweight scripting language;
  106. luajit, a Just-In-Time compiler for LUA;
  107. m4, the Gnu macro editor;
  108. mathematica, a programming language for symbolic computing;
  109. matlab, a programming language for numerical computing;
  110. matlab_parallel, how a MATLAB computation can be submitted to the batch system for parallel execution;
  111. matplotlib, a graphics library for Python;
  112. meep, a finite-difference time-domain (FDTD) software package for simulating electromagnetic systems.
  113. metis, partition graphs and meshes, reorder sparse matrices;
  114. minia, ultra-low memory DNA sequence assembly;
  115. mkl, the Intel Math Kernel Library;
  116. mkl_ifort, the Intel Math Kernel Library, used with the Intel Fortran compiler ifort;
  117. mothur, a Python-based bioinformatics tool for analyzing 16S rRNA gene sequences and is focussed on the microbial ecology community.
  118. mpe2, MPI performance visualization tools;
  119. mpi4py, allows Python programs to run in parallel under MPI.
  120. mpich, an implementation of the MPI interface for distributed parallel programming;
  121. mpip, a utility for monitoring MPI program performance;
  122. mrbayes, Bayesian inference for evolutionary and phylogenetic models;
  123. mvapich2, an implementation of the MPI interface for distributed parallel programming;
  124. mvapich2-test, an implementation of the MPI interface for distributed parallel programming (a variant test version);
  125. namd, a parallel, object-oriented molecular dynamics code;
  126. namd-gpu, a GPU version of the NAMD code;
  127. nastran, finite element structural analysis program;
  128. ncbi-blast+, basic local alignment search tool;
  129. ncl, NCAR Command Language for graphics;
  130. nco, NETCDF Operators to manipulate data in NETCDF files;
  131. ncview, reads and displays the data in a NETCDF file;
  132. netcdf, NETCDF portable datafile library;
  133. netcdf-c, C interface to the NETCDF portable datafile library;
  134. netcdf-c-par, C interface to the NETCDF portable datafile library including parallelism;
  135. netcdf-cxx, C++ interface to the NETCDF portable datafile library;
  136. netcdf-fortran, FORTRAN interface to the NETCDF portable datafile library;
  137. netcdf-fortran-par, FORTRAN interface to the parallel NETCDF portable datafile library;
  138. netcdf-par, interface to the NETCDF portable datafile library including parallelism;
  139. normal_q, the "normal_q".
  140. nose, automatic unit-testing facility for Python;
  141. numpy, a numerical library for Python;
  142. octave, an interactive program for scientific and numerical calculation;
  143. open_q, a queue available on all systems, to all users, but with limited resources; access to this queue does not require an allocation;
  144. openacc, a parallel programming system;
  145. openblas, an optimized version of the Basic Linear Algebra Subprogram (BLAS) package;
  146. opencv, a C++ library for real-time applications involving computer vision;
  147. openfoam, a computational fluid dynamics package;
  148. openmp, a set of directives and functions for shared memory parallel programming;
  149. openmpi, an implementation of the MPI interface for distributed parallel programming;
  150. openmpi-test, an implementation of the MPI interface for distributed parallel programming (Test Version);
  151. opensees, an earthquake engineering simulation program;
  152. p100, the P100 GPU nodes;
  153. p100_dev_q, the "development" queue for the P100 GPU's, available only on the NewRiver cluster.
  154. p100_normal_q, the "normal" queue for the P100 GPU's, available only on the NewRiver cluster.
  155. p2fa, Penn Phonetics Lab Forced Aligner;
  156. p4est, dynamically manage a collection of octrees;
  157. p7zip, lossless compression program;
  158. pango, a library for text layout and rendering;
  159. papi, performance application programming interface;
  160. parallel, GNU Parallel scripting command;
  161. parallel-netcdf, parallel version of NETCDF;
  162. parmetis, parallel program to partition nodes in a sparse graph or matrix;
  163. pbdr, highly scalable R packages for distributed computing and profiling in data science;
  164. pbs, a job scheduler.
  165. 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.
  166. pcl, the Point Cloud Library;
  167. perl, a high level dynamic programming language;
  168. pgf90, Portland Group Fortran90 compiler;
  169. pgi, Portland Group Fortran, C, and C++ compilers;
  170. phdf5, Parallel HDF5 library, for large, complex data files with MPI;
  171. picard, tools for manipulating high throughput sequencing data;
  172. pigz, a parallel data compression program;
  173. proj, a program to poject geographic longitude/latitude to various cartesian coordinate systems;
  174. pycuda, a Python interface for CUDA programming;
  175. python, a high-level programming language;
  176. python-ucs2, the Python programming language;
  177. python3gdal, Geospatial Data Abstraction Library;
  178. r, a programming language for statistical applications;
  179. r-parallel, parallel R libraries pbdr, rmpi, snow, snowfall;
  180. rutils, the R utils package;
  181. sac, seismic analysis program;
  182. samtools, tools for high throughput sequencing data;
  183. scalapack, distributed parallel linear algebra algorithms;
  184. scipy, a Python library for scientific computing;
  185. scons, a software construction tool;
  186. seqtk, a toolkit for FASTA and FASTQ sequence data files;
  187. singular, a computer algebra system for polynomial computations;
  188. slurm, a job scheduler.
  189. sox, a program for the manipulation of sound data;
  190. spades, St Petersburg genome assembler;
  191. sparsehash, a space-efficient hash-table utility;
  192. sprai, correct sequencing errors in single-pass reads;
  193. stata, an interactive statistical analysis package;
  194. swig, call C and C++ functions from other languages;
  195. szip, a lossless compression algorithm for HDF5;
  196. tbb, threading building blocks for C++;
  197. tecplot, interactive scientific illustration, animation and visualization program;
  198. tensorflow, an interface for expressing machine learning algorithms on heterogeneous systems;
  199. test_suite_blueridge, runs the BlueRidge test codes;
  200. test_suite_cascades_broadwell, runs the Cascades Broadwell test codes;
  201. test_suite_cascades_skylake, runs the Cascades Skylake test codes;
  202. test_suite_dragonstooth, runs the DragonsTooth test codes;
  203. test_suite_huckleberry, runs the Huckleberry test codes;
  204. test_suite_newriver_broadwell, runs the NewRiver/Broadwell test codes;
  205. test_suite_newriver_haswell, runs the NewRiver/Haswell test codes;
  206. test_suite_newriver_ivybridge, runs the NewRiver/Ivybridge test codes;
  207. theano, a deep learning package written in Python;
  208. tophat, a spliced read mapper for RNA-Seq;
  209. torch, a scientific computing framework for LUAJIT;
  210. trilinos, an extensive library for multiphysics problems;
  211. trimmomatic, a read trimming tool for Illumina NGS data;
  212. trinityrnaseq, RNA-Seq de novo assembly;
  213. uuid, generate universally unique identifiers;
  214. v100_dev_q the "development" queue for the V100 GPU's, available only on the Cascades cluster.
  215. v100_large_q a large memory queue for the V100 GPU's, available only on the Cascades cluster.
  216. v100_normal_q, the research and production queue for the V100 GPU's, available only on the Cascades cluster.
  217. valgrind, checks programs for illegal memory references, uninitialized variable use, and memory leaks;
  218. vasp, ab-initio quantum-mechanical molecular dynamics (MD) simulations;
  219. vasp-gpu, GPU version of VASP;
  220. velvet, genomic assembler;
  221. viennacl, scientific library for CUDA/OpenCL/OpenMP;
  222. 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.
  223. wannier90, maximally localized Wannier functions;
  224. x264, a library for converting video formats;
  225. yasm, an assembler with multiple output formats;
  226. zip, lossless compression program;
  227. zlib, lossless compression and uncompression;

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Last revised on 17 June 2018.