What Runs Where on Athena: Simulation and Modeling

AFNI

Description: collection of programs for viewing and analyzing functional magnetic resonance images of the brain. Supplied with many associated command-line utility functions

TO RUN:

athena% add seven

athena% afni data-directory (main application)

athena% command options files (utilities)

Please see documentation for usage of utility commands

Local documentation starts here; there is also a central information site and a resource site

See also: clustalw, GENSCAN, NetPBM Utilities, xv

Biopython

Description: collection of Python tools for computational molecular biology- allows processing of biological sequences and databases

To run in interactive mode:

athena% add seven

athena% biopython

followed by commands from the Biopython package, for example:

>>> from Bio.Seq import Seq

>>> new_seq = Seq('GATC')

>>> new_seq[0:2]

To run as a stand-alone application, you can write python scripts that contain Biopython commands

There is a documentation site

See also: BLAST, CLC Sequence Viewer , clustalw, COPASI, emboss, Geneious, GENSCAN, hmmer, meme/mast, Osprey, phylip, primer3, python, R

BLAST

Description: BLAST (Basic Local Alignment Search Tool) is an application for finding regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. BLAST can be run standalone, as an NCBI Web client, via a local BLAST server and via a Web form at the NCBI Website. This installation contains the standalone and Web client versions from NCBI

TO RUN:

athena% blastcl3 -i query options > outfile (Web client: to run query query, with output in outfile)

athena% formatdb -i data options (standalone: to index a database data)

athena% program options -d data -i query > outfile (standalone: use program to run query query against database data, output in outfile)

There is documentation, tutorial information (see section 19.3 for BLAST), Wiki and a Web page

See also: Biopython, CLC Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, phylip, primer3, R

CLC Sequence Viewer

Description: tool for bioinformatics analysis including: alignment creation and editing, interactive restriction site analysis, phylogenetics, integrated GenBank searches, DNA to protein translation and other features

TO RUN:

athena% add clcbio

athena% clcseqview6 &

There is a local pdf manual and Website

See also: Biopython, BLAST, clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, Net Entrez, phylip

clustalw

Description: general purpose multiple sequence alignment program for DNA or proteins

TO RUN:

athena% clustalw

There is a Web page

See also: AFNI, Biopython, BLAST, CLC Sequence Viewer , emboss, Geneious, GENSCAN, hmmer, meme/mast, phylip, primer3, R

COPASI

Description: software application for simulation and analysis of biochemical networks and their dynamics

TO RUN:

athena% add copasi

athena% CopasiUI & (GUI interface)

athena% CopasiSE options file (command line interface)

There is a Web page and local online manual

See also: Biopython, NEURON, Osprey

emboss

Description: the European Molecular Biology Suite is a large collection of tools for molecular analysis of genomic data. It can handle data in a variety of formats and allows transparent retrieval of sequence data from the Web. A GUI Java-based interface, jemboss, is also available

TO RUN:

athena% runJemboss.csh (to run GUI)

athena% command options file(s) (command is one of the emboss commands; see docs for list)

There is documentation at the development site and a Web page

See also: Biopython, BLAST, CLC Sequence Viewer , clustalw, Geneious, GENSCAN, hmmer, meme/mast, phylip, primer3, R

Note: This application is no longer installed. You can install it from the emboss and jemboss Ubuntu packages using aptitude or synaptic

Geneious

Description: integrated bioinformatics tool suite for manipulating, finding, sharing and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information and publications

TO RUN:

athena% add geneious

athena% geneious &

There is a local pdf manual, and Web site

See also: Biopython, BLAST, CLC Sequence Viewer , clustalw, emboss, GENSCAN, hmmer, meme/mast, Net Entrez, phylip

Note: The version of Geneious on Athena is the free, basic version, not the more advanced Pro version

GENSCAN

Description: tool for predicting the locations and exon-intron structures of genes in genomic sequences

TO RUN:

athena% add seven

athena% genscan /mit/seven/share/HumanIso.smat sequence-file options (vertebrates)

athena% genscan /mit/seven/share/Maize.smat sequence-file options (maize)

athena% genscan /mit/seven/share/Arabidopsis.smat sequence-file options (arabidopsis)

Local documentation starts here

See also: AFNI, Biopython, BLAST, CLC Sequence Viewer , clustalw, emboss, Geneious, hmmer, meme/mast, phylip

hmmer

Description: set of tools that profile hidden Markov models for protein sequence analysis. This can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus

TO RUN:

athena% hmmfetch options database name

athena% hmmalign options hmmfile seqfile

athena% hmmsearch options hmmfile seqfile

athena% hmmbuild options hmmfile seqfile

(other commands exist; see man hmmer for documentation)

There is documentation and a Web page

See also: Biopython, BLAST, CLC Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, meme/mast, phylip, primer3, R

meme/mast

Description: meme is a tool for discovering motifs in a group of related DNA or protein sequences. mast is a tool for searching molecular sequence databases for sequences that contain one or more of a group of known motifs. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences

TO RUN:

athena% add meme

athena% meme dataset options

athena% mast motif-file options

There is local documentation for meme and mast; there is also a Web page

See also: Biopython, BLAST, CLC Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, hmmer, phylip, primer3

NEURON

Description: simulator of neurons and networks of neurons, with an extensible library of biophysical mechanisms

TO RUN:

athena% add neuron

athena% nrngui (to run GUI)

athena% neurondemo (to run a demo)

Look below /mit/neuron/bin to see launch commands for various components and utilities; local tutorials and documentation are available. There is an author Web page and pointers to additional documentation

See also: COPASI, Osprey

Osprey

Description: tool for graphically representing biological interaction networks, drawing on data from various interaction databases. Osprey is integrated with the BioGRID

TO RUN:

athena% add osprey

athena% osprey &

There is an author page with documentation

See also: Biopython, COPASI, NEURON

phylip

Description: phylip (Phylogeny Inference Package) is a collection of separate programs for inferring phylogenies (evolutionary trees). It can infer phylogenies by parsimony, compatibility, distance matrix methods and likelihood. It can also compute consensus trees, compute distances between trees, draw trees, resample data sets by bootstrapping or jackknifing, edit trees and compute distance matrices. It can handle data that are nucleotide sequences, protein sequences, gene frequencies, restriction sites, restriction fragments, distances, discrete characters and continuous characters.

TO RUN:

athena% phylip command file(s) (command is one of the phylip commands; see docs for list)

generally a data file named intree or infile is expected as input in the current directory; output is produced in files outtree and outfile in the same directory. drawtree and drawgram additionally require a font file in the current directory

There is documentation and a Web page

See also: Biopython, BLAST, CLC Sequence Viewer , clustalw, emboss, Geneious, GENSCAN, hmmer, meme/mast, primer3

Note: this application is no longer installed. You can install it from the phylip Ubuntu package using aptitude or synaptic

primer3

Description: program for designing Polymerase Chain Reaction primers. It can also design hybridization probes and sequencing primers

TO RUN:

athena% primer3_core < inputdata

There is an author page and documentation

See also: Biopython, BLAST, clustalw, emboss, hmmer, meme/mast, phylip

CalculiX

Description: 3d structural analysis finite-element program, incorporating a pre- and post-processor (Graphix, cgx) and solution engine (CrunchiX, ccx_2.4). The cfd computation application isaac is also installed. A vda to fdb conversion utility vda2fbd is also in the locker

TO RUN:

athena% add calculix

athena% ccx_2.4 file (to run ccx_2.4 on model file file.inp)

athena% cgx model.frd (to view model in file model.frd; use left mouse button outside drawing rectangle for popup menu)

athena% cgx -b model.fbd (to preprocess model in file model.fbd; use left mouse button outside drawing rectangle for popup menu)

athena% vda2fbd file.vda > file.fbd (to convert file.vda to file.fbd)

athena% isaac < file.dat (to run isaac on input data file file.dat)

There is an online ccx manual, cgx manual, cgx tutorial and an author Web page; there is also a discussion group

For isaac, there is a Web page and online manual

See also: Elmer, FreeFem++, Mathematica (IMTEK Mathematica supplement), OpenFOAM

EasyMesh

Description: 2d Delaunay mesh generator that supports a variety of features, including materials containing holes, domains composed of more than one material and Laplacian smoothing. Output can be generated in a variety of file formats. ShowMesh is a viewer for displaying meshes created by EasyMesh

TO RUN:

athena% add easymesh

athena% easymesh infile options (to run EasyMesh on input data file infile)

athena% showmesh infile (to run ShowMesh on input data file infile)

There is EasyMesh documentation, ShowMesh documentation and an author Web page

EasyMesh is used by some of the demos in the IMTEK Mathematica supplement added to our Mathematica installation

See also: Mathematica, tetgen, triangle

Elmer

Description: multiphysics/finite-element application capable of solving problems that can be described by partial differential equations in fields such as fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics. It includes a front end, solver and post-processor, and can import data from a variety of commercial finite-element applications

TO RUN:

athena% ElmerGUI (to run the main GUI)

athena% ElmerGrid options (to run the mesh generator)

athena% ElmerFront (to run front end)

athena% ElmerSolver (to run solver on model file file.sif, where this file is in the current directory)

athena% ElmerPost (to run post-processor; needs to read data in file.ep generated by solver)

There is a Web page

See also: CalculiX, FreeFem++, Mathematica (IMTEK Mathematica supplement), oof, OpenFOAM, OpenModelica, Stanford University Unstructured, TAO/PETSc

Note: This application is no longer installed. You can install it from the elmer and elmer-doc Ubuntu packages using aptitude or synaptic

This application is technical and complex and generally requires multiple solutions steps involving a number of distinct programs. You need to read the documentation and work through some of the tutorials to learn how to use it

FreeFem++

Description: finite-element method solver for partial differential equations that incorporates an internal scripting language. It can output graphics directly

TO RUN:

athena% add freefempp

athena% FreeFem++ file.edp (to run FreeFem++ on model file file.edp

There is an online manual and an author Web page

See also: CalculiX, Elmer, Mathematica (IMTEK Mathematica supplement), OpenFOAM, Stanford University Unstructured

OpenFOAM

Description: OpenFOAM is primarily a C++ library used to create executables, known as applications. The applications fall into two categories: solvers, that are each designed to solve a specific problem in continuum mechanics; and utilities, that are designed to perform tasks that involve data manipulation. The OpenFOAM distribution contains numerous solvers and utilities covering a wide range of problems. New solvers and utilities can be created by its users with some prerequisite knowledge of the underlying method, physics and programming techniques involved. OpenFOAM is supplied with pre- and post-processing environments. The interfaces to the pre- and post-processing are themselves OpenFOAM utilities

TO RUN:

athena% program options file(s)

Many utilities and solvers can be run directly from the command line.

There is a home page with html documentation, and a Wiki

See also: CalculiX, Elmer, FreeFem++, Mathematica (IMTEK Mathematica supplement), Stanford University Unstructured

Note: This application is no longer installed. The vendor has set up repositories to allow it to be installed in Ubuntu package form. Please follow these instructions.

This application is technical and complex and generally requires multiple solutions steps involving a number of distinct programs. You need to read the documentation and work through some of the tutorials to learn how to use it.

tetgen

Description: 3d tetrahedral mesh generator and Delaunay triangulator. These meshes can be used in finite-element and finite-volume simulations. tetview is a 3d viewer for viewing meshes created by tetgen as well as other objects and triangular and tetrahedral meshes in other formats

TO RUN:

athena% add tetgen

athena% tetgen options infile (to run tetgen on input data file infile)

athena% tetview options infile (to run tetview on input data file infile)

There is a pdf manual and author site

tetgen is used by some of the demos in the IMTEK Mathematica supplement added to our Mathematica installation

See also: EasyMesh, Mathematica, triangle

Note: Also available as a Ubuntu package, but without tetview; tetview is broken on debathena-precise

triangle

Description: 2d mesh generator and Delaunay triangulator that supports a variety of file formats. showme is a viewer for meshes generated by triangle

TO RUN:

athena% add triang

athena% triangle options infile (to run triangle on input data file infile)

athena% showme options infile (to run showme on input data file infile)

There is triangle documentation, showme documentation

triangle is used by some of the demos in the IMTEK Mathematica supplement added to our Mathematica installation

See also: EasyMesh, Mathematica, tetgen

ArcExplorer

Description: lightweight Java-based client for viewing GIS maps and related data

TO RUN:

athena% add arcims

athena% aejava

Documentation is here

babel

Description: converts molecular description files between a variety of formats

TO RUN:

athena% babel -iinput type input file -ooutput type output file

athena% babel -H (for options and supported formats)

See also: Cambridge Structural Database, Discovery Studio Visualizer, Jmol, molekel, molscript, Net Entrez, rasmol, VMD

Cambridge Structural Database

Description: database of bibliographic, chemical and crystallographic information for organic molecules and metal-organic compounds. It is distributed with a number of client applications:

• Conquest (cq): search and information retrieval utility
• Mercury (mercury): structure visualization application
• Vista (vista): statistical analysis and display of geometric data
• PreQuest (prequest): database creation in CSD format
• Mogul (mogul): knowledge base for molecular geometry
• IsoStar (run_isostar): knowledge base of intermolecular interactions
• Hermes (hermes): 3d visualizer with emphasis on functionality for the analysis of protein-ligand interactions
• SuperStar (superstar): produces maps of interaction sites in proteins or around small molecules

TO RUN:

athena% setup cambsd

athena% cq & (to run ConQuest)

athena% mercury & (to run Mercury)

athena% vista -j jobname (to run Vista)

athena% prequest (to run PreQuest)

athena% mogul (to run Mogul)

athena% run_isostar (to run IsoStar)

athena% hermes & (to run Hermes; SuperStar is usually run from within Hermes by selecting Calculate -> SuperStar)

There is now a Web version (MIT only)

There are local manuals for Mercury, Mogul, IsoStar, ConQuest, Vista, Hermes, SuperStar; also a CSD home page and MIT Library support site

See also: Deep View, Discovery Studio Visualizer, molscript, rasmol, Star Biochem, VMD, XCrySDen

Note: only the IsoStar client is installed, not the server component

CPMD

Description: computational molecular chemistry application; specifically, a parallelized plane wave/pseudopotential implementationof Density Functional Theory, particularly designed for ab-initio molecular dynamics computations

TO RUN:

athena% add cpmd

athena% cpmd.x file.inp [pseudopotential-path] >file.out (to run commands in file.inp, generating file.out using pseudopotential in pseudopotential-path directory; if omitted, looks for pseudopotential file(s) in current directory)

There is an online manual and author site

See also: Espresso, Gaussian, molden, VMD

Deep View

Description: tool for structural analysis and display of molecular chemistry models of proteins. It can read molecular density maps and interface to a variety of tools that generate them; output in POV-Ray format is possible, allowing for the generation of ray-traced images

TO RUN:

athena% add deepview

athena% spdbv &

athena% ppov10 -w width -h height file.pov (rendered image output, file.pov made by spdbv output via File -> Save -> Pov-Ray3 Scene in ~/SPDBV/PPOV)

There is documentation and a tutorial at the author's Website

See also: Cambridge Structural Database, Discovery Studio Visualizer, Jmol, molden, molekel, molscript, Net Entrez, pymol, rasmol, Star Biochem, VMD, XCrySDen

Discovery Studio Visualizer

Description: application that allows visualizing, analyzing and sharing biological and chemical data. Data can be viewed in multiple ways, including visually, from sequences and from data tables

TO RUN:

athena% add dsvisualizer

athena% DiscoveryStudio35 &

There is a vendor site and support forum

See also: babel, Cambridge Structural Database, Deep View, Jmol, molekel, molscript, pymol, rasmol, Star Biochem, VMD, XCrySDen

Espresso

Description: computational molecular chemistry applications: programs for quantum-mechanical simulations of extended or isolated systems based on density functional theory, periodic boundary conditions, plane-waves and norm-conserving or ultrasoft pseudopotentials

TO RUN:

athena% setup espresso

and in the terminal that opens:

athena% pw.x options < file.in > file.out (to run commands in file.in, generating file.out) (and similarly for other commands like ph.x etc.)

athena% pwgui & (to run pwgui interface)

There is an Espresso Website and User Guide

To run examples: see end of README.athena file

See also: CPMD, Gaussian, NAMD, XCrySDen

Gaussian, Gaussview

Description: computational molecular chemistry application. Gaussian is the command-line computational engine. Gaussview is a 3d molecular structure visualizer add-on to  Gaussian

TO RUN:

athena% setup gaussian (for default 03-D01 version)

followed by:

athena% g03 <file.com (to run Gaussian from a command file file.com)

athena% gv & (for Gaussview interface)

See also: Cambridge Structural Database, CPMD, Espresso, molden, molekel, NAMD

Note: We do not have access to Gaussian 09 due to a licensing issue with the vendor. We do not know if or when this will be resolved

Jmol

Description: 3d molecular viewing application written in Java that can read a variety of molecular file description formats. Can be integrated as a component into other Java applications. can also export snapshot images directly, and render images using POV-Ray

TO RUN:

athena% jmol &

There is an author site with demonstration pages

See also: babel, Cambridge Structural Database, Deep View, Discovery Studio Visualizer, molekel, molscript, pymol, rasmol, Star Biochem, NAMD, XCrySDen

molden

Description: molden is a chemistry application for displaying molecular density computed from various ab-initio packages. It can output image description files in .pov format, suitable for input to the POV-Ray ray tracer

TO RUN:

athena% add molden

athena% molden options file

athena% gmolden options file (OpenGL-enabled version)

athena% mpfit.molden options file (mpfit-enabled version)

athena% moldenogl file.ogl (utility for displaying molden-format .ogl files)

There is an online user's Guide; see also the molden Web page

See also: CPMD, Deep View, Gaussian, molekel, platon, povray

molekel

Description: Molecular graphics visualization package for displaying 3d images of molecular model and electronic structure data. Reads molecule description files in a variety of standard formats (pdb, xyz) and output data from molecular chemistry computation packages (Gaussian, adf, zindo, molden...)

TO RUN:

athena% add molekel

athena% molekel

There is 5.x online documentation, msms documentation also a Molekel home page

See also: babel, Cambridge Structural Database, Deep View, Discovery Studio Visualizer, Gaussian, Jmol, molden, molscript, pymol, rasmol, Star Biochem, VMD, XCrySDen

molscript

Description: application for creating schematic or detailed molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures

TO RUN:

athena% add molscript

athena% molscript options -in input file -out output file

athena% molauto file.pdb | molscript -gl (to generate interactive 3d image)

To build examples:

athena% cp -r /afs/athena/software/molscript_v2.1.2/examples /var/tmp

athena% setenv LD_LIBRARY_PATH /afs/athena/software/molscript_v2.1.2/lib

athena% cd /var/tmp/examples

athena% make

There is a molscript home page

See also: babel, Cambridge Structural Database, Deep View, Discovery Studio Visualizer, Jmol, molekel, Net Entrez, platon, pymol, rasmol, Star Biochem, VMD

platon

Description: platon is a crystallographic computational chemistry tool incorporating a variety of computations and image generation formats. It can output image description files in .pov format, suitable for input to the POV-Ray ray tracer, and in rasmol format for the rasmol viewer

TO RUN:

athena% add platon

athena% platon options datafile

There is local online documentation. See also the platon Web page

See also: Cambridge Structural Database, molden, molscript, povray, rasmol

pymol

Description: tool for displaying and manipulating 3d molecular images

TO RUN:

athena% pymol

There is online html documentation; also a Website

See also: Cambridge Structural Database, Deep View, Discovery Studio Visualizer, FreeWRL, geomview, Jmol, molekel, molscript, Net Entrez, rasmol, Star Biochem, VMD, XCrySDen

rasmol

Description: 3d imaging tool for displaying 3d molecular images that can be rotated in space. Reads molecule description files in standard formats such as Brookhaven Protein Databank (pdb) which is the default, as well as others (alchemy, mdl)

TO RUN:

athena% rasmol -format description_file

See also: babel, Cambridge Structural Database, Deep View, Discovery Studio Visualizer, FreeWRL, geomview, Jmol, molekel, molscript, Net Entrez, pymol, Star Biochem, VMD, XCrySDen

Note: this application is no longer installed. You can install it from the rasmol Ubuntu package using aptitude or synaptic

Star Biochem

Description: Java-based 3d biomolecule viewer developed at MIT for use in courses and designed for easy, intuitive analysis commands. Accessible here through Java3D-enabled browsers

See also: Deep View, Cambridge Structural Database, Discovery Studio Visualizer, Jmol, molekel, molscript, pymol, rasmol, VMD, XCrySDen

VMD/NAMD

Description: VMD is an application designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies etc. It can also view more general molecules in standard representations (such as pdb and other standard molecular description files). It provides a wide variety of methods for visualizing and rendering molecules, and can also be used to animate and analyze the trajectory of molecular dynamics simulations. NAMD is a parallel molecular dynamics code based on Charm++. NAMD uses VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM and X-PLOR. It can be used on Athena but with limited performance as current Athena machines don't have parallel computing hardware or access to parallel computing resources on the network

TO RUN:

athena% add vmd

athena% vmd (to run VMD)

athena% charmrun ++local options `athdir /mit/vmd`/namd2 configfile (to run NAMD with input data specified in configfile)

athena% run-alanin-demo (to run a simple NAMD demo)

athena% run-apoa1-demo (to run a longer NAMD demo)

Sample VMD data files are in the /afs/athena.mit.edu/software/vmd_v1.8.7/distrib/vmd-1.8.7/proteins directory

There are VMD 1.8.7 release notes, User's Guide and a tutorial and NAMD 2.8b1 release notes and User's Guide

See also: babel, Cambridge structural Database, CPMD, Deep View, Discovery Studio Visualizer, Espresso, Gaussian, Jmol, molekel, molscript, Net Entrez, pymol, rasmol, Star Biochem, XCrySDen

XCrySDen

Description: crystalline and molecular structure visualization program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated

TO RUN:

athena% setup xcrysden

athena% xcrysden

There is local online documentation and an author home page

See also: Cambridge Structural Database, Deep View, Discovery Studio Visualize , Espresso, Jmol, molekel, pymol, rasmol, Star Biochem, VMD

XDrawChem

Description: 2d molecule drawing program similar to ChemDraw  in functionality. Can input and output a variety of chemical structure formats using openbabel translator also installed in locker. Can also read structures from a database on the Internet.

TO RUN:

athena% xdrawchem

There is online documentation and an author home page

Note: This application is no longer installed. You can install it from the xdrawchem Ubuntu package using aptitude or synaptic

Alloy

Description: MIT-developed language for describing structures and a tool for exploring them. An Alloy model is a collection of constraints that describes (implicitly) a set of structures, for example: all the possible security configurations of a web application,or all the possible topologies of a switching network. Alloy’s tool, the Alloy Analyzer, is a solver that takes the constraints of a model and finds structures that satisfy them

TO RUN:

athena% add alloy

athena% alloy

For tests and samples, select File -> Open Sample Models and choose one of the models from the file selection dialog that opens

There is online documentation and more at the Alloy Website

See also: sketch, spin

AVL, XFOIL

Description: AVL is a program for the aerodynamic and flight-dynamic analysis of rigid aircraft of arbitrary configuration. XFOIL is an interactive program for the design and analysis of subsonic isolated airfoils

TO RUN:

athena% add aeroutil

athena% avl parameter_file (to run AVL)

athena% xfoil (to run XFOIL)

There is AVL documentation and a Web page; also XFOIL documentation and a Web page

See also: Stanford University Unstructured

CHEMKIN/CHEMKIN PRO

Description: package to investigate problems in elementary gas-phase chemical kinetics. Can be used via a GUI interface or in batch mode. CHEMKIN PRO incorporates more advanced functionality not available in CHEMKIN

TO RUN CHEMKIN:

athena% add chemkin

athena% chemkin (to run CHEMKIN GUI interface)

TO RUN CHEMKIN PRO:

athena% add chemkinpro

athena% chemkinpro (to run CHEMKIN PRO GUI interface)

CHEMKIN PRO manuals are here

CHEMKIN manuals are here

To build the 3.7 version examples without running the GUI (you will need 5-6 meg. of free disk space in your home directory):

athena% add chemkin_v3.7

athena% source /mit/chemkin_v3.7/cshrc

athena% cd ~/reaction/chemkin37/samples

athena% buildsamples

Electric VLSI

Description: VLSI circuit design and simulation application written in Java that incorporates many features and optional add-ons. Design features include custom IC layouts (ASICs), schematic drawing and hardware description language specifications

TO RUN:

athena% electric &

There is an Electric home page, online manual and a GNU Electric information page

See also: dia, eagle, gEDA, gerbv, Magic, ngspice, xcircuit

Note: This application is no longer installed. You can install it from the electric Ubuntu package using aptitude or synaptic

gEDA

Description: suite of electronic design tools, currently offering schematic capture and simulation tools. There are numerous tools in the suite. All can, and some must be invoked independently from the command line. Major available components include:

• gattrib (attribute editor)
• gerbv (Gerber circuit board viewer)
• gnetlist (netlister- textual representation of a schematic)
• gnucap (GNU circuit analysis package)
• gschem (schematic editor)
• gsch2pcb (interfaces gEDA schematics to PCB layout files)
• gtkwave (digital waveform viewer)
• iverilog (Icarus Verilog compiler)
• pcb (PCB layout editor)
• vvp (Icarus Verilog simulation runtime engine)

TO RUN:

athena% gnetlist options files(s)

athena% gsch2pcb options files(s)

To run other components, consult the documentation. There is a gEDA home page and a documentation Wiki

See also: eagle, Electric VLSI, Magic, ngspice

Note: ngspice is also part of the gEDA suite

GNU Linear Programming Kit

Description: set of routines packaged up into a library (libglpk.a) and a solver (glpsol) for solving linear programming (LP), mixed integer linear programming (MIP) and other related problems. The solver processes directives in a language called the "GNU MathProg modeling language" that is a subset of AMPL

TO RUN:

athena% glpsol -m sample.mod > sample.sol (to solve a MathProg model sample.mod, with results in sample.sol)

To create executable binaries, add the following line to your code:

#include <glpk.h>

and compile as:

athena% gcc -o sample sample.c -lglpk -lgmp -lm (C source file sample.c, dynamic linking)

athena% gcc -o sample sample.c /usr/lib/libglpk.a /usr/lib/x86_64-linux-gnu/libgmp.a -lm-lz -lltdl -ldl (C source file sample.c, static linking, 64 bit systems)

athena% gcc -o sample sample.c /usr/lib/libglpk.a /usr/lib/i386-linux-gnu/libgmp.a -lm-lz -lltdl -ldl (C source file sample.c, static linking, 32 bit systems)

For dynamic linking, you may or may not need to include the -lgmp link, depending on your code

There is a GLPK home page and a tutorial article at IBM; local docs are at file:///usr/share/doc/glpk-doc on debathena machines

See also: AMPL, ipopt, lpsolve, snopt

ipopt

Description: application for solving general nonlinear programming problems. It is supplied as a library/API that you can link against (C/C++/FORTRAN code), and as a solver than can be invoked from within AMPL

TO RUN:

athena% add ipopt

athena% gcc -O3 -o sample -I/mit/ipopt/include/coin sample.c -L/mit/ipopt/lib -lipopt -lblas -ldl -lm \

               -lgcc_s -lstdc++ -lgfortran -lpthread (C source file sample.c)

athena% g++ -O3 -o sample -I/mit/ipopt/include/coin sample.cpp [other.cpp] -L/mit/ipopt/lib \

               -lipopt -lblas -ldl -lm -lgcc_s -lstdc++ -lgfortran -lpthread (C++ source file(s) sample.cpp, other.cpp)

athena% gfortran -O3 -o sample -I/mit/ipopt/include/coin sample.f -L/mit/ipopt/lib -lipopt -lblas -ldl -lm \

               -lstdc++ -lpthread (FORTRAN source file sample.f)

athena% add ampl (to run within AMPL)

athena% ampl

ampl: model mymodel.mod;

ampl: data mymodel.dat;

ampl: option solver ipopt;

ampl: solve;

There is an ipopt Website, online documentation

See also: AMPL, GNU Linear Programming Kit, lpsolve, snopt, TAO/PETSc

lpsolve

Description: Mixed Integer Linear Programming solver; can run via a standalone solver, a library with accompanying API which can be used to produce C, C++ and Java code and as a plugin to mathematical applications like Matlab (the latter has been installed in the matlab locker). It comes with multiple converters to convert models written in other solver's modeling languages to its native format, and can be used as a solver within AMPL

TO RUN:

athena% add lpsolve

athena% source /mit/lpsolve/set-environment

athena% lp_solve sample.lp (to use solver to solve a model sample.lp)

athena% gcc -o sample sample.c -I/mit/lpsolve/include -L/mit/lpsolve/lib -llpsolve55 -lm (C source file sample.c)

Please read this for other ways of invoking lpsolve

There is an FAQ, version 5.5 changes, online manual, Matlab guide, Java guide and API index

See also: AMPL, GNU Linear Programming Kit, ipopt, matlab, snopt, TAO/PETSc

Magic

Description: interactive editor for VLSI layouts. The IRSIM add-on is an event-driven logic level simulator for MOS circuits

TO RUN:

athena% add magic-vlsi

athena% magic options & (to launch magic)

% irsim (to start IRSIM from the Tcl prompt within Magic)

There is a Magic home page, local pdf manuals and local internal command descriptions

See also: dia, eagle, Electric VLSI, gEDA, gerbv, ngspice, xcircuit

Meep, MPB, Harminv

Description: related utilities for analysis of time-domain signals. Meep is a finite-difference time domain signal simulator. MPB (MIT Photonic-Bands) is an application for computing definite-frequency eigenstates of Maxwell's equations in periodic dielectric structures. Harminv is a program for performing harmonic inversion of discrete-time, finite-length signals

TO RUN:

athena% meep (to run Meep interactively)

athena% meep options file.ctl (to run Meep from command file file.ctl)

athena% mpb (to run MPB interactively)

athena% mpb options file.ctl (to run MPB from command file file.ctl)

athena% harminv options < input.dat (to run Harminv with input data in input.dat)

There are home pages for Meep, MPB and Harminv with further links to documentation and tutorials

See also: matlab

Note: mpb may be broken. You may be able to fix this by making a link: /usr/share/libctl3 -> /usr/share/libctl as root

ngspice

Description: mixed-level/mixed-signal circuit simulator based on Spice, Cider and Xspice

TO RUN:

athena% ngspice options infile (to run ngspice using circuit design data in infile)

athena% ngspice (to run ngspice interactively from a command prompt)

Other components are available; see man page for each for explanation and usage:

• ngmultidec
• ngnutmeg
• ngsconvert

Author site is here

See also: eagle, Electric VLSI, gEDA, Magic

Note: This application is part of the gEDA suite and is no longer installed. You can install it from the ngspice and ngspice-doc Ubuntu packages using aptitude or synaptic

oof

Description: oof is a tool designed to help materials scientists calculate macroscopic properties from images of real or simulated microstructures. the current release is called oof2, to distinguish it from an earlier release with significantly different functionality

TO RUN:

athena% add oof

athena% oof2 options infile (to run oof2 on data in infile)

Author site is here, and documentation starts here

See also: Elmer

OpenModelica

Description: language and development environment that allows specification of mathematical models of complex natural or man-made systems; has built-in plotting capabilities. There are a number of components that can be run from the command line or invoked internally from the Modelica shell (OMShell). There is documentation

TO RUN:

athena % OMShell (primary shell interface)

From within the shell, a typical command sequence to read in a Modelica simulation file, run the simulation and plot the results looks something like this:

>> loadFile("/var/tmp/helloworld.mo")

>> simulate(HelloWorld, stopTime=2)

>> plot(x)

Other components that can also be launched from the command line include:

• OMShell-terminal (terminal shell)
• OMEdit (connection editor)
• OMNotebook (basic notebook interface, with built-in tutorial)
• OMOptim (optimization tool)
• OMPlot (plotting system)
• omc (compiler, translates Modelica code to C)

See also: Elmer, euler, Julia, Mathematica, matlab, SAGE, Stanford University Unstructured

Note: This application is not installed. The authors have prepared a Ubuntu repository with installation instructions

sketch

Description: software synthesis tool allowing for rapid development of tuned, bug-free algorithm implementations. The programmer develops a "sketch", or partial implementation, and a separate specification of the desired functionality. The synthesizer them completes the sketch to behave like the specification

TO RUN:

athena% setup sketch

athena% sketch options file.sk (to generate code for sketch in input script file.sk)

For samples, look in the /mit/sketch_v1.3/examples directory

See also: Alloy, spin

snopt

Description: general purpose system for constrained optimization. Minimizes a linear or nonlinear function subject to bounds on the variables and sparse linear or nonlinear constraints. It is suitable for large-scale linear and quadratic programming and for linearly constrained optimization, as well as for general nonlinear problems. Supplied as a library that you can link against to generate C/C++/FORTRAN code. It can also be used within matlab and as a solver in AMPL

TO RUN:

athena% setup snopt

Please read /mit/snopt/current/README.to-run for detailed usage instructions; there is also a snopt home page

There is an online pdf manual and pointers to additional documentation in /mit/snopt/current/README.athena

See also: AMPL, GNU Linear Programming Kit, ipopt, lpsolve, matlab, TAO/PETSc

spin

Description: spin is an on-the-fly LTL model checking system for proving properties of asynchronous software systems designs. xspin is a Tcl-based GUI front end to spin, with some added bells and whistles

TO RUN:

athena% add spin

athena% spin options data_file (for command line version)

athena% xspin & (for GUI interface version)

For tests and samples, look in the /mit/spin_v4.2.5/Test directory

There is local online documentation and more at the spin Website

See also: Alloy, sketch

Note: spin in some modes generates C code that must be compiled into a binary that you subsequently run- generally gcc is the preferred compiler as commercial compiler preprocessors tend to have trouble with the syntax

Stanford University Unstructured

Description: The Stanford University Unstructured (SU2) suite is an open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind, but it is extensible to treat arbitrary sets of governing equations such as potential flow, electrodynamics, chemically reacting flows, and many others

TO RUN:

athena% add su2

athena% su2_program config_file (see documentation for su2_program naming and usage)

athena% python_script options file (see documentation for python_script naming and usage)

There is a Web page, online documentation and local README.athena and technical summary paper

See also:AVL,XFOIL, Elmer, FreeFem++, OpenFOAM, OpenModelica, TAO/PETSc

TAO/PETSc

Description: PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It supports MPI, shared memory pthreads, and NVIDIA GPUs, as well as hybrid MPI-shared memory pthreads or MPI-GPU parallelism. The version on Athena is built for uniprocessor use only and does not support GPU computation. TAO is software for solving large-scale optimization problems. It uses an object-oriented design to create a flexible toolkit with strong emphasis on the reuse of external tools (it is designed to run on top of PETSc). The design enables bi-directional connection to lower level linear algebra support (for example, parallel sparse matrix data structures) as well as higher level application frameworks. It has algorithms for unconstrained and bound-constrained optimization. petsc4py is a Python binding for PETSc

TO RUN: (selected examples)

athena% setup tao-petsc

PETSc tutorials/python/ex1:

compile: g++ -o ex1.o -c options -Iincludefilelocation ex1.c; g++ options -o ex1 ex1.o -Llinkfilelocation libraries

run: ./ex1 -ksp_monitor_short -ksp_view > ex1.out

PETSc tutorials/python/ex1.py:

run: python ./ex1.py -ksp_monitor_short -ksp_view > ex1py.out

TAO examples/rosenbrock1:

compile: g++ -o rosenbrock1.o -c options -Iincludefilelocation rosenbrock1.c; g++ options -o rosenbrock1 rosenbrock1.o -Llinkfilelocation libraries

run: ./rosenbrock1 -tao_monitor -tao_view > rosenbrock1.out

To run examples, run the locker setup command, copy the desired example or tutorial subtree to a location where you have write permission and run the desired makefile from there. vec_serial.py in the tao-petsc_v2.1 locker is a Python executable that can be run directly to demonstrate petsc4py commands

There is a local TAO manual, PETSc manual, petsc4py manual,  TAO Web page and PETSc Web page. See also the README.athena file

See also: AMPL, Elmer, ipopt, lpsolve, snopt, Stanford University Unstructured

These are very complex command-line applications and involve compiling binaries that make calls to TAO and PETSc routines. You will need to study the documentation and examples contained in the tao-petsc_v2.1 locker in order to learn how to use them