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Vol. 1, No. 1 Fall 1997 Supercomputing Institute Software Newsletter Sofware Newsletter of the Supercomputing Institute Introduction The pages of Cray Supercomputer resources are differ- ent. To use these, you will need to set up a password There are many software packages available to from your cray account. For instructions on setting up researchers at the Supercomputing Institute, and this this password, see: newsletter lists them. This listing does not contain com- http://www.msi.umn.edu/msci/msci_guide.html mon Unix commands, mail programs, text editors and such. Most common programs of this type are installed; if not, ask us. If it is in the public domain, we will try to get and install it. However, the focus in this software Contents newsletter is primarily our applications software. Introduction . . . . . . . . . . . . . . . . . . . . . . .1 All software listed here, and more, is described in our web pages. Software is installed frequently making a Documentation . . . . . . . . . . . . . . . . . . . . .2 printed document such as this out-of-date almost as soon as it is published. Therefore, we maintain web pages that continuously reflect the ever changing software installed Software Purchase Policy . . . . . . . . . . . . . ..2 at the Supercomputing Institute. These web pages are always current and contain more information than is in Software Listing . . . . . . . . . . . . . . . . . . . . .2 this list: where to find documentation, the version num- Chemistry and Molecular Modeling . . . .3 ber, links to related information, and instructions describing how to use the software. Nevertheless, it still Computational Fluid Dynamics . . . . . . .7 seems worthwhile to occasionally prepare a printed doc- ument to be sure that the software opportunities avail- Graphics, Image Processing, and able to researchers do not go unnoticed. Scientific Visualization . . . . . . . . . . . .8 For a listing of all software available on Institute work- stations, see: Mathematics . . . . . . . . . . . . . . . . . . . .12 http://www.msi.umn.edu/user_support/ Miscellaneous . . . . . . . . . . . . . . . . . . .16 Click on “Software Listing”. Parallel Programming Libraries . . . . . .16 For a listing of software at the individual labs of the Structural Analysis . . . . . . . . . . . . . . .17 Supercomputing Institute, first go to the above web page, then select the desired computing resource (lab). Feedback and Steering Committees . . . . . .19 From here, click on “Software”. Once this password is set up, you may access the web pages that contain software listings in addition to hard- Software Purchase Policy ware information and a summary of services available. The Supercomputing Institute purchases software as These web pages are located at:: directed by the faculty steering committees. Each of the labs has its own steering committee. If there is software http://www.networkcs.com/msi that you would like the Supercomputing Institute to pur- chase, please contact a member of the steering commit- A wide range of compilers is available to researchers. tee, the laboratory manager, or the head of technical sup- Fortran77 and Fortran90 compilers are available at all port. The names of these people are listed at the end of Laboratories. High Performance Fortran (HPF) is this newsletter. If unsure who to contact, you may installed on the machines at the University of always call the Head of Technical Support, Barry Minnesota-IBM Shared Research Project. C and C++ Schaudt. Please note: The Institute does not purchase compilers are available on all machines. The Fortran 90 software for single individual principal investigators. extension F- - will soon be available on the Origin 2000. Instead, the Institute tries to purchase software that will Java is installed at the Scientific Development and benefit a wide range of principal investigators, but indi- Visualization Laboratory, the Medicinal Chemistry/ vidual recommendations are one way we learn which Supercomputing Institute Visualization/Workstation software is likely to be widely useful. In addition, please Laboratory, and the Basic Sciences Computing Labora- let us know if you recommend that a package we do have tory. Perl is installed at the Scientific Development and should be made available on another platform or should Visualization Laboratory, the Basic Sciences Computing be upgraded to a newer version. Laboratory, the Medicinal Chemistry/Supercomputing Institute Visualization/Workstation Laboratory, and the University of Minnesota–IBM Shared Research Project Software Listing Laboratory. For purposes of presentation, each software package or For more information, see the software web pages for library is loosely placed into one of the following cate- the individual laboratories. gories: • Chemistry and Molecular Modeling Documentation • Computational Fluid Dynamics • Graphics, Image Processing and Scientific Most of the newer software packages have on-line doc- Visualization umentation that can be accessed from within the appli- • Mathematics cation. If there is a printed manual, it can be checked • Miscellaneous out for a short period of time. Manuals for software • Parallel Programming Libraries installed at the Supercomputing Institute are at the • Structural Analysis Technical Documentation Center at the Scientific Development and Visualization Laboratory and at the Software listed here is installed in one or more of the Basic Sciences Computing Laboratory. Cray manuals are computing laboratories or on one or more platforms. in the reference room at the Minnesota Supercomputing The following abbreviations are used: Center. Researchers with Cray accounts may ask the security guard at the front desk for a key to this room in BSCL Basic Sciences Computing Laboratory order to check out manuals. C90 Cray C90 For information on documentation of individual IBM University of Minnesota–IBM Shared Research packages, consult the software web pages mentioned ear- Project lier in this newsletter SDVL Scientific Development and Visualization Laboratory page 2 SMP Symmetric Multiprocessing Laboratory BABEL T3E Cray T3E BABEL is a molecular structural data file format con- VWL Medicinal Chemistry/Supercomputing version program from the University of Arizona. It con- Institute Visualization/ Workstation verts amongst over thirty different molecular file formats Laboratory producing ready and near-ready input files for such applications as MOPAC, GAMESS, GAUSSIAN 92, Minnesota Supercomputer Center, Inc. (MSCI) now MM2, MM3, and Alchemy. has the new name of Network Computing Services, Inc., and will be referred to in the software listing as Labs: BSCL, C90, and T3E NetworkCS. In the listings below, “Labs” is used as a synonym for Biosym (Molecular Simulations, Inc) labs or platforms. Biosym is a molecular modeling package consisting of several programs. The following modules are available to Chemistry and Molecular researchers: Insight II Modeling Insight creates, modifies, manipulates, displays, and analyzes the molecular systems and related data and ACES II provides the core requirements for all Insight II soft- ware modules. ACES II is a series of programs for performing ab ini- tio computational chemistry calculations. The package Discover has a high degree of flexibility, and it supports many Discover is a simulation program available within kinds of calculations at a number of levels of theory. The Insight II. It incorporates a range of well validated major strengths of the program are in performing calcu- forcefields for dynamics simulations, minimization, lations using many-body methods to treat electron corre- and conformational searches, allowing you to predict lation. These approaches, broadly categorized as many- the structure, energetics and properties of organic, body perturbation theory (MBPT) and coupled-cluster inorganic, organometallic, and biological systems, (CC) approximation, offer a reliable treatment of elec- Discover also implements IPC (Inter Process tron correlation and have the property of size-extensivity, Communications), which allows users to instruct meaning that energies scale properly with the size of the Discover to turn processing control over to external system. As a result, MBPT and CC methods are well programs, and retrieve the results of those external suited for the study of chemical reactions. The vendor processes, incorporating them into the continuing requires that any user of the software first acquire a usage Discover computations. license Biopolymer Labs: C90 Biopolymer constructs models of peptides, proteins, carbohydrates, and nucleic acids for visualizing com- AMSOL plex macromolecular structures and for use in further AMSOL is an enhanced version of the general semi- simulation work. empirical molecular orbital package AMPAC. In addi- DelPhi tion to the capabilities of AMPAC, AMSOL includes DelPhi calculates electrostatic potentials and solva- code for calculating solvation energies of molecules and tion energies of both large and small molecules, ions in aqueous solution. including nucleic acids. You can use DelPhi to rigor- Labs: C90 ously examine the effects of charge distribution, ionic strength, and dielectric constant on the electrostatic potentials of macromolecules. page 3 Consensus be performed using direct techniques, or in parallel on Consensus builds a 3D model of a protein from its appropriate hardware. amino acid sequence and the known structures of Labs: C90, IBM, and T3E related proteins using distance constraints derived from the reference protein structures. Gaussian94 and Gaussian92 Homology Gaussian 94 and Gaussian 92 are a connected systems Homology builds a 3D model of a protein from its of programs for performing semiempirical and ab initio amino acid sequence and the known structure of molecular orbital (MO) calculations. They represent fur- related proteins. Standard techniques of backbone ther development of the Gaussian 82, Gaussian 76 and building, loop modeling, structural overlay and sta- Gaussian 80 systems. G92 and G94 features include: cal- tistical analysis of the resulting models are available. culation of one- and two-electron integrals over s, p, d, and f contracted gaussian functions; self-consistent field Labs: BSCL, SDVL, SMP, and VWL calculations; evaluation of various one-electron proper- (Not all programs are available at all labs. See the ties of the Hartree-Fock wavefunction; automated geom- lab’s web pages for more details). etry optimization to either minima or saddle points, etc. CHARMM Labs: C90, IBM, SMP, and T3E CHARMM is a molecular dynamics package for sim- ulating biomolecular structures. Equilibrium properties, HONDO 95.3/KGNGRAF such as radial distribution functions and free energies, Hondo is a system designed for electronic structure and dynamical properties, such as diffusion constants, studies. KGNGRAF provides general capabilities to visu- are be computed by solving Newton’s equation with alize data generated with the HONDO program and forces derived from an empirical force field. The vendor some limited capabilities for the GAUSSIAN and requires that any user of the software first acquire a usage MOPAC programs, along with integration with license which requires the payment of a license fee. HONDO such as automatic creation and display of Woodward-Hoffman correlation diagrams for standard- Labs: IBM and T3E with-disk, standard-in-core, semi-direct and direct algo- rithms serial implementations. Most have parallel imple- GAMESS mentations, thus expanding the range of applications of General Atomic and Molecular Electronic Structure these methods. System is a general ab initio quantum chemistry package. GAMESS can compute wavefunctions ranging from Labs: IBM RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections available for some of these. MacroModel Analytic gradients are available for these SCF functions, MacroModel consists of several programs. for automatic geometry optimization, transition state Macromodel is one of the programs and is used to build, searches, or reaction path following. Computation of the manipulate and display organic chemical structures. energy hessian permits prediction of vibrational frequen- BatchMin is a non-interactive, batch-mode modeling cies. A variety of molecular properties, ranging from sim- program used to minimize the energy of one structure or ple dipole moments to frequency dependent hyperpolar- a series of structures, to eliminate duplicate conforma- izabilities may be computed. Many basis sets are stored tions and to conduct molecular dynamics simulations internally, and together with effective core potentials, all with calculation of average enthalpy. BatchMin is called elements up to Radon may be included in molecules. by MacroModel and is its use is usually transparent. Several graphics programs are available for viewing of the However, for advanced applications, an understanding of final results. Many of the computational functions can page 4 BatchMin may be necessary. MacroModel can read files and on-line help. The display possibilities include con- in its own format and PDB files. ventional presentations, as well as novel schematic draw- ings, with the option of displaying different presenta- Labs: BSCL and SDVL tions in one view. The covalent molecular structures can be modified by addition or removal of individual atoms Midas Plus and bonds; the three-dimensional structure can be The Molecular Interactive Display and Simulation manipulated by interactive rotation about individual (MIDAS) System is a collection of programs developed dihedral angles. Special efforts were made to allow for by the Computer Graphics Laboratory at UCSF. The appropriate display and analysis of sets of (typically 20- major component of the MIDAS system is an interactive 40) conformers that are conventionally used to represent graphics display program, MidasPlus, designed for the the result of a NMR structure determination, using display and manipulation of macromolecules such as functions for superimposing sets of conformers, calcula- proteins and nucleic acids. Several ancillary programs are tion of root mean square distance (RMSD) values, iden- also part of the system and allow for such features as tification of hydrogen bonds, checking and displaying computing the surface of a molecule, the selection of an violations of NMR constraints, and identification and active region within a molecule, computation of electro- listing of short distances between pairs of hydrogen static charge potentials, etc. At the core of MIDAS is an atoms. unusually coherent hierarchical database system, designed specifically for macromolecules and both com- Labs: BSCL, SDVL, and VWL pact in its storage requirements and fast in its data access. MIDAS is capable of displaying molecular structures MOPAC from information contained in either a Protein Data MOPAC is a general-purpose semi-empirical molecu- Bank (PDB) format file or a binary MIDAS database lar orbital package for the study of chemical structures (created from a PDB file using the midas.in program). and reactions. MOPAC calculates vibrational spectra, MIDAS can display molecules as line (bond) drawings, thermodynamic quantities, isotopic substitution effects, ribbons-type cartoons (“Jane Richardson drawings”), and and force constants for molecules, radicals, ions and space-filling drawings. MIDAS takes advantage of the polymers. MOPAC was written with the non-theoreti- graphics hardware available on these SGI systems to cian in mind. deliver high-speed display of complex molecular models. It also has virtual trackball interaction, shadow genera- Labs: C90 tion from multiple light sources, annotation, stereo view- ing, enhanced control of van der Waals surfaces, interac- Oxford Molecular tive monitoring for inter-atomic contacts during bond- The Supercomputing Institute has a collection of soft- ing and dihedral angles rotations, and direct support of ware from Oxford Molecular installed. The following MS surface files. table contains the name of the software packages installed at the Supercomputing Institute, and a brief Labs: BSCL, SDVL, and VWL description of each package. AbM Molmol Antibody modeling program: builds 3-D structures starting from only a sequence for humanization and MolMol - MOLecule analysis and MOLecule display mutagenesis studies. MOLMOL is a molecular graphics program for dis- Amber play, analysis, and manipulation of three-dimensional Amber is a collection of a set of programs used for structures of biological macromolecules, with special molecular modeling and molecular simulations, par- emphasis on nuclear magnetic resonance (NMR) solu- ticularly of biomolecules. The package includes a tion structures of proteins and nucleic acids. MOLMOL number of database of force field parameters, togeth- has a graphical user interface with menus, dialog boxes er with the required preparation, calculation and page 5 analysis tools for these studies. Ribbons Anaconda The Ribbons software package displays molecular A graphically oriented molecular comparison and models as rendered images on an SGI workstation. The alignment tool. molecules are rendered using a ribbon representation of the secondary structure similar to a “Jane Richardson” Asp type drawing. The data required consists of atomic coor- A numerical molecular comparison tool for lead dinates in Protein Data Bank format and files of color- compound optimization; aligns molecules and exam- coding information. Version 2.0 allows the manipulation ines sterics and electrostatics. of complicated smooth shaded images in near real-time. Cameleon Features include: display of multiple chains of proteins A sequence alignment tool connecting sequence with and/or nucleic acids, interactive control of the style and structure using dynamic links and displays. texture of ribbon models, color coding by a wide variety of biological and geometrical properties, display of Cobra spheres and cylinders with interceptively-set radii, dis- 2-D to 3-D structure conversion and molecular con- play of triangular and dot surfaces, interactive control formation prediction. over the colors and the light source, and output suitable Corina for use with the WaveFront ray-tracer. A 3-D structure generator. Labs: SDVL Iditis A relation protein data base searching tool for dis- Setor covery of loops, interactions, active sites, etc. Setor is designed to allow the display of secondary, ter- tiary and quaternary structures of molecules, and to Iditis Architect allow a wide variety of rendering models to be used. Adds your own structures to Iditis Labs: SDVL Tsar Program for QSAR and QSPR studies with numer- VMD - Visual Molecular Dynamics ous molecular descriptors and statistical tools. VMD is a molecular graphics program designed for VAMP the interactive visualization and analysis of biopolymers Semi-empirical quantum mechanics including NMR such as proteins, nucleic acids, and lipids and mem- chemical shift predictions. branes. It recognizes many file formats, provides many types of molecule representation, 3D display and pho- Labs: BSCL, SDVL, SMP, and VWL torealistic output. RasMol Labs: BSCL and VWL RasMol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small mol- XMOL ecules. RasMol can read in files in the following formats: XMOL uses the X Window System to display 3-D pdb (Brookhaven Protein Databank), -mdl (MDL’s molecular models produced by other software packages, MOL File Format), mol2 (Tripos’ Sybyl MOL2 Format), and prints copies of molecular displays to PostScript xyz (MSC’s XYZ format), alchemy (Alchemy File devices. Animations of multi-step data files are possible, Format) and charmm (CHARMm File Format). It can as are calculations of atom-to-atom distances, bond display depth-cued wireframes, ‘Dreiding’ sticks, space- angles, and torsion angles. XMOL is currently capable of filling (CPK) spheres, ball and stick, solid and strand reading ALCHEMY, CHEMLAB, GAUSSIAN, and biomolecular ribbons, atom labels and dot surfaces. MOPAC input files, MOPAC output files, MOLSIM and MOPAC archive files, and PDB and XYZ data files. Labs: BSCL, SDVL, and VWL page 6 XMOL is capable of writing ALCHEMY, CHEMLAB, experiment with new ideas without being restricted to MOLSIM, and MOPAC input files, and XYZ data files. standard or ``hard-wired” protocols. X-PLOR was designed to provide user friendliness, machine portabili- Labs: BSCL, C90, SDVL, T3E, and VWL ty, and highly efficient algorithms for modern comput- ers. X-PLOR (from the X-PLOR Manual) X-PLOR is a program system for computational struc- Labs: BSCL, C90, SDVL, and SMP tural biology. X-PLOR stands for exploration of confor- mational space of macromolecules restrained to regions XVIBS allowed by combinations of empirical energy functions XVIBS takes raw GAUSSIAN 92 or GAUSSIAN 94 and experimental data. But it also stands for exploration frequency calculation output files, extracts the normal of modern concepts of structured programming in modes, and generates XMOL-compatible XYZ coordi- macromolecular simulation. nate files for animation in XMOL. As long as there were no machines, programming Labs: C90 and T3E was no problem at all; when we had a few weak computers, programming became a mild problem and now that we have gigantic computers, program- Computational Fluid ming has become an equally gigantic problem. In this sense the electronic industry has not solved a Dynamics single problem, it has only created them—-it has created the problem of using its product. (E.W. Fast Dijkstra, Turing Award Lecture, 1972) Fast is an interactive computational fluid dynamics X-PLOR’s main focus is the three-dimensional struc- Post-Processing software package from NASA for SGI ture determination of macromolecules using crystallo- workstations. Due to its many features, it is used by graphic diffraction or nuclear magnetic resonance researchers at the Supercomputing Institute from many (NMR) data. The program is based on an energy func- different fields. Features of FAST include: Drawing shad- tion approach: arbitrary combinations of empirical, geo- ed meshes, isosurfaces, streamlines, vector fields, particle metric and effective energy terms describing experimen- traces and contours. It can output Postscript. Annotation tal data may be used. The combined energy function can and legends are easy to add. FAST specializes in curvilin- be minimized by a variety of gradient descent, simulated ear grids and reads in PLOT3D data files. annealing, and conformational search procedures. The Labs: BSCL and SDVL first version of X-PLOR (1.0) was published in the fall of 1987; it had evolved from a modified CRAY version of FIDAP the CHARMM program (Brooks et al. 1983). X-PLOR FIDAP uses the finite element method to simulate was the first program to combine X-ray crystallographic many classes of incompressible fluid flows, such as 2-D diffraction data and molecular dynamics for refinement axisymmetric and 3-D steady-state or transient simula- (BrŸnger, Kuriyan, and Karplus 1987). Since then the tions that include the effects of temperature. program has undergone extensive development, and the focus has shifted from refinement to structure determi- Labs: C90 nation. Major features of computational X-ray crystal- lography and solution NMR-spectroscopy have been FLUENT included. Future development of X-PLOR is aimed at FLUENT uses a finite volume numerical procedure to providing a comprehensive system for all computational solve the differential equations governing fluid flow, as aspects of macromolecular structure determination. well as conservation of energy and chemical species X-PLOR is more than a program: it is a macromolec- therein. Both compressible and incompressible flows can ular language. This flexible language allows the user to be modeled, as can turbulence by way of the k-e turbu- page 7 lence model. The numerical technique subdivides the Data files must be in the PLOT3D format and the out- domain of interest into control volumes or cells. The put from UFAT can be displayed using FAST governing partial differential equations are then dis- Labs: SDVL cretized over these cells to obtain a set of simultaneous algebraic equations which is solved using the SIMPLE iterative solution technique. In FLUENT version 4.0, a body-fitted coordinate pre-processor allows generation of Graphics, Image meshes within geometrically irregular domains. Earlier versions support only Cartesian meshes. Processing, and Scientific Labs: C90 Visualization NEKTON 4d2 NEKTON simulates steady and unsteady incompress- Developed by the National Center for ible fluid flow and heat transfer, as well as optional con- Supercomputing Applications, 4d2 is an interactive visu- vective-diffusive passive scalar quantities. NEKTON alization tool for time-dependent 3D CFD data on rec- uses the spectral element method, a high-order finite ele- tangular grids containing scalar and vector fields, and for ment technique for the solution of partial differential particle data. It is displays contours, vector fields, slices, equations. The computational domain can be either sta- isosurfaces and stream traces: it does vector fields and tionary or moving (free surfaces, moving walls, fluid lay- stream traces quite well. It has some volume rendering ers, or melting fronts are supported). If both the fluid capabilities, however, other packages are recommended flow and heat transfer simulation capabilities are used, over 42d for volume rendering. Data must use the HDF they can be coupled via forced and/or natural convection format. heat transfer. A conjugate heat transfer, solid and fluid problem can also be solved. Labs: BSCL and SDVL Labs: C90 Adobe Photoshop Adobe Photoshop allows you to create color images PHOENICS and edit all or part of an existing images. With PHOENICS is a general-purpose computational fluid Photoshop you can add text, change the color balance, dynamics program for the simulation of fluid flow, heat replace colors, change the brightness, blur or sharpen, transfer, mass transfer, and chemical reaction processes. and adjust an image or part of an image in hundreds of A finite-volume method is employed for the efficient different ways. Photoshop can also resize or change the solution of the Navier Stokes equations governing fluid resolution of an image. It is the most powerful image flow phenomena. PHOENICS can be applied to a large manipulation tool at the Supercomputing Institute. variety of problems using the built-in models and options provided. PHOENICS has applicability in the Labs: SDVL aerospace, nuclear, process, defense, marine, environ- mental, turbomachinery, and automotive industries. Bob/Animabob Bob (Brick-of-Bytes) has been installed on the SGI Labs: C90 workstations. Bob is a tool for browsing three dimen- sional data sets. The program was designed to render UFAT portions of potentially large time-dependent volumes UFAT (unsteady flow analysis toolkit) generates parti- quickly. Bob can also create a series of images that can be cle traces, stream surfaces, color contoured walls, and later compiled into a movie. Animabob is the latest vector plots from time-dependent (unsteady) flow fields. release of bob and adds animation capabilities. Labs: BSCL and SDVL page 8 Composer document to another format and its use is transparent to Composer from Alias/Wavefront is software that the user (e.g. The image display programs xv and display allows you to create and edit videos. Composer can read use ghostscript). Ghostview provides a user X11 user in a sequence of images or movies. Composer accepts a interface to ghostscript. From ghostview, you can view a wide range of formats, including tiff for images and PostScript document or image, and save or print selected quicktime for movies. Once read in, titles can be easily pages. added. Images or sequence of images can be annotated Labs: BSCL, SDVL, and VWL or adjusted (cropped, scaled, sharpened, blurred, colors adjusted). You can use composer to add transitions, such Gnuplot as fading in and then out, from one sequence to another. Gnuplot is a command-driven interactive function Composer can also warp an image or a sequence and can plotting program. If files are given, gnuplot loads each morph one image into another. Composer outputs file with the load command, in the order specified. gnu- movies in many different formats. For web pages, the MPEG is available. Movies produced by composer can plot exits after the last file is processed. It plots any num- also be put to VHS or S-VHS tape using the hardware at ber of functions, built up of C operators, C library func- the workstation I4. tions, and some things C doesn’t have, such as **, sgn(), etc. It also provides support for plotting data files, to Labs: SDVL compare actual data to theoretical curves, user-defined X and Y ranges (optional auto-ranging), smart axes scaling, Contours and smart tick marks. A public domain program from NCSA, Contours is Labs: BSCL, C90, SDVL, and VWL used to generate contour plots from data generated by other programs. IBM Data Visualization Explorer Labs: SDVL IBM Data Visualization Explorer (dx) is a general pur- pose, easy to use, visualization tool. You control dx by Cricket Graph III linking a modules together with the mouse. It can read Cricket Graph has the ability to create different types in both structured and unstructured data in many differ- of graphs (Scatter, line bar, pie, polar and more), fit ent formats, as well as TIFF images. Once the data is read curves, display error bars, and several types of data in, the individual modules handle both structured and manipulation, including annotation. It is also very easy unstructured data. to use and is flexible. • With 2D data, dx can produce shaded contours, con- Labs: SDVL tour lines, graphs, .... • With 3D data sets, dx can volume render, display Geomview arbitrary slices of the data and isosurfaces. The trans- Geomview is an interactive 3-D geometry viewer writ- parence of the slices and the isosurfaces can be set ten at the University of Minnesota’s federally-funded according to data values, along with their colors. Geometry Center. It displays the objects in the files given on the command line and allows the user to view and • Vector fields and stream traces can be drawn with 2D manipulate them interactively. or 3D data. Text and color bars are easily added. Labs: SDVL • DX can be programmed to read in a sequence of files, or write a sequence of files. If the output files Ghostscript/Ghostview are images, these can be put together into an anima- Ghostscript (gs) is an interpreter for PostScript. It can tion. be used to translate Postscript to other formats. More often, it is used by other programs to convert a PostScript page 9 • Chemistry extensions are installed that allow dx to MediaConvert read and manipulate molecules stored in the PDB Use Mediaconvert to convert movies to and from format. Quicktime movies , MPEG movies and SGI’s movie for- mats. Labs: BSCL, IBM, and SDVL Labs: SDVL and VWL Igor MovieConvert Igor is an integrated graphing and data analysis envi- Movieconvert converts a movie file into a group of ronment. It generates waves, graphs, tables, and page lay- separate images, and to convert movies from one format outs. to another. Movieconvert will also crop or resize images, and convert from one image format to another. Labs: SDVL Labs: SDVL and VWL ImageMagick ImageMagick is a collection of programs to display, NCAR Graphics manipulate and convert images from one format to NCAR 4.0 is a library of C and FORTRAN 77 another. It can handle many different image formats, callable functions that allow applications to generate 2-D including PostScript, GIF, JPEG, TIFF, PICT,and SGI’s and 3-D graphics on a number of output devices, includ- rgb. ImageMagick consists of display, montage, convert, ing X windows, PostScript, Tektronix 4010 and 4014 mogrify, animate, import, combine, segment, and iden- and 4107, and HP Pen Plotters and SunTools. The tify programs. NCAR 4.0 library provides such functions as 2-D line and color-shaded contours with labeling, 2-D halftone Labs: BSCL, SDVL, and VWL contours, 2-D vector fields and streamlines, simple 2-D Cartesian graphs with linear or logarithmic scaling, his- KaleidaGraph tograms, 2-D and 3-D (plane projected) text in a num- KaleidaGraph is an easy-to-use graphing package. It ber of fonts at any size or angle with superscripting and can porduce many types of plots, including line, scatter, subscripting, 3-D mesh surfaces, 3-D contoured iso-sur- histogram, probability (graph of a variable normalized to faces with hidden lines removed, 3-D axes systems, 3-D either a linear or normal probability distribution), polar curves, world-coastline, U.S. state, and world political and pie. New features include the use of scripts, addition map database, and ten cartographic projections. of macro libraries, enhanced data table tools and new Contours, vector fields, streamlines, and grids can under- curve fits. go map projections and can optionally be masked by Labs: SDVL continents, state, and world political boundaries (e.g., contours can be drawn over land masses only). This Khoros makes NCAR 4.0 well-suited for atmospheric applica- Visualization software with an emphasis on image pro- tions. NCAR 4.0 also provides limited supported for ani- cessing applications. Khoros uses a visual programming mation and scrolled or stationary titles. In addition, paradigm for its user interface (i.e., similar to AVS and NCAR 4.0 comes with a public domain software pack- Explorer). There are too many modules in Khoros to list age called BIVAR that performs bivariant interpolation here but a sample might include: a 2-D graphing mod- of random 2-D scalar data into a regular 2-D scalar grid. ule, a 3D surface/contour rendering module, dozens of Labs: SDVL and C90 (NCAR 3.0) 1-D and 2-D image processing modules, data importing modules, data exporting modules, etc. Khoros is based PV~Wave on the X Windows system (athena widgets). PV~WAVE provides a powerful interpreted com- Labs: SDVL mand-language interface to a set of procedures that pro- vide capabilities of data access, reduction, and analysis; 2-D and 3-D graphics; animation; and image processing. page 10 Some of the procedures provided with PV~WAVE com- make up the San Diego Supercomputer Center’s Image mand language include an extensive library of math Tools. functions (trigonometric functions, Bessel functions, Labs: BSCL and SDVL logarithms, statistical functions, interpolations, complex number arithmetic, vector functions, numerical differen- tiation, matrix functions, Fast Fourier Transform, SciAn gamma function, Gaussian fit, Hilbert transformation, SciAn can create 3-D visualizations from many differ- polynomial evaluation, least squares), axis-drawing pro- ent types of scientific data using various simple and cedures (linear and logarithmic), 2-D contouring, 3-D advanced visualization techniques. The program has mesh surfaces, 3-D light-shaded surfaces, 3-D data-shad- both a Graphics User Interface (GUI) and a scripting ed surfaces, 3-D iso-surface construction and rendering, language. The various techniques can be integrated ray tracing, 2-D vector fields, image processing (scaling, together in a single image. SciAn accepts many popular interpolation, digital filters, convolutions, smoothing, data and object formats including netCDF, Plot3D, spatial warping, etc.), 2-D Cartesian graphs (line plots, HDF, STF, NFF, PDB, and MSC, Inc.’s XYZ format. scatter plots, bars, error bars), random data to regular Techniques employed include ball and stick, space filling grid interpolation, histograms, legends, file I/O, and for molecular display, groups of spheres, cylinders, and more. Output from PV~WAVE can be directed to a points, colored meshes, contours, isosurfaces. The pro- number of devices including X windows, PostScript, gram also allows the ability to use subsets of data, has CGM (Computer Graphics Metafile), HPGL, and good animation facilities for time-dependent datasets, Tektronix compatible terminals. and good presentation tools such as text placement, over- lay graphics, and clocks. Labs: SDVL Labs: SDVL Raz/Xraz Raz is a GL based program for animating a series of Tecplot raster or byte based pseudo-colored images using a user Tecplot is a powerful interactive plotting program for supplied color map which can be edited interactively. Raz visualizing and analyzing engineering and scientific data. is controlled by commands in a script file or by the pro- It integrates XY plotting with two- and three- dimen- gram xraz which offers a Motif based Graphical User sional surface data-visualization capabilities into a single Interface (GUI). Raz and xraz allow varying the frame easy-to-use program. Tecplot allows the user to create rate for animation, zooming the images, and adding a plots with contours, iso-surfaces, mesh lines, vectors, variable size border to make live recordings of the ani- streamlines, light-source shaded surfaces, and scatter mations look more professional. Raz can play from mem- symbols. ory or off disk. Labs: BSCL and SDVL Labs: SDVL Tgif San Diego Supercomputer Center’s Image Tgif is a drawing program. One of the main features Tools of tgif: it is one of the few programs that can annotate an encapsulated postscript image. In addition to annotating The SDSC image tools are tools developed at the San an encapsulated postscript file, tgif can be used to scale, Diego Supercomputer Center (SDSC) to handle image rotate or flip the image. It is probably the best tool at the manipulation and file format conversion for a wide range Supercomputing Institute for annotating PostScript vec- of file formats. There are a number of programs to han- tor graphics (Here a line is stored as two endpoints, dle the different operations available. One widely used rather than all the pixels that make up a line. Thus rota- program is imconv, which is used to convert from one tion and scaling are simple and precise operations.) As image format to another. The programs imconv, imcopy, with most drawing programs, tgif can draw lines, rectan- imfile, imflip, imgray, immono, impaste, and imscale gles, arc, polygons, splines, and text. Tgif can output the page 11 drawing in one of 4 different formats: PostScript, XV Encapsulated Postscript, X11 bitmaps and X11 pixmaps. XV is used to display, manipulate and convert images Tgif can also save the objects in its own format for later from one format to another. XV reads and writes images manipulation. in many formats including PostScript, GIF, JPEG, TIFF, and SGI’s rgb. XV can be used to interactively resize, Labs: BSCL, SDVL, and VWL crop, reflect and rotate images. Transform Labs: BSCL, SDVL, and VWL Transform is an easy to use visualization tools. The only somewhat confusing operation is reading in data Xfig files. Transform works best with Matrix data and accepts Xfig is a menu-driven tool that allows the user to draw several types of data formats, including binary, ascii and and manipulate objects interactively in an X window. hdf. Transform can create contours and surface plots. The pictures that are drawn with xfig may be converted Labs:SDVL to one of several formats, including encapsulated PostScript which allows their inclusion in LaTeX docu- ments. With xfig, you can also annotate images, includ- Vis5D (from the README for vis5d-4.2) ing encapsulated postscript, X11 bit and pixmap, GIF Vis5D is a software system for visualizing data made and JPEG images. When used in conjunction with by numerical weather models and similar sources. Vis5D LaTeX, it is possible to send the pictures directly to post- works on data in the form of a five- dimensional rectan- script, and the text to LaTeX so that fonts in the image gle. That is, the data are real numbers at each point of a will be the same as in the LaTeX document. “grid” or “lattice” which spans three space dimensions, one time dimension and a dimension for enumerating Labs: BSCL, SDVL, and VWL multiple physical variables. Of course, Vis5D works per- fectly well on data sets with only one variable or one time Xmgr step (i.e. no time dynamics). However, your data should Xmgr is the interactive program of ACE/gr. ACE/gr is have some depth in all three spatial dimensions. an XY plotting tool for workstations or X-terminals The Vis5D system includes the vis5d visualization using X. Features include Linear regression, splines, run- program, several programs for managing and analyzing ning averages, DFT/FFT, and cross/auto-correlation five-dimensional data grids, and instructions and sample source code for converting your data into its file format. Labs: BSCL, SDVL, and VWL Labs: BSCL and SDVL Mathematics VolVis VolVis is a volume rendering software package created AMPL at the Visualization Lab at SUNY Stony Brook. With AMPL is an integrated software package for the state- VolVis, you can render volumes and extract isosurfaces ment and solution of linear, integer network, and some from 3-D data. VolVis produces very high quality nonlinear optimization problems. The software consists images; the volume rendering capabilities are the most of a command and model interpreter (AMPL) that works sophisticated of any volume rendering software installed with various solution generators such as MINOS and at the Supercomputing Institute. The user can control CPLEX. The command and model interpreter provides many aspects of the volume rendering, the trade-off: it is an interactive facility for defining models and data, and not as easy to use as the other packages. for controlling the execution of the solution generators. AMPL is both a software package and a modeling lan- Labs: BSCL and SDVL guage. Each problem formulation can be divided into three parts: data structure definitions, model definitions page 12 and data declarations. Allowable data types include sets, EISPACK parameters and variables. Sets are defined as ordered The EISPACK library is a collection of Fortran sub- groups of constants. Parameters may be singular or may routines that compute the eigenvalues and eigenvectors be single or multidimensional arrays. Variables are used of nine classes of matrices. The package can determine to represent decision variables within the model. Once the eigensystems of complex general, complex defined, these data types are used to declare objective Hermitian, real general, real symmetric, real symmetric functions and constraints. band, real symmetric tridiagonal, special real tridiagonal, generalized real, and generalized real symmetric matrices. Labs: C90 In addition, there are two routines which use the singu- lar value decomposition to solve certain least squares BESPACK problems. BESPACK contains subprograms for computing Bessel and Airy functions. Labs: BSCL, C90, SDVL, SMP, T3E, and VWL Labs: C90 ESSL/6000 Engineering and Scientific Subroutine Library, a state- BLAS of-art collection of 441 subroutines providing a wide BLAS is a library of routines that perform basic oper- range of mathematical functions for many different sci- ations involving matrices and vectors. They were entific and engineering applications. The mathematical designed as a way of achieving efficiency in the solution subroutines, in nine computational areas, are tuned for of linear algebra problems. performance on RS/6000 architecture. Labs: BSCL, C90, SDVL, SMP, T3E, and VWL Labs: IBM BSPLINE IMSL (from the IMSL web pages) BSPLINE contains Fortran subprograms for calculat- The IMSL FORTRAN 77 Numerical Libraries ing values characterizing B-splines, and for representing Version 3.0 - a comprehensive resource of more than 900 splines as combinations of B-splines. FORTRAN 77 subroutines for applications in general Labs: C90 applied mathematics and for analyzing and presenting statistical data in scientific and business applications. CPLEX Here is a comprehensive alphabetical listing of the rou- CPLEX is a tool for solving linear optimization prob- tines with links to GAMS for documentation and code lems, otherwise known as linear programs. CPLEX pro- examples. vides the user with several solving techniques including • Version 3.0 includes more efficient online documenta- the primal simplex method, dual simplex method, net- tion and enhancements to linear algebra, optimization work simplex method, barrier method, and mixed inte- and linear equations. ger method. CPLEX has a robust linear optimizer (fast, and capable of handling a large number of elements), a • Routines and interfaces consistent over 65 supported mixed integer optimizer, and a network optimizer. computer platforms. CPLEX can be used stand-alone or in conjunction with IMSL C Numerical Libraries Version 2.0 - written in AMPL. CPLEX also has a library of subroutines to sup- C for C programmers and based on the world's most port the Fortran programming environment. widely called numerical subroutines. Labs: C90 • Version 2.0 includes nearly 100 new functions, includ- ing partial differential equation support, additions for sparse and band matrices, expanded statistical func- tions and reorganized and expanded documentation. page 13 positive definite, triangular, and tridiagonal square. In • Online documentation provides powerful search capa- addition, the package computes the QR and singular bilities with quick cut-and-paste examples. value decompositions of rectangular matrices and applies IMSL Exponent Graphics - Powerful interactive them to least squares problems. graphics libraries for scientific, engineering and business Labs: BSCL, SDVL, SMP, and VWL applications. • Reduce source code by 75% to 95%. MAPLE • 2D and 3D graphing and charting. See XMAPLE. • Interactively manipulate graphs for quick results, Labs: C90 without recompiling. • Plot Types ° 2D MASS 2.2 -polar plots Mathematical Acceleration SubSystem. MASS is a set -spline plots of subroutines for the computation of mathematical -bar charts and plots functions that may provide improved performance for -pie charts certain FORTRAN and C intrinsic functions over those -error bars in the conventional libraries. MASS was developed by -box plots IBM inside of IBM and released for general use. -Pareto plots Labs: IBM -Bode plots ° 2D and 3D MINOS -scatter plots MINOS is a tool used to solve large-scale linear and -contour plots nonlinear optimization problems. MINOS uses the pri- -histograms mal simplex method to solve linear problems and the the -function plots reduced-gradient algorithm and projected Lagrangian Labs: BSCL, C90, IBM, SDVL, SMP, and T3E algorithm to solve nonlinear problems. MINOS can be used stand-alone or in conjunction with AMPL. LAPACK 2.0 MINOS also has a library of subroutines to support the LAPACK provides routines for solving systems of Fortran programming environment. The vendor simultaneous linear equations, least-squares solutions of requires that any user of the software first acquire a usage linear systems of equations, eigenvalue problems, and license. Often, this requires the payment of a license fee. singular value problems. The associated matrix factoriza- Labs: C90 tions (LU, Cholesky, QR, SVD, Schur, generalized Schur) are also provided, as are related computations Mathematica such as reordering of the Schur factorizations and esti- Mathematica is a widely used software package for mating condition numbers. Dense and banded matrices numerical and symbolic mathematical computations. are handled, but not general sparse matrices. In all areas, similar functionality is provided for real and complex Labs: BSCL, SDVL, and VWL matrices, in both single and double precision. Labs: BSCL, C90, IBM, SDVL, SMP, T3E, and VWL NAG NAG, from the Numerical Algorithms Group, con- LINPACK tains subprograms for solving many classes of problems, including zeros of polynomials, roots of transcendental The LINPACK library is for linear equations and lin- equations, differential equations, integral equations, ear least squares problems, linear systems whose matrices are general, banded, symmetric indefinite, symmetric page 14 matrix operations, eigenvalues and eigenvectors, analysis PRO-MATLAB of variance, and time-series analysis. PRO-MATLAB (matrix laboratory) is an interactive Labs: C90 tool for tasks involving matrices, graphics and general numerical computation. PRO-MATLAB is also a scien- tific programming language, with some of the elements NSPCG of languages like Algol, Fortran, Pascal, and C. One NSPCG solves large, sparse systems of linear equa- important distinction is that the only data type in PRO- tions, using any of a number of iterative methods and MATLAB is the matrix, a rectangular array of possibly preconditioning techniques. The iterative methods complex floating point values, which need not be dimen- available are: ORTHOMIN, restarted generalized conju- sioned, and whose size and shape can vary dynamically. gate residual method, Lanczos, LSQR, biconjugate gra- Toolboxes that extend PRO-MATLAB’s applicability to dient squared, conjugate gradient, Chebyshev accelera- specialized fields are also available. tion, generalized minimal residual method, and succes- sive overrelaxation. The preconditioning techniques Labs: C90 available are: incomplete LU factorization, Jacobi, sym- metric successive overrelaxation, least squares polynomi- SLATEC al, and Neumann polynomial. SLATEC Common Mathematical Library is a com- Labs: C90 prehensive software library containing over 1400 gener- al-purpose mathematical and statistical routines written in Fortran 77. OSL The Optimization Subroutine Library (OSL) is an Labs: C90 IBM product for manipulating and analyzing optimiza- tion problems. The emphasis in OSL is on solving opti- SMPAK mization problems. SMPAK contains subprograms for solving systems of Labs: IBM linear equations using direct methods, in which the coef- ficient matrix is large and sparse. OSLP Labs: C90 Parallel Optimization Subroutine Library (OSLp) is a collection of high performance mathematical subrou- WGPP tines used by application programmers to solve large WGPP is a multipurpose package developed at IBM optimization problems. It includes all of the functions of Research that incorporates state-of-the art graph parti- the AIX OSL/6000 product but solves linear and mixed- tioning and sparse matrix ordering algorithms. In addi- integer programming problems in parallel on the IBM tion to a user callable subroutine interface, WGPP pro- RISC System/6000 Scalable POWERparallel Systems vides automatic acceleration for the Barrier Methods in (SP) processor achieving a significant performance OSL and OSLp for solving Linear Programming prob- improvement. lems. Labs: IBM Labs: IBM PESSL XMAPLE Parallel Engineering and Scientific Subroutine Library MAPLE is an X Window System-based interactive sys- (Parallel ESSL) is a mathematical subroutine library tem for algebraic computation. It is designed for com- designed to provide high performance for numerically putation using integers, rational numbers, polynomials, intensive computing jobs running on the IBM RISC equations, sets, derivatives, and indefinite integrals. System/6000 Scalable POWERparallel (SP) processor. MAPLE can perform computations such as integer and Labs: IBM page 15 polynomial factorization, differentiation, integration, TeX, LaTeX Taylor series expansion, and matrix algebra. TeX and LaTeX are installed at the Supercomputing Institute, along with many packages, style files and fonts. Labs: C90 AMS-TeX and revtex are two of the packages. Also installed are xdvi (to preview TeX and LaTeX documents) Miscellaneous and dvips (to convert to PostScript). The Supercomputing Institute’s Technical Documentation Center has many books on TeX and LaTeX. Information ASPEN PLUS on various packages installed is in /usr/local/tex/doc, and ASPEN PLUS is a process simulation software system. is in PostScript form. It performs steady-state material and energy balances, estimates equipment and capital costs for proposed or Labs: BSCL, SDVL, and VWL existing plants, and predicts project costs and profits. The vendor requires that any user of the software first TeXtures acquire a usage license. Often, this requires the payment TeXtures is typesetting software which is particularly of a license fee. useful when mathematical formulae must be integrated with text. It is a full implementation of Donald Knuth’s Labs:C90 TeX typesetting language with a Macintosh interface, and includes the AMS-TeX and LaTeX macros. Data Thief Data Thief allows users to reverse engineer a data set Labs: SDVL from a scanned graph in MacPaint or PICT format. It will automatically trace graphs, accepts either log or lin- ear scale, and will calculate error from error bars if they Parallel Programming are present. It enables users to retrieve data for which they have only the graph. Libraries Labs: SDVL FORGE DISCO FORGE xhpf is Applied Parallel Research’s (APR) par- allelizing pre-compiler for distributed memory, multi- The DISCO seismic processing system provides mod- ular software for processing land and marine seismic processor systems. xhpf can automatically parallelize a Fortran program to produce an immediately compilable data. It is designed to meet all processing requirements, SPMD (Single Program Multiple Data) parallelized such as migration, DMO, velocity analysis, statics, deconvolution, etc. It provides modules for all processing Fortran 77 code containing calls to APR’s library inter- stages, from demultiplexing through stacking and plot- face. It can accept as input serial Fortran 77 source code, Fortran 77 with with subset High Performance Fortran ting. The system accommodates almost any field record- (HPF) data decomposition directives and Fortran 90 ing format and all variations of recording parameters. array syntax, and Fortran 77 with APR directives for loop The methodology includes swath processing, and gather selection and array partitioning. and non-gather stacking. Special quality control features include cable feathering displays, coverage maps, sem- Labs: IBM blance displays of dip and velocity, time slices, oblique line displays and triangulation displays. The vendor MPI requires that a royalty be charged for the use of the soft- Message Passing Interface (MPI) is a new library spec- ware. NetworkCS will charge this royalty to your ification for message-passing, proposed as a standard by account automatically when you use the software. a broadly based committee of vendors, implementors, Labs: C90 and users. We have MPICH 1.0.11 (a portable public- page 16 domain implementation of the MPI standard) as well as program include integrated solid modeling, design opti- IBM’s MPI implementation installed on all of the mization, coupled analyses, and handling of fluid-flow machines in the RS6000 Cluster. You need to load the and multi-field elements. The vendor requires that any mpi module to use MPICH. user of the software first acquire a usage license. Often, this requires the payment of a license fee. The vendor Labs: C90, IBM, and T3E also requires that a royalty be charged for the use of the software. NetworkCS will charge this royalty to your PVM account automatically when you use the software. PVM (Parallel Virtual Machine) is a software package that permits a heterogeneous collection of Unix comput- Labs: C90 ers hooked together by a network to be used as a single large parallel computer. PVM is one of the most popular CSA/NASTRAN message passing solutions for running parallel programs CSA/NASTRAN is a large-scale, structural analysis on distributed parallel computers in use today. The cur- computer program that solves a wide variety of engineer- rent installed version is 3.3.11. You need to load the ing problems by the finite-element method. CSA/NAS- pvm3 module to use PVM. TRAN has capabilities similar to MSC/NASTRAN. Labs: BSCL, C90, IBM, and T3E Labs: C90 SHMEM Hypermesh The logically shared memory access (SHMEM) rou- HyperMesh is a full-featured, linear and non-linear tines perform various operations on remote and local pre- and post-processor, designed for use by analysis memory on Cray MPP systems. These routines can min- engineers. HyperMesh can output models created in imize overhead and latency and can maximize data band- HyperMesh to analysis solvers such as MSC/NASTRAN width. Supported operations include remote data trans- and ABAQUS. HyperMesh then can be used as a post- fer, atomic swap, work-shared broadcast and reduction, processor to view the results graphically. HyperMesh and barrier synchronization. interfaces with ABAQUS, ANSYS, IGES,LS-DYNA, MARC, MSC/NASTRAN, PAMCRASH and Labs: T3E MSC/PATRAN. Labs: SDVL Structural Analysis LS-DYNA3D ABAQUS LS-DYNA3D is an explicit, three-dimensional, finite ABAQUS is a general-purpose finite-element program element code for analyzing the large deformation designed for advanced linear and nonlinear engineering dynamic response of inelastic solids and structures. A analysis applications. The program features very general contact-impact algorithm permits gaps and sliding along geometric modeling capabilities, a large library of mate- material interfaces with friction. Using a specialization rials, and a broad range of procedures. of this algorithm, such interfaces can be rigidly tied to admit variable zoning without the need of transition Labs: C90 regions. Spatial discretization is achieved by the use of eight-node solid elements, two-node beam elements, ANSYS four-node shell elements, and rigid bodies. The equa- ANSYS is a general-purpose finite-element program tions of motion are integrated in time by the central dif- for engineering analysis, and includes preprocessing, ference method. LS-DYNA3D currently contains 39 solution, and postprocessing functions. ANSYS is used material models and ten equations of state to cover a in a wide range of disciplines for solutions to mechanical, wide range of material behavior. The vendor requires thermal, and electronic problems. The capabilities of the that any user of the software first acquire a usage license. page 17 Often, this requires the payment of a license fee. The can be translated back to be used by Patran for post-pro- vendor also requires that a royalty be charged for the use cessing analysis including the generation of graphical of the software. NetworkCS will charge this royalty to images. your account automatically when you use the software. Labs: BSCL and SDVL Labs: C90 MTR/SASSI MARC MTR/SASSI consists of a number of interrelated com- MARC is a general-purpose finite-element system for puter programs that can be used to solve a wide range of linear and non-linear analyses. It supports structural, dynamic soil-structure interaction problems in two or thermal, and coupled thermal-mechanical analyses. The three dimensions. The vendor requires that a royalty be program is applicable to large strain and large displace- charged for the use of the software. NetworkCS will ment problems such as creeping and buckling. It is also charge this royalty to your account automatically when applicable to incompressible material behavior such as you use the software. tires and rubber engine mounts. Labs: C90 Labs: C90 NIKE2D MSC/NASTRAN NIKE2D is an implicit finite element code for analyz- MSC/NASTRAN is a large-scale finite-element pro- ing the finite deformation, static and dynamic response gram for engineering analysis. Its capabilities include of two-dimensional, axisymmetric, plane strain, and static and dynamic structural analysis, material and geo- plane stress solids. The code is fully vectorized. A num- metric nonlinearity, heat transfer, aeroelasticity, acoustics ber of material models are incorporated to simulate a and electromagnetism. Its features include sparse matrix wide range of material behavior including elastoplastici- routines, multilevel superelements, cyclic symmetry, gen- ty, anisotropy, creep, thermal effects, and rate depen- eralized dynamic reduction, and automatic singularity dence. Slideline algorithms model gaps and sliding along suppression. The vendor requires that a royalty be material interfaces, including interface friction and single charged for the use of the software. NetworkCS will surface contact. Interactive graphics and rezoning is charge this royalty to your account automatically when included for analyses with large mesh distortions. In you use the software. addition to quasi-Newton and arclength procedures, adaptive algorithms can be defined to solve the implicit Labs: C90 equations using the solution language ISLAND. MSC/PATRAN Labs: C90 MSC/PATRAN is a general purpose 3D Mechanical Computer-Aided Engineering (MCAE) software system. ORION It includes finite element pre- and post-processing soft- Orion is the graphics post-processor for NIKE2D. ware, as well as solid modeling capabilities, and interfaces Labs: C90 to various other popular analysis codes, such as ABAQUS, MSC-NASTRAN, and ANSYS. The pre-pro- cessing functionality allows a person to create a model or ProE read in an IGES file, help mesh the object, assign prop- Pro/ENGINEER (Pro/E for short) is a powerful CAD erties, set boundary conditions, etc. It supports input package that allows you to create 3D solid models of graphically, from a command line, and from a file. You parts from 2D drawings. Pro/E is a product of can also save the current state to an editable file, so it is Parametric Technology Corporation and it is a feature- easy to make modifications. After setting up your prob- based, parametric solid modelling system. It is written to lem, you can translate the information to work with ease tho process of frequent design changes characteristic your’s or other’s analysis code. The output of these codes of the manufacturing industry. Pro/E is feature-based in page 18 the sense that parts are created by specifying features e.g. Roger Fosdick slots, holes, etc.; as opposed to specifying geometry e.g. Department of Aerospace Engineering and lines, surfaces, etc. Pro/E is parametric in the sense that Mechanics the shape of a part is controlled primarily by its feature George Rapp, Jr. dimensions. In other words, the shape of a part can be Department of Geology and Archaeometry Lab significantly, even radically, changed simply by altering Charles C.S. Song its dimensions. Pro/E is essentially a collection of modes, Department of Civil Engineering and Scientific each mode complete by itself; all modes of course can Computation interact. The basic Pro/E modes are Sketcher (to create David Yuen 2D sections), Part (to create 3D solid model of parts), Department of Geology and Geophysics and Sheet Metal (to create thin-walled, sheet metal parts), Scientific Computation Assembly (to assemble parts), Drawing (to create engi- neering drawings of parts and assemblies produced in Symmetric Multiprocessing Laboratory: Pro/E) and lastly, Manufacture (to define machining operations required for manufacturing a part created in Lab Manager: Pro/E). For comprehensive info on how to use Pro/E, Erik Jacobson refer to the reference manuals which can be accessed on the system using a program called proguide (part of Assistant Lab Manager: Pro/E package). John Makosky Labs: SDVL Steering Committee: Vipin Kumar (Committee Chair) Feedback Department of Computer Science and Engineering and Scientific Computation Graham Candler We appreciate your feedback. If you have any sugges- tions for software, please don’t hesitate to contact the lab Department of Aerospace Engineering and Mechanics and Scientific Computation managers or the Steering Committees. Christopher Cramer Department of Chemistry Head of Technical Support is: John Lowengrub Department of Mathematics Barry Schaudt Yousef Saad Department of Computer Science and Scientific Development and Visualization Engineering and Scientific Computation Laboratory David Yuen Department of Geology and Geophysics and Lab Manager: Scientific Computation Barry Schaudt Basic Sciences Computing Laboratory: Steering Committee: Thomas W. Jones (Committee Chair) Lab Manager: Department of Astronomy Bob Milius Lynne Edwards Department of Educational Psychology and Scientific Computation page 19 Steering Committee: University of Minnesota-IBM Shared (Named by Structural Biology) Research Project Edward Egelman (Committee Chair) Department of Cell Biology and Neuroanatomy User Support Manager: Leonard Banaszak Amidu Oloso Department of Biochemistry (Medical School) Steering Committee: Kevin Mayo (Named by Computer Science) Department of Biochemistry (Medical School) David Du (Committee Chair) Steering Committee: Department of Computer Science and (Named by the Supercomputing Institute) Engineering Mitchell Luskin Vipin Kumar Department of Mathematics and Scientific Department of Computer Science and Computation Engineering and Scientific Computation Alon McCormick Anand Tripathi Department of Chemical Engineering and Department of Computer Science and Materials Science Engineering George Wilcox Department of Pharmacology Steering Committee: (Named by the Supercomputing Institute) Medicinal Chemistry/Supercomputing Christopher J. Cramer Institute Visualization/Workstation Department of Chemistry Laboratory David Lilja Department of Electrical Engineering Lab Manager: David Yuen Kirk Wolff Department of Geology and Geophysics and Scientific Computation Steering Committee: (Named by Medicinal Chemistry) Steering Committee: David Ferguson (Committee Chair) (Named by Academic Affairs Computing and Information Department of Medicinal Chemistry and Technologies) Scientific Computation Ernest Retzel Department of Cell Biology and Neuroanatomy Steering Committee: (Named by the Supercomputing Institute) To be determined Steering Committee: (Named Jointly) David Grant Department of Pharmaceutics Carston Wagner Department of Medicinal Chemistry page 20 Head of Technical Support Barry Schaudt (schaudt@msi.umn.edu) Office: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Room 2091, SCC Phone: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .626-1765 Scientific Development and Visualization Laboratory Web Page http://www.msi.umn.edu/sdvl/index.html Laboratory Manager Barry Schaudt (schaudt@msi.umn.edu) Office: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Room 2091, SCC Phone: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .626-1765 Symmetric Multiprocessing Laboratory Web Page http://www.msi.umn.edu/smp/index.html Laboratory Manager Erik Jacobson (erikj@smp.msi.umn.edu) Office: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Room 2075, SCC Phone: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .624-0532 Assistant Manager John Makosky (makosky@smp.msi.umn.edu) Office: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Room 2079, SCC Phone: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .624-7552 Basic Sciences Computing Laboratory Web Page http://www.msi.umn.edu/bscl/index.html Laboratory Manager Bob Milius (milius@msi.umn.edu) Office: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Room 1-280B BSCL Phone: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .626-2771 page 21 Medicinal Chemistry/Supercomputing Institute Visualization/Workstation Laboratory Web Page http://www.msi.umn.edu/vwl/index.html Laboratory Manager Kirk Wolff (wolff@msi.umn.edu) Office: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Room 7-123 WDH Phone: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .626-3612 University of Minnesota-IBM Shared Research Project Web Page http://www.cs.umn.edu/Research/ibm-cluster/ Laboratory Manager Amidu Oloso (oloso@msi.umn.edu) Office: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Room 1-229 EE/CSci Phone: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .624-2376 This publication is available in alternative formats, upon request, to individuals with disabilities. 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