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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printed document such as this out-of-date almost as soon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




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