Software installed on /usr/addedon on the SGI's and /usr/local/lib on the Linux workstations. Unfortunately not all software is available on both platforms.
| a2ps | This program can convert other files into Postscript - a2ps means "Any to PostScript filter". There is a html manual available. |
|---|---|
| acroread | Adobe's viewer for PDF files (i.e. Adobe Acrobat). |
| Allen & Tildesley |
The Fortran programs mentioned in the book "Computer Simulation of Liquids" by M.P. Allen and D.J. Tildesley has been installed in the directory /usr/addedon/lib/Allen-Tildesley. They are also available as web-pages . |
| bash | GNU Bourne-Again SHell. An alternative shell - sh-compatible command language interpreter that incorporates useful features from the Korn and C shells (ksh and csh). Two more manuals are available: bash and bash-reference |
| biosym | Issue the command source /biosym/cshrc
and the necessary environment variables will be set up for using
the biosym-package, e.g. the command insightII can be
issued. Please see the note about the licenses we have available. |
| bison | Gnu compiler compiler. A manual is also available. |
| bsplit | Works like split - but for binary files. |
| cerius | Use the command
/people/polymer/cerius/cerius2 to start version 3.5 of the
visualizer and /usr/addedon/cerius2_3.9/cerius2 to start version 3.9. Please see the note about the licenses we have available. |
| chemtool | chemtool: Graphical tool for drawing chemical structures with similar functionality as ChemDraw and ISISdraw. |
| CSD | Cambridge Crystallographic Database. The database is installed on junction only but the software displays in a X-window. Issue the command source /usr/addedon/CSD/cshrc and you are ready to run quest. |
| cplot | C-PLOT: Scientific Graphics and Data Analysis Software. |
| elm | Interactive screen-oriented mailer program. |
| emacs | Screen oriented editor. |
| evolver | Interactive program for studying surfaces shaped by surface tension and other energy functionals. |
| f2c | Converts Fortran 77 programs to C or C++. The procedure for
using f2c in connection with a C compiler is:
|
| formulc | Utility which can transform crystallographic unit cells into different space group settings. sginfo generates matrices to do the transformation - formulc takes the matrix and applies it to your coordinates. |
| ftnchek | Fortran 77 program checker. Ftnchek is designed to detect certain errors in a Fortran program that a compiler usually does not. |
| fudgit | A Multi-purpose data-processing and fitting program. Look in /usr/addedon/lib/fudgit for examples. |
| gaussian98 | Gaussian 98 is a connected system of programs for performing a variety of semi-empirical and ab initio molecular orbital (MO) calculations. Please read the help page. |
| geomview | Interactive geometry viewer (can be used in conjunction with evolver). A reference manual is also available. Try visit the The Geometry Center. |
| ghostview | GNU's postscript previewer. |
| gifmerge | Merge single GIFs into an GIF89a Animation, which can be included in a web-page. The command-line options are very simple - just type gifmerge without any arguments to see a list. |
| gimp | General Image Manipulation Program - with some of the same functionality as Adobe Photoshop. Before you can use the program issue the command cp /usr/addedon/lib/gimp/gimprc ~/.gimprc |
| gmemusage | Graphical tool to view the memory usage on a system. |
| gnuinfo | GNU's hypertext browser. |
| gnumake | GNU's alternative make facility. A reference manual is also available. |
| gnuplot | All-purpose plotting facility (useful demos can be found in /usr/addedon/lib/gnuplot). |
| groff | nroff,troff, ... Typesetting facility. |
| grok | Desktop Database Manager and GUI Builder. A reference manual is also available. |
| gs | GNU's postscript interpreter (ghostscript). |
| gzip | File compression facility. gunzip uncompresses gzip'ed files. |
| hpgl2ps | A HP (Hewlett Packard) plot command filter to PostScript . |
| html2latex | Converts html documents into LaTeX documents. |
| idl | Interactive Data Language - Version 4.0 is installed.
Use the commands:
|
| icol | Interactive tool for sketching and modifying color maps. |
| ispell | Spell-checker. |
| kermit | File transfer tool for modem connections. A manual is also available. |
| khoros | A software environment for data processing and visualization. Run 'cantata' to use a spreadsheet-like environment. On the linux machines you have to run the command: /usr/local/lib/khoros/bin/kconfigure to create a .khoros_env in your home-directory, which has to be sourced before running cantata - i.e. source ~/.khoros_env |
| latex2html | Tool for conversion of LaTeX documents into html documents. |
| less | GNU's version of a file browser - but it has more functionality than unix's 'more'. |
| lha, zoo | Popular file compress/uncompress utilities from the dos-world. |
| m4 | Gnu's macro processor. A reference manual is also available. |
| mathematica | Mathematica is an interactive system for doing mathematical computation. It handles numeric, symbolic, and graphical calculations. A line oriented version of Mathematica can be invoked by math. A hypertext help system is available by starting mathematica and use the pull-down help menu. |
| matlab | There are 2 floating licenses for matlab on the Linux machines. |
| mcvert | File conversion utility: MacBinary <=> BinHex 4.0 and other file formats. |
| mkisofs | Utility to create a iso9660 image from a directory structure. This is used when writing a CD-ROM. |
| mopac93 | Semi-classical minimization package. The command '/usr/addedon/mopac_bin/mopac.csh' will set up the necessary commands to run mopac. |
| moria | D&D style game. |
| Mosaic | NCSA WWW document browser. |
| mpeg_encode | mpeg-1 video stream encoder - accepts the following formats: YUV, PPM, PNM. A default parameter file can be found in /usr/addedon/lib/mpeg_encode. |
| mpeg_play | Mpeg movie viewer. |
| nedit | NEdit - Motif GUI style text editor. More info is available at Fermi Lab. |
| netcdf | NetCDF (network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. The netCDF libraries are installed in /usr/local/lib/netcdf. |
| nethack | D&D style game. |
| netpbm | Portable Bit Map (incl. pbm-plus) - look at
pbm,
ppm,
pgm, and
pnm. Converts anything -> pbm -> anything (for graphics formats). |
| nmrPipe | Offline processing of 1D-4D nmr data. Issue the commands: source /usr/addedon/lib/nmrPipe/nmrInit.sgi6x.com and source /usr/addedon/lib/nmrPipe/font.com before using the software. A manual is available here. |
| netscape | WWW document browser. |
|
Numerical Recipes |
Source code in C can found in /usr/addedon/lib/cc_recipes and source code in FORTAN can found in /usr/addedon/lib/f77_recipes on the SGI's. On the linux machines the directories are: /usr/local/lib/cc_recipes and /usr/local/lib/f77_recipes respectively. |
| onall | Executes commands on all machines in the MRL cluster: e.g. onall uptime will show you the loadlevel on each machine. |
| patch | A program to apply diff's to upgrade sources. |
| perl | Language making text-analyzing easy. A reference manual is also available. |
| plan | Interactive X/Motif calendar and day planner. Copy /usr/addedon/lib/plan/holiday/holiday_us to ~/.holiday to get started. |
| pgp | PGP (Pretty Good Privacy) is a public key encryption package to protect E-mail and data files. |
| pgplot | The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable,
device-independent graphics package for making simple scientific
graphs. It is intended for making graphical images of publication
quality with minimum effort on the part of the user. For most
applications, the program can be device-independent, and the output
can be directed to the appropriate device at run time.
The libraries are installed in: /usr/local/lib/pgplot on the linux systems /usr/addedon/lib/pgplot on the SGI cluster. |
| povray | Ray-tracer. Also look at The Persistence of Vision homepage. |
| pymol | pymol is a molecular graphics system designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. There is a manual available. |
| psutils | Collection of usefull utilities for manipulation of Postscript files. See e.g. the man-page for pstops. |
| rasmol | RasMol is a software package for looking at molecular structures.
You must download a PDB data file for each molecule you wish to view.
It can rotate a protein or a DNA molecule to show its 3D structure.
You can find out about downloading PDB files
here.
A manual for rasmol is available. On the Linux machines the X-windows must be in 8 bit color mode - thus use the following command to start X: startx -- -bpp 8 |
| rn | Text-screen based news read program. |
| run | Command to start up jobs: run -h 'machine' 'command' executes 'command' on 'machine' in the current directory. Automatically renices jobs to the lowest priority. |
| sginfo | Utility which can transform crystallographic unit cells into different space group settings. sginfo generates matrices to do the transformation - formulc takes the matrix and applies it to your coordinates. |
| Staroffice | Staroffice has been installed on the Linux machines. An overview of the features is available here. In short Staroffice is compatible with and 'equivalent' to Microsoft Office 97. Type the command soffice - the first time it will ask you to install some files: Choose Workstation Installation (it will use 1,7MB of diskspace in your home directory). |
| ssh | ssh allows users to connect to other computers over a network using strong authentication and secure communications over insecure channels. Please also read the manpage for ssh |
| sm | SuperMongo - plotting package. |
| spip | Scanning Probe Image Processor. Demo-images in /usr/addedon/lib/spip_demoimages. |
| SYBYL | The molecular simulation software package from Tripos is installed on oxygen (the SGI O2 in the teamroom) - just type the command sybyl to start it up. To read and search the documentation type the command sybyl_bookshelf. |
| sz, sx, sy | Z,X,Y - modem. |
| term | Server for multiple communication channels on a serial link (say modem connection). Popular with Linux people. |
| TeX | latex,tex,bibtex + xdvi + dvitps. Also RevTeX-4 has been installed (for those who want to submit directly to Phys. Rev.). |
| vort | Ray-tracer (demos in /usr/addedon/lib/vort_demo). Also look at the man page for art. |
| vrweb | VRweb is a browser for 3D worlds and objects modeled in the Virtual
Reality Modeling Language (VRML). Start vrweb with
the command: vrweb -helpDir /usr/addedon/lib/vrweb/help (On the SGI's) |
| x3270 | IBM 3270 terminal emulator - type: x3270 ccnh.ucsb.edu to use the Pegasus services at the UCSB Library |
| xanim | Multiformat animation viewer for X (mpeg, flc, ...). |
| xemacs | Emacs with better GUI support, but can only be used on a X-terminal. |
| xfig | Facility for Interactive Generation of figures under X11. |
| xmfract | X interface to display fractal images e.g. Mandelbrot & Julia sets. Online help is available. |
| xmgrace | Formerly xmgr: Graphics program for plotting/drawing. |
| xrn | X-interface to USENET news system. |
| xv | Tool to display *.gif, *.jpg and *.tiff pictures. |
| zip, unzip | Popular file compress/uncompress utilities from the dos-world |