Documentation and Getting Help
Besides the usual man (manual) pages (for example, type man ls to get the description of the ls command), this machine has it's entire documentation (> 100MB) online and searchable via the insight command (not to be confused with insightII, the command that starts the BIOSYM viewer). insight uses only X11 graphics, so can be used with any Xserver; you do not have to be at the console.
In the directory /usr/local/man there are several directories:
html/ man1/ man5/ man7/ man8/ postscript/ txt/
The man#
directories are searched automatically by the man command. The html/,
postscript/ and text/ directories contain documentation that
came with certain programs, so if you cannot get information about a command or
program via the man command, look in those locations for info.
NB: If you are at an X display, you can use ghostview to view the postscript files. At an X display or the console, type gv postscriptfile to view it.
There are some very useful Web pages describing the use and abuse of Unix, especially for beginners: (if this link proves too slow, we may make the pages local).
OAC also has an Online Intro to Unix that may be helpful.
Silicon Graphics has very splashy Web page in which you can find information on the system hardware and software.
Possibly more useful (he said, blushing) is Harry Mangalam's SGI WAIS page which allows you to query the complete back-postings of the comp.sys.sgi newsgroup, allowing you benefit from all (admitted) mistakes and foolish questions ever submitted to the group. Try it before you try to get answers from anyone else (even before RTFM!)
If you're considering buying one of these machines your$elf, you can get reasonably up to date information from OAC's Workstation Acquisition Service, including academic pricing for SGIs.
There are 3 modes of access to this machine - GL/OpenGL/DGL mode , X window mode, or character mode.
GL/OpenGL/DGL
mode
For realtime graphics and other niceties that depend on the fast transfer of data from the cpu to the monitor, you have to be at the console (the 19" color monitor directly connected to the cpu). From here you can access all 3 modes mentioned above. In addition, attached to the console are also Crystal Eyes 3D glasses and a Dials Box for easier manipulation of 3D objects in many applications. Since the release of the OpenGL specification, a few vendors have releases OpenGL for Linux and OpenGL applications will soon arrive for Macs and Windows, allowing you to run these applications remotely, but slowly because of network latency.
X
window mode
Many programs are available via the X window system, which allows you to open a graphical (bitmapped) window to programs (like the native Mac or Windows interface) on remote machines (unlike the native Mac or Windows interface). This mode can be used with Macs and Windows PCs using an X server program, available from OAC (free for Macs, about $75 for PCs) or from other vendors.
Character
mode
Character mode is like the old DOS or Unix command line interface (still prefered by people , especially those who can touch type) who know exactly what they want to do and how to do it. Many programs still rely on this interface or the related 'curses'-like interface which uses ascii characters to create a pseudo graphical interface for controlling programs. The best bet for this type of mode is 'NCSA Telnet' for the Mac (68K version or fat binary for both 68K and PowerMac-native) or ewan for Microsoft Windows.
We are providing a number of text editors for mamba so as to make interacting with your files as painless as possible. Aside from the default unix editors vi and emacs (both powerful in their own way, but relatively impenetrable as far as a user interface), we have or will soon provide (NYI=Not Yet Installed):
jot - SGI's very fast, but GL-based editor (only works at the console)
joe - a character based editor that uses the old WordStar-like commands
pico - another simple, character-based editor, familiar to many from the elm/pine mail programs
sedt - an edt-like editor, for those of you from the VMS world (NYI)
nedit (aka ned)and asWedit - pretty good X-based editors; asWedit is also an HTML editor, and
crisp - a commercial editor that does just about everything one
might hope an editor to do (with complete online help from within the editor, in
both X (mcr) and character modes (cr). As an example, here's its
X toolbar:
All the editors mentioned above can be started by typing their names, much like starting a program in DOS. ie
joe file.to.be.edited
The X editors should be started in background mode by appending the '&' character:
ned file.to.be.edited &,
although the jot editor knows enough to start itself in background mode anyway. If you have requirements that are not met by the preceding, we will try to accomodate you. Some of the character based editors (notably sedt and crisp) require substantial changes or tuning of the TERM environment variable or your termcap file (if you don't know what these are, don't worry....yet).
Printing from this machine is possible to the local laser printer in BSII Rm 5205, as well as to other Novell print queues, to Mac-compatible, ethertalk laser printers (via the Mac application lpdaemon - Click here to download it), to MS Windows for Workgroups-available printers via the SMB software Samba, as well as any lp/lpr compatible printers.
In general, all files in the /usr/local/bin directory can be executed by anyone. However, it is advisable to find out about the display requirements for each as many require either X or GL displays. If you cannot find information about it, send me mail, and I'll try to answer your questions.
We will also be maintaining and adding to this Web homepage for this machine that describes how to accomplish various things that might be of interest to the biocomputing community. Future plans include the possibility of setting up NIS (so that you can have one login for all your biocomputing accounts), load sharing software so that large jobs are executed on other idle processors around the university, and multiple platter CD library for large databases. We are trying to make this system as easy to use as possible, and so welcome suggestions and questions about its use. Please send email to Harry Mangalam .