THE SGI SCREAM-SAVER
Chemistry Department, Indiana University, Winter 1995
This newsletter is available at the beginning of each quarter and covers the chemistry
SGI cluster and the software available on it. If you want to subscribe, contact Marty Pagel
(mpagel@indiana.edu, 5-6492, C237C) or Kathrine Mann (A421).
Items Covered in this Edition:
This issue initiates several changes. Publication of the Scream Saver will occur 3 times per year,
usually in January, May, and September; additional issues may also be published. ON-line SGI news
is no longer maintained; important messages will appear in the "Message of the Day". Finally, the
series of SGI Users Meetings has been canceled; however, the Molecular Visualization Staff is still
available for consultation and training.
Several new X window applications are available on departmental SGI workstations courtesy of Jack
Duan, Biochemistry Computing System Administrator. While all of these applications work with
IRIX 5.x, they may NOT work with IRIX 4.x. XV version 3.1 (type xv_31) has several new
features for viewing images, can now view postscript files, and is great for converting between
different graphics formats. ghostscript (type gs) is also available for viewing postscript files.
Netscape (type netscape) can be used instead of mosaic, and has been reported to be faster. xanim
(type xanim) is also available for viewing movie files (see below). Cerius2 version 1.6, CSD version
2.3.7, and InsightII version 2.3.5 have replaced earlier versions. The CSD has been transferred to
chemlib, but this change has been transparent to users.
IRIX 5.3, the latest UNIX operating system for SGI workstations, is available. All workstations
running IRIX 5.2 will be upgraded. Contact Marty or Ken if you want to upgrade your IRIX 4.x
operating system. All printing via the network travels through the departmental Novell server,
improving printing reliability and allowing for an automatic log of all printing. Changes to the
ethernet network have reduced many network problems, which also improves reliability.
User files on several research SGIs are now backed up on a weekly basis. Cost = 1 or 2 DAT tapes.
This backup is meant to prevent catastrophic loss if a system were to fail; users should still back up
their own files. Other research SGIs can be added to the list of weekly backups upon request.
The following is taken from notes compiled by Jack Duan, Biochemistry Computing System
Administrator.
- Make sure that your Mac is networked to the campus network and it is using EtherTalk.
- Launch the Fetch application on the Mac. Fetch is usually under the Communication folder
under the Apple menu (the colorful Apple icon on the Mac menu bar). Fetch is a Mac-based
program which uses the FTP (File Transfer Protocol) transfer method.
- When the Open Connection window pops up, type the correct entries in the corresponding input
boxes. For example:
HOST: type the name of the UNIX machine you want to connect to
(e.g., splatter.chem.indiana.edu), then press <TAB>
USER ID: Type your username (e.g., jdoe), then press <TAB>
PASSWORD: Type in your password for your account on the UNIX
machine, then press <ENTER>
- After you have successfully logged into your account, you can browse through your account
using the user-friendly interface.
- If you are making a binary transfer (anything that is not ASCII text files), check the option
Binary on the Fetch window. Otherwise, choose the Text option.
- To transfer a file:
- Macintosh ---> UNIX
- Click on the Put button in the Fetch window
Choose a file to be opened---transferred.
After selecting a file, a pop-up window appears which asks for a file format. Choose Raw Data
for binary transfers, Text for text transfers.
Hit and the transfer will begin.
- UNIX ---> Mac
- Select a file in your UNIX account in Fetch, and click on the GET button.
If Fetch asks where to save the file on the Mac, select the Desktop.
If Fetch doesn't ask where to save the transferring file, and a running dog icon appears, check the
Customize Menu / Preference / Download option to determine the default downloading folder
for Fetch.
Transfer additional files between the SGI/Mac
Choose Close Connection under Fetch when you are done.
Converting Graphics File Formats
The following is taken from notes compiled by Jack Duan, Biochemistry Computing System
Administrator.
It is always a good idea to choose a graphics format that is multi-Operating System supported if you
want to transfer these files across platforms. to convert a file from one format to another, first make
sure that the program you use supports both file formats. Then, open the file under that program.
After that, save a copy of the file under a different file format (usually there is a command such as
"Save as..."). Here are some suggestions on selecting the best graphics formats:
Category I: Pixel-based graphics formats:
These formats are very portable (can be transferred between different computer operating systems),
preserving the best image quality. Lines, polygons, characters, fonts are all pixel-based, so that they
cannot be edited separately from the rest of the picture.
- GIF (*.gif files)
- The most supported 256-color graphics format. It can be viewed using XV on
the SGI's or using GIF Converter on the Mac's. Its file size is small. Most people like to use
this format for WorldWideWeb pages.
- TIFF (*.tif files)
- It has very good image quality, supports 24-bit color. It is supported
using GIF Converter, Canvas, or PhotoShop, etc., on the Mac, and it is also supported using
Showcase or XV on the SGI. The image size is relatively large since it contains 24-bit color
information.
- EPS (*.eps files)
- It is one of the best formats for graphics. The disk space requirement for this
format is huge; sometimes it is 300-400% larger than a comparable sized TIFF file. Many
graphics professionals like to use this format to retain all the information for the picture.
- JPEG(*.jpeg or *.jpg files)
- One of the most compact 24-bit color formats. It is supported on the
SGI's using XV and on the Macs using JPEG View or GIF-Converter. It is very good for
live-color pictures. It uses loosy compression method which sometimes reduces a multi-
megabyte image file to a less-than-200 kilobyte JPEG file. It is another widely used image
format for WWW pages.
Category II: Vector-based graphics formats
As opposed to pixel-based graphics formats, vector-based pictures have different layers, fonts, lines,
polygons, etc. as separate objects. Users can easily move or edit these objects within the picture.
There are a lot of proprietary formats used by different drawing packages, and they are normally
very limited-supported. Adobe Illustrator, Canvas, MacDraw Pro all have their own vector-based
formats; unfortunately, they are not easily exchangeable.
- PICT (*.pic files)
- Supported by MacDraw and Canvas on Macs. It is also supported by Showcase
on the SGIs. Vector-based PICT files are sometimes confused with pixel-based PIC files, but
they are different.
Category III: Special language formats
- Postscript (*.ps files)
- This is a format based upon a universal printer language. All printers which
support postscript can print this format without much trouble. Please do not choose
this format if you want to edit your graphics file later because they cannot be edited
using any of the graphics packages. However, you can view postscript files using
xpsview or XV (version 3.1a) on the SGIs.
Category IV: Movie formats
- MPEG: (*.mpg)
- A movie (animation) file. Most MPEGprograms don't support sound. On a Mac,
use the utility Sparkle; use 16-bit or 24-bit color for best results. On a 24-bit color SGI
(our Indys are only 8-bit color), use mpeg_play to view *.mpg files:
mpeg_play -dither color filename.mpg.
- AVI
- Supported by Microsoft, mainly made for Windows on PCs. Can be played on an SGI
using xanim. AVI supports sounds, but our version of xanim does not support sounds.
- QuickTime Movies
- Supported by Apple for the Mac, can be played using MoviePlayer or Sparkle
on a Mac (16-bit color for optimal performance). xanim on the SGIs will also play
these files (without sound).
Some Hints:
- For WorldWideWeb pages, use GIF or JPEG formats.
- For color prints, use postscript format
- For color pictures to be transferred between platforms, use TIFF or EPS formats.
- For computer-aided designs and drawings, make sure that a particular file
format is supported by other drawing packages. A PIC format can be a safer bet for these purposes.
These programs support the following kinds of graphics formats:
- XV (SGI and most UNIX workstations)
- JPEG, GIF, TIFF, BMP, PICT, postscript, Raw, and SGI
- Showcase (SGI)
- EPS, SGI, PICT, RTF
- ImageWorks (SGI)
- TIFF, SGI, GIF, JPEG, FIT, PhotoCD
- PhotoShop (Mac, supported by UCS at Student Building and Fine Arts)
- JPEG, GIF, EPS, BMP
- PICT (pixel-based)
- Raw, PhotoShop native formats.
- Canvas (Mac)
- MacDraw, PICT, TIFF, MacPaint
- GIF Converter (Mac)
- JPEG, GIF, BMP, MacPaint, PICT (pixel-based)
- JPEG View (Mac)
- JPEG, GIF, MacPaint, PICT (pixel-based)
The SGI workstations have both versions of UNIX printing software: lp and lpr.
The Big News: If you have a local printer, use lp. To use the default remote printer, use
either lp or lpr. To choose a printer that is NOT the default printer, use lpr.
Table 1 lists the default printer for each version of printing. If a printer is directly attached to the
workstation, this local printer is the default lp printer. If the workstation does not have a local
printer, lp printing is directed to one departmental printer via the departmental Novel server. All
departmental printers can be accessed via the departmental Novell server using lpr.
Printing via the Novell server has two consequences (with either lp or lpr). First, print requests do
NOT appear in the print queue, but are still printed. Also, huge files larger than 4 MBytes (such as
large color postscript files) will NOT print and NO error message will appear. This size limitation
may disappear in the future.
Some programs, such as Cerius2 and InsightII, allow you to type lp or lpr within the program
window to automatically print from the program. Other programs, such as PC-MODEL and Midas,
generate a postscript file. Files can be printed using lp or lpr from a UNIX window, or via the
WorkSpace window (which always uses lp). Printing from programs, from the UNIX window, or
from WorkSpace is very easy. See the Sept. 94 issue of the ScreamSaver for more information.
To use lp:
lp filename prints filename on the default lp printer
lpstat display the status of the print queue of the
default lp printer
cancel printername-## cancel print job printername-## (displayed by
typing lpstat)
To use lpr:
lpr the workstation assists you with lpr
printing commands
lpr filename prints filename on the default lpr printer
lpr printername filename print filename on printer printername
lpr help displays lpr help file
ALL print requests are logged by the workstation. While there is no charge for Laser Jet output, you
may be asked for retribution (in the form of paper or toner cartridges). Please limit your printing to
research activities only. Please DO NOT abuse your privilege to print, or we may be forced to charge
for each print-out. There IS a formal $1 charge for color Paint Jet printout requests.
Table 1. Printers (bold = local printers)
workstation default lpr printer default lp printer
chemvgx chemmsc chemmsc
floater1 chemmsc chemmsc
chemlib chemlib liblp1
pchem01-06 chemlp2 chemlp2
nmrsg1 chemnmr nmrlp1
iumsc1 chemmsc chemmsc
iumsc2 chemmsc msclp1
iumsc3 chemmsc HPLaserjet4
iumsc4 chemmsc chemmsc
acniris chembio chembio
dwilliams chemmsc chemmsc
grieco chemlp2 macpr_9600
inorganic3 chemnmr Inorganic3
jwz1 chemnmr chemnmr
mdholl2 chemnmr HPLaserjet4M
montgomery chemmsc HP
roush chembio PostScript
rustico chemlib chemlib
splatter chembio hounds_hind
widlanski chembio chembio
All departmental printers can be accessed using lpr print commands from MOST SGI workstations.
PCHEM01-06 CAN ONLY PRINT TO CHEMLP2 OR CHEMLXY.
Departmental Printers:
chemlp2 Room A202
chemlxy Room A202
chemlib Chemistry Library (also known as liblp1 on chemlib)
chemnmr NMR Facility, room 237 (also known as nmrlp1 on nmrsg1)
chemmsc MSC, room A421 (also known as msclp1 on iumsc2)
chembio Room A663 (also known as hounds_hind on splatter)
mscpj1 MSC, room A421
* subject to change
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Last updated: 01/23/2001