Information for New Users of Molecular Modeling Facility
Please change the password using the command 'passwd' when
you log in the first time.
Your account is good on the following machines in Rowland
room 517: model1 through model6.
You can log in remotely using F-Secure ssh to:
modelx.ps.uci.edu where x is a number 1-6.
If you want to get an orientation to the Facility or any of
the software, please contact me. I am available to help make
the Facility work for you. If you have any questions or
problems, please contact me at X 1204 or e-mail to model@uci.edu .
You will receive e-mail updates approximately quarterly. The
updates will contain info about new hardware and software,
tips for using the Facility, policy issues, and information
about short classes and tutorials. If you wish paper mail
instead, please let me know.
General Admonitions
-
One key is issued to each group that has an account. The
Facility door is never to be unlocked or propped open
under any circumstances.
-
Manuals on the bookshelves of the Facility are not to
leave the room unless they are checked out.
-
Please bring no food or drink into the Facility. We don't
want sticky coke or coffee spills on the tables, floors,
or keyboards.
-
The last user to leave the room is to turn off the lights
and verify that the door is locked before leaving--day or
night.
-
Please do not share your personal account with someone
else.
Access
Here is a description of Modeling Facility assets and guidelines.
An account gives you access to the following
- **Access to at least one Octane2 for interactive jobs controlled
from the SGI terminal itself or from an X-terminal or X-terminal emulator
on the UCINet.** A given group will be able to access more than one
Octane2 for interactive jobs only if no other interactive users are
waiting for access. Unattended interactive jobs are subject to being
killed by another prospective user, if no other machines are available.
Users may not log in remotely for more than 24 hours; this is an annoyance
to other users. Logins older than 24 hours may be summarily killed.
Before logging on from a remote terminal, users should survey the current
usage pattern and logon to a vacant or lightly used machine. This can
be done with the command "ruptime".
- **Access to the latest versions of software maintained by the Facility.**
Packages and commands to invoke them are listed below:
*Mathematica:
> mathematica (for Xwindows version)
Help: manuals on shelf in rm. 517; > man mathematica
*Macromodel(molecular mechanics, etc.):
> macromodel
Help: Tutorial and manuals in rm 517.
Right mouse button gives online help. Short course available.
*Spartan(molecular orbital package):
>spartan
Manuals and tutorial on shelf in rm. 517.
*Biosym(approximately 6 program modules
for molecular modeling of many flavors)
>insightII
Help: Manuals on shelf in rm. 517. Short course available.
Tutorials online: type
Note: we have one license for Biosym software.
Please do not leave Biosym running when you're doing something else.
*Gaussian(Molecular orbital package)
>nice +10 g98 inputfile ( or submit through Spartan) &
Help: Manuals on shelf in rm. 517.
*ISIS reaction database software from MDL.
IRDAS (ISIS/Base) and ISIS/Draw
run on Macintosh computers.
The database is accessed via ethernet and resides in the modeling
facility.
*Cambridge Structure Database (CSD)
>ssh model0 (First log into model0)
>quest -j filename
Also available: The SGI Varsity package of developer software
including C, C++, Fortran77, Webmagic HTML web page editor and CASEVision/WorkShop
debugging/profiling tools, utilities, and compilers from SGI, as well
as DCSLIB utilities and communications software such as the gnu package,
netscape etc. I will consider purchasing and/or installing additional
software at your request.
Most of this software can be accessed on your local SGI from the network(NFS)
disk /apps on the Facility server so that you can run it without competition
from other users if you have your own SGI machine(s). See me to arrange
this. Facility software will be available only to groups that have Facility
accounts.
- **Authority to run at least one job in batch mode at any one time.**
* Interactive processes from remote logins that use more than 10 minutes
of CPU are considered batch jobs and must be reniced accordingly.
*Users may run one batch job on one Facility computer at priority 30--that's
+10 from interactive: the command is ">renice 10 PID" (where PID
is the ID no. of the process, which can be found by typing: >psinfo)
*Users may run additional jobs, one to a computer, at priority 40 (that's+20
from interactive) if no batch jobs are currently running on that computer.
Policing of Facility CPU usage will be the mutual responsibility of
the user community. Use the commands "top", and "psinfo." Offending
users or research groups should be brought to the attention of the Facility
Manager.
- **Access to a HP Color LaserJet printer.**
Files can be printed from SGI's by typing:
lp -dclaser filename
For the black and white printer:
lp -dbwlaser filename
Text files can be printed by typing:
> lptops filename | lpr
Users should record their printer usage on the clipboard by the printer.
Currently there is no recharge. Facility users can also print from Macintoshes
by going to the chooser, choosing LaserWriter 8 driver, and the 'Modeling
Facility Color Laser' printer in zone 'model'. If you need the updated
printer driver, ask the facility manager.
*Printing of black and colored backgrounds uses huge amounts of toner
and should be avoided when not absolutely neccessary.
- **Access to 300 MB of hard disk storage space per user account**
(Subject to change) Overages are OK for a short time; disk write access
is automatically denied for overages that persist over a week. If you
need more disk space, use the scratch directory in your home directory.
This scratch directory is actually a link to a scratch volume on each
of the model computers.
- **Access to up-to-date manuals for the software maintained by the
Facility** and information concerning where these manuals can be purchased
should you wish copies for your own group. Manuals can be checked out
for 2 hours. Some duplicate manuals are available-- these can be checked
out overnight. Removal of manuals from the Facility without checking
out may result in cancellation of the user's account.
- **Access to a HP ScanJet 4 color scanner for text and image scanning,
and a G3 Mac for image manipulation.**
- **Access to a camera system capable of photographic capture of screen
images from the Macintosh or Mastermodel.** Available cameras are 35
mm (for color prints, color transparencies, or black and white) plus
a Polaroid camera that can make prints or transparencies. Instructions
for use of the camera system is posted behind the camera device. Cameras
and cables are in the drawers of the desk under the Macintosh.
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