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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

  1. 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.
  2. Manuals on the bookshelves of the Facility are not to leave the room unless they are checked out.
  3. Please bring no food or drink into the Facility. We don't want sticky coke or coffee spills on the tables, floors, or keyboards.
  4. 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.
  5. 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
  1. **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".
  2. **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.
  3. **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.
  4. **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.
  5. **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.
  6. **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.
  7. **Access to a HP ScanJet 4 color scanner for text and image scanning, and a G3 Mac for image manipulation.**
  8. **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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