Rules for Use of PFD Computing Facility

1. Shared Resource

   The SGI Onyx 3400, known as proteome, is a shared resource and this fact must be a guiding principle in your use of the system. There are only 4 graphical "heads" (display terminals) on this system. You must not leave yourself logged in when you leave the room for anything longer than a bathroom break (well, okay let's say 15 minutes). If you really need to do this, then you must leave a note indicating where you can be found otherwise your session is liable to be logged out, potentially losing the work that was in progress.

2. Limited Licenses

   Some software packages installed on this system have licenses that limit the number of users that can be using the software at any one time.

   License limits for InsightII and Sybyl

   InsightII module	Licenses	Sybyl module	Licenses
   Affinity	1	BioPolymer	2
   Binding_Site	1	CPU	1
   Biopolymer	2	CScore	1
   Charmm	1	Dynamics	2
   DeCipher	1	FlexX	1
   DelPhi	1	FlexX_drugscore	1
   Discover	1	FlexX_PVM	1
   Homology	1	MatchMaker	1
   InsightII	4	MOLCAD	2
   Modeler	2	ProTable	1
   QUANTA	1	SybylBasic	2
   		XDEV	2

   Given the limited number of licenses, it is improper for one user to use two terminals running the same software at the same time, especially if that person also does not follow the rules of the next paragraph.

3. Batch Job Submission

   Software such as "InsightII" and "Sybyl", with their graphical user interfaces, tend to promote the concept of running calculations in the foreground (i.e. you sit and wait for a result to appear in a matter of seconds or maybe a few minutes). Unfortunately, computing speed is not infinite and some calculations really will take anywhere from hours to days or even weeks. These jobs must be run in the background (i.e. batch mode). You definitely must not start a calculation that will run for hours and walk away from the terminal leaving yourself logged in. In InsightII look for the "Background_Job" pull-down menu item. In Sybyl, look for a button that you can select to "Run in Batch" or when setting up dynamics look for the "Netbatch" button. (More details will be given separately.)

4. Exceptions

   Exceptions to the rules 2 and 3 can be granted if you are working at non-peak hours and nobody else is using the system and your jobs will finish before anyone else is likely to use the system.