December
Cluster News:
- Parallel G03 with Linda is here! As one may recall, we announced in the month of November the intensive efforts made at the Chemistry Computer Center to configure and build parallel computing capabilities of several major chemistry software packages, including Gaussian 03 with Linda and parallel Jaguar. We now have successfully built and been able to run parallel G03 with Linda! Preliminary testings show significant improvements (in terms of CPU time). Further testing and implementation of scheduling scripts are underway, in order to port the program to a couple of new clusters for production work in the Spring 2005.
- Parallel Jaguar is also a success! Preliminary tests also show that we have successfully built and are now able to run parallel Jaguar using Message Passing Interface (MPI). Ryan Nelson (Professor Clark Landis group) is currently porting this capability to his group's Beowulf cluster for production work. How sweet it is!
Personnel Changes:
- Baby on board! Since the end of November, Steve Barnet has become a first-time daddy of a beautiful baby daughter! Congratulations to Steve and his wife, Jodi!
November
Personnel Changes:
Departures:
- Paul McGuire has started a new position as an Associate Information Processing Consultant at the Physical Sciences Laboratory, UW-Madison at the beginning of 11/2004.
- Jesse Stroik has started a position as a Network Administrator at the Space Science and Engineer Center, UW-Madison.
Arrivals:
- Gavin Edwards and Jonathan Popper are the Center's new 'comphelp' students, who will help with troubleshooting computer-related problems.
- Kara Hartmann is our new technical writer who is currently working on expanding the Computer Center's web site, which is scheduled to be published in the near future.
Cluster News:
- The month of November marks a handful of significant ventures in research and development at the Computer Center. We are currently working on reconfiguration and testing of the two clusters Curie and Moore, in order to facilitate parallel computing capabilities of several major chemistry software packages, including Gaussian 03, Jaguar, and MacroModel.
October
What's Arrived:
New Software:
- Network license of Mathematica 5.0! The Computer Center now has network license of Mathematica 5.0. More information can be found at Mathematica 5.0 network license.)
- Sybyl Virtual Screening Modules (FlexX, FlexX_E, FlexX_Pharm, CScore, and Concord) have been installed on the SGI computer (Remsen - Room 9311) and on those SGI owned by several research groups. These powerful modules have upgraded tremendously the computing resources of the Chemistry Department.
- Both the PC and Mac computers at the Center now have Mathematica 5.0 (Room 9311).
- Web site: The old sites have been redirected to this location.
- Gallery Spotlights: Several home-made pictures from Hieu Tran's archives of molecules are currently available in the Galleries. More are coming.
What's Coming:
- Top priority: Gaussian 03 and Linda will be of top interest for this month. Despite previous plans to have these two packages the main priority of the month of September, popular demands on the docking modules have won over. Now that those have been done, these two packages will certainly be of highest priority again!
- Parallel Computing: Jaguar 5.5 will be tested for parallel computing capabilities.
- More graphic software packages will be made available at the Center.
September
The Chemistry Computer Center Welcomes New Graduate Students!
What's Arrived:
New Software:
- Maestro 6.0, MacroModel 8.5, and Jaguar 5.5 are now available on the cluster Moore.
- UW-Madison now has site license for ChemDraw Std 8.0. (More information at ChemDraw Std UW-Madison site license.)
- Both the PC and Mac computers at the Center now have ChemDraw Std. The PC also has ChemSketch and ISIS/Draw (Room 9311).
- MathCad 11 is now available on the PC at the Center (Room 9311).
- VMD (Visual Molecular Dynamics) is now available on the graphics cluster (GFX) at the Center (Room 9311).
- CHARMM is now available on the graphic cluster (GFX) for students enrolled in Chem860 with Prof. Cui only. (Research groups have to buy their own licenses.)
- Sybyl Virtual Screening Modules: The long-waited FlexX, FlexX_E, FlexX_Pharm, CScore, and Concord have just arrived and are being configured for research computers of the department.
Computer Teaching Classroom: now has several new software products, including ChemDraw Std, ChemSketch, ISIS/Draw (for Windows) and Maestro 6.0, MacroModel 8.5, Jaguar 5.5, and Chemtool (for Linux). More information is available here.
Cluster News: Testing for Jaguar 5.5 and MacroModel 8.5 on the new cluster Moore is now done (for non-parallel jobs only).
What's Coming:
- Top priority: Gaussian 03 and Linda will be of top interest for this month.
- Sybyl Virtual Screening Modules: Configuring FlexX, FlexX_E, FlexX_Pharm, CScore, and Concord for research computers of the department.
- Parallel Computing: Jaguar 5.5 will be tested for parallel computing capabilities.
- More graphic software packages will be made available at the Center.
- Web site: Continuing to migrate and update information from the old web sites to the current one. The old sites will be redirected or removed.
August
New Software:
MacroModel 8.5 is now available on the graphics cluster (GFX) at the Center (Room 9311).
What's Coming:
- New Cluster: The new cluster (Moore) is scheduled to be put in use starting the Fall 2004 semester, with Jaguar 5.5 (Release 11) and MacroModel 8.5 currently being tested.
- Computer Teaching Classroom: Jaguar 5.5, MacroModel 8.5, ISIS/Draw, and ChemSketch are scheduled to be installed in the Computer Teaching Classroom (Room 1381).
Web site:
- Migrating and updating information from the old web sites to the current one. The old sites will be redirected or removed.
- The web site is given major updates both in contents and appearance to welcome new graduate students in the Fall semester 2004.
- Grand opening of the new web site of the Chemistry Computer Center
July
What's Arrived:
- New Software: MacroModel 8.5 has arrived and is being installed/configured on the departmental computers.
What's Coming:
- Information of major computing software packages available at the Chemistry Department
June
What's Arrived:
- June 2, 2004: New Chemistry Computer Center Web Site
What's Coming:
- More contents updated
- Tripos SYBYL demonstration: Tuesday 6/22/2004 - Poster (pdf)