From chemistry-request@ccl.net Mon Mar 25 16:51:46 1991 Date: Mon, 25 Mar 91 16:21:52 EST From: G. Ravishanker To: mwitten@cerberus.chpc.utexas.edu Subject: chemistry benchmark query Status: R Hi We purchased three IBM RISC/6000 Powerstations last fall. Our primary research is in the area of molecular simulations, using Molecular Dynamics and Monte Carlo simulations. We also have another group doing electrostatic models for proteins. The time hog in all these are the molecular simulations. The molecules we study are DNA and protein and our systems range in size from 600 atoms (for vacuum simulations) to about 7000 (for aqueous solutions). We also run the MD simulations for about 200-300 picosecond range. Our experience so far has been extremely good. We use a program called WESDYN, which was derived from another MD program called GROMOS. Our typical benchmarks show that the speed we get is between 1/8 to 1/10th of the CRAY Y-MP time. Given that we have these boxes give 24 hrs of dedicated processor time, compared to getting 2-3 hrs of CRAY time a day, we are sort of breaking even in terms of throughput. We are able to run 10 picosecond of dynamics on a system of 6000 atoms in 24 hours (clock time). The machine is very easy to install. The service engineers are extremely helpful, though they are not fully knowledgeable. They try all sorts of channels to get the problems solved quickly. The OS is pretty stable and the on-line documentation called info-explorer takes a while to get used to, but is great. X-Windows works great for the most part. (It is only X11 Rev. 3 compliant) Silicon Graphics GL programs work great for the most part. The scheme of opening and resizing windows does not work exactly the way it does on Silicon Graphics machines, but most other operations work just fine. We have had Polygen Quanta, a molecular modeling program up and running on the IBM RISC for the past two months and are pretty happy with it. Overall, we are very pleased with the speed of the machine and its overall stability. We have had instances where the student runs the machine continuously for a week to 10 days. The only complaint we have is the lack of manuals. One needs to purchase it for a price. IBM wants everyone to use the info-explorer. This is fine when the machine is up and running. When one has only one machine and the machine goes down, it creates a big problem. The price is very attractive for the MFLOPS/MIPS ratio of the Powerstation 530. There are reasonable public domain software already available, such as TeX and emacs. Hope this is useful and if you need further info, please feel free to let me know. Ravi