>From my browsing of list archives I can only recall seeing advice that >hyperthreading cannot offer more Gromacs performance. For all I know this remains true if you're trying to use MPI to accelerate single calculations on hyperthreaded processors. However, I have discovered that it may be possible to increase throughput by running two independent jobs on a recent hyperthreaded processor, and I don't recall seeing this mentioned on the list before.
My typical job involves ~790 DNA atoms, a few Na+ ions, and 13000-14000 water molecules. I use Gromacs with the Amber force field ported by the Pande group. My simulation machines are 3.2 Ghz Pentium machines with 2 MB of cache (Pentium 640, I think) and 1 GB RAM. Typical performance for one of these systems running on an unloaded machine is 64.3 hours/ns, 1.4 gflop/s. I accidentally started some pairs of simulations on some of these machines this week and discovered that the performance of each job was *not* cut in half. With two systems running simultaneously, each shows performance of about 98.8 hours/ns, 908 mflop/s. Running two of these jobs on each machine thus appears to increase throughput by about 30%. If like me you run many independent calculations, throughput is more important than turnaround, and you have hyperthreaded machines but have not previously tried to take advantage of them, it may be worth testing. I suppose this issue may have been covered on the mailing list before, but all I ever remember seeing were advisements that hyperthreaded processors won't help performance, or even advice to disable hyperthreading in the BIOS. A brief web search indicates that some [EMAIL PROTECTED] participants have discovered comparable throughput advantages to running two client instances on hyperthreaded processors. Matt Ernst Washington State University _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
