AMBER Archive (2003)

Subject: AMBER: PMEMD Performance on IBM SP

From: David Skinner (dskinner_at_nersc.gov)
Date: Tue Dec 23 2003 - 14:00:45 CST

Hi,

The recent discussions about the parallel scaling of PMEMD led me to
finalizes some test timings done on our IBM SP. In particular there's a
comparison of PMEMD and NAMD for the JAC benchmark. Nearly ideal up to
32 tasks and reasonable speedups into 64 tasks. While the scalar
performance on this machine is far behind today's workstations, PMEMD
seems to make good use of the interconnect.

Here are the timings:

http://hpcf.nersc.gov/software/apps/chemistry/amber/seaborg_jac_t.gif
http://hpcf.nersc.gov/software/apps/chemistry/amber/seaborg_jac_s.gif

This is on POWER3 (375 Mhz) with Colony switch. Compiled using -O3
-qstrict under AIX 5.1 using xlf 8.1 and xlc 6.0.

-David

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