apoa1 slow Phase 1

From: Jan Fredin (jfredin_at_sgi.com)
Date: Thu Aug 15 2013 - 16:25:11 CDT

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Hi,

I am working with a customer using an SGI shared memory UV machine and an SGI MPT build of NAMD following the MPI build method. They are seeing the standard 500 step apoa1 test run with slow WallClock time but the seconds/step is basically correct. Can you tell me what contributes to the Startup phase 1 part of the computation and what might be causing the excess time usage there?

Customer site: Info: Finished startup at 194.537 s, 82.7031 MB of memory in use
Standard SGI: Info: Finished startup at 1.56274 s, 82.7031 MB of memory in use

Customer site: Info: Startup phase 1 took 186.643 s, 64.5078 MB of memory in use
Standard SGI: Info: Startup phase 1 took 0.175269 s, 64.5078 MB of memory in use

Customer site: TIMING: 500 CPU: 25.7678, 0.0468977/step Wall: 25.7678, 0.0468977/step, 0 hours remaining, 82.703125 MB of memory in use.
Standard SGI: TIMING: 500 CPU: 25.8591, 0.0466062/step Wall: 25.8591, 0.0466062/step, 0 hours remaining, 82.703125 MB of memory in use.

Thanks,
Jan

-- 
Dr. Jan Fredin 
SGI, Member Technical Staff - Technical Lead 
Austin, TX 
512-331-2860 
jfredin_at_sgi.com 

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