Trying to profile namd to look for memory leaks

From: Scott Atchley (
Date: Fri Jan 27 2006 - 10:33:04 CST

Hi all,

This is a follow on to "Re: NAMD memory problems on ASC's SGI Altix
machine" but not related to SGI. I am running namd2 (2.6) on dual
Opterons with 2 GB of memory. I have run namd over mpich-p4 (TCP),
mpich-gm and mpich-mx. In each case memory usage grows rapidly for
about 90 minutes then the rate of memory growth slows down. With all
three version, the initial rate of growth is about 45% in the 90
minute range. For mpich-p4 and mpich-gm, the rate then drops to about
4% over 3 hours. For mpich-mx, the rate drops down to 17% over 3 hours.

I would like to profile namd using mpich's MPE library but I am not
having any luck. We have added "-mpilog" to mpicc and mpiCC in conv- nm reports that the PMPI_ symbols are in namd2, but when I
run it, I do not get any logs. I can get logs from the example files
in mpich/share/examples using my mpicc and mpirun.

Can anyone give some suggestions for profiling, tracing, etc?



Scott Atchley
Myricom Inc.

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