Re: namd cvs memory leak?

From: Axel Kohlmeyer (
Date: Thu Oct 22 2009 - 19:24:52 CDT

On Thu, 2009-10-22 at 16:12 -0700, BIN ZHANG wrote:
> Dear all:

dear bin,

> While using the NAMD CVS version, I found a memory leak problem. After
> 500,000 steps simulation, the memory usage goes from 76.781250 MB to
> 93.515625 MB. The relatively small amount of increase might not be a
> big deal. However, I do intend to run long simulations, and the
> clearly increasing trend would become a problem then.

have you looked at what your system does, particularly
does it get more dense? or more structured? even if
only in part?

this kind of memory increase can happen when neighbor lists
have to be grown. i don't know about NAMD, but it is quite
common to only increase those lists and never shrink them.
for a typical system this should level out during equilibration.


> Has anyone else noticed this also?
> Best,
> Bin
> Here is some detail info about the cluster I'm testing on:
> Info: NAMD 2.7b1 for Linux-amd64-MPI
> Info:
> Info: Please visit
> Info: and send feedback or bug reports to
> Info:
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 60000 for mpi-linux-amd64-icc-mpich
> Info: 1 NAMD 2.7b1 Linux-amd64-MPI 24 compute-3-13.local bingo
> Info: Running on 24 processors.
> Info: Charm++/Converse parallel runtime startup completed at 0.019257
> s
> Info: 62.3398 MB of memory in use based on /proc/self/stat
> Info: Configuration file is relax.namd
> TCL: Suspending until startup complete.

Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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