Re: namd cvs memory leak?

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Thu Oct 22 2009 - 19:57:08 CDT

Dear axel:

Actually, what you said makes a lot of sense. This system is
undergoing a non-equilibrium process, and indeed becomes more dense.
Also, a closer look at the timing seems to show that it would plateau
after some time. So thank you very much for the clarification.

Best,
Bin

On Oct 22, 2009, at 5:24 PM, Axel Kohlmeyer wrote:

> 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.
>
> cheers,
> axel.
>
>>
>>
>> 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 http://www.ks.uiuc.edu/Research/namd/
>> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
>> 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 akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>

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