Re: Memory leak and crash before first step

From: Pedro Gonnet (gonnet_at_maths.ox.ac.uk)
Date: Tue Jul 12 2011 - 15:00:45 CDT

Hi Erik,

The diff of the two input files would be pretty much the two files
themselves. They are outputs of a different simulation and hence no
molecules overlap.

I've rolled a .tar.gz of the input files and uploaded it to
http://people.maths.ox.ac.uk/gonnet/bulk.tar.gz. Can you check if you
can reproduce this or if it's something on my machines/installations?

Cheers, Pedro

On Sun, 2011-07-10 at 05:02 -0400, Erik Nordgren wrote:
> Pedro -- at a glance, not sure what the problem might be... but
> perhaps you could send us a "diff" type comparison of your NAMD input
> files for the smaller vs. the larger systems, and also a direct
> comparison of the output files from those two cases, in order to see
> exactly what changed.
>
> Also, when you say you "scaled up" your system, how exactly did you do
> this?
>
> -Erik
>
>
> On Fri, Jun 24, 2011 at 3:28 PM, Pedro Gonnet <gonnet_at_maths.ox.ac.uk>
> wrote:
>
> Hi,
>
> I'm new to NAMD and was trying to run some simulations of bulk
> TIP3P
> water. This worked just fine in a 8x8x8 nm cube, but when I
> scaled it up
> to 16x16x16 nm (387072 atoms), NAMD crashed as follows:
>
> Info: Startup phase 7 took 0.0791871 s, 203.889 MB of
> memory in use
> Info: Startup phase 8 took 0.00410999 s, 370.621 MB of
> memory in use
> Info: Finished startup at 7856.1 s, 370.621 MB of
> memory in use
>
> ------------- Processor 0 Exiting: Called CmiAbort
> ------------
> Reason: Could not malloc() 93454760 bytes--are we out
> of memory?
> Charm++ fatal error:
> Could not malloc() 93454760 bytes--are we out of
> memory?
> [0] Stack Traceback:
> [0:0] CmiOutOfMemory+0x3c [0x85d9a38]
>
> which is odd since I have 4 GB of RAM on my local machine and
> the 8x8x8
> nm simulation only required a few hundred MB. I tried running
> the
> simulation on a machine with 64 GB with the same result
> (although it
> took significantly longer to fill-up the memory).
>
> In both cases I could watch namd2 gobble-up the memory on
> "top" before
> it crashed.
>
> This happens both with NAMD 2.7 for Linux-x86 and NAMD 2.8 for
> Linux-x86_64-MPI, both on a single CPU (e.g. without mpirun).
>
> I have attached the configuration file. Since the .pdb
> and .psf files
> are rather large, I will only send them on request.
>
> Am I doing anything wrong or could this be a bug?
>
> Cheers,
> Pedro
>
>
>
>
>
> --
> C. Erik Nordgren, Ph.D.
> University of Pennsylvania

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