Re: Memory leak and crash before first step

From: Pedro Gonnet (
Date: Tue Jul 05 2011 - 08:25:34 CDT

Hi again,

Just thought I'd re-send this as I haven't received and replies yet and
I still haven't been able to solve the problem myself.

Please do let me know if you have a fix/workaround.


> 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

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