Memory leak and crash before first step

From: Pedro Gonnet (
Date: Fri Jun 24 2011 - 14:28:08 CDT


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?


# Physical characteristics of the system
structure flexible.psf
coordinates flexible.pdb
paraTypeCharmm on
parameters par_all22_prot.inp

# Set the temperature
temperature 300
# langevin on
# langevinTemp 300
# langevinDamping 0.1
# tCouple on
# tCoupleTemp 300
rescaleFreq 50
rescaleTemp 300

# Set some domain parameters
cellBasisVector1 160.0 0.0 0.0
cellBasisVector2 0.0 160.0 0.0
cellBasisVector3 0.0 0.0 160.0
cellOrigin 80.0 80.0 80.0

# Integration stuff
numsteps 1000
cutoff 10
pairlistdist 12.0
stepspercycle 10
switching on
switchdist 8
splitPatch hydrogen
timestep 2.0
rigidBonds water
exclude 1-3

# Output
outputname flexible_namd
binaryoutput no
outputEnergies 1
outputTiming 1

# PME params
PME off
PMEGridSizeX 64
PMEGridSizeY 64
PMEGridSizeZ 64

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:21 CST