From: Pedro Gonnet (gonnet_at_maths.ox.ac.uk)
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?
 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
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
# Set the temperature
# langevin on
# langevinTemp 300
# langevinDamping 0.1
# tCouple on
# tCoupleTemp 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
# PME params
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:30 CST