[gmx-users] gromacs memory usage

Alexey Shvetsov alexxyum at gmail.com
Thu Mar 4 08:55:11 CET 2010


Looks like your system simply runs out of memory. So power cycling nodes isnt 
needed. If your cluster runs linux then it already has OOM Killer that will 
kill processes that runs out of memory. Also having swap on nodes is a good 
idea even with huge amount  of memory.
Memory usage for mpi processes will strongly depend on mpi implentation 
because some of them are usualy caching slave process memory (like usualy do 

So can you provide info about youre cluster setup.
OS version (including kernel version)  uname -a 
mpi version  mpirun --version or mpiexec --version
also compiler version that was used for compiling gromacs

On Четверг 04 марта 2010 03:15:53 Amit Choubey wrote:
> Hi Roland,
> I was using 32 nodes with 8 cores, each with 16 Gb memory. The system was
> about 154 M particles. This should be feasible according to the numbers.
> Assuming that it takes 50bytes per atoms and 1.76 KB per atom per core then
> Masternode -> (50*154 M + 8*1.06)bytes ~ 16GB (There is no leverage here)
> All other nodes 8*1.06 ~ 8.5 GB
> I am planning to try the same run on 64 nodes with 8 cores each again but
> not until i am a little more confident. The problem is if gromacs crashes
> due to memory it makes the nodes to hang and people have to recycle the
> power supply.
> Thank you,
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru
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