[gmx-users] Replica Exchange MD on more than 64 processors

Sebastian Breuers breuerss at uni-koeln.de
Tue Feb 2 18:44:25 CET 2010

Dear list

I recently came up with a problem concerning a replica exchange simulation. The simulation is run 
with gromacs-mpi in Version 4.0.7 compiled with following flags
--enable-threads --enable-mpi --with-fft=mkl -enable-double,

intel compiler version 11.0
mvapich version 1.1.0
mkl version 10.1

The program is working fine in this cluster evironment consisting of 32 nodes with 8 processors and 
32GB each. I've already run several simulations using the MPI feature.

It seems that I stuck in a similar problem that was already announced on this list by bharat v. 
adkar in december 2009 without an eventual solution:


I am doing a replica exchange simulation on a simulation box with 5000 molecules (81 atoms each) and 
4 different temperatures. The simulation runs nicely with 64 processors (8 nodes) but stops with an 
error message on 128 processors (16 nodes).

Taking the following four points into account:

         1. every cluster node has at least 28GB memory in a usable way available
         2. the system I am working with should only use
            5000*81*900B=347.614MB (according to the FAQ)
         3. even if every replica (4) is run on the same node the memory usage
            should be less than 2GB
         4. the simulation works fine with 64 processors

it seems to me the following error

Program mdrun, VERSION 4.0.7
Source code file: smalloc.c, line: 179

Fatal error:
Not enough memory. Failed to realloc 790760 bytes for nlist->jjnr, nlist->jjnr=0xae70b7b0
(called from file ns.c, line 503)

has to be caused by another issue than missing memory.

I am wondering if there is anyone else who is still facing the same problem or has already found a 
solution for this issue.

Kind regards



Sebastian Breuers                    Tel: +49-221-470-4108
EMail: breuerss at uni-koeln.de

Universität zu Köln                  University of Cologne
Department für Chemie                Department Chemistry
Organische Chemie                    university of Cologne

Greinstr. 4                          Greinstr. 4
D-50939 Köln                         D-50939 Cologne, Federal Rep. of Germany

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