[gmx-users] parallel GROMACS question: more the nodes, slower Gromacs ... :-(

[Luca Mollica]

Dear all,

we are installing parallel GROMACS (double precision) on an IBM ppc64 
machine (28 64bit double processor), but we are experiencing some 
troubles with the test MD runs themselves (5 ps, by now).

We have followed the instructions posted on the GROMACS website by Choon 
Peng (http://www.gromacs.org/documentation/howtos/mpich_howto.html), and 
the compilation and installation were both fine after some additional 
set up optimized for our machine.

After the complete installation (MPICH, FFTW and GMX), a standard mdp 
file was used and compiled with grompp for a single processor in order 
to test the goodness of installation, and a 5ps simulation of a 300 
residues protein in explicit water was ended after ~200 s .

When we had tried to set up the simulation for many nodes (4, 12 and 24 
for testing), we had success compiling mdp file with -shuffle and -sort 
options. Everything was fine and all the nodes were recognised and log 
files written.
[Please note that the simulation is started from a machine that works as 
a node itself]
But, unfortunately, there was no way to get an increase in calculation 
speed with mdrun (specifing the complete path of mdrun) and activating 
MPI in the same line. We had even the impression that the calculation 
time was becoming ... longer as more nodes were added for calculation !!

Do you have any suggestion about this big problem ?? Or , better: do you 
think that the problem lies in the GMX installation, in the FFTW 
settings or in the MPI set up ?

Thanks in advance

Luca









..............................................................................................

Luca Mollica
Dulbecco Telethon Institute (Biomolecular NMR Lab)

DIBIT-HSR,Via Olgettina 58, 1B4
20132 Milano (Italy)

Tel: 0039-02-26434824(Office)/26433497(Lab)
Fax: 0039-02-26434153
E-mail: mollica.luca#hsr.it
	luca_mollica#virgilio.it

"There is something to be learned from a rainstorm. When meeting
with a sudden shower, you try not to get wet and run quickly along
the road. By doing such things as passing under the eaves of houses
one still gets wet. When you are resolved from the beginning,
you will not be perplexed, though you will get the same soaking.
This understanding extends to all things."

- Hagakure -

..............................................................................................