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

[David]

On Mon, 2005-01-24 at 19:13 +0100, Luca Mollica wrote:
> 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 .
Scaling to many processors is not optimal. However we need more details
about the calculation:
- PME
- Communication hardware
- Processor speed
- Scaling numbers


> 
> 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 -
> 
> ..............................................................................................
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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