[gmx-users] Poor parallel performance in Ubuntu 8.04

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Wed Feb 4 21:15:09 CET 2009

Quoting Jussi Lehtola <jussi.lehtola at helsinki.fi>:

> On Wed, 2009-02-04 at 18:01 -0200, Alexandre Suman de Araujo wrote:
>> Quoting Jussi Lehtola <jussi.lehtola at helsinki.fi>:
>> > That's highly unlikely: it would be a severe performance bug, which
>> > would have been picked up by the kernel packager.
>> >
>> > How did you configure the parallel version? What MPI environment 
>> did you use?
>> First I used Ubuntu binary packages for Gromacs (3.3.2) and LAM-MPI. After I
>> compiled both with Intel C and Fortran 11.0 compilers.
>> In both cases (binary and compiled), the performed is basicaly the same.
>> In further tests I compiled the Gromacs 4.0 and, again, the performance
>> was the
>> same.
> Please keep the discussion on the list.

Sorry. It was not my intention to open a private contact with you.

> Try compiling against OpenMPI (or using the binary compiled against it).
> LAM has been deprecated for many years, and should not be used anymore.

Ok. I used LAM because it is recommended in GROMACS documentation, but 
I´ll try

> Also, is your system big enough to allow efficient scaling?

Yes. It scales at 100% in an OpenSuse box with equivalent hardware 

> --
> ------------------------------------------------------
> Jussi Lehtola, FM, Tohtorikoulutettava
> Fysiikan laitos, Helsingin Yliopisto
> jussi.lehtola at helsinki.fi, p. 191 50632
> ------------------------------------------------------
> Mr. Jussi Lehtola, M. Sc., Doctoral Student
> Department of Physics, University of Helsinki, Finland
> jussi.lehtola at helsinki.fi
> ------------------------------------------------------
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Best Regards

Alexandre Suman de Araujo
Instituto de Física de São Carlos
Universidade de São Paulo
São Carlos - Brasil

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