Arthur Roberts wrote:
Hi, David,
One question. I know that fftw3 can not be enabled
with mpi, while fftw2 can. Your email implies that
fftw3 without mpi can be used with gromacs that is mpi
enabled. I guess my question is. Can you use fftw3
without mpi with mpi enabled gromacs? I appreciate
your help.
yes, that's right. the parallellism is now handled by gromacs itself.
Best wishes,
Art
--- David van der Spoel <[EMAIL PROTECTED]> wrote:
Arthur Roberts wrote:
To Whom It May Concern:
I have checked the archives, but I have not found
a
good solution for the following problem:
When I try to compile Gromacs 3.3.1, I get
complaints
from the compiler that I have undefined symbols.
The
symbols are present in the libraries, so I don't
know
why ld can not seem to find them. I checked the
libraries with the following command.
nm library.a | grep undefined_symbol
the missing symbols are from FFTW2.
First you'll get slightly better performance from
FFTW3
Second it may be necessary to link in the mpi
version of the FFTW libs
as well, check which libs are in the fftw/lib
directory
Third, with FFTW3 you only have one library to link
to, which may make
it slightly simpler
Fourth, it seems that configure for gromacs doesn't
add a -lfftw to the
link command line, but instead puts the library
itself on the command
line, which is strange.
Perhaps, there is a flag that I need to see on the
LD
command or something. There is a detailed
description
of the problem at:
http://cetus.mchem.washington.edu/pub/supercomputer/Gromacs-compiling-problems.html
I appreciate input that any you could give.
Perhaps,
you know someone that has installed Gromacs on a
computer system that runs AIX 5.2.
Appreciate your help...
Best wishes,
Art Roberts
Department of Medicinal Chemistry
University of Washington
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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
[EMAIL PROTECTED] [EMAIL PROTECTED]
http://folding.bmc.uu.se
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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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
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