[gmx-users] Problems Installing Gromacs 3.3.1 on AIX 5.2

[Arthur Roberts]

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.

Best wishes,
Art

--- David van der Spoel <spoel at xray.bmc.uu.se> 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
> spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://folding.bmc.uu.se
>
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