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

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 26 10:05:05 CEST 2006

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 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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