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

[David van der Spoel]

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 <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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-- 
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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