[gmx-users] Gromacs on Pathscale/Infiniband?

[David van der Spoel]

Mark Abraham wrote:
> Susan Chacko wrote:
>> Hi all,
>>
>> We have a bunch of Opterons connected with Infiniband. I'm trying to  
>> get Gromacs compiled for these nodes. I successfully built FFTW  
>> 3.1.2, but my Gromacs 3.3.1 config goes about halfway and then fails  
>> with
>>
>> checking size of int... configure: error: cannot compute sizeof  
>> (int), 77
>>
>> These are the flags I'm using:
>> ./configure --with-fft=fftw3 --enable-float --prefix=/usr/local/src/ 
>> gromacs/gromacs-ib --enable-mpi
>>
>> Any suggestions? Has anyone else successfully built/run Gromacs with  
>> Pathscale/IB?
> 
> I don't have anything hardware-specific to say, but you do need to build 
> a float-enabled fftw. You can get more insight into the problem from the 
> last few hundred lines of config.log.
> 
In addition you should probably disable fortran everywhere. Pathscale 
does not improve the performance of gromacs (when last tested). So try 
it with gcc first.

-- 
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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