[gmx-users] Gromacs on Pathscale/Infiniband?

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 13 09:38:26 CEST 2006

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 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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