[gmx-users] Re. Re: How to complie gromacs on sgi Altix450? (Martin Hoefling)

Martin Höfling mhoefli at gwdg.de
Mon Sep 14 14:35:51 CEST 2009

Am 14.09.2009 um 14:01 schrieb 石子枫:

> Thanks for your help.
> I compiled the fftw3 like this :
> export CPPFLAGS=-I/opt/mpich2/include
> export LDFLAGS=-L/opt/mpich2/lib
> ./configure --prefix=/opt/fftw3 --enable-float --enable-mpi
> make
> make install

OK, I don't think that an MPI version of the fftw library will give  
you any advantage. In fact - I am not even sure if it's possible to  
use it from gromacs, in particular when gromacs itself is compiled  
with mpi.

> for gromacs :
> export CPPFLAGS='-I/opt/mpich2/include -I/opt/fftw3/include'
> export LDFLAGS='-L/opt/mpich2/lib -L/opt/fftw3/lib'
> ./configure --prefix=/opt/gmx45 --enable-mpi --disable-float -- 
> enable-shared --program-suffix=_mpi
> make
> make install

2 things - if you compile it dynamically, also make sure that your  
libraries are in the search path of the runtime linker.  
LD_LIBRARY_PATH on linux I think, on Mac DYLD_LIBRARY_PATH. You have -- 
enable-float set for fftw configure and --disable-float for gromacs.  
The double precision fftw library is called fftw while the float  
version is called fftwf afair. Gromacs looks for the matching one,  
thus you need to compile fftw with the same precision (or with both)  
matching to gromacs.

> =================
> And mpt(A version of mpich2 for SGI ) and openmp have been  
> installed  in the system.
> But I don't kown how to use them,because I can't find the mpicc or  
> mpif90  in these '/bin' directory.

If this is a bigger machine, I suggest using the installed mpi  
libraries. You can get hints about the useage in the cluster /  
computation center documentation. Just as a general advice, I would  
not recommend using dynamic linking on the cluster, in particular when  
mpi is involved.

Best wishes

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