[gmx-users] Compiling with MPICH

David spoel at xray.bmc.uu.se
Sun Sep 26 22:35:25 CEST 2004

On Sun, 2004-09-26 at 17:50, Amadeu Sum wrote:
> I am having some problems compiling Gromacs with MPICH. When I run
> configure, it stops at:
> checking whether the MPI cc command works... configure: error: Cannot
> compile and link MPI code with mpicc
> I have read previous posting with similar problem, but I believe I
> have been setting the correct path and variables as suggested. Here is
> how I am running configure:
> > PATH=$PATH:/usr/local/mpich/bin CPPFLAGS="-I/usr/local/fftw-mpi/include -I/usr/local/mpich/include -I/usr/local/gm/include" LDFLAGS="-L/usr/local/fftw-mpi/lib -L/usr/local/mpich/lib -L/usr/local/gm/lib" LIBS="-lmpich -lgm -lm -static"  ./configure --prefix=/usr/local/gromacs_mpi --disable-float --enable-mpi --enable-all-static --without-x --without-xml
Add -lpthread to your LIBS variable.

> I have also tried to export those variables instead of specifying as
> show above and I still get the same problem. I also tried not
> specifying the path to mpicc, but instead use MPICC=cc, and that got
> me to the same place too.
> If I look at the config.log file, I see:
> configure:3422: mpicc -o conftest -g -O2 -I/usr/local/fftw-mpi/include -I/usr/lo
> cal/mpich/include -I/usr/local/gm/include -L/usr/local/fftw-mpi/lib -L/usr/local
> /mpich/lib -L/usr/local/gm/lib conftest.c -lmpich -lgm -lm -static >&5
> /usr/local/mpich/lib/libmpich.a(gmpi_malloc.o)(.text+0x46): In function `malloc_
> atfork':
> : undefined reference to `pthread_self'
> /usr/local/mpich/lib/libmpich.a(gmpi_malloc.o)(.text+0xa9): In function `malloc_
> atfork':
> (** and a bunch more of similar undefined references **)
> Can anyone give me some clues to what may be the problem?
> I am doing this in a P4 machine with RH9 and the GNU compiler.
> Thanks in advance,
>             --Amadeu
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
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://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list