[gmx-users] Re: Problem compiling gromacs-4.0.5 against mvapich2-1.4rc1

[chris.neale at utoronto.ca]

Found it.

Jerry got the solution here:  
http://mail.cse.ohio-state.edu/pipermail/mvapich-discuss/2009-July/002403.html

Thanks Jerry,
Chris.

Quoting chris.neale at utoronto.ca:

> Hi Jerry,
>
> did you have any luck solving this? I have run into the same problem
> compiling gromacs-4.0.5 with MVAPICH2-1.4rc1 using the intel compiler.
> I was able to successfully compile gromacs-4.0.5 using openmpi-1.3.2
> and the intel compiler. In both cases, the MPI libraries were compiled
> using the intel compiler v11.0.081.
>
> make errors out with:
>
> ...
> mpicc -DHAVE_CONFIG_H -I. -I../../src  -I../../include
> -DGMXLIBDIR=\"/scratch/cneale/exe/intel/gromacs-4.0.5/exec/share/top\"
> -I/scratch/cneale/exe/intel/fftw-3.1.2/exec/include
> -I/scinet/gpc/mpi/mvapich2/1.4rc1-3378_intel-v11.0_ofed/include
> -I/scinet/gpc/mpi/mvapich2/1.4rc1-3378_intel-v11.0_ofed/lib
> -I/usr/local/include  -O3 -tpp7 -axW -ip -w -funroll-all-loops
> -std=gnu99 -MT grompp.o -MD -MP -MF .deps/grompp.Tpo -c -o grompp.o
> grompp.c
> grompp.c(983): (col. 5) remark: LOOP WAS VECTORIZED.
> mv -f .deps/grompp.Tpo .deps/grompp.Po
> /bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3 -tpp7 -axW -ip
> -w -funroll-all-loops -std=gnu99
> -L/scratch/cneale/exe/intel/fftw-3.1.2/exec/lib   -o grompp grompp.o
> libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la
> -lnsl -lfftw3f
> mpicc -O3 -tpp7 -axW -ip -w -funroll-all-loops -std=gnu99 -o grompp
> grompp.o  -L/scratch/cneale/exe/intel/fftw-3.1.2/exec/lib
> ./.libs/libgmxpreprocess_mpi.a ../mdlib/.libs/libmd_mpi.a
> /scratch/cneale/exe/intel/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a
> ../gmxlib/.libs/libgmx_mpi.a -lnsl
> /scratch/cneale/exe/intel/fftw-3.1.2/exec/lib/libfftw3f.a -lm
> /scinet/gpc/mpi/mvapich2/1.4rc1-3378_intel-v11.0_ofed/lib/libmpich.a(ibv_channel_manager.o):(.bss+0x18): multiple definition   
> of
> `debug'
> /scratch/cneale/exe/intel/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a(gmx_fatal.o):(.bss+0x530): first   
> defined
> here
> make[3]: *** [grompp] Error 1
> make[3]: Leaving directory
> `/scratch/cneale/exe/intel/gromacs-4.0.5/src/kernel'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/scratch/cneale/exe/intel/gromacs-4.0.5/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/scratch/cneale/exe/intel/gromacs-4.0.5/src'
> make: *** [all-recursive] Error 1
>
>
> could this 'debug' be the one int calls like this? I at first looked
> for a debug() function but didn't find any.
>
> $ grep debug src/gmxlib/*.c
> ...
> main.c:  if (debug) {
> main.c:    fprintf(debug,"This is simulation %d",cr->ms->sim);
> main.c:      fprintf(debug,", local number of nodes %d, local nodeid %d",
> main.c:    fprintf(debug,"\n\n");
> ...
>
> Thanks,
> Chris
>
> #####################################3
>
> -- original message --
>
> Hello all,
>
> I have built MVAPICH2-1.4rc1 with Infiniband support on a CentOS 5.3 box and
> am trying to build gromacs-4.0.5 with MPI support.
>
> make is failing with the following error message:
>
> mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
> -funroll-all-loops -std=gnu99 -o grompp grompp.o
> ./.libs/libgmxpreprocess_mpi.a -L/usr/lib64 ../mdlib/.libs/libmd_mpi.a
> /<...snip..>/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a
> ../gmxlib/.libs/libgmx_mpi.a -lxml2 -lnsl -lfftw3f -lm -lX11
>
> /usr/local/lib/libmpich.a(ibv_channel_manager.o):(.bss+0x10): multiple
> definition of `debug'
> <..snip..>/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a(gmx_fatal.o):(.bss+0x0):
> first defined here
> collect2: ld returned 1 exit status
> make[3]: *** [grompp] Error 1
>
> It looks like 'debug' is conflicting in both MVAPICH2 and in Gromacs.
>
> Any suggestions?
>
> Thanks,
>
> Jerry.
> Research Systems Administrator
> SBGrid
>
>
>