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

[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