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.ne...@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
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