$ mpif90 -show
xlf90 -I/users/yf4/UTILS/OPENMPI/1.4.3/include
-I/users/yf4/UTILS/OPENMPI/1.4.3/lib
-L/users/yf4/UTILS/OPENMPI/1.4.3/lib -lmpi_f90 -lmpi_f77 -lmpi
-lopen-rte -lopen-pal -lrdmacm -libverbs -ltorque -lnuma -ldl
-Wl,--export-dynamic -lnsl -lutil -lpthread
$
I changed LOADCC and LOADLIB but got the same error. I will try to
recompile OpenMPI and NetCDF again.
Thanks,
Yubo
On Mon, Mar 26, 2012 at 2:51 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, 2012-03-26 at 13:44 -0500, Yubo Fan wrote:
>
>> ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
>> ../lib/nxtsec.o ../lib/sys.a ../netcdf/lib/libnetcdf.a
>> -L/users/yf4/UTILS/OPENMPI/1.4.3/lib -lmpi_f90 -lmpi_f77 -lmpi
>> -lopen-rte -lopen-pal -libverbs -ltorque -lnuma -ldl
>> -Wl,--export-dynamic -lnsl -lutil -lpthread
>> /usr/bin/ld: cannot find -lrdmacm
>> make: *** [sander.MPI] Error 1
>
> One thing that confuses me here is that I don't see where -lrdmacm is
> actually linked in from anywhere (that is, it must be hidden somewhere).
> The problem is that the linker can't find the librdmacm.so or
> librdmacm.a files. Are these files anywhere on your system? If so,
> where?
>
> To help, what is the output of:
>
> mpif90 -show
>
>> $(AMBERBUILDFLAGS)
>> LOADCC= xlc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
>
> Try changing this line to:
>
> LOADCC= /users/yf4/UTILS/OPENMPI/1.4.3/bin/mpicc $(LOCALFLAGS)
> $(AMBERBUILDFLAGS)
>
>> LOADLIB= -L/users/yf4/UTILS/OPENMPI/1.4.3/lib -lmpi_f90 -lmpi_f77
>> -lmpi -lopen-rte -lopen-pal -lrdmacm -libverbs -ltorque -lnuma -ldl
>> -Wl,--export-dynamic -lnsl -lutil -lpthread
>
> Try changing this line to:
>
> LOADLIB= -Wl,--export-dynamic -lnsl -lutil -lpthread
>
> The MPI compiler wrapper (mpif90) should pull in the actual MPI
> libraries and include headers without having to specify them here.
>
>
>> #NETCDF=/users/yf4/APPS/AMBER10/NETCDF/include/netcdf.mod
>> #NETCDFLIB=/users/yf4/APPS/AMBER10/NETCDF/lib/libnetcdf.a
>
> Yikes! Where did this come from?? I thought you said you were
> compiling Amber 9 (and indeed, other references in your message indicate
> you're working with AMBER9) -- but these NetCDF variables appear to
> point to an Amber 10 installation. While I realize these lines are
> commented out, it makes me suspect that you took many non-standard steps
> when you attempted to configure and build Amber 9...
>
>
>> xlf and xlc has been loaded and OpenMPI/NetCDF have been precompiled correctly.
>
> Are you sure? One thing you could try is to download AmberTools 1.5 and
> use the "configure_openmpi" or "configure_mpich2" scripts in there to
> make sure you build a compatible MPI, and use that to build Amber 9.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Mar 26 2012 - 14:00:02 PDT
