> testing [C++ / fortran] cross-compile with MPI libs
> Error! Could not link C++ mpi code using mpi fortran linker:
> "mpif90 -lstdc++ -lmpi_cxx"
> [C++ / fortran / MPI] cross-linking is needed for cuda_parallel and EMIL
> builds.
> Try: "mpif90 -show"
> Configure failed due to the errors above!
>
> own.arrakis ~/Documents/simulations/restart_holo $ mpif90 -show
> gfortran -I/usr/lib/openmpi/include -pthread -I/usr/lib/openmpi/lib
> -L/usr/lib/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal
-ldl
> -Wl,--export-dynamic -lnsl -lutil -lm -ldl
>
> What should be done here?
>>Install a working MPI.
Or try commenting out the check in AmberTools/src/configure2
"
echo "[C++ / fortran / MPI] cross-linking is needed for cuda_parallel
and EMIL builds."
echo "Try: \"mpif90 -show\""
this line-----> exit 1
fi
"
and hope that the functionality which you need will then still compile OK.
Not ideal, I know, but if you are building for execution on your local
machine then CUDA_PARALLEL and EMIL are probably not going to be used
anyway these are heavy-duty crunching utilities that would normally be on a
cluster.
Josh
On 1 May 2014 15:15, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, 2014-05-01 at 13:05 +0400, James Starlight wrote:
> > Jason,
> >
> > mpirun -np 4 MMPBSA.py.MPI
> > resulted in
> > mpirun was unable to launch the specified application as it could not
> find
> > an executable:
> >
> > Executable: MMPBSA.py.MPI
>
> Then you do not have AmberTools installed in parallel.
>
> >
> > Previously I faced with the problems of compilation of amber using
> > ./configure -mpi
> >
> > resulted in
> > testing [C++ / fortran] cross-compile with MPI libs
> > Error! Could not link C++ mpi code using mpi fortran linker:
> > "mpif90 -lstdc++ -lmpi_cxx"
> > [C++ / fortran / MPI] cross-linking is needed for cuda_parallel and EMIL
> > builds.
> > Try: "mpif90 -show"
> > Configure failed due to the errors above!
> >
> > own.arrakis ~/Documents/simulations/restart_holo $ mpif90 -show
> > gfortran -I/usr/lib/openmpi/include -pthread -I/usr/lib/openmpi/lib
> > -L/usr/lib/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal
> -ldl
> > -Wl,--export-dynamic -lnsl -lutil -lm -ldl
> >
> > What should be done here?
>
> Install a working MPI. The configure_openmpi and configure_mpich
> scripts can help. Getting a working MPI can be tricky and requires a
> bit of Linux savvy to get your environment set up correctly, however.
> If you can't install one from your package manager or get one working
> yourself, I suggest trying to find an experienced Linux user near you to
> help.
>
> Or, of course, just run in serial.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri May 02 2014 - 00:00:02 PDT
