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
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Received on Thu May 01 2014 - 06:30:02 PDT
