[Openmd-users] OpenMD stuntDoubles and visualizing the result

[Dan Gezelter]

Dear Kasun,

  These errors all refer with the parallel (MPI) implementation of these routines.  It sounds like cmake was able to find the MPI libraries, but built and linked the code using a compiler that wasn't aware of MPI.  One of the ways to fix this is to specify the compiler directly.  If your MPI compiler is mpicxx, then you can set the CXX environment variable to force cmake to use that compiler:

cd build
export CXX=mpicxx
cmake ../path-to-openmd-directory
make

This assumes you are building in the "build" directory, and that the OpenMD directory is in ../path-to-openmd-directory

This should force cmake to rebuild the project using your specified MPI-aware compiler.

Best regards,

 --Dan Gezelter




> [ 96%] Built target openmd_parallel
> Linking CXX executable bin/openmd_MPI
> 
> error massage is too long i took only a short part here
> 
> i_comm_world'
> /home/kasun/openmd-2.2/src/rnemd/RNEMD.cpp:1106: undefined reference to `ompi_mpi_op_sum'
> /home/kasun/openmd-2.2/src/rnemd/RNEMD.cpp:1106: undefined reference to `ompi_mpi_double'
> /home/kasun/openmd-2.2/src/rnemd/RNEMD.cpp:1106: undefined reference to `MPI_Allreduce'
> /home/kasun/openmd-2.2/src/rnemd/RNEMD.cpp:1108: undefined reference to `ompi_mpi_comm_world'
> /home/kasun/openmd-2.2/src/rnemd/RNEMD.cpp:1108: undefined reference to `ompi_mpi_op_sum'
> /home/kasun/openmd-2.2/src/rnemd/RNEMD.cpp:1108: undefined reference to `ompi_mpi_double'
> .
> .
> .
> .
> .
> 
> GradientNormValue(OpenMD::DynamicVector<double, std::allocator<double> >&)':
> /home/kasun/openmd-2.2/src/optimization/Problem.cpp:28: undefined reference to `ompi_mpi_comm_world'
> /home/kasun/openmd-2.2/src/optimization/Problem.cpp:28: undefined reference to `ompi_mpi_op_sum'
> /home/kasun/openmd-2.2/src/optimization/Problem.cpp:28: undefined reference to `ompi_mpi_double'
> /home/kasun/openmd-2.2/src/optimization/Problem.cpp:28: undefined reference to `MPI_Allreduce'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/openmd_MPI] Error 1
> make[1]: *** [CMakeFiles/openmd_MPI.dir/all] Error 2
> make: *** [all] Error 2




***********************************************
  J. Daniel Gezelter
  Associate Professor of Chemistry
  Department of Chemistry and Biochemistry
  251 Nieuwland Science Hall
  University of Notre Dame
  Notre Dame, IN 46556-5670

  phone:  +1 (574) 631-7595
  e-mail: gezelter at nd.edu
  web:    http://www.nd.edu/~gezelter
************************************************