Allow CubeGenerator to use multiple MPI processes

[montrie]

Extended the CubeGenerator class to allow for using more than 1 MPI process.

Boundary condition 7 works as expected, however using boundary condition 6 leads to exponential growth in the elastic energy output when using more than 1 MPI process. This also happens with the NetcdfReader and meshes generated with the cubeGenerator located in preprocessing/meshing/cube_c/. I added a warning to the CubeGenerator class which warns the user of this issue when using at least 2 MPI processes and boundary condition 6.

[davschneller]

Hi, thanks for the PR! Would it be possible to upgrade to the current master branch? There may still be some file conflicts/file moves there.

[montrie]

I merged the upstream changes into the current master branch. After fixing the merge-related issues, I ran into the following error when I tried to compile SeisSol:

[ 97%] Building CXX object CMakeFiles/SeisSol-bin.dir/src/main.cpp.o
/dss/dsshome1/lxc0B/ga27koz2/apps/fork_SeisSol/src/main.cpp(100): error: namespace "MPI" has no member "mpi"
    MPI::mpi.init(argc, argv);
         ^

/dss/dsshome1/lxc0B/ga27koz2/apps/fork_SeisSol/src/main.cpp(101): error: namespace "MPI" has no member "mpi"
    const int rank = MPI::mpi.rank();
                          ^

/dss/dsshome1/lxc0B/ga27koz2/apps/fork_SeisSol/src/main.cpp(132): error: namespace "MPI" has no member "mpi"
      MPI::mpi.finalize();
           ^

compilation aborted for /dss/dsshome1/lxc0B/ga27koz2/apps/fork_SeisSol/src/main.cpp (code 2)
make[2]: *** [CMakeFiles/SeisSol-bin.dir/build.make:76: CMakeFiles/SeisSol-bin.dir/src/main.cpp.o] Error 2
make[1]: *** [CMakeFiles/Makefile2:146: CMakeFiles/SeisSol-bin.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 98%] Linking CXX static library libSeisSol-proxy-core.a
[ 98%] Built target SeisSol-proxy-core
make: *** [Makefile:136: all] Error 2

I fixed it locally by adding the seissol:: namespace to the calls to the MPI class above. Should I include these changes in this PR as well, or is this just an issue on my end?

[davschneller]

I merged the upstream changes into the current master branch. After fixing the merge-related issues, I ran into the following error when I tried to compile SeisSol:

[ 97%] Building CXX object CMakeFiles/SeisSol-bin.dir/src/main.cpp.o
/dss/dsshome1/lxc0B/ga27koz2/apps/fork_SeisSol/src/main.cpp(100): error: namespace "MPI" has no member "mpi"
    MPI::mpi.init(argc, argv);
         ^

/dss/dsshome1/lxc0B/ga27koz2/apps/fork_SeisSol/src/main.cpp(101): error: namespace "MPI" has no member "mpi"
    const int rank = MPI::mpi.rank();
                          ^

/dss/dsshome1/lxc0B/ga27koz2/apps/fork_SeisSol/src/main.cpp(132): error: namespace "MPI" has no member "mpi"
      MPI::mpi.finalize();
           ^

compilation aborted for /dss/dsshome1/lxc0B/ga27koz2/apps/fork_SeisSol/src/main.cpp (code 2)
make[2]: *** [CMakeFiles/SeisSol-bin.dir/build.make:76: CMakeFiles/SeisSol-bin.dir/src/main.cpp.o] Error 2
make[1]: *** [CMakeFiles/Makefile2:146: CMakeFiles/SeisSol-bin.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 98%] Linking CXX static library libSeisSol-proxy-core.a
[ 98%] Built target SeisSol-proxy-core
make: *** [Makefile:136: all] Error 2

I fixed it locally by adding the seissol:: namespace to the calls to the MPI class above. Should I include these changes in this PR as well, or is this just an issue on my end?

Hi, I'm gonna embed the namespace fixes also into #1112—if that's good for you. (it appeared now in other contexts as well, cf. #1113 ; I'll probably just namespace the main SeisSol class)

[davschneller]

Hi, thank you for your PR.
I've added some minor comments regarding the code.
Fixing boundary condition 6 may be a bit more involved in the end—so it's not required for this PR.

[montrie]

Thank you for the suggestions, let me know if I missed something!

[davschneller]

Ok, thanks for the changes! I've mirrored the branch to run it through the tests (we currently need to do that for external branches). And it passed.