OK, just to answer the question: If you are running with petsc you should 
not call

dealii::Utilities::MPI::MPI_InitFinalize
mpi_initialization(argc, argv, dealii::numbers::invalid_unsigned_int);

since this will invoke threading if you start a number of mpi processes 
that is not equal the number of cores you use. Instead one should pass 
(when using generic linear algebra)

#ifdef USE_PETSC_LA
dealii::Utilities::MPI::MPI_InitFinalize
mpi_initialization(argc, argv, /* disable threading for petsc */ 1);
#else
dealii::Utilities::MPI::MPI_InitFinalize
mpi_initialization(argc, argv, dealii::numbers::invalid_unsigned_int);
#endif

I guess that was the bug.

Best,
Konrad

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