>
> > After that no more segmentation error and step-17 works on
> > 1 processor, but 'mpiexec -n 2 ./step-17' reports an error (link to this
> > at bottom).
>
> It appears as if both processors still think that they are processor zero
> since they both produce output, and they appear to both think that no
> other processor is around. But there is a second processor.
>
> I believe this is due to the fact that you download mpich when configuring
> and building petsc, but you don't pass the --with-mpi=1 switch. Does
> adding this switch help? Alternatively, does it make a difference if you
> configure deal.II using --enable-mpi?
>
Thank you for help. Passing --enable-mpi to deal.II configure solved the
problem. Now, step-17 works in parallel.
This time I stumbled on step-18. Again runtime problem. Printout at the
bottom.
Mate Kosor
m...@r12:/home/1/mate/software/deal.II.source/examples/step-18$ make
Makefile:171: Makefile.dep: No such file or directory
============================ Remaking Makefile.dep
==============debug========= step-18.cc
In file included from
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpi.h:1143,
from
/home/1/mate/software/deal.II.source/base/include/base/utilities.h:24,
from step-18.cc:21:
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:383:
warning: unused parameter 'oldtype'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:383:
warning: unused parameter 'keyval'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:383:
warning: unused parameter 'ex'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:383:
warning: unused parameter 'attr_in'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:383:
warning: unused parameter 'attr_out'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:385:
warning: unused parameter 'type'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:385:
warning: unused parameter 'keyval'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:385:
warning: unused parameter 'attr'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:385:
warning: unused parameter 'ex'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:387:
warning: unused parameter 'oldtype'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:387:
warning: unused parameter 'keyval'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:387:
warning: unused parameter 'ex'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1435:
warning: unused parameter 'oldcomm'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1435:
warning: unused parameter 'keyval'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1435:
warning: unused parameter 'ex'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1435:
warning: unused parameter 'attr_in'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1435:
warning: unused parameter 'attr_out'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1437:
warning: unused parameter 'comm'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1437:
warning: unused parameter 'keyval'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1437:
warning: unused parameter 'attr'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1437:
warning: unused parameter 'ex'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1439:
warning: unused parameter 'oldcomm'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1439:
warning: unused parameter 'keyval'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1439:
warning: unused parameter 'ex'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1869:
warning: unused parameter 'oldwin'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1869:
warning: unused parameter 'keyval'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1869:
warning: unused parameter 'ex'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1869:
warning: unused parameter 'attr_in'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1869:
warning: unused parameter 'attr_out'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1871:
warning: unused parameter 'win'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1871:
warning: unused parameter 'keyval'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1871:
warning: unused parameter 'attr'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1871:
warning: unused parameter 'ex'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1873:
warning: unused parameter 'oldwin'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1873:
warning: unused parameter 'keyval'
/home/1/mate/software/petsc-3.0.0-p11/linux-gnu-cxx-debug/include/mpicxx.h:1873:
warning: unused parameter 'ex'
In file included from
/home/1/mate/software/deal.II.source/lac/include/lac/petsc_parallel_sparse_matrix.h:20,
from step-18.cc:27:
/home/1/mate/software/deal.II.source/lac/include/lac/petsc_matrix_base.h:1078:
warning: type qualifiers ignored on function return type
In file included from step-18.cc:29:
/home/1/mate/software/deal.II.source/lac/include/lac/petsc_precondition.h:83:
warning: type qualifiers ignored on function return type
============================ Linking step-18
m...@r12:/home/1/mate/software/deal.II.source/examples/step-18$ mpiexec -n 2
./step-18
Timestep 1 at time 1
Cycle 0:
Number of active cells: 3712 (by partition: 1856+1856)
Number of degrees of freedom: 17226 (by partition: 8488+8738)
Assembling system... norm of rhs is 2.31518e+10
Solver converged in 133 iterations.
Updating quadrature point data...
Cycle 1:
--------------------------------------------------------
An error occurred in line <670> of file
</home/1/mate/software/deal.II.source/deal.II/include/grid/tria_objects.h>
in function
unsigned int&
dealii::internal::Triangulation::TriaObjects<G>::user_index(unsigned int)
[with G = dealii::internal::Triangulation::TriaObject<3>]
The violated condition was:
user_data_type == data_unknown || user_data_type == data_index
The name and call sequence of the exception was:
ExcPointerIndexClash()
Additional Information:
(none)
Stacktrace:
-----------
#0 /home/1/mate/software/deal.II.source/lib/libdeal_II_3d.g.so.6.2.1:
dealii::internal::Triangulation::TriaObjects<dealii::internal::Triangulation::TriaObject<3>
>::user_index(unsigned int)
#1 /home/1/mate/software/deal.II.source/lib/libdeal_II_3d.g.so.6.2.1:
dealii::TriaAccessor<3, 3, 3>::user_index() const
#2 /home/1/mate/software/deal.II.source/lib/libdeal_II_3d.g.so.6.2.1
[0x7ff002dbcf59]:
/home/1/mate/software/deal.II.source/lib/libdeal_II_3d.g.so.6.2.1
[0x7ff002dbcf59]
#3 /home/1/mate/software/deal.II.source/lib/libdeal_II_3d.g.so.6.2.1:
dealii::Triangulation<3, 3>::save_user_indices_hex(std::vector<unsigned int,
std::allocator<unsigned int> >&) const
#4 /home/1/mate/software/deal.II.source/lib/libdeal_II_3d.g.so.6.2.1:
dealii::Triangulation<3, 3>::save_user_indices(std::vector<unsigned int,
std::allocator<unsigned int> >&) const
#5 /home/1/mate/software/deal.II.source/lib/libdeal_II_3d.g.so.6.2.1: void
dealii::GridTools::get_face_connectivity_of_cells<3,
3>(dealii::Triangulation<3, 3> const&, dealii::SparsityPattern&)
#6 /home/1/mate/software/deal.II.source/lib/libdeal_II_3d.g.so.6.2.1: void
dealii::GridTools::partition_triangulation<3, 3>(unsigned int,
dealii::Triangulation<3, 3>&)
#7 ./step-18: QuasiStaticElasticity::TopLevel<3>::refine_initial_grid()
#8 ./step-18: QuasiStaticElasticity::TopLevel<3>::do_initial_timestep()
#9 ./step-18: QuasiStaticElasticity::TopLevel<3>::run()
#10 ./step-18: main
--------------------------------------------------------
[0]0:Return code = 0, signaled with Aborted
[0]1:Return code = 0, signaled with Interrupt
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