Output the solution to .h5 file (hdf5)
Judy Lee
For the step-3 hdf5 to output the solution data, I have an error message returned, like the following:
[ 66%] Built target step-3
[100%] Run step-3 with Debug configuration
Number of active cells: 1024
Number of degrees of freedom: 1089
DEAL:cg::Starting value 0.121094
DEAL:cg::Convergence step 48 value 5.33692e-13
terminate called after throwing an instance of 'dealii::StandardExceptions::ExcMessage'
what():
--------------------------------------------------------
An error occurred in line <7799> of file </home/debianlinux4dealii/Downloads/dealii-9.3.2/source/base/data_out_base.cc> in function
void dealii::DataOutBase::write_hdf5_parallel(const std::vector<dealii::DataOutBase::Patch<dim, spacedim> >&, const dealii::DataOutBase::DataOutFilter&, bool, const string&, const string&, const MPI_Comm&) [with int dim = 2; int spacedim = 2; std::string = std::__cxx11::basic_string<char>; MPI_Comm = int]
The violated condition was:
false
Additional information:
HDF5 support is disabled.
--------------------------------------------------------
make[3]: *** [CMakeFiles/run.dir/build.make:77: CMakeFiles/run] Aborted
make[2]: *** [CMakeFiles/Makefile2:237: CMakeFiles/run.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:244: CMakeFiles/run.dir/rule] Error 2
make: *** [Makefile:202: run] Error 2
My modified step-3.cc is attached. I added in the main function (Line 685-687), in the class step3 to declare *n_refinement_steps* (Line 100), in the function void step3::make_grid() (Line 164-165), and in the function void step3::output_results() (Line 606-610). Thank you very much.
Best regards,
Judy
Timo Heister
https://www.dealii.org/developer/readme.html#optional-software
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Timo Heister
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Timo Heister
install the library afterwards?
I am asking because the error message should only show up if you are
using deal.II without HDF5 support enabled.
On Wed, Sep 7, 2022 at 9:36 PM Judy Lee <reader....@gmail.com> wrote:
>
> Thank you, Dr. Heister.
>
> This is what I did to link hdf5 library to dealii-9.3.2 version:
>
> find usr -iname “*hdf5.h” returned /usr/include/hdf5/mpich/hdf5.h
>
> export CPATH="/usr/include/hdf5/mpich/"
>
> export CPATH="/Downloads/dealii-9.3.2/"
>
> cmake -DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=/usr/include/hdf5/mpich -DHDF5_LIBRARY=/usr/lib/x86_64-linux-gnu/libhdf5_mpich.so -DHDF5_HL_LIBRARY=/usr/lib/x86_64-linux-gnu/libhdf5_mpich_hl.so -DDEAL_II_WITH_MPI=ON ../
>
> I have the same error message returned. How to link hdf5 to dealii correctly?
> Thank you very much.
>
> Best regards,
>
> Judy
>