Uclus,
the usual style is to create the DataOut object every time you are writing
into a file, and then let the variable die at the end of the scope again,
rather than keeping it around for the next time you want to create output. You
might want to take a look at how time dependent programs do this, say step-26.
Of course, in that case you will want to write to a different file in each
iteration. Right now, your code snippet suggests that you don't actually ever
write into the f_output stream.
For your particular error, I don't know whether that is going to solve the
problem. It may be that you have no cells on a particular MPI process and that
that is what the error indicates -- that would be a bug. But I would first try
to address the issue mentioned above.
Best
W.
On 2/16/22 03:07, Uclus Heis wrote:
*** Caution: EXTERNAL Sender ***
Dear Timo,
Thank you for the comments.
I am doing now one file per iteration. However, when running with mpirun more
tha 1 MPI ranks I get an error in the writing function.
My code right now looks :
DataOut<dim> data_out;
data_out.attach_dof_handler(dof_handler);
for(int freq_iter=0 ... ) ///solver loop, /
{
... ///computes the solution per frequency/
string nname = "rb";
string nit = to_string(freq_iter);
string fitame =nname+nit;
string f_output("./solution-" + std::to_string(freq_iter) + ".h5");
data_out.add_data_vector(locally_relevant_solution, fitame);
data_out.build_patches();
DataOutBase::DataOutFilterFlags flags(true, true);
DataOutBase::DataOutFilter data_filter(flags);
data_out.write_filtered_data(data_filter);
data_out.write_hdf5_parallel(data_filter, "solution.h5", MPI_COMM_WORLD);
}
The error is the following:
/An error occurred in line <7811> of file
</zhome/32/9/115503/dealii-candi/tmp/unpack/deal.II-v9.3.1/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&,
ompi_communicator_t* const&) [with int dim = 2; int spacedim = 2; std::string
= std::__cxx11::basic_string<char>; MPI_Comm = ompi_communicator_t*]/
/The violated condition was: /
/patches.size() > 0/
/Additional information: /
/You are trying to write graphical data into a file, but no data is available
in the intermediate format that the DataOutBase functions require. /
/Did you forget to call a function such as DataOut::build_patches()?/
My intention is to save the whole domain, for each iteration when using a
parallel distributed implemeentation
Could you please help me or point me what am I doing wrong?
Thank you again
El martes, 15 de febrero de 2022 a las 23:45:39 UTC+1, Timo Heister escribió:
What we do typically in this situation is that we write one visualization
output file per iteration with a different filename. This is done in many
of the examples, especially for time dependent problems.
I don't think there is an easy way to append data to an existing file like
you suggested. This would overwrite existing data. With the hdf5 data, you
can store the mesh only once, assuming it doesn't change. See the
DataOutBase::DataOutFilterFlags.
On Tue, Feb 15, 2022, 15:02 Uclus Heis <[email protected]> wrote:
Thank you very much for the answer.
I need to evaluate a high number of frequencies, so in that case I
would need to have a large number of vectors to track the results,
which is not optimal in my case.
Is it any other way to do that? Would be possible to call
data_out.add_data_vector() and data_out.write_hdf5_parallel() in each
iteartion? Would that keep the previous written information?
Thank you
El martes, 15 de febrero de 2022 a las 19:43:02 UTC+1, Timo Heister
escribió:
The call to data_out.add_data_vector() does not copy the contents
of the vector but it just keeps track of it until the data is
actually written.
You will need to store your solutions in different vectors without
touching the old ones.
On Tue, Feb 15, 2022, 11:05 Uclus Heis <[email protected]> wrote:
Good afternoon,
I want to store my results in a hdf5 file using a distributed
implementation. I am computing different frequencies, so I
have a loop in my run() function where I solve for each
frequency. When for example computing 5 frequencies, I get 5
results with the same value in my hdf5 file, however, the
solution vector inside dealii is correct. Can I ask for help,
I do not know what am I doing wrong when exporting the
results, my code looks like the following:
DataOut<dim> data_out;
data_out.attach_dof_handler(dof_handler);
for(int freq_iter=0 ... ) ///solver loop, /
{
... ///computes the solution per frequency/
string nname = "rb";
string nit = to_string(freq_iter);
string fitame =nname+nit;
data_out.add_data_vector(locally_relevant_solution, fitame);
}
data_out.build_patches();
DataOutBase::DataOutFilterFlags flags(true, true);
DataOutBase::DataOutFilter data_filter(flags);
data_out.write_filtered_data(data_filter);
data_out.write_hdf5_parallel(data_filter, "solution.h5",
MPI_COMM_WORLD);
Thank you for you time.
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