Dear Wolfgang,
Thank you for the suggestions. I updated the code as you mentioned. I do
not fully understand what you mentioned about that I am not writing into
the f_output stream. Is data_out.write_hdf5_parallel() not writing the
data? However, I still have the error when running more than 1 MPI rank. If
it is a bug I can not do much about it.
At this point I do not care much if the output file is hdf5 or not. I just
need to export the raw data of the whole domain for each frequency using
parallel approach. Do you have any suggestion how to do that?
I tried also to save the local_relevant_solution vector into a FullMatrix
that stores each dof and frequency and then print it in the end, but the
data is wrong also for more than 1 MPI rank:
for(int freq_iter=0 ... ) *//solver loop, *
{
// solve...
testvec.operator=(locally_relevant_solution); // testvec is a vector of
size dof.
for ( int j= 0; j < dof_handler.n_dofs(); ++j)
testsol(freq_iter, j)+=testvec(j); // testsol is a FullMatrix of size
number_frequencies x dof
}
if(Utilities::MPI::this_mpi_process (mpi_communicator)==0){
testsol.print_formatted(mydomain,12,true,0,"0"); // my domain is ofstream
Is there anything wrong in this approach of exporting the results?
Thank you
El miércoles, 16 de febrero de 2022 a las 17:09:02 UTC+1, Wolfgang Bangerth
escribió:
>
> 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.
> >
> > --
> > The deal.II project is located at http://www.dealii.org/
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> ------------------------------------------------------------------------
> Wolfgang Bangerth email: [email protected]
> www: http://www.math.colostate.edu/~bangerth/
>
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