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Upgrade write_vtu_in_parallel based on mpi large IO update #13673

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May 30, 2022
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Upgrade write_vtu_in_parallel based on mpi large IO update #13673

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67 changes: 49 additions & 18 deletions source/base/data_out_base.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
#include <deal.II/base/data_out_base.h>
#include <deal.II/base/memory_consumption.h>
#include <deal.II/base/mpi.h>
#include <deal.II/base/mpi_large_count.h>
#include <deal.II/base/parameter_handler.h>
#include <deal.II/base/thread_management.h>
#include <deal.II/base/utilities.h>
Expand Down Expand Up @@ -7673,6 +7674,7 @@ DataOutInterface<dim, spacedim>::write_svg(std::ostream &out) const
out);
}


template <int dim, int spacedim>
void
DataOutInterface<dim, spacedim>::write_vtu_in_parallel(
Expand All @@ -7688,8 +7690,8 @@ DataOutInterface<dim, spacedim>::write_vtu_in_parallel(
write_vtu(f);
#else

const int myrank = Utilities::MPI::this_mpi_process(comm);

const unsigned int myrank = Utilities::MPI::this_mpi_process(comm);
const unsigned int n_ranks = Utilities::MPI::n_mpi_processes(comm);
MPI_Info info;
int ierr = MPI_Info_create(&info);
AssertThrowMPI(ierr);
Expand All @@ -7707,21 +7709,24 @@ DataOutInterface<dim, spacedim>::write_vtu_in_parallel(
ierr = MPI_Info_free(&info);
AssertThrowMPI(ierr);

// Define header size so we can broadcast later.
unsigned int header_size;
std::uint64_t footer_offset;

// write header
if (myrank == 0)
{
std::stringstream ss;
DataOutBase::write_vtu_header(ss, vtk_flags);
header_size = ss.str().size();
// Write the header on rank 0 and automatically move the
// shared file pointer to the location after header;
ierr = MPI_File_write_shared(
fh, ss.str().c_str(), header_size, MPI_CHAR, MPI_STATUS_IGNORE);
// Write the header on rank 0 at the starting of a file, i.e., offset 0.
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Suggested change
// Write the header on rank 0 at the starting of a file, i.e., offset 0.
// Write the header on rank 0 at the start of a file, i.e., offset 0.

ierr = Utilities::MPI::LargeCount::MPI_File_write_at_c(
fh, 0, ss.str().c_str(), header_size, MPI_CHAR, MPI_STATUS_IGNORE);
AssertThrowMPI(ierr);
}

ierr = MPI_Bcast(&header_size, 1, MPI_UNSIGNED, 0, comm);
AssertThrowMPI(ierr);
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{
const auto &patches = get_patches();
Expand All @@ -7741,21 +7746,47 @@ DataOutInterface<dim, spacedim>::write_vtu_in_parallel(
vtk_flags,
ss);

ierr = MPI_File_write_ordered(
fh, ss.str().c_str(), ss.str().size(), MPI_CHAR, MPI_STATUS_IGNORE);
// using prefix sum to find specific offset to write at.
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// using prefix sum to find specific offset to write at.
// Use prefix sum to find specific offset to write at.

const std::uint64_t size_on_proc = ss.str().size();
std::uint64_t prefix_sum = 0;
ierr =
MPI_Exscan(&size_on_proc, &prefix_sum, 1, MPI_UINT64_T, MPI_SUM, comm);
AssertThrowMPI(ierr);

// Locate specific offset for each processor.
const MPI_Offset offset = static_cast<MPI_Offset>(header_size) + prefix_sum;

ierr =
Utilities::MPI::LargeCount::MPI_File_write_at_all_c(fh,
offset,
ss.str().c_str(),
ss.str().size(),
MPI_CHAR,
MPI_STATUS_IGNORE);
AssertThrowMPI(ierr);

if (myrank == n_ranks - 1)
{
// Locating Footer with offset on last rank.
footer_offset = size_on_proc + offset;

std::stringstream ss;
DataOutBase::write_vtu_footer(ss);
const unsigned int footer_size = ss.str().size();

// Writing Footer.
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// Writing Footer.
// Writing footer:

ierr =
Utilities::MPI::LargeCount::MPI_File_write_at_c(fh,
footer_offset,
ss.str().c_str(),
footer_size,
MPI_CHAR,
MPI_STATUS_IGNORE);
AssertThrowMPI(ierr);
}
}

// write footer
if (myrank == 0)
{
std::stringstream ss;
DataOutBase::write_vtu_footer(ss);
unsigned int footer_size = ss.str().size();
ierr = MPI_File_write_shared(
fh, ss.str().c_str(), footer_size, MPI_CHAR, MPI_STATUS_IGNORE);
AssertThrowMPI(ierr);
}

ierr = MPI_File_close(&fh);
AssertThrowMPI(ierr);
#endif
Expand Down