From: Pengfei Jia Date: Thu, 5 May 2022 00:15:23 +0000 (-0400) Subject: Upgrade write_vtu_in_parallel based on mpi large IO update X-Git-Tag: v9.4.0-rc1~117^2 X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=44bdb8e0dfc6d15b02ecaf027cdfd80b0f9d3f7c;p=dealii.git Upgrade write_vtu_in_parallel based on mpi large IO update Updating author name fixing work update indent Remove the broadcast and fix some comment and fix author name updates updates! last fix fixing indent fixing unmatched int type fixing indent trying to fix the broadcast error Trying to fix broadcast error II adding _c to write_at functions fixing rank issue fixing footer_offset last fix on rank indent removing some unused line --- diff --git a/source/base/data_out_base.cc b/source/base/data_out_base.cc index ae7ba13fcb..5db3b1bcb6 100644 --- a/source/base/data_out_base.cc +++ b/source/base/data_out_base.cc @@ -34,6 +34,7 @@ #include #include #include +#include #include #include #include @@ -7673,6 +7674,7 @@ DataOutInterface::write_svg(std::ostream &out) const out); } + template void DataOutInterface::write_vtu_in_parallel( @@ -7688,8 +7690,8 @@ DataOutInterface::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); @@ -7707,7 +7709,9 @@ DataOutInterface::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) @@ -7715,13 +7719,14 @@ DataOutInterface::write_vtu_in_parallel( 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. + 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); { const auto &patches = get_patches(); @@ -7741,21 +7746,47 @@ DataOutInterface::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. + 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(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. + 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