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Add HDF5 input and output files to eigensolver miniapp #973

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merged 11 commits into from
Sep 13, 2023
Merged

Add HDF5 input and output files to eigensolver miniapp #973

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b20cefc
add HDF5 input and output files to eigensolver miniapp
RMeli Sep 7, 2023
3c4e156
Update miniapp/miniapp_eigensolver.cpp
RMeli Sep 7, 2023
d4c1c27
support I/O for distributed matrices too
RMeli Sep 7, 2023
52baa3b
Merge branch 'eig-hdf5' of https://github.com/RMeli/DLA-Future into e…
RMeli Sep 7, 2023
22563fb
cleanup
RMeli Sep 7, 2023
8505ef7
use filesystem::path
RMeli Sep 8, 2023
1d81e2e
format
RMeli Sep 8, 2023
92812e3
Update miniapp/miniapp_tridiag_solver.cpp
RMeli Sep 11, 2023
04b16bd
allow input dataset selection and add input to output
RMeli Sep 12, 2023
0823937
Merge branch 'eig-hdf5' of https://github.com/RMeli/DLA-Future into e…
RMeli Sep 12, 2023
6477f73
enable dataset name in tridiag solver too
RMeli Sep 12, 2023
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74 changes: 66 additions & 8 deletions miniapp/miniapp_eigensolver.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,10 @@
//

#include <cstdlib>
#include <filesystem>
#include <iostream>
#include <limits>
#include <string>

#include <pika/init.hpp>
#include <pika/program_options.hpp>
Expand All @@ -27,6 +29,7 @@
#include <dlaf/eigensolver/internal/get_band_size.h>
#include <dlaf/init.h>
#include <dlaf/matrix/copy.h>
#include <dlaf/matrix/hdf5.h>
#include <dlaf/matrix/matrix.h>
#include <dlaf/matrix/matrix_mirror.h>
#include <dlaf/miniapp/dispatch.h>
Expand All @@ -50,6 +53,10 @@ using dlaf::common::Ordering;
using dlaf::matrix::MatrixMirror;
using pika::this_thread::experimental::sync_wait;

#ifdef DLAF_WITH_HDF5
using dlaf::matrix::internal::FileHDF5;
#endif

/// Check results of the eigensolver
template <typename T>
void checkEigensolver(CommunicatorGrid comm_grid, blas::Uplo uplo, Matrix<const T, Device::CPU>& A,
Expand All @@ -60,12 +67,33 @@ struct Options
SizeType m;
SizeType mb;
blas::Uplo uplo;
#ifdef DLAF_WITH_HDF5
std::filesystem::path input_file;
std::string input_dataset;
std::filesystem::path output_file;
#endif

Options(const pika::program_options::variables_map& vm)
: MiniappOptions(vm), m(vm["matrix-size"].as<SizeType>()), mb(vm["block-size"].as<SizeType>()),
uplo(dlaf::miniapp::parseUplo(vm["uplo"].as<std::string>())) {
DLAF_ASSERT(m > 0, m);
DLAF_ASSERT(mb > 0, mb);

#ifdef DLAF_WITH_HDF5
if (vm.count("input-file") == 1) {
input_file = vm["input-file"].as<std::filesystem::path>();

if (!vm["matrix-size"].defaulted()) {
std::cerr << "Warning! "
"Specified matrix size will be ignored because an input file has been specified."
<< std::endl;
}
}
input_dataset = vm["input-dataset"].as<std::string>();
if (vm.count("output-file") == 1) {
output_file = vm["output-file"].as<std::filesystem::path>();
}
#endif
}

Options(Options&&) = default;
Expand All @@ -87,19 +115,28 @@ struct EigensolverMiniapp {
Communicator world(MPI_COMM_WORLD);
CommunicatorGrid comm_grid(world, opts.grid_rows, opts.grid_cols, Ordering::ColumnMajor);

// Allocate memory for the matrix
GlobalElementSize matrix_size(opts.m, opts.m);
TileElementSize block_size(opts.mb, opts.mb);

ConstHostMatrixType matrix_ref = [matrix_size, block_size, comm_grid]() {
ConstHostMatrixType matrix_ref = [comm_grid, &opts]() {
TileElementSize block_size(opts.mb, opts.mb);
#ifdef DLAF_WITH_HDF5
if (!opts.input_file.empty()) {
auto infile = FileHDF5(opts.input_file, FileHDF5::FileMode::readonly);
if (opts.local)
return infile.read<T>(opts.input_dataset, block_size);
else
return infile.read<T>(opts.input_dataset, block_size, comm_grid, {0, 0});
}
#endif
using dlaf::matrix::util::set_random_hermitian;

HostMatrixType hermitian(matrix_size, block_size, comm_grid);
HostMatrixType hermitian(GlobalElementSize(opts.m, opts.m), block_size, comm_grid);
set_random_hermitian(hermitian);

return hermitian;
}();

auto matrix_size = matrix_ref.size();
auto block_size = matrix_ref.blockSize();

for (int64_t run_index = -opts.nwarmups; run_index < opts.nruns; ++run_index) {
if (0 == world.rank() && run_index >= 0)
std::cout << "[" << run_index << "]" << std::endl;
Expand Down Expand Up @@ -127,6 +164,22 @@ struct EigensolverMiniapp {
DLAF_MPI_CHECK_ERROR(MPI_Barrier(world));
double elapsed_time = timeit.elapsed();

#ifdef DLAF_WITH_HDF5
if (run_index == opts.nruns - 1) {
if (!opts.output_file.empty()) {
auto outfile = [&]() {
if (opts.local)
return FileHDF5(opts.output_file, FileHDF5::FileMode::readwrite);
else
return FileHDF5(world, opts.output_file);
}();
outfile.write(matrix_ref, opts.input_dataset);
outfile.write(eigenvalues, "/evals");
outfile.write(eigenvectors, "/evecs");
}
}
#endif

matrix.reset();

// print benchmark results
Expand Down Expand Up @@ -174,8 +227,13 @@ int main(int argc, char** argv) {

// clang-format off
desc_commandline.add_options()
("matrix-size", value<SizeType>() ->default_value(4096), "Matrix size")
("block-size", value<SizeType>() ->default_value( 256), "Block cyclic distribution size")
("matrix-size", value<SizeType>() ->default_value(4096), "Matrix size")
("block-size", value<SizeType>() ->default_value( 256), "Block cyclic distribution size")
#ifdef DLAF_WITH_HDF5
("input-file", value<std::filesystem::path>() , "Load matrix from given HDF5 file")
("input-dataset", value<std::string>() -> default_value("/input") , "Name of HDF5 dataset to load as matrix")
("output-file", value<std::filesystem::path>() , "Save eigenvectors and eigenvalues to given HDF5 file")
#endif
;
// clang-format on
dlaf::miniapp::addUploOption(desc_commandline);
Expand Down
17 changes: 11 additions & 6 deletions miniapp/miniapp_tridiag_solver.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,10 @@
//

#include <cstdlib>
#include <filesystem>
#include <iostream>
#include <limits>
#include <optional>
#include <string>

#include <pika/init.hpp>
#include <pika/program_options.hpp>
Expand Down Expand Up @@ -59,7 +60,8 @@ struct Options
SizeType m;
SizeType mb;
#ifdef DLAF_WITH_HDF5
std::optional<dlaf::matrix::internal::FileHDF5> input_file;
std::filesystem::path input_file;
std::string input_dataset;
#endif

Options(const pika::program_options::variables_map& vm)
Expand All @@ -69,14 +71,15 @@ struct Options

#ifdef DLAF_WITH_HDF5
if (vm.count("input-file") == 1) {
input_file = FileHDF5(vm["input-file"].as<std::string>(), FileHDF5::FileMode::readonly);
input_file = vm["input-file"].as<std::filesystem::path>();

if (!vm["matrix-size"].defaulted()) {
std::cerr << "Warning! "
"Specified matrix size will be ignored because an input file has been specified."
<< std::endl;
}
}
input_dataset = vm["input-dataset"].as<std::string>();
#endif

if (do_check != dlaf::miniapp::CheckIterFreq::None) {
Expand All @@ -100,8 +103,9 @@ struct TridiagSolverMiniapp {

Matrix<const T, Device::CPU> tridiag_ref = [&opts]() {
#ifdef DLAF_WITH_HDF5
if (opts.input_file) {
Matrix<T, Device::CPU> tridiag = opts.input_file->read<T>("/tridiag", {opts.mb, 2});
if (!opts.input_file.empty()) {
auto infile = FileHDF5(opts.input_file, FileHDF5::FileMode::readonly);
Matrix<T, Device::CPU> tridiag = infile.read<T>(opts.input_dataset, {opts.mb, 2});
return tridiag;
}
#endif
Expand Down Expand Up @@ -196,7 +200,8 @@ int main(int argc, char** argv) {
("matrix-size", value<SizeType>() ->default_value(4096), "Matrix size")
("block-size", value<SizeType>() ->default_value( 256), "Block cyclic distribution size")
#ifdef DLAF_WITH_HDF5
("input-file", value<std::string>() , "Load matrix from given HDF5 file")
("input-file", value<std::filesystem::path>() , "Load matrix from given HDF5 file")
("input-dataset", value<std::string>() ->default_value("/tridiag") , "Name of HDF5 dataset to load as matrix")
#endif
;
// clang-format on
Expand Down
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