diff --git a/CMakeLists_files.cmake b/CMakeLists_files.cmake index 272572545..f0a4fc0de 100644 --- a/CMakeLists_files.cmake +++ b/CMakeLists_files.cmake @@ -172,6 +172,9 @@ if(MPI_FOUND) opm/simulators/utils/ParallelSerialization.cpp opm/simulators/utils/SetupZoltanParams.cpp) endif() +if(HDF5_FOUND) + list(APPEND MAIN_SOURCE_FILES opm/simulators/utils/HDF5File.cpp) +endif() # originally generated with the command: # find tests -name '*.cpp' -a ! -wholename '*/not-unit/*' -printf '\t%p\n' | sort @@ -218,6 +221,9 @@ endif() if(ROCALUTION_FOUND) list(APPEND TEST_SOURCE_FILES tests/test_rocalutionSolver.cpp) endif() +if(HDF5_FOUND) + list(APPEND TEST_SOURCE_FILES tests/test_HDF5File.cpp) +endif() list (APPEND TEST_DATA_FILES tests/equil_base.DATA @@ -430,6 +436,12 @@ list (APPEND PUBLIC_HEADER_FILES opm/simulators/wells/WGState.hpp ) +if(HDF5_FOUND) + list(APPEND PUBLIC_HEADER_FILES + opm/simulators/utils/HDF5File.hpp + ) +endif() + list (APPEND EXAMPLE_SOURCE_FILES examples/printvfp.cpp ) diff --git a/opm-simulators-prereqs.cmake b/opm-simulators-prereqs.cmake index c0d8d2536..904ce4f98 100644 --- a/opm-simulators-prereqs.cmake +++ b/opm-simulators-prereqs.cmake @@ -48,6 +48,7 @@ set (opm-simulators_DEPS "opm-grid REQUIRED" "opm-models REQUIRED" "Damaris 1.7" + "HDF5" ) find_package_deps(opm-simulators) diff --git a/opm/simulators/utils/HDF5File.cpp b/opm/simulators/utils/HDF5File.cpp new file mode 100644 index 000000000..cc6cdb40b --- /dev/null +++ b/opm/simulators/utils/HDF5File.cpp @@ -0,0 +1,126 @@ +/* + This file is part of the Open Porous Media project (OPM). + + OPM is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 2 of the License, or + (at your option) any later version. + + OPM is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with OPM. If not, see . + + Consult the COPYING file in the top-level source directory of this + module for the precise wording of the license and the list of + copyright holders. +*/ + +#include +#include + +#include +#include + +namespace { + +bool groupExists(hid_t parent, const std::string& path) +{ + // turn off errors to avoid cout spew + H5E_BEGIN_TRY { +#if H5_VERS_MINOR > 8 + return H5Lexists(parent, path.c_str(), H5P_DEFAULT) == 1; +#else + return H5Gget_objinfo(static_cast(parent), path.c_str(), 0, nullptr) == 0; +#endif + } H5E_END_TRY; + return false; +} + +} + +namespace Opm { + +HDF5File::HDF5File(const std::string& fileName, OpenMode mode) +{ + bool exists = std::filesystem::exists(fileName); + if (mode == OpenMode::OVERWRITE || + (mode == OpenMode::APPEND && !exists)) { + m_file = H5Fcreate(fileName.c_str(), + H5F_ACC_TRUNC, + H5P_DEFAULT, H5P_DEFAULT); + } else { + m_file = H5Fopen(fileName.c_str(), + mode == OpenMode::READ ? H5F_ACC_RDONLY : H5F_ACC_RDWR, + H5P_DEFAULT); + } + if (m_file == H5I_INVALID_HID) { + throw std::runtime_error(std::string("HDF5File: Failed to ") + + ( mode == OpenMode::OVERWRITE || + (mode == OpenMode::APPEND && !exists) ? "create" : "open") + + fileName); + } +} + +HDF5File::~HDF5File() +{ + if (m_file != H5I_INVALID_HID) { + H5Fclose(m_file); + } +} + +void HDF5File::write(const std::string& group, + const std::string& dset, + const std::vector& buffer) +{ + hid_t grp; + if (groupExists(m_file, group)) { + grp = H5Gopen2(m_file, group.c_str(), H5P_DEFAULT); + } else { + grp = H5Gcreate2(m_file, group.c_str(), 0, H5P_DEFAULT, H5P_DEFAULT); + } + + hsize_t size = buffer.size(); + hsize_t start = 0; + + hid_t space = H5Screate_simple(1, &size, nullptr); + hid_t dataset_id = H5Dcreate2(grp, dset.c_str(), H5T_NATIVE_CHAR, space, + H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + if (dataset_id == H5I_INVALID_HID) { + throw std::runtime_error("HDF5File: Trying to write already existing dataset " + group + '/' + dset); + } + + if (size > 0) { + hid_t filespace = H5Dget_space(dataset_id); + hsize_t stride = 1; + H5Sselect_hyperslab(filespace, H5S_SELECT_SET, &start, &stride, &size, nullptr); + hid_t memspace = H5Screate_simple(1, &size, nullptr); + H5Dwrite(dataset_id, H5T_NATIVE_CHAR, memspace, filespace, H5P_DEFAULT, buffer.data()); + H5Sclose(memspace); + H5Sclose(filespace); + } + H5Dclose(dataset_id); + H5Sclose(space); + H5Gclose(grp); +} + +void HDF5File::read(const std::string& group, + const std::string& dset, + std::vector& buffer) +{ + hid_t dataset_id = H5Dopen2(m_file, (group + "/"+ dset).c_str(), H5P_DEFAULT); + if (dataset_id == H5I_INVALID_HID) { + throw std::runtime_error("HDF5File: Trying to read non-existing dataset " + group + '/' + dset); + } + + hid_t space = H5Dget_space(dataset_id); + hsize_t size = H5Sget_simple_extent_npoints(space); + buffer.resize(size); + H5Dread(dataset_id, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer.data()); + H5Dclose(dataset_id); +} + +} diff --git a/opm/simulators/utils/HDF5File.hpp b/opm/simulators/utils/HDF5File.hpp new file mode 100644 index 000000000..1b236179d --- /dev/null +++ b/opm/simulators/utils/HDF5File.hpp @@ -0,0 +1,73 @@ +/* + This file is part of the Open Porous Media project (OPM). + + OPM is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 2 of the License, or + (at your option) any later version. + + OPM is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with OPM. If not, see . + + Consult the COPYING file in the top-level source directory of this + module for the precise wording of the license and the list of + copyright holders. +*/ +#ifndef HDF5_FILE_HPP +#define HDF5_FILE_HPP + +#include + +#include +#include + +namespace Opm { + +//! \brief Class handling simple output to HDF5. +class HDF5File { +public: + //! \brief Enumeration of file opening modes. + enum class OpenMode { + APPEND, //!< Append to an existing file (creates new if not) + OVERWRITE, //!< Overwrite and write to an existing file + READ //!< Open existing file for reading + }; + + //! \brief Opens HDF5 file for I/O. + //! \param fileName Name of file to open + //! \param mode Open mode for file + HDF5File(const std::string& fileName, OpenMode mode); + + //! \brief Destructor clears up any opened files. + ~HDF5File(); + + //! \brief Write a char buffer to a specified location in file. + //! \param group Group ("directory") to write data to + //! \param dset Data set ("file") to write data to + //! \param buffer Data to write + //! \details Throws exception on failure + void write(const std::string& group, + const std::string& dset, + const std::vector& buffer); + + //! \brief Read a char buffer from a specified location in file. + //! \param group Group ("directory") to read data from + //! \param dset Data set ("file") to read data from + //! \param buffer Vector to store read data in + //! \details Throws exception on failure + void read(const std::string& group, + const std::string& dset, + std::vector& buffer); + +private: + hid_t m_file = H5I_INVALID_HID; //!< File handle +}; + +} + +#endif diff --git a/tests/test_HDF5File.cpp b/tests/test_HDF5File.cpp new file mode 100644 index 000000000..2d243dff2 --- /dev/null +++ b/tests/test_HDF5File.cpp @@ -0,0 +1,96 @@ +/* + Copyright 2021 Equinor. + + This file is part of the Open Porous Media project (OPM). + + OPM is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + OPM is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with OPM. If not, see . +*/ + +#include + +#include + +#include + +#define BOOST_TEST_MODULE HDF5FileTest +#include + +#include +#include + +using namespace Opm; + +BOOST_AUTO_TEST_CASE(ReadWrite) +{ + auto path = std::filesystem::temp_directory_path() / Opm::unique_path("hdf5test%%%%%"); + std::filesystem::create_directory(path); + auto rwpath = (path / "rw.hdf5").string(); + const std::vector test_data{1,2,3,4,5,6,8,9}; + { + Opm::HDF5File out_file(rwpath, Opm::HDF5File::OpenMode::OVERWRITE); + BOOST_CHECK_NO_THROW(out_file.write("/test_data", "d1", test_data)); + } + { + Opm::HDF5File in_file(rwpath, Opm::HDF5File::OpenMode::READ); + std::vector data; + BOOST_CHECK_NO_THROW(in_file.read("/test_data", "d1", data)); + BOOST_CHECK_EQUAL_COLLECTIONS(data.begin(), data.end(), + test_data.begin(), test_data.end()); + } + std::filesystem::remove(rwpath); + std::filesystem::remove(path); +} + +BOOST_AUTO_TEST_CASE(ThrowOpenNonexistent) +{ + BOOST_CHECK_THROW(Opm::HDF5File out_file("no_such_file.hdf5", Opm::HDF5File::OpenMode::READ), std::runtime_error); +} + +BOOST_AUTO_TEST_CASE(ReadNonExistentDset) +{ + auto path = std::filesystem::temp_directory_path() / Opm::unique_path("hdf5test%%%%%"); + std::filesystem::create_directory(path); + auto rwpath = (path / "existent_dset.hdf5").string(); + const std::vector test_data{1,2,3,4,5,6,8,9}; + { + Opm::HDF5File out_file(rwpath, Opm::HDF5File::OpenMode::OVERWRITE); + BOOST_CHECK_NO_THROW(out_file.write("/test_data", "d1", test_data)); + } + { + Opm::HDF5File in_file(rwpath, Opm::HDF5File::OpenMode::READ); + std::vector data; + BOOST_CHECK_NO_THROW(in_file.read("/test_data", "d1", data)); + BOOST_CHECK_EQUAL_COLLECTIONS(data.begin(), data.end(), + test_data.begin(), test_data.end()); + BOOST_CHECK_THROW(in_file.read("/test_data", "d2", data), std::runtime_error); + } + std::filesystem::remove(rwpath); + std::filesystem::remove(path); +} + +BOOST_AUTO_TEST_CASE(WriteExistentDset) +{ + auto path = std::filesystem::temp_directory_path() / Opm::unique_path("hdf5test%%%%%"); + std::filesystem::create_directory(path); + auto rwpath = (path / "existent_dset.hdf5").string(); + const std::vector test_data{1,2,3,4,5,6,8,9}; + { + Opm::HDF5File out_file(rwpath, Opm::HDF5File::OpenMode::OVERWRITE); + BOOST_CHECK_NO_THROW(out_file.write("/test_data", "d1", test_data)); + BOOST_CHECK_THROW(out_file.write("/test_data", "d1", test_data), std::runtime_error); + } + std::filesystem::remove(rwpath); + std::filesystem::remove(path); +} +