added: simple HDF5File class

bare minimum to enable reading and writing byte arrays

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
   )

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)

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 <http://www.gnu.org/licenses/>.
+
+  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 <config.h>
+#include <opm/simulators/utils/HDF5File.hpp>
+
+#include <filesystem>
+#include <stdexcept>
+
+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<hid_t>(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<char>& 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<char>& 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);
+}
+
+}

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 <http://www.gnu.org/licenses/>.
+
+  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 <hdf5.h>
+
+#include <string>
+#include <vector>
+
+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<char>& 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<char>& buffer);
+
+private:
+    hid_t m_file = H5I_INVALID_HID; //!< File handle
+};
+
+}
+
+#endif

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 <http://www.gnu.org/licenses/>.
+*/
+
+#include <config.h>
+
+#include <opm/common/utility/FileSystem.hpp>
+
+#include <opm/simulators/utils/HDF5File.hpp>
+
+#define BOOST_TEST_MODULE HDF5FileTest
+#include <boost/test/unit_test.hpp>
+
+#include <filesystem>
+#include <stdexcept>
+
+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<char> 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<char> 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<char> 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<char> 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<char> 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);
+}
+