Encapsulate HDF5 module

Rewrite h5xx and hdf5 bindings such that they no longer propagate
their compiler flags to the entire codebase.

src/core/io/writer/CMakeLists.txt

@@ -30,5 +30,5 @@ if(ESPRESSO_BUILD_WITH_HDF5)
     PRIVATE h5xx hdf5 espresso::cpp_flags espresso::h5xx_cpp_flags MPI::MPI_CXX
             Boost::mpi Boost::filesystem espresso::utils espresso::config
             espresso::instrumentation)
-  target_link_libraries(espresso_core PRIVATE espresso_hdf5)
+  target_link_libraries(espresso_core PUBLIC espresso_hdf5)
 endif()

src/core/io/writer/h5md_core.cpp

@@ -19,11 +19,14 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#include "hdf5_patches.hpp" // must appear first
+
 #include "h5md_core.hpp"
+#include "h5md_dataset.hpp"
+#include "h5md_specification.hpp"
 
 #include "BoxGeometry.hpp"
 #include "Particle.hpp"
-#include "h5md_specification.hpp"
 #include "lees_edwards/LeesEdwardsBC.hpp"
 
 #include "config/version.hpp"
@@ -35,6 +38,8 @@
 #include <boost/mpi/collectives.hpp>
 #include <boost/multi_array.hpp>
 
+#include <h5xx/h5xx.hpp>
+
 #include <mpi.h>
 
 #include <algorithm>
@@ -46,6 +51,11 @@
 #include <string>
 #include <vector>
 
+namespace h5xx {
+template <typename T, std::size_t size>
+struct is_array<Utils::Vector<T, size>> : std::true_type {};
+} // namespace h5xx
+
 namespace Writer {
 namespace H5md {
 
@@ -141,12 +151,12 @@ void File::load_datasets() {
   for (auto const &d : m_h5md_specification.get_datasets()) {
     if (d.is_link)
       continue;
-    datasets[d.path()] = h5xx::dataset(m_h5md_file, d.path());
+    datasets[d.path()] = h5xx::dataset(*m_h5md_file, d.path());
   }
 }
 
 void File::create_groups() {
-  h5xx::group group(m_h5md_file);
+  h5xx::group group(*m_h5md_file);
   for (auto const &d : m_h5md_specification.get_datasets()) {
     h5xx::group new_group(group, d.group);
   }
@@ -190,13 +200,13 @@ void File::create_datasets() {
     auto dataspace = h5xx::dataspace(create_dims(d.rank, d.data_dim), maxdims);
     auto storage = hps::chunked(create_chunk_dims(d.rank, d.data_dim))
                        .set(hps::fill_value(-10));
-    datasets[d.path()] = h5xx::dataset(m_h5md_file, d.path(), d.type, dataspace,
+    datasets[d.path()] = h5xx::dataset(*m_h5md_file, d.path(), d.type, dataspace,
                                        storage, H5P_DEFAULT, H5P_DEFAULT);
   }
 }
 
 void File::load_file(const std::string &file_path) {
-  m_h5md_file = h5xx::file(file_path, m_comm, MPI_INFO_NULL, h5xx::file::out);
+  *m_h5md_file = h5xx::file(file_path, m_comm, MPI_INFO_NULL, h5xx::file::out);
   load_datasets();
 }
 
@@ -259,7 +269,7 @@ void File::create_hard_links() {
         from = path_time.c_str();
       }
       assert(from != nullptr);
-      if (H5Lcreate_hard(m_h5md_file.hid(), from, m_h5md_file.hid(),
+      if (H5Lcreate_hard(m_h5md_file->hid(), from, m_h5md_file->hid(),
                          ds.path().c_str(), H5P_DEFAULT, H5P_DEFAULT) < 0) {
         throw std::runtime_error("Error creating hard link for " + ds.path());
       }
@@ -271,10 +281,10 @@ void File::create_file(const std::string &file_path) {
   if (m_comm.rank() == 0)
     write_script(file_path, m_absolute_script_path);
   m_comm.barrier();
-  m_h5md_file = h5xx::file(file_path, m_comm, MPI_INFO_NULL, h5xx::file::out);
+  m_h5md_file = std::make_unique<h5xx::file>(file_path, m_comm, MPI_INFO_NULL, h5xx::file::out);
   create_groups();
   create_datasets();
-  write_attributes(m_h5md_file);
+  write_attributes(*m_h5md_file);
   write_units();
   create_hard_links();
 }
@@ -478,7 +488,27 @@ void File::write_connectivity(const ParticleRange &particles) {
                 offset_bonds, count_bonds);
 }
 
-void File::flush() { m_h5md_file.flush(); }
+void File::flush() { m_h5md_file->flush(); }
+
+std::string File::file_path() const { return m_h5md_file->name(); }
+
+File::File(std::string file_path, std::string script_path,
+           std::vector<std::string> const &output_fields, std::string mass_unit,
+           std::string length_unit, std::string time_unit, std::string force_unit,
+           std::string velocity_unit, std::string charge_unit)
+      : m_script_path(std::move(script_path)),
+        m_mass_unit(std::move(mass_unit)),
+        m_length_unit(std::move(length_unit)),
+        m_time_unit(std::move(time_unit)), m_force_unit(std::move(force_unit)),
+        m_velocity_unit(std::move(velocity_unit)),
+        m_charge_unit(std::move(charge_unit)),
+        m_comm(boost::mpi::communicator()),
+        m_fields(fields_list_to_bitfield(output_fields)),
+        m_h5md_specification(m_fields) {
+    init_file(file_path);
+  }
+
+File::~File() = default;
 
 } /* namespace H5md */
 } /* namespace Writer */

src/core/io/writer/h5md_core.hpp

@@ -30,8 +30,6 @@
 #include <boost/filesystem.hpp>
 #include <boost/mpi/communicator.hpp>
 
-#include <h5xx/h5xx.hpp>
-
 #include <cstddef>
 #include <stdexcept>
 #include <string>
@@ -40,8 +38,8 @@
 #include <utility>
 
 namespace h5xx {
-template <typename T, std::size_t size>
-struct is_array<Utils::Vector<T, size>> : std::true_type {};
+class file;
+class dataset;
 } // namespace h5xx
 
 namespace Writer {
@@ -88,7 +86,7 @@ static std::unordered_map<std::string, H5MDOutputFields> const fields_map = {
 inline auto fields_list_to_bitfield(std::vector<std::string> const &fields) {
   unsigned int bitfield = H5MD_OUT_NONE;
   for (auto const &field_name : fields) {
-    if (fields_map.count(field_name) == 0) {
+    if (not fields_map.contains(field_name)) {
       throw std::invalid_argument("Unknown field '" + field_name + "'");
     }
     bitfield |= fields_map.at(field_name);
@@ -112,24 +110,12 @@ class File {
    * @param force_unit The unit for force.
    * @param velocity_unit The unit for velocity.
    * @param charge_unit The unit for charge.
-   * @param comm The MPI communicator.
    */
   File(std::string file_path, std::string script_path,
        std::vector<std::string> const &output_fields, std::string mass_unit,
        std::string length_unit, std::string time_unit, std::string force_unit,
-       std::string velocity_unit, std::string charge_unit,
-       boost::mpi::communicator comm = boost::mpi::communicator())
-      : m_script_path(std::move(script_path)),
-        m_mass_unit(std::move(mass_unit)),
-        m_length_unit(std::move(length_unit)),
-        m_time_unit(std::move(time_unit)), m_force_unit(std::move(force_unit)),
-        m_velocity_unit(std::move(velocity_unit)),
-        m_charge_unit(std::move(charge_unit)), m_comm(std::move(comm)),
-        m_fields(fields_list_to_bitfield(output_fields)),
-        m_h5md_specification(m_fields) {
-    init_file(file_path);
-  }
-  ~File() = default;
+       std::string velocity_unit, std::string charge_unit);
+  ~File();
 
   /**
    * @brief Method to perform the renaming of the temporary file from
@@ -151,7 +137,7 @@ class File {
    * @brief Retrieve the path to the hdf5 file.
    * @return The path as a string.
    */
-  auto file_path() const { return m_h5md_file.name(); }
+  std::string file_path() const;
 
   /**
    * @brief Retrieve the path to the simulation script.
@@ -272,9 +258,9 @@ class File {
   unsigned int m_fields;
   std::string m_backup_filename;
   boost::filesystem::path m_absolute_script_path;
-  h5xx::file m_h5md_file;
+  std::unique_ptr<h5xx::file> m_h5md_file;
   std::unordered_map<std::string, h5xx::dataset> datasets;
-  H5MD_Specification m_h5md_specification;
+  Specification m_h5md_specification;
 };
 
 struct incompatible_h5mdfile : public std::exception {

src/core/io/writer/h5md_dataset.hpp

@@ -0,0 +1,45 @@
+/*
+ * Copyright (C) 2010-2025 The ESPResSo project
+ * Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
+ *   Max-Planck-Institute for Polymer Research, Theory Group
+ *
+ * This file is part of ESPResSo.
+ *
+ * ESPResSo 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.
+ *
+ * ESPResSo 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 this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#pragma once
+
+#include "hdf5_patches.hpp"
+
+#include <hdf5.h>
+
+#include <string>
+
+namespace Writer {
+namespace H5md {
+
+struct Dataset {
+    std::string path() const { return group + "/" + name; }
+
+    std::string group;
+    std::string name;
+    hsize_t rank;
+    hid_t type;
+    hsize_t data_dim;
+    bool is_link;
+};
+
+} // namespace H5md
+} // namespace Writer

src/core/io/writer/h5md_specification.cpp

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2010-2022 The ESPResSo project
+ * Copyright (C) 2010-2025 The ESPResSo project
  * Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
  *   Max-Planck-Institute for Polymer Research, Theory Group
  *
@@ -19,17 +19,24 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "h5md_specification.hpp"
+#include "hdf5_patches.hpp" // must appear first
+
 #include "h5md_core.hpp"
+#include "h5md_dataset.hpp"
+#include "h5md_specification.hpp"
+
+#include <h5xx/h5xx.hpp>
 
 #include <hdf5.h>
 
+#include <algorithm>
+#include <string>
 #include <utility>
 
 namespace Writer {
 namespace H5md {
 
-H5MD_Specification::H5MD_Specification(unsigned int fields) {
+Specification::Specification(unsigned int fields) {
   auto const add_time_series = [this](Dataset &&dataset, bool link = true) {
     auto const group = dataset.group;
     m_datasets.push_back(std::move(dataset));
@@ -89,5 +96,19 @@ H5MD_Specification::H5MD_Specification(unsigned int fields) {
   }
 }
 
+bool Specification::is_compliant(std::string const &filename) const {
+  h5xx::file h5md_file(filename, h5xx::file::in);
+
+  auto const all_groups_exist =
+      std::ranges::all_of(m_datasets, [&h5md_file](auto const &d) {
+        return h5xx::exists_group(h5md_file, d.group);
+      });
+  auto const all_datasets_exist =
+      std::ranges::all_of(m_datasets, [&h5md_file](auto const &d) {
+        return h5xx::exists_dataset(h5md_file, d.path());
+      });
+  return all_groups_exist and all_datasets_exist;
+}
+
 } // namespace H5md
 } // namespace Writer

src/core/io/writer/h5md_specification.hpp

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2010-2022 The ESPResSo project
+ * Copyright (C) 2010-2025 The ESPResSo project
  * Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
  *   Max-Planck-Institute for Polymer Research, Theory Group
  *
@@ -21,62 +21,26 @@
 
 #pragma once
 
-// guard for hdf5.h
-#if not defined(_H5public_H)
-#ifdef OMPI_SKIP_MPICXX
-#undef OMPI_SKIP_MPICXX
-#endif
-#ifdef MPICH_SKIP_MPICXX
-#undef MPICH_SKIP_MPICXX
-#endif
-#endif // not defined(_H5public_H)
-#include <H5public.h>
-
-#include <h5xx/h5xx.hpp>
-
-#include <algorithm>
 #include <string>
 #include <vector>
 
 namespace Writer {
 namespace H5md {
 
+struct Dataset;
+
 /**
  * @brief Layout information for H5MD files.
  * In order to add a new particle property you have to add an entry to the
  * H5MD_Specification::DATASETS member and extend the File::write() and the
  * File::write_units() functions accordingly.
  */
-struct H5MD_Specification {
-
-  struct Dataset {
-    std::string path() const { return group + "/" + name; }
-
-    std::string group;
-    std::string name;
-    hsize_t rank;
-    hid_t type;
-    hsize_t data_dim;
-    bool is_link;
-  };
-
-  H5MD_Specification(unsigned int fields);
+struct Specification {
+  Specification(unsigned int fields);
 
   auto const &get_datasets() const { return m_datasets; }
 
-  bool is_compliant(std::string const &filename) const {
-    h5xx::file h5md_file(filename, h5xx::file::in);
-
-    auto const all_groups_exist = std::all_of(
-        m_datasets.begin(), m_datasets.end(), [&h5md_file](auto const &d) {
-          return h5xx::exists_group(h5md_file, d.group);
-        });
-    auto const all_datasets_exist = std::all_of(
-        m_datasets.begin(), m_datasets.end(), [&h5md_file](auto const &d) {
-          return h5xx::exists_dataset(h5md_file, d.path());
-        });
-    return all_groups_exist and all_datasets_exist;
-  }
+  bool is_compliant(std::string const &filename) const;
 
 private:
   std::vector<Dataset> m_datasets;