closeHDF5HandlesForFile

C++ Function Reference

1 Signature

void BigDataStatMeth::closeHDF5HandlesForFile(const std::string &filename)

2 Description

Close all HDF5 handles associated with a specific file.

3 Parameters

• filename (const std::string &): Absolute path to the HDF5 file.

4 Details

Finds all open HDF5 file handles matching filename (by absolute path), closes their associated datasets/groups/attributes, then closes the file handles themselves. Pre-defined HDF5 library types are never touched.

5 Source Code

NoteImplementation

File: inst/include/hdf5Utilities/hdf5CheckClose.hpp • Lines 135-170

inline void closeHDF5HandlesForFile(const std::string& filename) {
        try {
            // Get all open file handles
            ssize_t n_files = H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_FILE);
            if (n_files <= 0) return;
            
            std::vector<hid_t> file_ids(static_cast<size_t>(n_files));
            H5Fget_obj_ids(H5F_OBJ_ALL, H5F_OBJ_FILE,
                           static_cast<size_t>(n_files), file_ids.data());
            
            for (hid_t fid : file_ids) {
                if (H5Iis_valid(fid) <= 0) continue;
                
                // Get the absolute path HDF5 stored for this handle
                ssize_t len = H5Fget_name(fid, nullptr, 0);
                if (len <= 0) continue;
                std::string hdf5_name(static_cast<size_t>(len + 1), '\0');
                H5Fget_name(fid, &hdf5_name[0], static_cast<size_t>(len + 1));
                hdf5_name.resize(static_cast<size_t>(len));
                
                if (hdf5_name != filename) continue;
                
                // Close datasets, groups, attributes for this file only
                // Never touch H5F_OBJ_DATATYPE — pre-defined types are library-internal
                const unsigned types = H5F_OBJ_DATASET | H5F_OBJ_GROUP | H5F_OBJ_ATTR;
                ssize_t n = H5Fget_obj_count(fid, types);
                if (n > 0) {
                    std::vector<hid_t> ids(static_cast<size_t>(n));
                    H5Fget_obj_ids(fid, types, static_cast<size_t>(n), ids.data());
                    for (hid_t id : ids)
                        if (H5Iis_valid(id) > 0) H5Oclose(id);
                }
                H5Fclose(fid);
            }
        } catch (...) {}
    }

6 Usage Example

#include "BigDataStatMeth.hpp"

// Example usage
auto result = closeHDF5HandlesForFile(...);