How to append a string to HDF5 dataset with C++?

Question

I'd like to append a string to an HDF5 dataset of dimension 1. The following code works for appending doubles to the "doubles" dataset in file test-doubles.h5 but the code segfaults in the dataset.write(str, string_type, mspace, fspace) call:

#include "H5Cpp.h"
const int RANK = 1;
H5::StrType string_type(H5::PredType::C_S1, H5T_VARIABLE);

void append_double(H5::DataSet &dataset, double value) {
    // dataspace
    hsize_t dims[RANK] = { 1 };
    hsize_t maxdims[RANK] = { H5S_UNLIMITED };
    H5::DataSpace mspace(RANK, dims, maxdims);

    H5::DataSpace space = dataset.getSpace();
    const hsize_t actual_dim = space.getSimpleExtentNpoints();

    // extend the dataset
    hsize_t new_size[RANK];
    new_size[0] = actual_dim + 1;
    dataset.extend(new_size);

    // select hyperslab.
    H5::DataSpace fspace = dataset.getSpace();
    hsize_t offset[RANK] = { actual_dim };
    hsize_t dims1[RANK] = { 1 };
    fspace.selectHyperslab(H5S_SELECT_SET, dims1, offset);

    dataset.write(&value, H5::PredType::NATIVE_DOUBLE, mspace, fspace);
}

void append_string(H5::DataSet &dataset, string value) {
    // dataspace
    hsize_t dims[RANK] = { 1 };
    hsize_t maxdims[RANK] = { H5S_UNLIMITED };
    H5::DataSpace mspace(RANK, dims, maxdims);

    H5::DataSpace space = dataset.getSpace();
    const hsize_t actual_dim = space.getSimpleExtentNpoints();

    // extend the dataset
    hsize_t new_size[RANK];
    new_size[0] = actual_dim + 1;
    dataset.extend(new_size);

    // select hyperslab.
    H5::DataSpace fspace = dataset.getSpace();
    hsize_t offset[RANK] = { actual_dim };
    hsize_t dims1[RANK] = { 1 };
    fspace.selectHyperslab(H5S_SELECT_SET, dims1, offset);

    const char *str = value.c_str();
    dataset.write(str, string_type, mspace, fspace);

}

int main(int argc, char *argv[]) {
    cout << "start" << endl;
    {
        H5::H5File h5_file("test-doubles.h5", H5F_ACC_TRUNC);

        // create data space with unlimited dimensions for doubles
        hsize_t doubles_dims[RANK] = { 0 };
        hsize_t doubles_maxdims[RANK] = { H5S_UNLIMITED };
        H5::DataSpace doubles_fspace(RANK, doubles_dims, doubles_maxdims);

        // enable chunking for this dataset
        H5::DSetCreatPropList cparms;
        hsize_t chunk_dims[RANK] = { 1 };
        cparms.setChunk(RANK, chunk_dims);

        // create dataset for doubles:
        H5::DataSet d_dataset = h5_file.createDataSet("doubles",
        H5::PredType::NATIVE_DOUBLE, doubles_fspace, cparms);

        // append values to this dataset:
        append_double(d_dataset, 1.0);
        append_double(d_dataset, 2.0);
        append_double(d_dataset, 3.0);

        cout << "doubles written." << endl;
    }

    {
        H5::H5File h5_file("test-strings.h5", H5F_ACC_TRUNC);

        // create data space with unlimited dimensions for strings
        hsize_t str_dims[RANK] = { 0 };
        hsize_t str_maxdims[RANK] = { H5S_UNLIMITED };
        H5::DataSpace str_fspace(RANK, str_dims, str_maxdims);

        // enable chunking for this dataset
        H5::DSetCreatPropList str_cparms;
        hsize_t str_chunk_dims[RANK] = { 1 };
        str_cparms.setChunk(RANK, str_chunk_dims);

        // create dataset for doubles:
        H5::DataSet str_dataset = h5_file.createDataSet("strings", string_type, str_fspace, str_cparms);

        // append strings to this dataset:
        append_string(str_dataset, "test1");
        append_string(str_dataset, "test2");
        append_string(str_dataset, "test3");
        cout << "strings written." << endl;
    }

    cout << "all done." << endl;
    return 0;
}

Thanks a lot for your help!

Answer 1

It all works if you replace

dataset.write(str, string_type, mspace, fspace);

with

dataset.write(&str, string_type, mspace, fspace);