Performance: Attribute reading in the HDF5 backend is implemented inefficiently

[franzpoeschel]

This issue should serve as documentation of a performance issue seen in our HDF5 backend.

Describe the issue

When parsing an HDF5 dataset, the majority of time will be spent reading attributes. The following graph was created by using openpmd-ls on a PIConGPU output with ~80 iterations:

Looking into the implementation of HDF5IOHandlerImpl::readAttribute():

void HDF5IOHandlerImpl::readAttribute(
    Writable *writable, Parameter<Operation::READ_ATT> &parameters)
{
    /* [ ... ] */

    auto res = getFile(writable);
    File file = res ? res.value() : getFile(writable->parent).value();

    /* [ ... ] */

    hid_t fapl = H5Pcreate(H5P_LINK_ACCESS);

    /* [ ... ] */

    obj_id =
        H5Oopen(file.id, concrete_h5_file_position(writable).c_str(), fapl);

    /* [ ... ] */

    H5S_class_t attr_class = H5Sget_simple_extent_type(attr_space);
    Attribute a(0);
    if (attr_class == H5S_SCALAR ||
        (attr_class == H5S_SIMPLE && ndims == 1 && dims[0] == 1))
    {
        if (H5Tequal(attr_type, H5T_NATIVE_CHAR))
        {
            char c;
            status = H5Aread(attr_id, attr_type, &c);
            a = Attribute(c);
        }
        else if (H5Tequal(attr_type, H5T_NATIVE_UCHAR))
        {
            unsigned char u;
            status = H5Aread(attr_id, attr_type, &u);
            a = Attribute(u);
        }

    /* [ ... ] */
    /* [ ... ] */
    /* [ ... ] */

        else
            throw error::ReadError(
                error::AffectedObject::Attribute,
                error::Reason::UnexpectedContent,
                "HDF5",
                "[HDF5] Unsupported scalar attribute type for '" + attr_name +
                    "'.");
    }
    else if (attr_class == H5S_SIMPLE)
    {
        if (ndims != 1)
            throw error::ReadError(
                error::AffectedObject::Attribute,
                error::Reason::UnexpectedContent,
                "HDF5",
                "[HDF5] Unsupported attribute (array with ndims != 1)");

        if (H5Tequal(attr_type, H5T_NATIVE_CHAR))
        {
            std::vector<char> vc(dims[0], 0);
            status = H5Aread(attr_id, attr_type, vc.data());
            a = Attribute(vc);
        }
        else if (H5Tequal(attr_type, H5T_NATIVE_UCHAR))
        {
            std::vector<unsigned char> vu(dims[0], 0);
            status = H5Aread(attr_id, attr_type, vu.data());
            a = Attribute(vu);
        }

    /* [ ... ] */
    /* [ ... ] */
    /* [ ... ] */

        else
        {

    /* [ ... ] */

        }
    }
    else
        throw std::runtime_error("[HDF5] Unsupported attribute class");

    /* [ ... ] */

    status = H5Tclose(attr_type);
    /* [ ... ] */
    status = H5Sclose(attr_space);
    /* [ ... ] */

    auto dtype = parameters.dtype;
    *dtype = a.dtype;
    auto resource = parameters.resource;
    *resource = a.getResource();

    status = H5Aclose(attr_id);
    /* [ ... ] */
    status = H5Oclose(obj_id);
    /* [ ... ] */
    status = H5Pclose(fapl);
    /* [ ... ] */
}

This exposes several problems:

1. For each read attribute, the object containing the attribute is opened and then closed. For subsequent attribute reads at the same object, this is unnecessary.
2. For each read attribute, a property is created and then closed. This is generally unnecessary, the property should be stored at the IOHandler level.
3. I've seen benchmarks before (though not the one above) where H5Tequal() was a sizeable portion of runtime. I'm not sure if we can find a better way to detect the attribute type.

To Reproduce Not needed as the cause of the inefficiency is understood.

Expected behavior Would a READ_ATTRIBUTES task help that reads all attributes in a group? --> Not fully since the frontend explicitly reads some attributes. Buffer the attributes of the last active group? Definitely buffer the attribute read property.

Additional context Not labeling as a a bug, since this is inefficient, but neither pathetically nor surprisingly so.