file printers/hdf5reader.hpp

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TODO: see if we can use this one:
Forward declaration.




DECLARE_RETRIEVE(r, data, i, elem)
Define the buffermanager getter specialisations.

Detailed Description



  • 2017 Jan
  • 2020 Dec

HDF5 printer retriever class declaration This is a class accompanying the HDF5Printer which takes care of reading from output created by the HDF5Printer.

Authors (add name and date if you modify):

Macros Documentation


bool _retrieve(elem&, const std::string&, const uint, const ulong);


      template<> \
      inline H5P_LocalReadBufferManager<TYPE>& \
        HDF5Reader::get_mybuffermanager() \
      { \
         return CAT(hdf5_localbufferman_,TYPE); \

Define the buffermanager getter specialisations.

Source code

//   GAMBIT: Global and Modular BSM Inference Tool
//   *********************************************
///  \file
///  HDF5 printer retriever class declaration
///  This is a class accompanying the HDF5Printer
///  which takes care of *reading* from output
///  created by the  HDF5Printer.
///  *********************************************
///  Authors (add name and date if you modify):
///  \author Ben Farmer
///          (
///  \date 2017 Jan
///  \author Tomas Gonzalo
///          (
///  \date 2020 Dec
///  *********************************************

#include "gambit/Printers/baseprinter.hpp"
#include "gambit/Printers/printer_id_tools.hpp"
#include "gambit/Printers/printers/hdf5types.hpp"
#include "gambit/Printers/printers/hdf5printer/hdf5tools.hpp"
#include "gambit/Printers/printers/hdf5printer/DataSetInterfaceScalar.hpp"
#include "gambit/Utils/cats.hpp"
#include "gambit/Utils/slhaea_helpers.hpp"

#include <boost/preprocessor/seq/for_each_i.hpp>

#ifndef __hdf5_reader_hpp__
#define __hdf5_reader_hpp__

namespace Gambit
  namespace Printers

    /// Length of dataset chunks read into memory during certain search operations.
    /// For maximum efficiency this should probably match the chunking length used
    /// to write the files in the first place.
    static const std::size_t CHUNKLENGTH = 100;

    template<class T>
    struct BuffPair
       DataSetInterfaceScalar<T,   CHUNKLENGTH> data;
       DataSetInterfaceScalar<int, CHUNKLENGTH> isvalid;
       BuffPair(DataSetInterfaceScalar<T, CHUNKLENGTH>& d,
                DataSetInterfaceScalar<int, CHUNKLENGTH>& v)
         : data(d)
         , isvalid(v)
       // Handy shortcut constructor
       BuffPair(hid_t location_id, const std::string& name)
         : data   (location_id,name,true,'r')
         , isvalid(location_id,name+"_isvalid",true,'r')
       // Default constructor, data uninitialised!
       BuffPair() {}

    // Forward declaration
    struct SLHAcombo;

    /// Keeps track of vertex buffers local to a retrieve function
    /// Similar to the buffer manager for HDF5Printer. I considered
    /// trying to re-use that, but it is too integrated with the
    /// printer.
    template<class T>
    class H5P_LocalReadBufferManager
        // Buffers local to a print function. Access whichever ones match the IDcode.
        std::map<VBIDpair, BuffPair<T>> local_buffers;

        /// Constructor

        /// Destructor. Close all datasets
          for(typename std::map<VBIDpair, BuffPair<T>>::iterator it=local_buffers.begin();
              it!=local_buffers.end(); ++it)

        /// Retrieve a buffer for an IDcode/auxilliary-index pair
        /// location_id used to access dataset if it has not yet been opened.
        BuffPair<T>& get_buffer(const int vID, const unsigned int i, const std::string& label, hid_t location_id);

    // A simple class to manage opening and closing a HDF5 file/group on construction and destruction
    class HDF5File
         HDF5File(const std::string& file, const std::string& group);
        const hid_t file_id;
        const hid_t location_id;

    class HDF5Reader : public BaseReader
        HDF5Reader(const Options& options);

        /// @{ Base class virtual interface functions
        virtual void reset(); // Reset 'read head' position to first entry
        virtual ulong get_dataset_length(); // Get length of input dataset
        virtual PPIDpair get_next_point(); // Get next rank/ptID pair in data file
        virtual PPIDpair get_current_point(); // Get current rank/ptID pair in data file
        virtual ulong    get_current_index(); // Get a linear index which corresponds to the current rank/ptID pair in the iterative sense
        virtual bool eoi(); // Check if 'current point' is past the end of the data file (and thus invalid!)
        /// Get type information for a data entry, i.e. defines the C++ type which this should be
        /// retrieved as, not what it is necessarily literally stored as in the output.
        virtual std::size_t get_type(const std::string& label);
        virtual std::set<std::string> get_all_labels(); // Get all dataset labels

        /// Retrieve functions
        using BaseReader::_retrieve; // Tell compiler we are using some of the base class overloads of this on purpose.
        #define DECLARE_RETRIEVE(r,data,i,elem) bool _retrieve(elem&, const std::string&, const uint, const ulong);
        #ifndef SCANNER_STANDALONE
        #undef DECLARE_RETRIEVE

        // Location of HDF5 datasets to be read
        const std::string file;
        const std::string group;
        HDF5File H5file; // contains file_id and location_id

        // Names of all datasets at the target location
        const std::vector<std::string> all_datasets;

        // MPIrank and pointID dataset wrappers
        DataSetInterfaceScalar<unsigned long, CHUNKLENGTH> pointIDs;
        DataSetInterfaceScalar<int, CHUNKLENGTH> pointIDs_isvalid;
        DataSetInterfaceScalar<int, CHUNKLENGTH> mpiranks;
        DataSetInterfaceScalar<int, CHUNKLENGTH> mpiranks_isvalid;

        ulong current_dataset_index; // index in input dataset of the current read-head position
        PPIDpair current_point;      // PPID of the point at the current read-head position

        // PPIDpair and dataset index of the last retrieved data.
        // Just to speed up "random access" retrieval of a lot of data from the same point
        ulong    mem_index;
        PPIDpair mem_point;

        // Search for the PPID supplied in the input data and return the index of the first match
        ulong get_index_from_PPID(const PPIDpair);

        template<class T>
        H5P_LocalReadBufferManager<T>& get_mybuffermanager();

        /// Buffer manager objects
        //  Need one for every directly retrievable type, and a specialisation
        //  of 'get_mybuffermanager' to access it. But the latter have to be
        //  defined outside the class declaration, so they can be found below.
        //  Could create all these with a macro, but I am sick of macros so
        //  will just do it the "old-fashioned" way.
        H5P_LocalReadBufferManager<int      > hdf5_localbufferman_int;
        H5P_LocalReadBufferManager<uint     > hdf5_localbufferman_uint;
        H5P_LocalReadBufferManager<long     > hdf5_localbufferman_long;
        H5P_LocalReadBufferManager<ulong    > hdf5_localbufferman_ulong;
        H5P_LocalReadBufferManager<longlong > hdf5_localbufferman_longlong;
        H5P_LocalReadBufferManager<ulonglong> hdf5_localbufferman_ulonglong;
        H5P_LocalReadBufferManager<float    > hdf5_localbufferman_float;
        H5P_LocalReadBufferManager<double   > hdf5_localbufferman_double;

        /// Helper function to parse a capability name to a dataset name
        void parse_capability_label(const std::string&, std::string&);

        /// "Master" templated retrieve function.
        template<class T>
        bool _retrieve_template(T& out, const std::string& label, int aux_id, const uint rank, const ulong pointID)
           // Retrieve the buffer manager for buffers with this type
           auto& buffer_manager = get_mybuffermanager<T>();

           // Parse the label to an actual parameter label
           std::string param_label;
           parse_capability_label(label, param_label);

           // Buffers are labelled by an IDcode, which in the printer case is a graph vertex.
           // In the reader case I think we can safely re-use this system to assign IDs:
           int IDcode = get_param_id(param_label);

           // Extract a buffer pair from the manager corresponding to this type + label
           auto& selected_buffer = buffer_manager.get_buffer(IDcode, aux_id, param_label, H5file.location_id);

           // Determine the dataset index from which to extract the input PPIDpair
           ulong dset_index = get_index_from_PPID(PPIDpair(pointID,rank));

           // Extract data value
           out =;

           // Extract data validity flag
           return selected_buffer.isvalid.get_entry(dset_index);

        /// Extra helper function for spectrum retrieval
        bool retrieve_and_add_to_SLHAea(SLHAstruct& out, bool& found, const std::string& spec_type, const std::string& entry, const SLHAcombo& item, const std::set<std::string>& all_dataset_labels, const uint rank, const ulong pointID);


    /// Buffer retrieve function
    template<class T>
    BuffPair<T>& H5P_LocalReadBufferManager<T>::get_buffer(const int vertexID, const unsigned int aux_i, const std::string& label, hid_t location_id)
     VBIDpair key;
     key.vertexID = vertexID;
     key.index    = aux_i;

     typename std::map<VBIDpair, BuffPair<T>>::iterator it = local_buffers.find(key);

     if( it == local_buffers.end() )
       error_if_key_exists(local_buffers, key, "local_buffers");
       // No local buffer exists for this output stream yet, so make one

       // Create the new buffer objects
          std::ostringstream errmsg;
          errmsg << "Failed to created HDF5 read buffer '"<<label<<"'! The suppied location_id does not point to a valid location in a HDF5 file!";
          printer_error().raise(LOCAL_INFO, errmsg.str());

       local_buffers[key] = BuffPair<T>(location_id,label);

       // Get the new buffer back out of the map
       it = local_buffers.find(key);

     if( it == local_buffers.end() )
       std::ostringstream errmsg;
       errmsg << "Error! Failed to retrieve newly created buffer (label="<<label<<") from local_buffers map! Key was: ("<<vertexID<<","<<aux_i<<")"<<std::endl;
       printer_error().raise(LOCAL_INFO, errmsg.str());

     return it->second;

    /// Define the buffermanager getter specialisations
      template<> \
      inline H5P_LocalReadBufferManager<TYPE>& \
        HDF5Reader::get_mybuffermanager() \
      { \
         return CAT(hdf5_localbufferman_,TYPE); \

    // Register reader so it can be constructed via inifile instructions
    // First argument is string label for inifile access, second is class from which to construct printer
    LOAD_READER(hdf5, HDF5Reader)



Updated on 2023-06-26 at 21:36:54 +0000