Adding missing files

src/HDF5_wr/HDF5_reader_gd.hpp

+/*
+ * HDF5_reader_gr.hpp
+ *
+ *  Created on: May 2, 2017
+ *      Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_GD_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_GD_HPP_
+
+
+#include "Packer_Unpacker/Pack_selector.hpp"
+#include "Packer_Unpacker/Packer.hpp"
+#include "Packer_Unpacker/Unpacker.hpp"
+#include "util/GBoxes.hpp"
+
+template <>
+class HDF5_reader<GRID_DIST>
+{
+	template<typename device_grid> void load_block(long int bid,
+			        hssize_t mpi_size_old,
+					int * metadata_out,
+					openfpm::vector<size_t> & metadata_accum,
+					hid_t plist_id,
+					hid_t dataset_2,
+					openfpm::vector<device_grid> & loc_grid_old,
+					openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext_old)
+	{
+		hsize_t offset[1];
+		hsize_t block[1];
+
+		if (bid < mpi_size_old && bid != -1)
+		{
+			offset[0] = metadata_accum.get(bid);
+			block[0] = metadata_out[bid];
+		}
+		else
+		{
+			offset[0] = 0;
+			block[0] = 0;
+		}
+
+	    hsize_t count[1] = {1};
+
+		//Select file dataspace
+		hid_t file_dataspace_id_2 = H5Dget_space(dataset_2);
+
+        H5Sselect_hyperslab(file_dataspace_id_2, H5S_SELECT_SET, offset, NULL, count, block);
+
+        hsize_t mdim_2[1] = {block[0]};
+
+		//Create data space in memory
+		hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
+
+		// allocate the memory
+		HeapMemory pmem;
+		//pmem.allocate(req);
+		ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
+		mem.incRef();
+
+	  	// Read the dataset.
+	    H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer());
+
+		mem.allocate(pmem.size());
+
+		Unpack_stat ps;
+
+		openfpm::vector<device_grid> loc_grid_old_unp;
+		openfpm::vector<GBoxes<device_grid::dims>> gdb_ext_old_unp;
+
+		Unpacker<typename std::remove_reference<decltype(loc_grid_old)>::type,HeapMemory>::unpack(mem,loc_grid_old_unp,ps,1);
+		Unpacker<typename std::remove_reference<decltype(gdb_ext_old)>::type,HeapMemory>::unpack(mem,gdb_ext_old_unp,ps,1);
+
+		for (size_t i = 0; i < loc_grid_old_unp.size(); i++)
+			loc_grid_old.add(loc_grid_old_unp.get(i));
+
+		for (size_t i = 0; i < gdb_ext_old_unp.size(); i++)
+			gdb_ext_old.add(gdb_ext_old_unp.get(i));
+
+		mem.decRef();
+		delete &mem;
+
+	}
+
+public:
+
+	template<typename device_grid> inline void load(const std::string & filename,
+													openfpm::vector<device_grid> & loc_grid_old,
+													openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext_old)
+	{
+		Vcluster & v_cl = create_vcluster();
+
+		MPI_Comm comm = v_cl.getMPIComm();
+		MPI_Info info  = MPI_INFO_NULL;
+
+		int mpi_rank = v_cl.getProcessUnitID();
+		//int mpi_size = v_cl.getProcessingUnits();
+
+		// Set up file access property list with parallel I/O access
+		hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
+		H5Pset_fapl_mpio(plist_id, comm, info);
+
+		//Open a file
+	    hid_t file = H5Fopen (filename.c_str(), H5F_ACC_RDONLY, plist_id);
+	    H5Pclose(plist_id);
+
+	    //Open dataset
+	    hid_t dataset = H5Dopen (file, "metadata", H5P_DEFAULT);
+
+	    //Create property list for collective dataset read
+	  	plist_id = H5Pcreate(H5P_DATASET_XFER);
+	  	H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+
+		//Select file dataspace
+		hid_t file_dataspace_id = H5Dget_space(dataset);
+
+		hssize_t mpi_size_old = H5Sget_select_npoints (file_dataspace_id);
+
+		//if (mpi_rank == 0)
+			//printf ("\nOld MPI size: %llu\n", mpi_size_old);
+
+	  	//Where to read metadata
+	  	int metadata_out[mpi_size_old];
+
+	  	for (int i = 0; i < mpi_size_old; i++)
+	  	{
+	  		metadata_out[i] = 0;
+	  	}
+
+		//Size for data space in memory
+		hsize_t mdim[1] = {(size_t)mpi_size_old};
+
+		//Create data space in memory
+		hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
+
+/*
+		if (mpi_rank == 0)
+		{
+			hssize_t size;
+
+			size = H5Sget_select_npoints (mem_dataspace_id);
+			printf ("\nmemspace_id size: %llu\n", size);
+			size = H5Sget_select_npoints (file_dataspace_id);
+			printf ("dataspace_id size: %llu\n", size);
+		}
+*/
+	  	// Read the dataset.
+	    H5Dread(dataset, H5T_NATIVE_INT, mem_dataspace_id, file_dataspace_id, plist_id, metadata_out);
+/*
+		if (mpi_rank == 0)
+		{
+			std::cout << "Metadata_out[]: ";
+			for (int i = 0; i < mpi_size_old; i++)
+			{
+				std::cout << metadata_out[i] << " ";
+			}
+			std::cout << " " << std::endl;
+		}
+*/
+
+	    openfpm::vector<size_t> metadata_accum;
+	    metadata_accum.resize(mpi_size_old);
+
+	    metadata_accum.get(0) = 0;
+	    for (int i = 1 ; i < mpi_size_old ; i++)
+	    	metadata_accum.get(i) = metadata_accum.get(i-1) + metadata_out[i-1];
+
+	    //Open dataset
+	    hid_t dataset_2 = H5Dopen (file, "grid_dist", H5P_DEFAULT);
+
+	    //Create property list for collective dataset read
+	  	plist_id = H5Pcreate(H5P_DATASET_XFER);
+	  	H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+
+	  	/////////////////////////////////////
+
+	  	openfpm::vector<size_t> n_block;
+	  	n_block.resize(v_cl.getProcessingUnits());
+
+
+	  	for(size_t i = 0 ; i < n_block.size() ; i++)
+	  		n_block.get(i) = mpi_size_old / v_cl.getProcessingUnits();
+
+	  	size_t rest_block = mpi_size_old % v_cl.getProcessingUnits();
+
+	  //	std::cout << "MPI size old: " << mpi_size_old << std::endl;
+	  	//std::cout << "MPI size: " << v_cl.getProcessingUnits() << std::endl;
+
+
+	  //	std::cout << "Rest block: " << rest_block << std::endl;
+
+	  	size_t max_block;
+
+	  	if (rest_block != 0)
+	  		max_block = n_block.get(0) + 1;
+	  	else
+	  		max_block = n_block.get(0);
+
+	  	//for(size_t i = 0 ; i < n_block.size() ; i++)
+	  	for(size_t i = 0 ; i < rest_block ; i++)
+	  		n_block.get(i) += 1;
+
+
+	  	//for(size_t i = 0 ; i < n_block.size() ; i++)
+	  		//std::cout << "n_block.get(i): " << n_block.get(i) << std::endl;
+
+	  	size_t start_block = 0;
+	  	size_t stop_block = 0;
+
+
+	  	if (v_cl.getProcessUnitID() != 0)
+	  	{
+			for(size_t i = 0 ; i < v_cl.getProcessUnitID() ; i++)
+				start_block += n_block.get(i);
+	  	}
+
+	  	stop_block = start_block + n_block.get(v_cl.getProcessUnitID());
+
+//	  	std::cout << "ID: " << v_cl.getProcessUnitID() << "; Start block: " << start_block << "; " << "Stop block: " << stop_block << std::endl;
+
+	  	if (mpi_rank >= mpi_size_old)
+	  		load_block(start_block,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,loc_grid_old,gdb_ext_old);
+	  	else
+	  	{
+	  		size_t n_bl = 0;
+	  		size_t lb = start_block;
+			for ( ; lb < stop_block ; lb++, n_bl++)
+				load_block(lb,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,loc_grid_old,gdb_ext_old);
+
+			if (n_bl < max_block)
+				load_block(-1,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,loc_grid_old,gdb_ext_old);
+	  	}
+
+	  	////////////////////////////////////
+
+		//std::cout << "LOAD: sum: " << sum << std::endl;
+
+	    // Close the dataset.
+	    H5Dclose(dataset);
+	    H5Dclose(dataset_2);
+	    // Close the file.
+	    H5Fclose(file);
+	    H5Pclose(plist_id);
+	}
+
+};
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_GD_HPP_ */