Several fix 2GB HDF5 + NO_POSITION wrong on GPU + CSV Writer + Adding DETERMINISTIC cell list

CMakeLists.txt

@@ -39,9 +39,12 @@ if(ENABLE_GPU)
         elseif ( CUDA_VERSION_MAJOR EQUAL 10 AND CUDA_VERSION_MINOR EQUAL 1 )
                 message("CUDA is compatible")
                 set(WARNING_SUPPRESSION_AND_OPTION_NVCC  -Xcudafe "--display_error_number --diag_suppress=2915 --diag_suppress=2912 --diag_suppress=2913 --diag_suppress=111 --diag_suppress=186 --diag_suppress=611 --diag_suppress=2928 --diag_suppress=2931 --diag_suppress=2929 --diag_suppress=2930" --expt-extended-lambda)
-
+        elseif ( CUDA_VERSION_MAJOR EQUAL 10 AND CUDA_VERSION_MINOR EQUAL 2 )
+                message("CUDA is compatible")
+                set(WARNING_SUPPRESSION_AND_OPTION_NVCC  -Xcudafe "--display_error_number --diag_suppress=2976 --diag_suppress=2977 --diag_suppress=2978 --diag_suppress=2979 --diag_suppress=1835 --diag_suppress=611 --diag_suppress=186 --diag_suppress=128" --expt-extended-lambda)
+                set(WARNING_SUPPRESSION_AND_OPTION_NVCC_TEXT  "-Xcudafe \"--display_error_number --diag_suppress=2976 --diag_suppress=2977 --diag_suppress=2978 --diag_suppress=2979 --diag_suppress=1835 --diag_suppress=611 --diag_suppress=186 --diag_suppress=128\" --expt-extended-lambda")
         else()
-                message(FATAL_ERROR "CUDA is incompatible, version 9.2 is only supported")
+                message(FATAL_ERROR "CUDA is incompatible, version 9.2 10.1 and 10.2 is only supported")
         endif()
 endif()
 

src/CSVWriter/CSVWriter.hpp

@@ -14,7 +14,7 @@
 #include <fstream>
 #include "util/common.hpp"
 #include <boost/mpl/range_c.hpp>
-#include "util/for_each_ref_host.hpp"
+#include <boost/mpl/for_each.hpp>
 #include "csv_multiarray.hpp"
 #include "util/util.hpp"
 #include "is_csv_writable.hpp"
@@ -57,7 +57,7 @@ struct csv_prp
     void operator()(T& t)
     {
 		// This is the type of the csv column
-		typedef decltype(obj.template get<T::value>()) col_type;
+		typedef typename boost::mpl::at<typename Tobj::type,T>::type col_type;
 
 		// Remove the reference from the column type
 		typedef typename boost::remove_reference<col_type>::type col_rtype;
@@ -183,7 +183,7 @@ class CSVWriter
 		csv_col<typename v_prp::value_type,has_attributes<typename v_prp::value_type>::value> col(str);
 
 		// Iterate through all the vertex and create the vertex list
-		boost::mpl::for_each_ref_host< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(col);
+		boost::mpl::for_each< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(col);
 
 		str << "\n";
 
@@ -225,7 +225,7 @@ class CSVWriter
 			csv_prp<decltype(obj)> c_prp(str,obj);
 
 			// write the properties to the stream string
-			boost::mpl::for_each_ref_host< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(c_prp);
+			boost::mpl::for_each< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(c_prp);
 
 			str << "\n";
 		}

src/CSVWriter/csv_multiarray.hpp

@@ -137,7 +137,8 @@ struct csv_value_str
 template<typename T,size_t N1, bool is_writable>
 struct csv_value_str<T[N1], is_writable>
 {
-	inline csv_value_str(const T v[N1], std::stringstream & str)
+	template<typename ArrObject>
+	inline csv_value_str(const ArrObject v, std::stringstream & str)
 	{
 		for (size_t i = 0 ; i < N1 ; i++)
 			str << "," << v[i];
@@ -148,7 +149,8 @@ struct csv_value_str<T[N1], is_writable>
 template<typename T,size_t N1,size_t N2, bool is_writable>
 struct csv_value_str<T[N1][N2], is_writable>
 {
-	inline csv_value_str(const T v[N1][N2], std::stringstream & str)
+	template<typename ArrObject>
+	inline csv_value_str(const ArrObject v, std::stringstream & str)
 	{
 		for (size_t i1 = 0 ; i1 < N1 ; i1++)
 		{
@@ -164,7 +166,8 @@ struct csv_value_str<T[N1][N2], is_writable>
 template<typename T,size_t N1,size_t N2,size_t N3, bool is_writable>
 struct csv_value_str<T[N1][N2][N3], is_writable>
 {
-	inline csv_value_str(const T v[N1][N2][N3], std::stringstream & str)
+	template<typename ArrObject>
+	inline csv_value_str(const  ArrObject v, std::stringstream & str)
 	{
 		for (size_t i1 = 0 ; i1 < N1 ; i1++)
 		{
@@ -183,7 +186,8 @@ struct csv_value_str<T[N1][N2][N3], is_writable>
 template<typename T,size_t N1,size_t N2,size_t N3,size_t N4, bool is_writable>
 struct csv_value_str<T[N1][N2][N3][N4],is_writable>
 {
-	inline csv_value_str(const T v[N1][N2][N3][N4], std::stringstream & str)
+	template<typename ArrObject>
+	inline csv_value_str(const ArrObject v, std::stringstream & str)
 	{
 		for (size_t i1 = 0 ; i1 < N1 ; i1++)
 		{

src/CSVWriter/is_csv_writable.hpp

@@ -141,5 +141,37 @@ struct is_csv_writable<bool>
 	};
 };
 
+//! Indicate if the property T is writable in CSV
+template<typename T, unsigned int N1>
+struct is_csv_writable<T[N1]>
+{
+	//! bool is writable
+	enum
+	{
+		value = true
+	};
+};
+
+//! Indicate if the property T is writable in CSV
+template<typename T, unsigned int N1, unsigned int N2>
+struct is_csv_writable<T[N1][N2]>
+{
+	//! bool is writable
+	enum
+	{
+		value = true
+	};
+};
+
+//! Indicate if the property T is writable in CSV
+template<typename T, unsigned int N1, unsigned int N2, unsigned int N3>
+struct is_csv_writable<T[N1][N2][N3]>
+{
+	//! bool is writable
+	enum
+	{
+		value = true
+	};
+};
 
 #endif /* OPENFPM_IO_SRC_CSVWRITER_IS_CSV_WRITABLE_HPP_ */

src/HDF5_wr/HDF5_reader_gd.hpp

@@ -19,7 +19,7 @@ class HDF5_reader<GRID_DIST>
 {
 	template<typename device_grid> void load_block(long int bid,
 			        hssize_t mpi_size_old,
-					int * metadata_out,
+					long int * metadata_out,
 					openfpm::vector<size_t> & metadata_accum,
 					hid_t plist_id,
 					hid_t dataset_2,
@@ -42,24 +42,37 @@ class HDF5_reader<GRID_DIST>
 
 	    hsize_t count[1] = {1};
 
+		// allocate the memory
+		HeapMemory pmem;
+		//pmem.allocate(req);
+		ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
+		mem.incRef();
+
 		//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);
+	    size_t to_read = block[0];
+	    size_t coffset = 0;
 
-        hsize_t mdim_2[1] = {block[0]};
+	    while (to_read)
+	    {
+			hsize_t block_c[1];
+			block_c[0] = std::min((size_t)(to_read),(size_t)0x7FFFFFFF);
 
-		//Create data space in memory
-		hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
+			hsize_t offset_c[1] = {offset[0] + coffset};
+			H5Sselect_hyperslab(file_dataspace_id_2, H5S_SELECT_SET, offset_c, NULL, count, block_c);
 
-		// allocate the memory
-		HeapMemory pmem;
-		//pmem.allocate(req);
-		ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
-		mem.incRef();
+			hsize_t mdim_2[1] = {block_c[0]};
 
-	  	// Read the dataset.
-	    H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer());
+			//Create data space in memory
+			hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
+
+			// Read the dataset.
+			H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer() + coffset);
+
+			coffset += std::min((size_t)(to_read),(size_t)0x7FFFFFFF);
+			to_read -= std::min((size_t)(to_read),(size_t)0x7FFFFFFF);
+	    }
 
 		mem.allocate(pmem.size());
 
@@ -72,7 +85,10 @@ class HDF5_reader<GRID_DIST>
 		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));
+		{
+			loc_grid_old.add();
+			loc_grid_old.last().swap(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));
@@ -120,7 +136,7 @@ public:
 			//printf ("\nOld MPI size: %llu\n", mpi_size_old);
 
 	  	//Where to read metadata
-	  	int metadata_out[mpi_size_old];
+	  	long int metadata_out[mpi_size_old];
 
 	  	for (int i = 0; i < mpi_size_old; i++)
 	  	{
@@ -133,30 +149,9 @@ public:
 		//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;
-		}
-*/
+	    H5Dread(dataset, H5T_NATIVE_LLONG, mem_dataspace_id, file_dataspace_id, plist_id, metadata_out);
+
 
 	    openfpm::vector<size_t> metadata_accum;
 	    metadata_accum.resize(mpi_size_old);
@@ -183,12 +178,6 @@ public:
 
 	  	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)

src/HDF5_wr/HDF5_writer_gd.hpp

@@ -92,12 +92,6 @@ public:
 		//Create data space in file
 		hid_t file_dataspace_id_2 = H5Screate_simple(1, fdim2, NULL);
 
-		//Size for data space in memory
-		hsize_t mdim[1] = {pmem.size()};
-
-		//Create data space in memory
-		hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
-
 		//if (mpi_rank == 0)
 			//std::cout << "Total object size: " << sum << std::endl;
 
@@ -105,7 +99,7 @@ public:
 		hid_t file_dataset = H5Dcreate (file, "grid_dist", H5T_NATIVE_CHAR, file_dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
 
 		//Create data set 2 in file
-		hid_t file_dataset_2 = H5Dcreate (file, "metadata", H5T_NATIVE_INT, file_dataspace_id_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+		hid_t file_dataset_2 = H5Dcreate (file, "metadata", H5T_NATIVE_LLONG, file_dataspace_id_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
 
 	    //H5Pclose(plist_id);
 	    H5Sclose(file_dataspace_id);
@@ -132,45 +126,51 @@ public:
 
 	//    std::cout << "MPI rank: " << mpi_rank << ", MPI size: " << mpi_size << ", Offset: " << offset[0] << ", Block: " << block[0] << std::endl;
 
-	    int metadata[mpi_size];
+	    long int metadata[mpi_size];
 
 	    for (int i = 0; i < mpi_size; i++)
 	    	metadata[i] = sz_others.get(i);
 
 	    //Select hyperslab in the file.
 	    file_dataspace_id = H5Dget_space(file_dataset);
-	    H5Sselect_hyperslab(file_dataspace_id, H5S_SELECT_SET, offset, NULL, count, block);
 
-	    file_dataspace_id_2 = H5Dget_space(file_dataset_2);
+            //Create property list for collective dataset write.
+            plist_id = H5Pcreate(H5P_DATASET_XFER);
+            H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
 
+	    // We slipt the write in chunk of 2GB maximum
+	    size_t to_write = block[0];
+	    size_t coffset = 0;
+	    while (to_write)
+	    {
+			hsize_t block_c[1];
+			block_c[0] = std::min((size_t)(to_write),(size_t)0x7FFFFFFF);
 
-	    //Create property list for collective dataset write.
-	    plist_id = H5Pcreate(H5P_DATASET_XFER);
-	    H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+			//Create data space in memory
+			hid_t mem_dataspace_id = H5Screate_simple(1, block_c, NULL);
 
-		//Write a data set to a file
-		H5Dwrite(file_dataset, H5T_NATIVE_CHAR, mem_dataspace_id, file_dataspace_id, plist_id, (const char *)pmem.getPointer());
+			hsize_t offset_c[1] = {offset[0] + coffset};
+			H5Sselect_hyperslab(file_dataspace_id, H5S_SELECT_SET, offset_c, NULL, count, block_c);
 
-		//Write a data set 2 to a file
-		H5Dwrite(file_dataset_2, H5T_NATIVE_INT, H5S_ALL, file_dataspace_id_2, plist_id, metadata);
-/*
-		for (size_t i = 0; i < gdb_ext.size(); i++)
-		{
-			Box<dim,long int> box = gdb_ext.get(i).Dbox;
-			std::cout << "Dboxes saved: (" << box.getLow(0) << "; " << box.getLow(1) << "); (" << box.getHigh(0) << "; " << box.getHigh(1) << ")" << std::endl;
-		}
-
-		for (size_t i = 0; i < loc_grid.size(); i++)
-		{
-			std::cout << "loc_grids saved: (" << loc_grid.get(i).getGrid().getBox().getLow(0) << "; " << loc_grid.get(i).getGrid().getBox().getLow(1) << "); (" << loc_grid.get(i).getGrid().getBox().getHigh(0) << "; " << loc_grid.get(i).getGrid().getBox().getHigh(1) << ")" << std::endl;
-		}
-*/
+			//Write a data set to a file
+			H5Dwrite(file_dataset, H5T_NATIVE_CHAR, mem_dataspace_id, file_dataspace_id, plist_id, (const char *)pmem.getPointer() + coffset);
+
+			coffset += std::min((size_t)(to_write),(size_t)0x7FFFFFFF);
+			to_write -= std::min((size_t)(to_write),(size_t)0x7FFFFFFF);
+
+			H5Sclose(mem_dataspace_id);
+	    }
+
+	    file_dataspace_id_2 = H5Dget_space(file_dataset_2);
+
+	    //Write a data set 2 to a file
+	    H5Dwrite(file_dataset_2, H5T_NATIVE_LLONG, H5S_ALL, file_dataspace_id_2, plist_id, metadata);
+	    
 	    //Close/release resources.
 	    H5Dclose(file_dataset);
 	    H5Sclose(file_dataspace_id);
 	    H5Dclose(file_dataset_2);
 	    H5Sclose(file_dataspace_id_2);
-	    H5Sclose(mem_dataspace_id);
 	    H5Pclose(plist_id);
 	    H5Fclose(file);
 	}