diff --git a/src/Grid/Iterators/grid_dist_id_iterator.hpp b/src/Grid/Iterators/grid_dist_id_iterator.hpp
index 7c80502a7d0860175b2dc9443bff7adb2a81715a..b44590e3ac6f2fa5a103bd8087e349423f96f142 100644
--- a/src/Grid/Iterators/grid_dist_id_iterator.hpp
+++ b/src/Grid/Iterators/grid_dist_id_iterator.hpp
@@ -8,49 +8,12 @@
#ifndef GRID_DIST_ID_ITERATOR_HPP_
#define GRID_DIST_ID_ITERATOR_HPP_
-/*! \brief This structure store the Box that define the domain inside the Ghost + domain box
- *
- \verbatim
-
- (Ghost + Domain)
- +------------------+
- | |
- | +------------+ <---------- (Domain)
- | | | |
- | | Domain | |
- | | Box | |
- | | | |
- | | | |
- | +------------+ |
- | |
- +------------------+
-(0,0) local coordinate ---> ( x, y )
-
- \endverbatim
-
- *
- * * Domain
- *
- * \tparam dim dimensionality
- *
- */
-template<unsigned int dim>
-struct GBoxes
-{
- //! Ghost + Domain ghost
- Box<dim,long int> GDbox;
- //! Domain box
- Box<dim,long int> Dbox;
- //! origin of GDbox in global grid coordinates
- Point<dim,long int> origin;
-};
-
#define FREE 1
#define FIXED 2
#include "Grid/grid_dist_key.hpp"
#include "VCluster/VCluster.hpp"
-
+#include "util/GBoxes.hpp"
/*! \brief Distributed grid iterator
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index e974dce4f28e85e755ce7f91eacc73e28695a622..81c435277af81e50682fdc8d9be0bf5ce3b2b164 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -21,6 +21,7 @@
#include "data_type/aggregate.hpp"
#include "hdf5.h"
#include "grid_dist_id_comm.hpp"
+#include "HDF5_wr/HDF5_wr.hpp"
//! Internal ghost box sent to construct external ghost box into the other processors
template<unsigned int dim>
@@ -1063,7 +1064,7 @@ public:
if (v_cl.getProcessUnitID() == 0)
{
- for (size_t i = 0; i < v_cl.getProcessingUnits(); i++)
+ for (size_t i = 1; i < v_cl.getProcessingUnits(); i++)
{
v_cl.send(i,0,gdb_ext_global);
}
@@ -1702,153 +1703,9 @@ public:
inline void save(const std::string & filename) const
{
- //std::cout << "Loc_grid.size() before save: " << loc_grid.size() << std::endl;
- //std::cout << "Gdb_ext.size() before save: " << gdb_ext.size() << std::endl;
-
- //Pack_request vector
- size_t req = 0;
-
- //Pack request
- Packer<decltype(loc_grid),HeapMemory>::packRequest(loc_grid,req);
- Packer<decltype(gdb_ext),HeapMemory>::packRequest(gdb_ext,req);
-
- //std::cout << "Req: " << req << std::endl;
-
- // allocate the memory
- HeapMemory pmem;
- //pmem.allocate(req);
- ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(req,pmem));
- mem.incRef();
-
- //Packing
-
- Pack_stat sts;
-
- Packer<decltype(loc_grid),HeapMemory>::pack(mem,loc_grid,sts);
- Packer<decltype(gdb_ext),HeapMemory>::pack(mem,gdb_ext,sts);
-
- /*****************************************************************
- * Create a new file with default creation and access properties.*
- * Then create a dataset and write data to it and close the file *
- * and dataset. *
- *****************************************************************/
-
- int mpi_rank = v_cl.getProcessUnitID();
- int mpi_size = v_cl.getProcessingUnits();
-
- MPI_Comm comm = v_cl.getMPIComm();
- MPI_Info info = MPI_INFO_NULL;
-
- // 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);
-
- // Create a new file collectively and release property list identifier.
- hid_t file = H5Fcreate (filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
- H5Pclose(plist_id);
-
- size_t sz = pmem.size();
- //std::cout << "Pmem.size: " << pmem.size() << std::endl;
- openfpm::vector<size_t> sz_others;
- v_cl.allGather(sz,sz_others);
- v_cl.execute();
-
- size_t sum = 0;
-
- for (size_t i = 0; i < sz_others.size(); i++)
- sum += sz_others.get(i);
-
- //Size for data space in file
- hsize_t fdim[1] = {sum};
-
- //Size for data space in file
- hsize_t fdim2[1] = {(size_t)mpi_size};
-
- //Create data space in file
- hid_t file_dataspace_id = H5Screate_simple(1, fdim, NULL);
-
- //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()};
+ HDF5_writer<GRID_DIST> h5s;
- //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;
-
- //Create data set in file
- 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);
-
- //H5Pclose(plist_id);
- H5Sclose(file_dataspace_id);
- H5Sclose(file_dataspace_id_2);
-
- hsize_t block[1] = {pmem.size()};
-
- //hsize_t stride[1] = {1};
-
- hsize_t count[1] = {1};
-
- hsize_t offset[1] = {0};
-
- for (int i = 0; i < mpi_rank; i++)
- {
- if (mpi_rank == 0)
- offset[0] = 0;
- else
- offset[0] += sz_others.get(i);
- }
-
- // std::cout << "MPI rank: " << mpi_rank << ", MPI size: " << mpi_size << ", Offset: " << offset[0] << ", Block: " << block[0] << std::endl;
-
- 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);
-
- //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());
-
- //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;
- }
-*/
- //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);
+ h5s.save(filename,loc_grid,gdb_ext);
}
void load_block(long int bid,
diff --git a/src/main.cpp b/src/main.cpp
index 6bdee796eaec9c4315bb4e5f10342068a0e1b7ea..7cf1c11787eaa5cd430064d805a7ec6980b0a8fc 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -37,7 +37,6 @@ int main(int argc, char* argv[])
#include "Graph/dist_map_graph.hpp"
#include "memory/HeapMemory.hpp"
#include "Space/Shape/Box.hpp"
-#include "util.hpp"
#include "unit_test_init_cleanup.hpp"
#include "Graph/CartesianGraphFactory_unit_test.hpp"