diff --git a/openfpm_data b/openfpm_data
index e9c615ab034051ea1bb666930189c9b0ee745fc4..6c8ba9db530c53c09c9212dff5098a5b4890fb23 160000
--- a/openfpm_data
+++ b/openfpm_data
@@ -1 +1 @@
-Subproject commit e9c615ab034051ea1bb666930189c9b0ee745fc4
+Subproject commit 6c8ba9db530c53c09c9212dff5098a5b4890fb23
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index 09efc279832eb640fc9ef986ad13a25617ace20d..e974dce4f28e85e755ce7f91eacc73e28695a622 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -1044,19 +1044,18 @@ public:
v_cl.execute();
size_t size_r;
+ size_t size = gdb_ext_global.size();
if (v_cl.getProcessUnitID() == 0)
{
- size_t size = gdb_ext_global.size();
- 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,&size,sizeof(size_t));
- }
+
+ size_r = size;
}
else
- {
v_cl.recv(0,0,&size_r,sizeof(size_t));
- }
+
v_cl.execute();
gdb_ext_global.resize(size_r);
@@ -1077,52 +1076,6 @@ public:
v_cl.execute();
}
- /*! \brief It gathers the local grids for all of the processors
- *
- *
- *
- */
- void getGlobalGrids(openfpm::vector<openfpm::vector<device_grid>> & loc_grid_global) const
- {
-#ifdef SE_CLASS2
- check_valid(this,8);
-#endif
- v_cl.SGather(loc_grid,loc_grid_global,0);
- v_cl.execute();
-
- size_t size_r;
-
- if (v_cl.getProcessUnitID() == 0)
- {
- size_t size = loc_grid_global.size();
- for (size_t i = 0; i < v_cl.getProcessingUnits(); i++)
- {
- v_cl.send(i,0,&size,sizeof(size_t));
- }
- }
- else
- {
- v_cl.recv(0,0,&size_r,sizeof(size_t));
- }
- v_cl.execute();
-
- loc_grid_global.resize(size_r);
-
-
- if (v_cl.getProcessUnitID() == 0)
- {
- for (size_t i = 0; i < v_cl.getProcessingUnits(); i++)
- {
- v_cl.send(i,0,loc_grid_global);
- }
- }
- else
- {
- v_cl.recv(0,0,loc_grid_global);
- }
-
- v_cl.execute();
- }
/*! \brief It return an iterator that span the full grid domain (each processor span its local domain)
*
@@ -1898,7 +1851,12 @@ public:
H5Fclose(file);
}
- 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)
+ 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)
{
/* if (mpi_size >= mpi_size_old)
{
@@ -2037,12 +1995,12 @@ public:
printf ("LOAD: dataspace_id_3 size: %llu\n", size2);
}
*/
- size_t sum = 0;
+/* size_t sum = 0;
for (int i = 0; i < mpi_size_old; i++)
{
sum += metadata_out[i];
- }
+ }*/
// std::cout << "LOAD: sum: " << sum << std::endl;
diff --git a/src/Grid/grid_dist_id_HDF5_chckpnt_restart_test.hpp b/src/Grid/grid_dist_id_HDF5_chckpnt_restart_test.hpp
index cfb08eee597377cd3b7f9fd82ed8f9ac7f17b3ea..fd63918ace57d8f4a9f4f65bda40651e83fec643 100644
--- a/src/Grid/grid_dist_id_HDF5_chckpnt_restart_test.hpp
+++ b/src/Grid/grid_dist_id_HDF5_chckpnt_restart_test.hpp
@@ -29,9 +29,6 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_save_test )
if (v_cl.getProcessingUnits() >= 32)
return;
- if (v_cl.getProcessUnitID() == 0)
- std::cout << "Saving Distributed 2D Grid..." << std::endl;
-
// grid size
size_t sz[2];
sz[0] = k;
@@ -67,8 +64,6 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_save_test )
count++;
}
- std::cout << "Count: " << count << std::endl;
-
openfpm::vector<size_t> count_total;
v_cl.allGather(count,count_total);
v_cl.execute();
@@ -78,15 +73,11 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_save_test )
for (size_t i = 0; i < count_total.size(); i++)
sum += count_total.get(i);
- std::cout << "Sum: " << sum << std::endl;
-
timer t;
t.start();
// Save the grid
g_dist.save("grid_dist_id.h5");
t.stop();
-
- std::cout << "Saving time: " << t.getwct() << std::endl;
}
BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_load_test )
@@ -106,9 +97,6 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_load_test )
if (v_cl.getProcessingUnits() >= 32)
return;
- if (v_cl.getProcessUnitID() == 0)
- std::cout << "Loading Distributed 2D Grid..." << std::endl;
-
// grid size
size_t sz[2];
sz[0] = k;
@@ -132,8 +120,6 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_load_test )
g_dist.write("Loaded_grid");
g_dist.getDecomposition().write("Loaded_grid_decomposition");
- std::cout << "Loading time: " << t.getwct() << std::endl;
-
auto it = g_dist.getDomainIterator();
size_t count = 0;
@@ -154,8 +140,6 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_load_test )
count++;
}
- std::cout << "COOOOOOUNT: " << count << std::endl;
-
openfpm::vector<size_t> count_total;
v_cl.allGather(count,count_total);
v_cl.execute();
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index f9ad21357004b694985bf088fffa5beb9900dbbc..781e12bd978988a7be54e7d5ed26d05437c1b42e 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -10,7 +10,7 @@
#include "../../openfpm_data/src/NN/CellList/CellListFast_gen.hpp"
#include "../../openfpm_data/src/NN/CellList/CellListFast_gen.hpp"
-#include "HDF5_XdmfWriter/HDF5_XdmfWriter.hpp"
+#include "HDF5_wr/HDF5_wr.hpp"
#include "VCluster/VCluster.hpp"
#include "Space/Shape/Point.hpp"
#include "Vector/Iterators/vector_dist_iterator.hpp"
@@ -745,21 +745,6 @@ public:
}
- /*! \brief Construct a cell list symmetric based on a cut of radius
- *
- * \tparam CellL CellList type to construct
- *
- * \param r_cut interation radius, or size of each cell
- *
- * \return the Cell list
- *
- */
- template<typename CellL = CellList<dim, St, FAST, shift<dim, St> > > CellL getCellListSymNoBind(St r_cut)
- {
- return getCellList(r_cut);
- }
-
-
/*! \brief Construct a cell list starting from the stored particles
*
* \tparam CellL CellList type to construct
@@ -1613,513 +1598,16 @@ public:
inline void save(const std::string & filename) const
{
- //Pack_request vector
- size_t req = 0;
-
- //std::cout << "V_pos.size() before save: " << v_pos.size() << std::endl;
-
- //Pack request
- Packer<decltype(v_pos),HeapMemory>::packRequest(v_pos,req);
- Packer<decltype(v_prp),HeapMemory>::packRequest(v_prp,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(v_pos),HeapMemory>::pack(mem,v_pos,sts);
- Packer<decltype(v_prp),HeapMemory>::pack(mem,v_prp,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;
-/*
- //Initialize MPI
- MPI_Comm_size(comm, &mpi_size);
- MPI_Comm_rank(comm, &mpi_rank);
-*/
- // 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()};
-
- //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, "vector_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()};
+ HDF5_writer<VECTOR_DIST> h5s;
- //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);
-
-
- //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);
- }
-
- 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)
- {
-/* if (mpi_size >= mpi_size_old)
- {
- if (mpi_rank >= mpi_size_old)
- block[0] = 0;
- else
- block[0] = {(size_t)metadata_out[mpi_rank]};
- }
- else
- {
- int x = mpi_size_old/mpi_size;
- int shift = mpi_rank*x;
- for (int i = 0; i < x; i++)
- {
- //block0.get(mpi_rank).add(metadata_out[shift]);
- block[0] += metadata_out[shift];
- shift++;
- }
- int y = mpi_size_old%mpi_size;
- if (mpi_rank < y)
- {
- block_add[0] += metadata_out[mpi_size*x+mpi_rank];
- //block_add0.get(mpi_rank).add(metadata_out[mpi_size*x+mpi_rank]);
- }
- }*/
-
-// std::cout << "BID: " << bid << std::endl;
-
- 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;
- }
-
-// std::cout << "Offset: " << offset[0] << "; Block: " << block[0]<< std::endl;
-// hsize_t offset_add[1] = {0};
-
-/* if (mpi_size >= mpi_size_old)
- {
- if (mpi_rank >= mpi_size_old)
- offset[0] = 0;
- else
- {
- for (int i = 0; i < mpi_rank; i++)
- offset[0] += metadata_out[i];
- }
- }
- else
- {
- int x = mpi_size_old/mpi_size;
- int shift = mpi_rank*x;
-
- for (int i = 0; i < shift; i++)
- {
- offset[0] += metadata_out[i];
- //offset0.get(mpi_rank).add(metadata_out[i]);
- }
-
- int y = mpi_size_old%mpi_size;
- if (mpi_rank < y)
- {
- for (int i = 0; i < mpi_size*x + mpi_rank; i++)
- {
- offset_add[0] += metadata_out[i];
- //offset_add0.get(mpi_rank).add(metadata_out[i]);
- }
- }
- }*/
-
- //hsize_t stride[1] = {1};
- hsize_t count[1] = {1};
-
- //std::cout << "LOAD: MPI rank: " << mpi_rank << ", MPI size: " << mpi_size << ", Offset: " << offset[0] << ", Offset_add: " << offset_add[0] << ", Block: " << block[0] << ", Block_add: " << block_add[0] << std::endl;
-/*
- std::cout << "LOAD: MPI rank: " << mpi_rank << ", MPI size: " << mpi_size << std::endl;
- for (size_t i = 0; i < offset0.get(mpi_rank).size(); i++)
- std::cout << ", Offset: " << offset0.get(mpi_rank).get(i) << std::endl;
- for (size_t i = 0; i < offset_add0.get(mpi_rank).size(); i++)
- std::cout << ", Offset_add: " << offset_add0.get(mpi_rank).get(i) << std::endl;
- for (size_t i = 0; i < block0.get(mpi_rank).size(); i++)
- std::cout << ", Block: " << block0.get(mpi_rank).get(i) << std::endl;
- for (size_t i = 0; i < block_add0.get(mpi_rank).size(); i++)
- std::cout << ", Block_add: " << block_add0.get(mpi_rank).get(i) << std::endl;
-*/
-
- //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);
-
- //Select file dataspace
-/* hid_t file_dataspace_id_3 = H5Dget_space(dataset_2);
-
- H5Sselect_hyperslab(file_dataspace_id_3, H5S_SELECT_SET, offset_add, NULL, count, block_add);*/
-
- hsize_t mdim_2[1] = {block[0]};
-// hsize_t mdim_3[1] = {block_add[0]};
-
-
- //Size for data space in memory
-
- /*if (mpi_rank >= mpi_size_old)
- mdim_2[0] = 0;
- else
- mdim_2[0] = metadata_out[mpi_rank];*/
-
- //Create data space in memory
- hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
-// hid_t mem_dataspace_id_3 = H5Screate_simple(1, mdim_3, NULL);
-
- //if (mpi_rank == 0)
-/* {
- hssize_t size2;
-
- size2 = H5Sget_select_npoints (mem_dataspace_id_2);
- printf ("\nLOAD: memspace_id_2 size: %llu\n", size2);
- size2 = H5Sget_select_npoints (file_dataspace_id_2);
- printf ("LOAD: dataspace_id_2 size: %llu\n", size2);
- }*/
-/*
- if (mpi_rank == 0)
- {
- hssize_t size2;
-
- size2 = H5Sget_select_npoints (mem_dataspace_id_3);
- printf ("\nLOAD: memspace_id_3 size: %llu\n", size2);
- size2 = H5Sget_select_npoints (file_dataspace_id_3);
- printf ("LOAD: dataspace_id_3 size: %llu\n", size2);
- }
-*/
- size_t sum = 0;
-
- for (int i = 0; i < mpi_size_old; i++)
- {
- sum += metadata_out[i];
- }
-
-// std::cout << "LOAD: sum: " << sum << std::endl;
-
- // allocate the memory
- HeapMemory pmem;
-// HeapMemory pmem2;
- //pmem.allocate(req);
- ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
- mem.incRef();
-// ExtPreAlloc<HeapMemory> & mem2 = *(new ExtPreAlloc<HeapMemory>(block_add[0],pmem2));
-// mem2.incRef();
-
- // Read the dataset.
- H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer());
-
- // Read the dataset.
-// H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_3, file_dataspace_id_3, plist_id, (char *)mem2.getPointer());
-
- mem.allocate(pmem.size());
-// mem2.allocate(pmem2.size());
-// std::cout << "Mem.size(): " << mem.size() << " = " << block[0] << std::endl;
-
- Unpack_stat ps;
-
- openfpm::vector<Point<dim, St>> v_pos_unp;
-
- openfpm::vector<prop> v_prp_unp;
-
- Unpacker<decltype(v_pos_unp),HeapMemory>::unpack(mem,v_pos_unp,ps,1);
- Unpacker<decltype(v_prp_unp),HeapMemory>::unpack(mem,v_prp_unp,ps,1);
-
-// Unpack_stat ps2;
-
-
-// Unpacker<decltype(v_pos),HeapMemory>::unpack(mem2,v_pos_unp,ps2,1);
-// Unpacker<decltype(v_prp),HeapMemory>::unpack(mem2,v_prp_unp,ps2,1);
-
-// std::cout << "V_pos.size(): " << v_pos.size() << std::endl;
-// std::cout << "V_pos_unp.size(): " << v_pos_unp.size() << std::endl;
-
- mem.decRef();
- delete &mem;
-
- for (size_t i = 0; i < v_pos_unp.size(); i++)
- v_pos.add(v_pos_unp.get(i));
-
- for (size_t i = 0; i < v_prp_unp.size(); i++)
- v_prp.add(v_prp_unp.get(i));
-
- g_m = v_pos.size();
+ h5s.save(filename,v_pos,v_prp);
}
inline void load(const std::string & filename)
{
- v_pos.clear();
- v_prp.clear();
-
- g_m = 0;
-
- 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 ("LOAD: memspace_id size: %llu\n", size);
- size = H5Sget_select_npoints (file_dataspace_id);
- printf ("LOAD: 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, "vector_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<openfpm::vector<hsize_t>> block0;
- openfpm::vector<openfpm::vector<hsize_t>> block_add0;
- openfpm::vector<openfpm::vector<hsize_t>> offset0;
- openfpm::vector<openfpm::vector<hsize_t>> offset_add0;
-
- block0.resize(mpi_size);
- offset0.resize(mpi_size);
- block_add0.resize(mpi_size);
- offset_add0.resize(mpi_size);
-*/
- 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);
- 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);
-
- if (n_bl < max_block)
- load_block(-1,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2);
- }
-
- // Close the dataset.
- H5Dclose(dataset);
- H5Dclose(dataset_2);
- // Close the file.
- H5Fclose(file);
- H5Pclose(plist_id);
-
- //std::cout << "V_pos.size() after merge: " << v_pos.size() << std::endl;
-
- // Map particles
- //map();
+ HDF5_reader<VECTOR_DIST> h5l;
- //std::cout << "V_pos.size() after merge and map: " << v_pos.size() << std::endl;
+ h5l.load(filename,v_pos,v_prp,g_m);
}
/*! \brief Output particle position and properties
diff --git a/src/Vector/vector_dist_HDF5_chckpnt_restart_test.hpp b/src/Vector/vector_dist_HDF5_chckpnt_restart_test.hpp
index 0c5da9f9b057b66e4833294420ddac61f1540a28..1ed0477ec6a402a514a00508d72e55fb96446187 100644
--- a/src/Vector/vector_dist_HDF5_chckpnt_restart_test.hpp
+++ b/src/Vector/vector_dist_HDF5_chckpnt_restart_test.hpp
@@ -19,21 +19,11 @@
BOOST_AUTO_TEST_SUITE( vd_hdf5_chckpnt_rstrt_test )
-// Input data
-
-// Number of particles
-size_t k = 1000000;
-
// Dimensionality
const size_t dim = 3;
BOOST_AUTO_TEST_CASE( vector_dist_hdf5_save_test )
{
- Vcluster & v_cl = create_vcluster();
-
- if (v_cl.getProcessUnitID() == 0)
- std::cout << "Saving distributed vector" << std::endl;
-
Box<dim,float> box;
for (size_t i = 0; i < dim; i++)
@@ -45,7 +35,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_hdf5_save_test )
// Boundary conditions
size_t bc[dim];
- const size_t Ng = cbrt(k);
+ const size_t Ng = 32;
// we create a Grid iterator
size_t sz[dim] = {Ng,Ng,Ng};
@@ -75,10 +65,6 @@ BOOST_AUTO_TEST_CASE( vector_dist_hdf5_save_test )
++it;
}
- //BOOST_REQUIRE_EQUAL(it.getSpacing(0),1.0f/(Ng-1));
- //BOOST_REQUIRE_EQUAL(it.getSpacing(1),1.0f/(Ng-1));
- //BOOST_REQUIRE_EQUAL(it.getSpacing(2),1.0f/(Ng-1));
-
vd.map();
// Put forces
@@ -96,13 +82,37 @@ BOOST_AUTO_TEST_CASE( vector_dist_hdf5_save_test )
++it2;
}
- timer t;
- t.start();
// Save the vector
vd.save("vector_dist.h5");
- t.stop();
- std::cout << "Saving time: " << t.getwct() << std::endl;
+ vector_dist<dim,float, aggregate<float[dim]>, CartDecomposition<dim,float> > vd2(0,box,bc,ghost);
+
+ vd2.load("vector_dist.h5");
+
+ // Check that vd and vd2 match
+
+ auto it3 = vd.getDomainIterator();
+
+ BOOST_REQUIRE_EQUAL(vd.size_local(),vd2.size_local());
+
+ bool check = true;
+ while (it3.isNext())
+ {
+ auto p = it3.get();
+
+ Point<3,float> p1 = vd.getPos(p);
+ Point<3,float> p2 = vd2.getPos(p);
+
+ check &= (p1 == p2);
+
+ check &= (vd.template getProp<0>(p)[0] == vd2.template getProp<0>(p)[0]);
+ check &= (vd.template getProp<0>(p)[1] == vd2.template getProp<0>(p)[1]);
+ check &= (vd.template getProp<0>(p)[2] == vd2.template getProp<0>(p)[2]);
+
+ ++it3;
+ }
+
+ BOOST_REQUIRE_EQUAL(check,true);
}
@@ -111,9 +121,6 @@ BOOST_AUTO_TEST_CASE( vector_dist_hdf5_load_test )
{
Vcluster & v_cl = create_vcluster();
- if (v_cl.getProcessUnitID() == 0)
- std::cout << "Loading distributed vector" << std::endl;
-
Box<dim,float> box;
for (size_t i = 0; i < dim; i++)
@@ -129,58 +136,24 @@ BOOST_AUTO_TEST_CASE( vector_dist_hdf5_load_test )
bc[i] = NON_PERIODIC;
- const size_t Ng = cbrt(k);
-
- // we create a Grid iterator
- size_t sz[3] = {Ng,Ng,Ng};
+ const size_t Ng = 32;
// ghost
Ghost<dim,float> ghost(1.0/(Ng-2));
vector_dist<dim,float, aggregate<float[dim]>, CartDecomposition<dim,float> > vd(0,box,bc,ghost);
- vd.load("vector_dist.h5");
-
- timer t;
- t.start();
- // Save the vector
- vd.load("vector_dist.h5");
- t.stop();
-
- std::cout << "Loading time: " << t.getwct() << std::endl;
+ // Load the vector
+ vd.load("test_data/vector_dist_24.h5");
/////////////////// Checking data ///////////////////////
// Check total number of particles
size_t n_part = vd.size_local();
- openfpm::vector<size_t> tot_n_part;
- v_cl.allGather(n_part,tot_n_part);
+ v_cl.sum(n_part);
v_cl.execute();
- size_t sum = 0;
-
- for (size_t i = 0; i < tot_n_part.size(); i++)
- sum += tot_n_part.get(i);
-
- BOOST_REQUIRE_EQUAL(sum,k);
-
- //std::cout << "Sum: " << sum << std::endl;
-
- // Check spacing (positions)
-
- auto it = vd.getGridIterator(sz);
-
- while (it.isNext())
- {
- //auto key = it.get();
-
- ++it;
- }
-
- BOOST_REQUIRE_EQUAL(it.getSpacing(0),1.0f/(Ng-1));
- BOOST_REQUIRE_EQUAL(it.getSpacing(1),1.0f/(Ng-1));
- BOOST_REQUIRE_EQUAL(it.getSpacing(2),1.0f/(Ng-1));
-
+ BOOST_REQUIRE_EQUAL(n_part,Ng*Ng*Ng);
// Check properties
@@ -190,9 +163,9 @@ BOOST_AUTO_TEST_CASE( vector_dist_hdf5_load_test )
{
auto key = it2.get();
- //Put the forces
+ // Check the properties
for (size_t i = 0; i < dim; i++)
- BOOST_CHECK_CLOSE(vd.template getProp<0>(key)[i],0.51234 + vd.getPos(key)[0] + vd.getPos(key)[1]+ vd.getPos(key)[2],0.0001);
+ BOOST_REQUIRE_EQUAL(vd.template getProp<0>(key)[i],(float)(0.51234 + vd.getPos(key)[0] + vd.getPos(key)[1]+ vd.getPos(key)[2]));
++it2;
}