From 5218dbe95705bdabb596e20c0d0e76830489c7c0 Mon Sep 17 00:00:00 2001
From: Yaroslav <beorn.90@gmail.com>
Date: Tue, 10 Jan 2017 11:43:32 +0100
Subject: [PATCH] Update modules
---
openfpm_data | 2 +-
openfpm_vcluster | 2 +-
src/Grid/grid_dist_id.hpp | 46 +++++++++----------
...grid_dist_id_HDF5_chckpnt_restart_test.hpp | 16 +++----
src/Grid/grid_dist_id_comm.hpp | 26 +++++------
src/Vector/vector_dist.hpp | 26 +++++------
.../vector_dist_HDF5_chckpnt_restart_test.hpp | 2 +-
7 files changed, 59 insertions(+), 61 deletions(-)
diff --git a/openfpm_data b/openfpm_data
index e62e281df..313e8ad01 160000
--- a/openfpm_data
+++ b/openfpm_data
@@ -1 +1 @@
-Subproject commit e62e281df21687cfa081d4ac9460a8abf4636ec0
+Subproject commit 313e8ad016ffe36da70d1f327dd71f90f646a580
diff --git a/openfpm_vcluster b/openfpm_vcluster
index 9d0986ae4..69e896667 160000
--- a/openfpm_vcluster
+++ b/openfpm_vcluster
@@ -1 +1 @@
-Subproject commit 9d0986ae448b22ada91ddcbb789ed58e270d4218
+Subproject commit 69e896667ab6d9f6027cd2fefd99ccdaa6f34206
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index e2147bd3e..37a09c5a2 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -1731,8 +1731,8 @@ 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;
+ //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;
@@ -1741,7 +1741,7 @@ public:
Packer<decltype(loc_grid),HeapMemory>::packRequest(loc_grid,req);
Packer<decltype(gdb_ext),HeapMemory>::packRequest(gdb_ext,req);
- std::cout << "Req: " << req << std::endl;
+ //std::cout << "Req: " << req << std::endl;
// allocate the memory
HeapMemory pmem;
@@ -1778,7 +1778,7 @@ public:
H5Pclose(plist_id);
size_t sz = pmem.size();
- std::cout << "Pmem.size: " << pmem.size() << std::endl;
+ //std::cout << "Pmem.size: " << pmem.size() << std::endl;
openfpm::vector<size_t> sz_others;
v_cl.allGather(sz,sz_others);
v_cl.execute();
@@ -1806,8 +1806,8 @@ public:
//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;
+ //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);
@@ -1835,7 +1835,7 @@ public:
offset[0] += sz_others.get(i);
}
- std::cout << "MPI rank: " << mpi_rank << ", MPI size: " << mpi_size << ", Offset: " << offset[0] << ", Block: " << block[0] << std::endl;
+ // std::cout << "MPI rank: " << mpi_rank << ", MPI size: " << mpi_size << ", Offset: " << offset[0] << ", Block: " << block[0] << std::endl;
int metadata[mpi_size];
@@ -1858,7 +1858,7 @@ public:
//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;
@@ -1869,7 +1869,7 @@ public:
{
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);
@@ -1907,7 +1907,7 @@ public:
}
}*/
- std::cout << "BID: " << bid << std::endl;
+// std::cout << "BID: " << bid << std::endl;
hsize_t offset[1];
hsize_t block[1];
@@ -1923,7 +1923,7 @@ public:
block[0] = 0;
}
- std::cout << "Offset: " << offset[0] << "; Block: " << block[0]<< std::endl;
+// std::cout << "Offset: " << offset[0] << "; Block: " << block[0]<< std::endl;
// hsize_t offset_add[1] = {0};
/* if (mpi_size >= mpi_size_old)
@@ -2000,14 +2000,14 @@ public:
// 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)
{
@@ -2026,7 +2026,7 @@ public:
sum += metadata_out[i];
}
- std::cout << "LOAD: sum: " << sum << std::endl;
+ // std::cout << "LOAD: sum: " << sum << std::endl;
// allocate the memory
HeapMemory pmem;
@@ -2045,7 +2045,7 @@ public:
mem.allocate(pmem.size());
// mem2.allocate(pmem2.size());
- std::cout << "Mem.size(): " << mem.size() << " = " << block[0] << std::endl;
+ // std::cout << "Mem.size(): " << mem.size() << " = " << block[0] << std::endl;
Unpack_stat ps;
@@ -2171,11 +2171,11 @@ 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 << "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;
+ // std::cout << "Rest block: " << rest_block << std::endl;
size_t max_block;
@@ -2189,8 +2189,8 @@ public:
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;
+ //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;
@@ -2204,7 +2204,7 @@ public:
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;
+// 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);
@@ -2232,11 +2232,11 @@ public:
// Map the distributed grid
map();
-
+/*
for (size_t i = 0; i < loc_grid.size(); i++)
{
std::cout << "loc_grids loaded: (" << 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;
- }
+ }*/
}
//! Define friend classes
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 2bf3fda54..cfb08eee5 100644
--- a/src/Grid/grid_dist_id_HDF5_chckpnt_restart_test.hpp
+++ b/src/Grid/grid_dist_id_HDF5_chckpnt_restart_test.hpp
@@ -16,12 +16,12 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_save_test )
{
// Input data
- size_t k = 1000;
+ size_t k = 2400;
float ghost_part = 0.0;
// Domain
- Box<2,float> domain({-1.0,-1.0},{1.0,1.0});
+ Box<2,float> domain({0.0,0.0},{1.0,1.0});
Vcluster & v_cl = create_vcluster();
@@ -41,7 +41,7 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_save_test )
Ghost<2,float> g(ghost_part);
// Distributed grid with id decomposition
- grid_dist_id<2, float, scalar<float[2]>, CartDecomposition<2,float>> g_dist(sz,domain,g);
+ grid_dist_id<2, float, scalar<float>, CartDecomposition<2,float>> g_dist(sz,domain,g);
// get the decomposition
auto & dec = g_dist.getDecomposition();
@@ -61,8 +61,7 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_save_test )
auto keyg = g_dist.getGKey(key);
- g_dist.template get<0>(key)[0] = keyg.get(0);
- g_dist.template get<0>(key)[1] = keyg.get(1);
+ g_dist.template get<0>(key) = keyg.get(0);
++it;
count++;
@@ -94,7 +93,7 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_load_test )
{
// Input data
- size_t k = 1000;
+ size_t k = 2400;
float ghost_part = 0.0;
@@ -119,7 +118,7 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_load_test )
Ghost<2,float> g(ghost_part);
// Distributed grid with id decomposition
- grid_dist_id<2, float, scalar<float[2]>, CartDecomposition<2,float>> g_dist(sz,domain,g);
+ grid_dist_id<2, float, scalar<float>, CartDecomposition<2,float>> g_dist(sz,domain,g);
g_dist.getDecomposition().write("Before_load_grid_decomposition");
g_dist.write("Before_Loaded_grid");
@@ -149,8 +148,7 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_hdf5_load_test )
auto keyg = g_dist.getGKey(key);
- BOOST_REQUIRE_EQUAL(g_dist.template get<0>(key)[0], keyg.get(0));
- BOOST_REQUIRE_EQUAL(g_dist.template get<0>(key)[1], keyg.get(1));
+ BOOST_REQUIRE_EQUAL(g_dist.template get<0>(key), keyg.get(0));
++it;
count++;
diff --git a/src/Grid/grid_dist_id_comm.hpp b/src/Grid/grid_dist_id_comm.hpp
index d1863a87e..b861fcaa8 100644
--- a/src/Grid/grid_dist_id_comm.hpp
+++ b/src/Grid/grid_dist_id_comm.hpp
@@ -82,7 +82,7 @@ public:
//device_grid gr_send(sz);
//gr_send.setMemory();
- std::cout << "B: (" << b.getLow(0) << "; " << b.getLow(1) << "); (" << b.getHigh(0) << "; " << b.getHigh(1) << "); " << "G: (" << g.getGrid().getBox().getHigh(0) << "; " << g.getGrid().getBox().getHigh(1) << ")" << std::endl;
+ //std::cout << "B: (" << b.getLow(0) << "; " << b.getLow(1) << "); (" << b.getHigh(0) << "; " << b.getHigh(1) << "); " << "G: (" << g.getGrid().getBox().getHigh(0) << "; " << g.getGrid().getBox().getHigh(1) << ")" << std::endl;
// Set the dimensions of the local grid
//g.resize(l_res);
@@ -130,7 +130,7 @@ public:
}
}
}
- std::cout << "Count after: " << count2 << std::endl;
+ //std::cout << "Count after: " << count2 << std::endl;
}
@@ -185,7 +185,7 @@ public:
count2++;
//////////////
- std::cout << "Inte_box: (" << inte_box.getLow(0) << "; " << inte_box.getLow(1) << "); (" << inte_box.getHigh(0) << "; " << inte_box.getHigh(1) << ")" << std::endl;
+ //std::cout << "Inte_box: (" << inte_box.getLow(0) << "; " << inte_box.getLow(1) << "); (" << inte_box.getHigh(0) << "; " << inte_box.getHigh(1) << ")" << std::endl;
auto inte_box_cont = cd_sm.convertCellUnitsIntoDomainSpace(inte_box);
@@ -199,23 +199,23 @@ public:
p_id = dec.processorID(p);
prc_sz.get(p_id)++;
- std::cout << "P_id: " << p_id << std::endl;
+ //std::cout << "P_id: " << p_id << std::endl;
// Transform coordinates to local
auto inte_box_local = inte_box;
inte_box_local -= gdb_ext_old.get(i).origin;
- std::cout << "gdb_ext_old.get(i): (" << sub_dom.getLow(0) << "; " << sub_dom.getLow(1) << "); (" << sub_dom.getHigh(0) << "; " << sub_dom.getHigh(1) << ")" << std::endl;
+ //std::cout << "gdb_ext_old.get(i): (" << sub_dom.getLow(0) << "; " << sub_dom.getLow(1) << "); (" << sub_dom.getHigh(0) << "; " << sub_dom.getHigh(1) << ")" << std::endl;
- std::cout << "gdb_ext_global.get(j): (" << sub_dom_new.getLow(0) << "; " << sub_dom_new.getLow(1) << "); (" << sub_dom_new.getHigh(0) << "; " << sub_dom_new.getHigh(1) << ")" << std::endl;
+ //std::cout << "gdb_ext_global.get(j): (" << sub_dom_new.getLow(0) << "; " << sub_dom_new.getLow(1) << "); (" << sub_dom_new.getHigh(0) << "; " << sub_dom_new.getHigh(1) << ")" << std::endl;
- std::cout << "Inte_box_local: (" << inte_box_local.getLow(0) << "; " << inte_box_local.getLow(1) << "); (" << inte_box_local.getHigh(0) << "; " << inte_box_local.getHigh(1) << ")" << std::endl;
+ //std::cout << "Inte_box_local: (" << inte_box_local.getLow(0) << "; " << inte_box_local.getLow(1) << "); (" << inte_box_local.getHigh(0) << "; " << inte_box_local.getHigh(1) << ")" << std::endl;
// Grid corresponding for gdb_ext_old.get(i) box
device_grid & gr = loc_grid_old.get(i);
- std::cout << "loc_grid_old.get(i): (" << gr.getGrid().getBox().getLow(0) << "; " << gr.getGrid().getBox().getLow(1) << "); (" << gr.getGrid().getBox().getHigh(0) << "; " << gr.getGrid().getBox().getHigh(1) << ")" << std::endl;
+ //std::cout << "loc_grid_old.get(i): (" << gr.getGrid().getBox().getLow(0) << "; " << gr.getGrid().getBox().getLow(1) << "); (" << gr.getGrid().getBox().getHigh(0) << "; " << gr.getGrid().getBox().getHigh(1) << ")" << std::endl;
//for (size_t l = 0; l < dim; l++)
//std::cout << "loc_grid_old.get(i).size on " << l << " dimension: " << gr.getGrid().size(l) << std::endl;
@@ -263,7 +263,7 @@ public:
std::string start2 = start.to_string();
std::string stop2 = stop.to_string();
- std::cout << "Start: " << start2 << "; Stop: " << stop2 << std::endl;
+ //std::cout << "Start: " << start2 << "; Stop: " << stop2 << std::endl;
auto it = gr.getSubIterator(start,stop);
@@ -304,8 +304,8 @@ public:
}
}
}
- std::cout << "Count for points: " << count << std::endl;
- std::cout << "Count for inte_boxes: " << count2 << std::endl;
+ //std::cout << "Count for points: " << count << std::endl;
+ //std::cout << "Count for inte_boxes: " << count2 << std::endl;
}
/*! \brief Moves all the grids that does not belong to the local processor to the respective processor
@@ -386,9 +386,9 @@ public:
// Vector for receiving of intersection grids
openfpm::vector<openfpm::vector<aggregate<device_grid,SpaceBox<dim,long int>>>> m_oGrid_recv;
- std::cout << "vcl.getProcessUnitID(): " << v_cl.getProcessUnitID() << "; prc_r.size(): " << prc_r.size() << std::endl;
+ //std::cout << "vcl.getProcessUnitID(): " << v_cl.getProcessUnitID() << "; prc_r.size(): " << prc_r.size() << std::endl;
- std::cout << "vcl.getProcessUnitID(): " << v_cl.getProcessUnitID() << "; m_oGrid_new.size(): " << m_oGrid_new.size() << std::endl;
+ //std::cout << "vcl.getProcessUnitID(): " << v_cl.getProcessUnitID() << "; m_oGrid_new.size(): " << m_oGrid_new.size() << std::endl;
/*
for (size_t i = 0; i < m_oGrid.size(); i++)
{
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 922becc6f..11b2554eb 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -1143,7 +1143,7 @@ public:
}
}*/
- std::cout << "BID: " << bid << std::endl;
+// std::cout << "BID: " << bid << std::endl;
hsize_t offset[1];
hsize_t block[1];
@@ -1159,7 +1159,7 @@ public:
block[0] = 0;
}
- std::cout << "Offset: " << offset[0] << "; Block: " << block[0]<< std::endl;
+// std::cout << "Offset: " << offset[0] << "; Block: " << block[0]<< std::endl;
// hsize_t offset_add[1] = {0};
/* if (mpi_size >= mpi_size_old)
@@ -1236,14 +1236,14 @@ public:
// 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)
{
@@ -1262,7 +1262,7 @@ public:
sum += metadata_out[i];
}
- std::cout << "LOAD: sum: " << sum << std::endl;
+// std::cout << "LOAD: sum: " << sum << std::endl;
// allocate the memory
HeapMemory pmem;
@@ -1281,7 +1281,7 @@ public:
mem.allocate(pmem.size());
// mem2.allocate(pmem2.size());
- std::cout << "Mem.size(): " << mem.size() << " = " << block[0] << std::endl;
+// std::cout << "Mem.size(): " << mem.size() << " = " << block[0] << std::endl;
Unpack_stat ps;
@@ -1420,11 +1420,11 @@ 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 << "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;
+ // std::cout << "Rest block: " << rest_block << std::endl;
size_t max_block;
@@ -1438,8 +1438,8 @@ public:
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;
+ //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;
@@ -1453,7 +1453,7 @@ public:
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;
+ //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);
@@ -1478,7 +1478,7 @@ public:
//std::cout << "V_pos.size() after merge: " << v_pos.size() << std::endl;
// Map particles
- map();
+ //map();
//std::cout << "V_pos.size() after merge and map: " << v_pos.size() << std::endl;
}
diff --git a/src/Vector/vector_dist_HDF5_chckpnt_restart_test.hpp b/src/Vector/vector_dist_HDF5_chckpnt_restart_test.hpp
index b166fb2b8..124728167 100644
--- a/src/Vector/vector_dist_HDF5_chckpnt_restart_test.hpp
+++ b/src/Vector/vector_dist_HDF5_chckpnt_restart_test.hpp
@@ -22,7 +22,7 @@ BOOST_AUTO_TEST_SUITE( vd_hdf5_chckpnt_rstrt_test )
// Input data
// Number of particles
-size_t k = 1000;
+size_t k = 1000000;
// Dimensionality
const size_t dim = 3;
--
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