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Commit c3e6ff5f authored by Pietro Incardona's avatar Pietro Incardona
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Adding ghost area, compiling and testing

parent 726c6d4c
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src/.deps/pdata-main.Po
View file @ c3e6ff5f
......@@ -1298,14 +1298,12 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
Grid/grid_dist_key.hpp \
../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp \
../../OpenFPM_data/src/Space/Matrix.hpp \
../../OpenFPM_data/src/Point_test.hpp \
../../OpenFPM_data/src/base_type.hpp \
../../OpenFPM_data/src/Point_orig.hpp \
../../OpenFPM_data/src/Grid/Encap.hpp \
Decomposition/CartDecomposition.hpp Decomposition/Decomposition.hpp \
../../OpenFPM_data/src/global_const.hpp SubdomainGraphNodes.hpp \
metis_util.hpp ../../metis_install/include/metis.h \
/usr/include/inttypes.h ../../OpenFPM_IO/src/VTKWriter.hpp \
../../OpenFPM_data/src/util/object_util.hpp \
../../OpenFPM_data/src/util/object_creator.hpp \
../../OpenFPM_data/src/util/object_s_di.hpp \
../../OpenFPM_data/src/util/object_si_d.hpp \
../../OpenFPM_devices/src/memory/ExtPreAlloc.hpp \
../../OpenFPM_IO/src/VTKWriter.hpp \
../../OpenFPM_IO/src/VTKWriter_graph.hpp \
../../OpenFPM_IO/src/VTKWriter_vector_box.hpp \
/usr/include/boost/math/special_functions/pow.hpp \
......@@ -1370,7 +1368,15 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
/usr/include/boost/iostreams/detail/config/dyn_link.hpp \
/usr/include/boost/iostreams/detail/path.hpp \
/usr/include/boost/config/abi_prefix.hpp \
/usr/include/boost/config/abi_suffix.hpp dec_optimizer.hpp \
/usr/include/boost/config/abi_suffix.hpp \
../../OpenFPM_data/src/Point_test.hpp \
../../OpenFPM_data/src/base_type.hpp \
../../OpenFPM_data/src/Point_orig.hpp \
../../OpenFPM_data/src/Grid/Encap.hpp \
Decomposition/CartDecomposition.hpp Decomposition/Decomposition.hpp \
../../OpenFPM_data/src/global_const.hpp SubdomainGraphNodes.hpp \
metis_util.hpp ../../metis_install/include/metis.h \
/usr/include/inttypes.h dec_optimizer.hpp \
/usr/include/c++/4.8.3/unordered_map \
/usr/include/c++/4.8.3/bits/hashtable.h \
/usr/include/c++/4.8.3/bits/hashtable_policy.h \
......@@ -1394,11 +1400,6 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
../../OpenFPM_devices/src/memory/PreAllocHeapMemory.hpp \
../../OpenFPM_devices/src/memory/HeapMemory.hpp \
../../OpenFPM_devices/src/memory/PtrMemory.hpp \
../../OpenFPM_data/src/util/object_util.hpp \
../../OpenFPM_data/src/util/object_creator.hpp \
../../OpenFPM_data/src/util/object_s_di.hpp \
../../OpenFPM_data/src/util/object_si_d.hpp \
../../OpenFPM_devices/src/memory/ExtPreAlloc.hpp \
../../OpenFPM_IO/src/CSVWriter.hpp \
../../OpenFPM_IO/src/csv_multiarray.hpp \
Decomposition/CartDecomposition_unit_test.hpp \
......@@ -4266,27 +4267,15 @@ Grid/grid_dist_key.hpp:
../../OpenFPM_data/src/Space/Matrix.hpp:
../../OpenFPM_data/src/Point_test.hpp:
../../OpenFPM_data/src/base_type.hpp:
../../OpenFPM_data/src/Point_orig.hpp:
../../OpenFPM_data/src/Grid/Encap.hpp:
Decomposition/CartDecomposition.hpp:
Decomposition/Decomposition.hpp:
../../OpenFPM_data/src/global_const.hpp:
../../OpenFPM_data/src/util/object_util.hpp:
SubdomainGraphNodes.hpp:
../../OpenFPM_data/src/util/object_creator.hpp:
metis_util.hpp:
../../OpenFPM_data/src/util/object_s_di.hpp:
../../metis_install/include/metis.h:
../../OpenFPM_data/src/util/object_si_d.hpp:
/usr/include/inttypes.h:
../../OpenFPM_devices/src/memory/ExtPreAlloc.hpp:
../../OpenFPM_IO/src/VTKWriter.hpp:
......@@ -4420,6 +4409,28 @@ metis_util.hpp:
/usr/include/boost/config/abi_suffix.hpp:
../../OpenFPM_data/src/Point_test.hpp:
../../OpenFPM_data/src/base_type.hpp:
../../OpenFPM_data/src/Point_orig.hpp:
../../OpenFPM_data/src/Grid/Encap.hpp:
Decomposition/CartDecomposition.hpp:
Decomposition/Decomposition.hpp:
../../OpenFPM_data/src/global_const.hpp:
SubdomainGraphNodes.hpp:
metis_util.hpp:
../../metis_install/include/metis.h:
/usr/include/inttypes.h:
dec_optimizer.hpp:
/usr/include/c++/4.8.3/unordered_map:
......@@ -4486,16 +4497,6 @@ Vector/vector_dist_key.hpp:
../../OpenFPM_devices/src/memory/PtrMemory.hpp:
../../OpenFPM_data/src/util/object_util.hpp:
../../OpenFPM_data/src/util/object_creator.hpp:
../../OpenFPM_data/src/util/object_s_di.hpp:
../../OpenFPM_data/src/util/object_si_d.hpp:
../../OpenFPM_devices/src/memory/ExtPreAlloc.hpp:
../../OpenFPM_IO/src/CSVWriter.hpp:
../../OpenFPM_IO/src/csv_multiarray.hpp:
......
src/Decomposition/CartDecomposition.hpp
View file @ c3e6ff5f
......@@ -74,6 +74,20 @@ class CartDecomposition
size_t proc;
};
struct Box_dom
{
// Intersection between the local sub-domain enlarged by the ghost and the contiguous processor
// sub-domains (External ghost)
openfpm::vector< ::Box<dim,T> > ebx;
// Intersection between the contiguous processor sub-domain enlarged by the ghost with the
// local sub-domain (Internal ghost)
openfpm::vector< ::Box<dim,T> > ibx;
// Domain id
size_t dom;
};
public:
//! Type of the domain we are going to decompose
......@@ -101,11 +115,15 @@ private:
//! List of near processors
openfpm::vector<size_t> nn_processors;
//! for each sub-domain, contain the list of the neighborhood processors
//! for each sub-domain (first vector), contain the list (nested vector) of the neighborhood processors
//! and for each processor contain the boxes calculated from the intersection
//! of the sub-domain + ghost with the near-by processor sub-domain ()
//! of the sub-domains + ghost with the near-by processor sub-domain () and the other way around
//! \see calculateGhostBoxes
openfpm::vector< openfpm::vector< Box_proc > > box_nn_processor_int;
//! It store the same information of box_nn_processor_int organized by processor id
openfpm::vector< Box_dom > proc_int_box;
//! for each sub-domain, contain the list of the neighborhood processors
openfpm::vector<openfpm::vector<long unsigned int> > box_nn_processor;
......@@ -328,6 +346,157 @@ private:
}
}
/*! \brief Create the box_nn_processor_int (bx part) structure
*
* This structure store for each sub-domain of this processors enlarged by the ghost size the boxes that
* come from the intersection with the near processors sub-domains (External ghost box)
*
* \param ghost margins
*
* \note Are the G8_0 G9_0 G9_1 G5_0 boxes in calculateGhostBoxes
* \see calculateGhostBoxes
*
*/
void create_box_nn_processor_ext(Ghost<dim,T> & ghost)
{
box_nn_processor_int.resize(sub_domains.size());
// For each sub-domain
for (size_t i = 0 ; i < sub_domains.size() ; i++)
{
SpaceBox<dim,T> sub_with_ghost = sub_domains.get(i);
// enlarge the sub-domain with the ghost
sub_with_ghost.enlarge(ghost);
// resize based on the number of contiguous processors
box_nn_processor_int.get(i).resize(box_nn_processor.get(i).size());
// For each processor contiguous to this sub-domain
for (size_t j = 0 ; j < box_nn_processor.get(i).size() ; j++)
{
// Contiguous processor
size_t p_id = box_nn_processor.get(i).get(j);
// get the set of sub-domains of the contiguous processor p_id
openfpm::vector< ::Box<dim,T> > & p_box = nn_processor_subdomains[p_id].bx;
// near processor sub-domain intersections
openfpm::vector< ::Box<dim,T> > & p_box_int = box_nn_processor_int.get(i).get(j).bx;
// for each near processor sub-domain intersect with the enlarged local sub-domain and store it
for (size_t b = 0 ; b < p_box.size() ; b++)
{
::Box<dim,T> bi;
bool intersect = sub_with_ghost.Intersect(::Box<dim,T>(p_box.get(b)),bi);
if (intersect == true)
{
struct p_box pb;
pb.box = bi;
pb.proc = p_id;
pb.lc_proc = ProctoID(p_id);
vb_ext.add(pb);
p_box_int.add(bi);
}
}
}
}
}
/*! \brief Create the box_nn_processor_int (nbx part) structure, the geo_cell list and proc_int_box
*
* This structure store for each sub-domain of this processors the boxes that come from the intersection
* of the near processors sub-domains enlarged by the ghost size (Internal ghost box). These boxes
* fill a geometrical cell list. The proc_int_box store the same information ordered by near processors
*
* \param ghost margins
*
* \note Are the B8_0 B9_0 B9_1 B5_0 boxes in calculateGhostBoxes
* \see calculateGhostBoxes
*
*/
void create_box_nn_processor_int(Ghost<dim,T> & ghost)
{
box_nn_processor_int.resize(sub_domains.size());
proc_int_box.resize(getNNProcessors());
// For each sub-domain
for (size_t i = 0 ; i < sub_domains.size() ; i++)
{
// For each processor contiguous to this sub-domain
for (size_t j = 0 ; j < box_nn_processor.get(i).size() ; j++)
{
// Contiguous processor
size_t p_id = box_nn_processor.get(i).get(j);
// get the set of sub-domains of the contiguous processor p_id
openfpm::vector< ::Box<dim,T> > & nn_p_box = nn_processor_subdomains[p_id].bx;
// get the local processor id
size_t lc_proc = nn_processor_subdomains[p_id].id;
// For each near processor sub-domains enlarge and intersect with the local sub-domain and store the result
for (size_t k = 0 ; k < nn_p_box.size() ; k++)
{
// enlarge the near-processor sub-domain
::Box<dim,T> n_sub = nn_p_box.get(k);
// local sub-domain
::SpaceBox<dim,T> l_sub = sub_domains.get(i);
// Create a margin of ghost size around the near processor sub-domain
n_sub.enlarge(ghost);
// Intersect with the local sub-domain
p_box b_int;
bool intersect = n_sub.Intersect(l_sub,b_int.box);
// store if it intersect
if (intersect == true)
{
// fill with the processor id
b_int.proc = p_id;
// fill the local processor id
b_int.lc_proc = lc_proc;
// near processor sub-domain intersections
openfpm::vector< ::Box<dim,T> > & p_box_int = box_nn_processor_int.get(i).get(j).nbx;
p_box_int.add(b_int.box);
vb_int.add(b_int);
// store the box in proc_int_box calculating the id
Box_dom & pr_box_int = proc_int_box.get(ProctoID(p_id));
pr_box_int.ibx.add(b_int.box);
// update the geo_cell list
// get the boxes this box span
const grid_key_dx<dim> p1 = geo_cell.getCellGrid(b_int.box.getP1());
const grid_key_dx<dim> p2 = geo_cell.getCellGrid(b_int.box.getP2());
// Get the grid and the sub-iterator
auto & gi = geo_cell.getGrid();
grid_key_dx_iterator_sub<dim> g_sub(gi,p1,p2);
// add the box-id to the cell list
while (g_sub.isNext())
{
auto key = g_sub.get();
geo_cell.addCell(gi.LinId(key),vb_int.size()-1);
++g_sub;
}
}
}
}
}
}
// Heap memory receiver
HeapMemory hp_recv;
......@@ -717,116 +886,9 @@ p1[0]<-----+ +----> p2[0]
// Get the sub-domains of the near processors
v_cl.sendrecvMultipleMessagesNBX(nn_processors,boxes,CartDecomposition<dim,T,device_l,Memory,Domain,data_s>::message_alloc, this ,NEED_ALL_SIZE);
box_nn_processor_int.resize(sub_domains.size());
// For each sub-domain
for (size_t i = 0 ; i < sub_domains.size() ; i++)
{
SpaceBox<dim,T> sub_with_ghost = sub_domains.get(i);
// enlarge the sub-domain with the ghost
sub_with_ghost.enlarge(ghost);
// resize based on the number of contiguous processors
box_nn_processor_int.get(i).resize(box_nn_processor.get(i).size());
create_box_nn_processor_ext(ghost);
// For each processor contiguous to this sub-domain
for (size_t j = 0 ; j < box_nn_processor.get(i).size() ; j++)
{
// Contiguous processor
size_t p_id = box_nn_processor.get(i).get(j);
// get the set of sub-domains of the contiguous processor p_id
openfpm::vector< ::Box<dim,T> > & p_box = nn_processor_subdomains[p_id].bx;
// near processor sub-domain intersections
openfpm::vector< ::Box<dim,T> > & p_box_int = box_nn_processor_int.get(i).get(j).bx;
// for each near processor sub-domain intersect with the enlarged local sub-domain and store it
for (size_t b = 0 ; b < p_box.size() ; b++)
{
::Box<dim,T> bi;
bool intersect = sub_with_ghost.Intersect(::Box<dim,T>(p_box.get(b)),bi);
if (intersect == true)
{
struct p_box pb;
pb.box = bi;
pb.proc = p_id;
pb.lc_proc = ProctoID(p_id);
vb_ext.add(pb);
p_box_int.add(bi);
}
}
}
// For each processor contiguous to this sub-domain
for (size_t j = 0 ; j < box_nn_processor.get(i).size() ; j++)
{
// Contiguous processor
size_t p_id = box_nn_processor.get(i).get(j);
// get the set of sub-domains of the contiguous processor p_id
openfpm::vector< ::Box<dim,T> > & nn_p_box = nn_processor_subdomains[p_id].bx;
// get the local processor id
size_t lc_proc = nn_processor_subdomains[p_id].id;
// near processor sub-domain intersections
openfpm::vector< ::Box<dim,T> > & p_box_int = box_nn_processor_int.get(i).get(j).nbx;
// For each near processor sub-domains enlarge and intersect with the local sub-domain and store the result
for (size_t k = 0 ; k < nn_p_box.size() ; k++)
{
// enlarge the near-processor sub-domain
::Box<dim,T> n_sub = nn_p_box.get(k);
// local sub-domain
::SpaceBox<dim,T> l_sub = sub_domains.get(i);
// Create a margin of ghost size around the near processor sub-domain
n_sub.enlarge(ghost);
// Intersect with the local sub-domain
p_box b_int;
bool intersect = n_sub.Intersect(l_sub,b_int.box);
// store if it intersect
if (intersect == true)
{
// fill with the processor id
b_int.proc = p_id;
// fill the local processor id
b_int.lc_proc = lc_proc;
p_box_int.add(b_int.box);
vb_int.add(b_int);
// update the geo_cell list
// get the boxes this box span
const grid_key_dx<dim> p1 = geo_cell.getCellGrid(b_int.box.getP1());
const grid_key_dx<dim> p2 = geo_cell.getCellGrid(b_int.box.getP2());
// Get the grid and the sub-iterator
auto & gi = geo_cell.getGrid();
grid_key_dx_iterator_sub<dim> g_sub(gi,p1,p2);
// add the box-id to the cell list
while (g_sub.isNext())
{
auto key = g_sub.get();
geo_cell.addCell(gi.LinId(key),vb_int.size()-1);
++g_sub;
}
}
}
}
}
create_box_nn_processor_int(ghost);
}
/*! \brief processorID return in which processor the particle should go
......@@ -1090,6 +1152,37 @@ p1[0]<-----+ +----> p2[0]
}
////////////// Functions to get decomposition information ///////////////
/*! \brief Get the number of Internal ghost boxes for one processor id
*
* \param id processor id (Carefully it is not the processor number)
* \return the number of internal ghost
*
*/
inline size_t getProcessorNIGhost(size_t id) const
{
return proc_int_box.get(id).ibx.size();
}
/*! \brief Get the j Internal ghost box for one processor id
*
* \param id processor id (Carefully it is not the processor number)
* \param j box
* \return the box
*
*/
inline const ::Box<dim,T> & getProcessorIGhostBox(size_t id, size_t j) const
{
proc_int_box.get(id).ibx.get(j);
}
/*! \brief Get the number of Near processor
*
* \return the number of near processors
*
*/
inline size_t getNNProcessors() const
{
return nn_processors.size();
......@@ -1198,7 +1291,7 @@ p1[0]<-----+ +----> p2[0]
//! p_sub_X.vtk domain for the processor X as union of sub-domain
VTKWriter<openfpm::vector<::SpaceBox<dim,T>>,VECTOR_BOX> vtk_box1;
vtk_box1.add(sub_domains);
vtk_box1.write(std::string("p_sub_") + std::to_string(v_cl.getProcessUnitID()) + std::string(".vtk"));
vtk_box1.write(output + std::string("p_sub_") + std::to_string(v_cl.getProcessUnitID()) + std::string(".vtk"));
//! sub_np_c_X.vtk sub-domain of the near processors contiguous to the processor X (Color encoded)
VTKWriter<openfpm::vector<::Box<dim,T>>,VECTOR_BOX> vtk_box2;
......@@ -1209,7 +1302,7 @@ p1[0]<-----+ +----> p2[0]
if (it != nn_processor_subdomains.end())
vtk_box2.add(nn_processor_subdomains.at(prc).bx);
}
vtk_box2.write(std::string("sub_np_c_") + std::to_string(v_cl.getProcessUnitID()) + std::string(".vtk"));
vtk_box2.write(output + std::string("sub_np_c_") + std::to_string(v_cl.getProcessUnitID()) + std::string(".vtk"));
//! sub_X_inte_g_np.vtk Intersection between the ghosts of the near processors and the processors X sub-domains (Color encoded)
VTKWriter<openfpm::vector<::Box<dim,T>>,VECTOR_BOX> vtk_box3;
......@@ -1220,7 +1313,7 @@ p1[0]<-----+ +----> p2[0]
vtk_box3.add(box_nn_processor_int.get(p).get(s).nbx);
}
}
vtk_box3.write(std::string("sub_") + std::to_string(v_cl.getProcessUnitID()) + std::string("_inte_g_np") + std::string(".vtk"));
vtk_box3.write(output + std::string("sub_") + std::to_string(v_cl.getProcessUnitID()) + std::string("_inte_g_np") + std::string(".vtk"));
//! sub_X_ghost.vtk ghost for the processor X (Color encoded)
......@@ -1232,7 +1325,9 @@ p1[0]<-----+ +----> p2[0]
vtk_box4.add(box_nn_processor_int.get(p).get(s).bx);
}
}
vtk_box4.write(std::string("sub_") + std::to_string(v_cl.getProcessUnitID()) + std::string("_ghost") + std::string(".vtk"));
vtk_box4.write(output + std::string("sub_") + std::to_string(v_cl.getProcessUnitID()) + std::string("_ghost") + std::string(".vtk"));
return true;
}
};
......
src/Grid/grid_dist_id.hpp
View file @ c3e6ff5f
......@@ -9,6 +9,9 @@
#include "grid_dist_id_iterator.hpp"
#include "grid_dist_key.hpp"
#include "NN/CellList/CellDecomposer.hpp"
#include "util/object_util.hpp"
#include "memory/ExtPreAlloc.hpp"
#include "VTKWriter.hpp"
#define SUB_UNIT_FACTOR 64
......@@ -100,11 +103,47 @@ class grid_dist_id
}
}
/*! \brief Create per-processor internal ghost box list in grid units
*
*/
void create_ig_box()
{
// Get the grid info
auto g = cd_sm.getGrid();
if (init_i_g_box == true) return;
// Get the number of near processors
for (size_t i = 0 ; i < dec.getNNProcessors() ; i++)
{
ig_box.add();
auto&& pib = ig_box.last();
pib.prc = dec.IDtoProc(i);
for (size_t j = 0 ; j < dec.getProcessorNIGhost(i) ; j++)
{
// Get the internal ghost boxes and transform into grid units
::Box<dim,St> ib = dec.getProcessorIGhostBox(i,j);
ib /= cd_sm.getCellBox().getP2();
// save the box and the sub-domain id (it is calculated as the linearization of P1)
// It is unique because it is ensured that boxes does not overlap
::Box<dim,size_t> cvt = ib;
Box_id bid_t(cvt);
bid_t.id = 0/*g.LinId(bid_t.box.getKP1())*/;
pib.bid.add(bid_t);
}
}
init_i_g_box = true;
}
public:
//! constructor
grid_dist_id(Vcluster v_cl, Decomposition & dec, const size_t (& g_sz)[dim], const Box<dim,St> & domain, const Ghost<dim,T> & ghost)
:domain(domain),cd_sm(domain,g_sz,0),ghost(ghost),loc_grid(NULL),v_cl(v_cl),dec(dec)
:domain(domain),ghost(ghost),loc_grid(NULL),cd_sm(domain,g_sz,0),v_cl(v_cl),dec(dec)
{
// fill the global size of the grid
for (int i = 0 ; i < dim ; i++) {this->g_sz[i] = g_sz[i];}
......@@ -125,6 +164,9 @@ public:
// Create local grid
Create();
// Calculate ghost boxes
dec.calculateGhostBoxes(ghost);
}
/*! \brief Constrcuctor
......@@ -133,8 +175,8 @@ public:
* \param domain
*
*/
grid_dist_id(const size_t (& g_sz)[dim],const Box<dim,St> & domain)
:domain(domain),cd_sm(domain,g_sz,0),ghost(0),dec(Decomposition(*global_v_cluster)),v_cl(*global_v_cluster)
grid_dist_id(const size_t (& g_sz)[dim],const Box<dim,St> & domain, const Ghost<dim,St> & g)
:domain(domain),ghost(g),dec(Decomposition(*global_v_cluster)),cd_sm(domain,g_sz,0),v_cl(*global_v_cluster)
{
// fill the global size of the grid
for (int i = 0 ; i < dim ; i++) {this->g_sz[i] = g_sz[i];}
......@@ -155,6 +197,9 @@ public:
// Create local grid
Create();
// Calculate ghost boxes
dec.calculateGhostBoxes(ghost);
}
/*! \brief Get the object that store the decomposition information
......@@ -177,6 +222,9 @@ public:
// Box used for rounding error
Box<dim,St> rnd_box;
for (size_t i = 0 ; i < dim ; i++) {rnd_box.setHigh(i,0.5); rnd_box.setLow(i,0.5);}
// Box used for rounding in case of ghost
Box<dim,St> g_rnd_box;
for (size_t i = 0 ; i < dim ; i++) {g_rnd_box.setHigh(i,0.5); g_rnd_box.setLow(i,-0.5);}