Fixing ghost get for distributed grids

src/.deps/pdata.Po

-# dummy

src/.deps/ppline-main.Po

-# dummy

src/Decomposition/CartDecomposition_unit_test.hpp

@@ -2,7 +2,7 @@
 #define CARTDECOMPOSITION_UNIT_TEST_HPP
 
 #include "CartDecomposition.hpp"
-#include "mathutil.hpp"
+#include "util/mathutil.hpp"
 
 BOOST_AUTO_TEST_SUITE( CartDecomposition_test )
 

src/Decomposition/ORB.hpp

@@ -9,7 +9,7 @@
 #define ORB_HPP_
 
 #include "data_type/scalar.hpp"
-#include "mathutil.hpp"
+#include "util/mathutil.hpp"
 
 /*! \brief this class is a functor for "for_each" algorithm
  *

src/Graph/CartesianGraphFactory.hpp

@@ -90,7 +90,7 @@ public:
 
 		T szd[dim];
 
-		for (int i = 0 ; i < dim ; i++)
+		for (size_t i = 0 ; i < dim ; i++)
 		{szd[i] = (dom.getHigh(i) - dom.getLow(i)) / sz[i];}
 
 		//! Construct an hyper-cube of dimension dim
@@ -137,7 +137,7 @@ public:
 
 			// Get the combinations of dimension d
 
-			for (int d = dim-1 ; d >= dim_c ; d--)
+			for (size_t d = dim-1 ; d >= dim_c ; d--)
 			{
 				// create the edges for that dimension
 
@@ -145,7 +145,7 @@ public:
 
 				// for each combination calculate a safe linearization and create an edge
 
-				for (int j = 0 ; j < c.size() ; j++)
+				for (size_t j = 0 ; j < c.size() ; j++)
 				{
 					// Calculate the element size
 
@@ -153,7 +153,7 @@ public:
 
 					// for each dimension multiply and reduce
 
-					for (int s = 0 ; s < dim ; s++)
+					for (size_t s = 0 ; s < dim ; s++)
 					{
 						ele_sz += szd[s] * abs(c[j][s]);
 					}
@@ -200,7 +200,7 @@ public:
 
 		T szd[dim];
 
-		for (int i = 0 ; i < dim ; i++)
+		for (size_t i = 0 ; i < dim ; i++)
 		{szd[i] = (dom.getHigh(i) - dom.getLow(i)) / sz[i];}
 
 		//! Construct an hyper-cube of dimension dim
@@ -247,7 +247,7 @@ public:
 
 			// Get the combinations of dimension d
 
-			for (int d = dim-1 ; d >= dim_c ; d--)
+			for (size_t d = dim-1 ; d >= dim_c ; d--)
 			{
 				// create the edges for that dimension
 
@@ -255,7 +255,7 @@ public:
 
 				// for each combination calculate a safe linearization and create an edge
 
-				for (int j = 0 ; j < c.size() ; j++)
+				for (size_t j = 0 ; j < c.size() ; j++)
 				{
 					// Calculate the element size
 
@@ -263,7 +263,7 @@ public:
 
 					// for each dimension multiply and reduce
 
-					for (int s = 0 ; s < dim ; s++)
+					for (size_t s = 0 ; s < dim ; s++)
 					{
 						ele_sz += szd[s] * abs(c[j][s]);
 					}

src/Grid/grid_dist_id_iterator.hpp

@@ -24,7 +24,7 @@
      |  +------------+  |
      |                  |
      +------------------+
-(0,0)
+(0,0) local coordinate ---> ( x, y )
 
 	\endverbatim
 
@@ -41,6 +41,8 @@ struct GBoxes
 	Box<dim,long int> GDbox;
 	//! Domain box
 	Box<dim,long int> Dbox;
+	//! origin of GDbox in global coordinates
+	Point<dim,long int> origin;
 };
 
 #include "grid_dist_key.hpp"
@@ -78,7 +80,7 @@ class grid_dist_iterator
 	 *
 	 */
 	grid_dist_iterator(Vcluster_object_array<device_grid> & gk, const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
-	:g_c(0),gList(gk),gdb_ext(gdb_ext),m(m)
+	:g_c(0),gList(gk),gdb_ext(gdb_ext),m(0)
 	{
 		// Initialize the current iterator
 		// with the first grid

src/Makefile

@@ -189,8 +189,8 @@ CC = gcc
 CCDEPMODE = depmode=gcc3
 CFLAGS = -g -O2
 CPPFLAGS = 
-CUDA_CFLAGS =  -I -I -I/usr/local/cuda-5.5/include
-CUDA_LIBS =  -L -L -L/usr/local/cuda-5.5/lib64 -lcuda -lcudart
+CUDA_CFLAGS =  -I -I -I/usr/local/cuda/include
+CUDA_LIBS =  -L -L -L/usr/local/cuda/lib64 -lcuda -lcudart
 CXX = mpic++
 CXXDEPMODE = depmode=gcc3
 CXXFLAGS =  --std=c++11 -march=native -mtune=native  -g3  -Wall -O0 
@@ -213,7 +213,7 @@ LIBS =
 LTLIBOBJS = 
 MAKEINFO = ${SHELL} /home/i-bird/Desktop/MOSAIC/OpenFPM_project/OpenFPM_pdata/missing makeinfo
 MKDIR_P = /usr/bin/mkdir -p
-NVCC = /usr/local/cuda-5.5/bin/nvcc
+NVCC = /usr/local/cuda/bin/nvcc
 NVCCFLAGS =    -g -O0 
 NVCC_EXIST = yes
 OBJEXT = o

src/Vector/vector_dist.hpp

@@ -16,7 +16,7 @@
 #include "memory/PreAllocHeapMemory.hpp"
 #include "memory/PtrMemory.hpp"
 #include "NN/CellList/CellList.hpp"
-#include "common.hpp"
+#include "util/common.hpp"
 #include "util/object_util.hpp"
 #include "memory/ExtPreAlloc.hpp"
 #include "CSVWriter.hpp"
@@ -102,7 +102,7 @@ public:
 		// Calculate the maximum number (before merging) of sub-domain on
 		// each dimension
 		size_t div[point::dims];
-		for (int i = 0 ; i < point::dims ; i++)
+		for (size_t i = 0 ; i < point::dims ; i++)
 		{div[i] = openfpm::math::round_big_2(pow(n_sub,1.0/point::dims));}
 
 		// Create the sub-domains
@@ -487,9 +487,9 @@ public:
 			for (size_t j = 0 ; j < opart.get(i).size() ; j++)
 			{
 				// source object type
-				typedef encapc<1,prop,typename openfpm::vector<prop>::memory_t> encap_src;
+				typedef encapc<1,prop,typename openfpm::vector<prop>::memory_conf> encap_src;
 				// destination object type
-				typedef encapc<1,prp_object,typename openfpm::vector<prp_object>::memory_t> encap_dst;
+				typedef encapc<1,prp_object,typename openfpm::vector<prp_object>::memory_conf> encap_dst;
 
 				// Copy only the selected properties
 				object_si_d<encap_src,encap_dst,ENCAP,prp...>(v_prp.get(INTERNAL).get(opart.get(i).get(j)),g_send_prp.get(i).get(j));

src/Vector/vector_dist_unit_test.hpp

@@ -113,7 +113,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
 	const auto & dec = vd.getDecomposition();
 
 	// Get the ghost external boxes
-	openfpm::vector<size_t> vb(dec.getNGhostBox());
+	openfpm::vector<size_t> vb(dec.getNEGhostBox());
 
 	// Get the ghost iterator
 	auto g_it = vd.getGhostIterator();
@@ -131,9 +131,9 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
 		size_t lb = 0;
 
 		// check if the received data is in one of the ghost boxes
-		for ( ; b < dec.getNGhostBox() ; b++)
+		for ( ; b < dec.getNEGhostBox() ; b++)
 		{
-			if (dec.getGhostBox(b).isInside(vd.getPos<s::x>(key)) == true)
+			if (dec.getEGhostBox(b).isInside(vd.getPos<s::x>(key)) == true)
 			{
 				is_in = true;
 
@@ -145,7 +145,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
 		BOOST_REQUIRE_EQUAL(is_in,true);
 
 		// Check that the particle come from the correct processor
-		BOOST_REQUIRE_EQUAL(vd.getProp<p::v>(key)[0],dec.getGhostBoxProcessor(lb));
+		BOOST_REQUIRE_EQUAL(vd.getProp<p::v>(key)[0],dec.getEGhostBoxProcessor(lb));
 
 		++g_it;
 	}
@@ -155,7 +155,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
 	for (size_t i = 0 ; i < vb.size() ; i++)
 	{
 		// Calculate how many particle should be in the box
-		size_t n_point = cd.getGridPoints(dec.getGhostBox(i)).getVolume();
+		size_t n_point = cd.getGridPoints(dec.getEGhostBox(i)).getVolumeKey();
 
 		BOOST_REQUIRE_EQUAL(n_point,vb.get(i));
 	}

src/dec_optimizer.hpp

@@ -115,7 +115,7 @@ private:
 	 */
 	void expand_one_wf(openfpm::vector<wavefront<dim>> & v_w, std::vector<comb<dim>> & w_comb , size_t d)
 	{
-		for (int j = 0 ; j < dim ; j++)
+		for (size_t j = 0 ; j < dim ; j++)
 		{
 			v_w.template get<wavefront<dim>::stop>(d)[j] = v_w.template get<wavefront<dim>::stop>(d)[j] + w_comb[d].c[j];
 			v_w.template get<wavefront<dim>::start>(d)[j] = v_w.template get<wavefront<dim>::start>(d)[j] + w_comb[d].c[j];
@@ -136,9 +136,9 @@ private:
 
 		// Eliminate the w_comb[d] direction
 
-		for (int k = 0 ; k < q_comb.size() ; k++)
+		for (size_t k = 0 ; k < q_comb.size() ; k++)
 		{
-			for (int j = 0 ; j < dim ; j++)
+			for (size_t j = 0 ; j < dim ; j++)
 			{
 				if (w_comb[d].c[j] != 0)
 				{
@@ -148,7 +148,7 @@ private:
 		}
 
 		// for all the combinations
-		for (int j = 0 ; j < q_comb.size() ; j++)
+		for (size_t j = 0 ; j < q_comb.size() ; j++)
 		{
 			size_t id = hyp.LinId(q_comb[j]);
 
@@ -158,7 +158,7 @@ private:
 
 			// is positive, modify the stop point or the starting point
 
-			for (int s = 0 ; s < dim ; s++)
+			for (size_t s = 0 ; s < dim ; s++)
 			{
 				if (is_pos == true)
 				{v_w.template get<wavefront<dim>::stop>(id)[s] = v_w.template get<wavefront<dim>::stop>(id)[s] + w_comb[d].c[s];}
@@ -257,7 +257,7 @@ private:
 		// Create an Hyper-cube
 		HyperCube<dim> hyp;
 
-		for (int d = 0 ; d < v_w.size() ; d++)
+		for (size_t d = 0 ; d < v_w.size() ; d++)
 		{
 			expand_one_wf(v_w,w_comb,d);
 			adjust_others_wf(v_w,hyp,w_comb,d);
@@ -265,7 +265,7 @@ private:
 
 		// for each expanded wavefront create a sub-grid iterator and add the sub-domain
 
-		for (int d = 0 ; d < v_w.size() ; d++)
+		for (size_t d = 0 ; d < v_w.size() ; d++)
 		{
 			// Create a sub-grid iterator
 			grid_key_dx_iterator_sub<dim> g_sub(gh,v_w.template get<wavefront<dim>::start>(d),v_w.template get<wavefront<dim>::stop>(d));
@@ -357,7 +357,7 @@ private:
 
 			// for each direction of expansion expand the wavefront
 
-			for (int d = 0 ; d < n_wf ; d++)
+			for (size_t d = 0 ; d < n_wf ; d++)
 			{
 				// number of processed sub-domain
 				size_t n_proc_sub = 0;
@@ -403,7 +403,7 @@ private:
 				if (w_can_expand == true)
 				{
 					// expand the wavefront
-					for (int j = 0 ; j < dim ; j++)
+					for (size_t j = 0 ; j < dim ; j++)
 					{
 						v_w.template get<wavefront<dim>::stop>(d)[j] = v_w.template get<wavefront<dim>::stop>(d)[j] + w_comb[d].c[j];
 						v_w.template get<wavefront<dim>::start>(d)[j] = v_w.template get<wavefront<dim>::start>(d)[j] + w_comb[d].c[j];
@@ -415,9 +415,9 @@ private:
 
 					// Eliminate the w_comb[d] direction
 
-					for (int k = 0 ; k < q_comb.size() ; k++)
+					for (size_t k = 0 ; k < q_comb.size() ; k++)
 					{
-						for (int j = 0 ; j < dim ; j++)
+						for (size_t j = 0 ; j < dim ; j++)
 						{
 							if (w_comb[d].c[j] != 0)
 							{
@@ -427,7 +427,7 @@ private:
 					}
 
 					// for all the combinations
-					for (int j = 0 ; j < q_comb.size() ; j++)
+					for (size_t j = 0 ; j < q_comb.size() ; j++)
 					{
 						size_t id = hyp.LinId(q_comb[j]);
 
@@ -437,7 +437,7 @@ private:
 
 						// is positive, modify the stop point or the starting point
 
-						for (int s = 0 ; s < dim ; s++)
+						for (size_t s = 0 ; s < dim ; s++)
 						{
 							if (is_pos == true)
 							{v_w.template get<wavefront<dim>::stop>(id)[s] = v_w.template get<wavefront<dim>::stop>(id)[s] + w_comb[d].c[s];}
@@ -451,7 +451,7 @@ private:
 
 		// get back the hyper-cube produced
 
-		for (int i = 0 ; i < dim ; i++)
+		for (size_t i = 0 ; i < dim ; i++)
 		{
 			// get the index of the wavefront direction
 			size_t p_f = hyp.positiveFace(i);
@@ -473,9 +473,9 @@ private:
 	{
 		// Wavefront to initialize
 
-		for (int i = 0 ; i < v_w.size() ; i++)
+		for (size_t i = 0 ; i < v_w.size() ; i++)
 		{
-			for (int j = 0 ; j < dim ; j++)
+			for (size_t j = 0 ; j < dim ; j++)
 			{
 				v_w.template get<wavefront<dim>::start>(i)[j] = start_p.get(j);
 				v_w.template get<wavefront<dim>::stop>(i)[j] = start_p.get(j);
@@ -517,7 +517,7 @@ private:
 			const grid_key_dx<dim> & gk = g_sub.get();
 
 			// if the subdomain has the id we are searching stop
-			if (graph.vertex(gh.LinId(gk)).template get<p_id>() == id)
+			if ((long int)graph.vertex(gh.LinId(gk)).template get<p_id>() == id)
 			{
 				return gk;
 			}