Latest modules

example/Vector/3_molecular_dynamic_gpu_opt/Makefile

@@ -8,9 +8,13 @@ else
         CUDA_CC=nvcc
 endif
 
-CC_SCOREP=scorep --nocompiler  --cuda --mpp=mpi nvcc
-CC=$(CUDA_CC) #${CC_SCOREP}
-CC_MPI=mpic++
+ifeq ($(PROFILE),ON)
+	CC=scorep --nocompiler  --cuda --mpp=mpi nvcc
+	CC_MPI=mpic++
+else
+	CC=$(CUDA_CC)
+	CC_MPI=mpic++
+endif
 
 LDIR =
 OPT=

example/Vector/7_SPH_dlb_gpu_opt/Makefile

@@ -13,8 +13,12 @@ else
         CUDA_CC_LINK=nvcc
 endif
 
-
-CC=mpic++
+ifeq ($(PROFILE),ON)
+	CUDA_CC=scorep --nocompiler  --cuda --mpp=mpi nvcc
+	CUDA_CC_LINK=nvcc
+else
+	CUDA_CC_LINK=nvcc
+endif
 
 LDIR =
 OPT=

example/Vector/7_SPH_dlb_gpu_opt/main.cu

@@ -348,7 +348,7 @@ __global__ void calc_forces_gpu(particles_type vd, NN_type NN, real_number W_dap
 		real_number r2 = norm2(dr);
 
 		// if they interact
-		if (r2 < FourH2)
+		if (r2 < FourH2 && dr >= 1e-8)
 		{
 			real_number r = sqrt(r2);
 
@@ -942,6 +942,8 @@ int main(int argc, char* argv[])
 				vd_out.getLastPos()[1] = vd.getPos(p)[1];
 				vd_out.getLastPos()[2] = vd.getPos(p)[2];
 
+				vd_out.template getLastProp<0>() = vd.template getProp<type>(p);
+
 				vd_out.template getLastProp<1>()[0] = vd.template getProp<velocity>(p)[0];
 				vd_out.template getLastProp<1>()[1] = vd.template getProp<velocity>(p)[1];
 				vd_out.template getLastProp<1>()[2] = vd.template getProp<velocity>(p)[2];

openfpm_vcluster @ e105e6ef

-Subproject commit 309c31433036534153366a27f8ad52c85c8dabb2
+Subproject commit e105e6ef793fa254da78c643c06bafdd858f0bb1

src/Decomposition/CartDecomposition_ext.hpp

@@ -218,6 +218,10 @@ public:
 	 */
 	void setParameters(const CartDecomposition<dim,T,Memory,layout_base,Distribution> & dec, const Ghost<dim,T> & g, const ::Box<dim,T> & ext_domain)
 	{
+		// Set the decomposition parameters
+		this->gr.setDimensions(dec.gr.getSize());
+		this->cd.setDimensions(ext_domain, dec.gr.getSize(), 0);
+
 		this->box_nn_processor = dec.box_nn_processor;
 
 		// Calculate new sub-domains for extended domain
@@ -225,7 +229,6 @@ public:
 
 		// Calculate fine_s structure for the extended domain
 		// update the cell decomposer and gr
-//		extend_fines(dec);
 		reconstruct_fine_s_from_extended_domain(ext_domain);
 
 		// Get the old sub-sub-domain grid extension

src/Vector/cuda/vector_dist_cuda_funcs.cuh

@@ -12,6 +12,7 @@
 #include "util/cuda/moderngpu/kernel_reduce.hxx"
 #include "util/cuda/moderngpu/kernel_scan.hxx"
 #include "Decomposition/common.hpp"
+#include "lib/pdata.hpp"
 
 template<unsigned int dim, typename St, typename decomposition_type, typename vector_type, typename start_type, typename output_type>
 __global__ void proc_label_id_ghost(decomposition_type dec,vector_type vd, start_type starts, output_type out)
@@ -349,6 +350,8 @@ void remove_marked(vector_type & vd)
 
 	// first we do a scan of the property
 	openfpm::vector_gpu<aggregate<unsigned int>> idx;
+
+	idx.setMemory(mem_tmp);
 	idx.resize(vd.size_local());
 
 	auto ite = idx.getGPUIterator();

src/Vector/tests/vector_dist_dlb_test.hpp

@@ -239,8 +239,21 @@ template<typename vector_type> void test_dlb_vector()
 	}
 
 	vd.map();
+
+	////////////// DEBUG ////////////////////////
+
+	vd.write("bug_test_init_before");
+
+	/////////////////////////////////////////////
+
 	vd.template ghost_get<>();
 
+	////////////// DEBUG ////////////////////////
+
+	vd.write("bug_test_init_after");
+
+	/////////////////////////////////////////////
+
 	// Get the neighborhood of each particles
 
 	auto VV = vd.getVerlet(0.01);
@@ -260,10 +273,24 @@ template<typename vector_type> void test_dlb_vector()
 
 	ModelSquare md;
 	md.factor = 10;
+	vd.map();
+
+	////////////// DEBUG ////////////////////////
+
+	vd.write("bug_test_before_dlb");
+
+	/////////////////////////////////////////////
+
 	vd.addComputationCosts(md);
 	vd.getDecomposition().decompose();
 	vd.map();
 
+	////////////// DEBUG ////////////////////////
+
+	vd.write("bug_test_after_dlb");
+
+	/////////////////////////////////////////////
+
 	vd.addComputationCosts(md);
 
 	openfpm::vector<size_t> loads;
@@ -299,9 +326,24 @@ template<typename vector_type> void test_dlb_vector()
 
 			++it;
 		}
+
 		vd.map();
+
+		////////////// DEBUG ////////////////////////
+
+		vd.write_frame("bug_test_before",i);
+
+		/////////////////////////////////////////////
+
 		vd.template ghost_get<>();
 
+		////////////// DEBUG ////////////////////////
+
+		vd.getDecomposition().write("dec_test");
+		vd.write_frame("bug_test_after",i);
+
+		/////////////////////////////////////////////
+
 		auto VV2 = vd.getVerlet(0.01);
 
 		auto it2 = vd.getDomainIterator();

src/Vector/vector_dist_comm.hpp

@@ -292,6 +292,9 @@ class vector_dist_comm
 
 		};
 		openfpm::vector<sh_box> reord_shift;
+		box_f.clear();
+		map_cmb.clear();
+		box_cmb.clear();
 
 		// Add local particles coming from periodic boundary, the only boxes that count are the one
 		// touching the border

src/lib/pdata.cpp

@@ -4,7 +4,7 @@
  *  Created on: Feb 5, 2016
  *      Author: Pietro Incardona
  */
-
+#include "pdata.hpp"
 #include "SubdomainGraphNodes.hpp"
 
 const std::string nm_v::attributes::name[] = {"x","migration","computation","global_id","id","sub_id","proc_id","id","fake_v"};
@@ -13,4 +13,3 @@ const std::string nm_part_v::attributes::name[] = {"id","sub_id"};
 const std::string nm_part_e::attributes::name[] = {"id"};
 
 
-

src/lib/pdata.hpp

+#include "config.h"
+