Release_0.8.0

CHANGELOG.md

@@ -5,10 +5,11 @@ All notable changes to this project will be documented in this file.
 
 ### Added
 - Dynamic Load balancing
-- Added SPH Dam break with Dynamic load balancing
+- Added SPH Dam break with Dynamic load balancing (7_sph_dlb)(7_sph_dlb_opt)
 - Added procedure for update ./install --update
   (From 0.8.0 version will be supported for bug fixing, version 0.X.0 will be supported untill
    0.X+2.0 will be out)
+- Added for debugging the options PRINT_STACKTRACE, CHECKFOR_POSNAN, CHECKFOR_POSINF, CHECKFOR_PROPINF, CHECKFOR_PROPNAN, SE_CLASS3 for debugging. Additional example added (7_sph_dlb_safe)
 
 ### Changed
 - BOOST updated to 1.63
@@ -27,7 +28,7 @@ All notable changes to this project will be documented in this file.
                 0.7.0 or apply the patch to upgrade to 0.6.1
 - Found and fixed a memory leak when using complex properties
 
-### Changed
+-### Changed
 - The file VCluster has been mooved #include "VCluster.hpp" must be changed to #include "VCluster/VCluster.hpp"
   BECAUSE OF THIS, PLEASE CLEAN THE OPENFPM FOLDER OTHERWISE YOU WILL END TO HAVE 2 VCLUSTER.HPP
 

example/SE/0_classes/main.cpp → example/Debugging/0_classes/main.cpp

@@ -187,7 +187,7 @@ int main(int argc, char* argv[])
 		vect_dist_key_dx vt(0);
 		auto it = vd1->getPos(vt);
     }
-	catch (size_t e)
+	catch (std::exception & e)
 	{
 		std::cerr << "Error notification of invalid usage of deleted object \n";
 	}

example/Vector/0_simple/main.cpp

@@ -12,6 +12,7 @@
  * \subpage Vector_5_md_vl_sym_crs
  * \subpage Vector_6_complex_usage
  * \subpage Vector_7_sph_dlb
+ * \subpage Vector_7_sph_dlb_opt
  *
  */
 
@@ -51,6 +52,7 @@
  */
 
 //! \cond [inclusion] \endcond
+#include <stddef.h>
 #include "Vector/vector_dist.hpp"
 //! \cond [inclusion] \endcond
 

example/Vector/7_SPH_dlb/main.cpp

@@ -13,6 +13,19 @@
  * decomposition to keep all the processor load and reduce idle time.
  *
  * \htmlonly
+ * <a href="#" onclick="hide_show('vector-video-3')" >Video 1</a>
+ * <div style="display:none" id="vector-video-3">
+ * <video id="vid1" width="1200" height="576" controls> <source src="http://openfpm.mpi-cbg.de/web/images/examples/7_SPH_dlb/sph_speed.mp4" type="video/mp4"></video>
+ * <script>video_anim('vid1',100,230)</script>
+ * </div>
+ * <a href="#" onclick="hide_show('vector-video-4')" >Video 2</a>
+ * <div style="display:none" id="vector-video-4">
+ * <video id="vid2" width="1200" height="576" controls> <source src="http://openfpm.mpi-cbg.de/web/images/examples/7_SPH_dlb/sph_speed2.mp4" type="video/mp4"></video>
+ * <script>video_anim('vid2',21,1590)</script>
+ * </div>
+ * \endhtmlonly
+ *
+ * \htmlonly
  * <img src="http://ppmcore.mpi-cbg.de/web/images/examples/7_SPH_dlb/dam_break_all.jpg"/>
  * \endhtmlonly
  *

images/Makefile.am

@@ -16,7 +16,7 @@ dom_box_CXXFLAGS = $(OPENMP_CFLAGS) $(AM_CXXFLAGS) $(PETSC_INCLUDE) $(METIS_INCL
 dom_box_CFLAGS = $(OPENMP_CFLAGS) $(CUDA_CFLAGS)
 dom_box_LDADD = $(LINKLIBS)
 
-vector_dist_SOURCES = vector.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_vcluster/src/VCluster/VCluster.cpp ../openfpm_devices/src/memory/PtrMemory.cpp
+vector_dist_SOURCES = vector.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_vcluster/src/VCluster/VCluster.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_devices/src/Memleak_check.cpp
 vector_dist_CXXFLAGS = $(OPENMP_CFLAGS) $(AM_CXXFLAGS) $(LIBHILBERT_INCLUDE) $(PETSC_INCLUDE) $(PARMETIS_INCLUDE) $(METIS_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(HDF5_CPPFLAGS) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function -Wno-unused-local-typedefs
 vector_dist_CFLAGS = $(OPENMP_CFLAGS) $(CUDA_CFLAGS)
 vector_dist_LDADD = $(LINKLIBS) -lparmetis -lmetis

images/vector.cpp

@@ -6,14 +6,34 @@ template<typename T> class Particle
 {
 public:
 
+#ifdef SE_CLASS3
+
+	typedef boost::fusion::vector<T,T[3],T[3][3],SE3_ADD_PROP(3)> type;
+
+#else
+
 	typedef boost::fusion::vector<T,T[3],T[3][3]> type;
 
+#endif
+
 	type data;
 
 	static const unsigned int s = 0;
 	static const unsigned int v = 1;
 	static const unsigned int t = 2;
+
+#ifdef SE_CLASS3
+
+	static const unsigned int max_prop = SE3_MAX_PROP(3);
+	static const unsigned int max_prop_real = 3;
+
+#else
+
 	static const unsigned int max_prop = 3;
+	static const unsigned int max_prop_real = 3;
+
+#endif
+
 };
 
 int main(int argc, char* argv[])

openfpm_data @ 63bfcfa6

-Subproject commit bcdc58554b1ff4b97c85479ac0869565bf76a0b6
+Subproject commit 63bfcfa657c6d9cd66eae064a115a08e4eaeb400

openfpm_devices @ b96708b8

-Subproject commit a0b02db5938003755b85c86fded64b107ac4e55d
+Subproject commit b96708b8c2ca93ef4a8754e58a28bbad506df932

openfpm_io @ 5dfcba90

-Subproject commit 4a5f8a2a4d13fe1e4e4537281c11979f3ac87e28
+Subproject commit 5dfcba90e49c58fa569f02475635938e285142b1

openfpm_vcluster @ dcf398d0

-Subproject commit 5b36046775ce3d7868f14450faade5effc256a14
+Subproject commit dcf398d040347c33163f349ffd3ab3f081affb01

src/DLB/DLB.hpp

@@ -11,10 +11,21 @@
 //! Time structure for statistical purposes
 typedef struct
 {
+	//! starting time of the simulation (0)
 	size_t simulationStartTime = 0;
+
+	//! End iteration of the simulation
 	size_t simulationEndTime;
+
+	//! integration time
 	double timeStep = 0.1;
+
+	//! Interval between teo rebalance
+
+	//! Start time
 	size_t iterationStartTime;
+
+	//! End time
 	size_t iterationEndTime;
 } Times;
 
@@ -89,7 +100,7 @@ private:
 
 	/*! \brief Function that gather times informations and decides if a rebalance is needed it uses the SAR heuristic
 	 *
-	 * \param t
+	 * \return true if re-balance is needed
 	 *
 	 */
 	inline bool SAR()
@@ -168,7 +179,12 @@ public:
 		heuristic = h;
 	}
 
-	/*! \brief Get the heuristic to use
+	/*! \brief Get the heuristic
+	 *
+	 * Indicate which heuristic model is used to calculate when a rebalance
+	 * is needed
+	 *
+	 * \return the Heuristic used by DLB
 	 *
 	 */
 	Heuristic getHeurisitc()
@@ -176,7 +192,9 @@ public:
 		return heuristic;
 	}
 
-	/*! \brief check if a re-balance is needed using the SAR heuristic
+	/*! \brief check if a re-balance is needed using the selected heuristic
+	 *
+	 * \return true if the rebalance is needed
 	 *
 	 */
 	bool rebalanceNeeded()
@@ -193,7 +211,7 @@ public:
 
 	/*! \brief Set start time for the simulation
 	 *
-	 * \param simulationStartTime time when the whole simulation starts
+	 * \param t time when the whole simulation starts
 	 */
 	void setSimulationStartTime(size_t t)
 	{
@@ -201,6 +219,8 @@ public:
 	}
 
 	/*! \brief Get start time for the simulation
+	 *
+	 * \return the start point of the simulation
 	 *
 	 */
 	size_t getSimulationStartTime()
@@ -210,7 +230,7 @@ public:
 
 	/*! \brief Set end time for the simulation
 	 *
-	 * \param simulationEndTime time when the whole simulation ends
+	 * \param t time when the whole simulation ends
 	 */
 	void setSimulationEndTime(size_t t)
 	{
@@ -218,6 +238,8 @@ public:
 	}
 
 	/*! \brief Get end time for the simulation
+	 *
+	 * \return the end time of the simulation
 	 *
 	 */
 	size_t getSimulationEndTime()
@@ -235,7 +257,7 @@ public:
 
 	/*! \brief Set start time for the single iteration
 	 *
-	 * \param iterationStartTime time when the single iteration starts
+	 * \param t time when the one iteration starts
 	 */
 	void startIteration(size_t t)
 	{
@@ -243,6 +265,8 @@ public:
 	}
 
 	/*! \brief Set end time for the single iteration
+	 *
+	 * \param time when one iteration is completed
 	 *
 	 */
 	void endIteration()
@@ -250,18 +274,18 @@ public:
 		timeInfo.iterationEndTime = clock();
 	}
 
-	/*! \brief Set end time for the single iteration
+	/*! \brief Set the end time when the previous rebalance has been performed
 	 *
-	 * \param iterationEndTime time when the single iteration ends
+	 * \param t time when one iteration ends
 	 */
 	void endIteration(size_t t)
 	{
 		timeInfo.iterationEndTime = t;
 	}
 
-	/*! \brief Set time step for the single iteration
+	/*! \brief Set delta time step for one iteration (Computation time)
 	 *
-	 * \param timestep value, can be also a 0.1 s
+	 * \param t timestep
 	 */
 	void setTimeStep(double t)
 	{
@@ -278,6 +302,8 @@ public:
 	}
 
 	/*! \brief Get how many time-steps have passed since the last re-balancing
+	 *
+	 * \return number of timesteos
 	 *
 	 */
 	size_t getNTimeStepSinceDLB()
@@ -287,16 +313,16 @@ public:
 
 	/*! \brief Set un-balance value
 	 *
-	 * \param computation value of the computation cost (default: 5)
+	 * \param u unbalance
 	 */
 	void setUnbalance(float u)
 	{
 		unbalance = u;
 	}
 
-	/*! \brief Set un-balance value
+	/*! \brief threshold of umbalance to start a rebalance
 	 *
-	 * \param computation value of the computation cost (default: 5)
+	 * \param t threshold level
 	 */
 	void setThresholdLevel(ThresholdLevel t)
 	{

src/DLB/LB_Model.hpp

@@ -32,6 +32,11 @@ struct ModelLin
 	{
 		dec.setSubSubDomainComputationCost(v, dec.getSubSubDomainComputationCost(v));
 	}
+
+	double setDistributionTol(size_t i)
+	{
+		return 1.01;
+	}
 };
 
 /*! \brief Linear model
@@ -52,6 +57,11 @@ struct ModelSquare
 	{
 		dec.setSubSubDomainComputationCost(v, dec.getSubSubDomainComputationCost(v) * dec.getSubSubDomainComputationCost(v));
 	}
+
+	double setDistributionTol(size_t i)
+	{
+		return 1.01;
+	}
 };
 
 

src/Decomposition/CartDecomposition.hpp

@@ -217,14 +217,6 @@ public:
 	 */
 	void createSubdomains(Vcluster & v_cl, const size_t (& bc)[dim], size_t opt = 0)
 	{
-#ifdef SE_CLASS1
-		if (&v_cl == NULL)
-		{
-			std::cerr << __FILE__ << ":" << __LINE__ << " error VCluster instance is null, check that you ever initialized it \n";
-			ACTION_ON_ERROR()
-		}
-#endif
-
 		int p_id = v_cl.getProcessUnitID();
 
 		// Calculate the total number of box and and the spacing
@@ -1028,7 +1020,7 @@ public:
 	 * \param ts number of time step from the previous load balancing
 	 *
 	 */
-	void rebalance(size_t ts)
+	void refine(size_t ts)
 	{
 		reset();
 
@@ -1044,13 +1036,34 @@ public:
 		domain_nn_calculator_cart<dim>::reset();
 	}
 
+	/*! \brief Refine the decomposition, available only for ParMetis distribution, for Metis it is a null call
+	 *
+	 * \param ts number of time step from the previous load balancing
+	 *
+	 */
+	void redecompose(size_t ts)
+	{
+		reset();
+
+		if (commCostSet == false)
+			computeCommunicationAndMigrationCosts(ts);
+
+		dist.redecompose();
+
+		createSubdomains(v_cl,bc);
+
+		calculateGhostBoxes();
+
+		domain_nn_calculator_cart<dim>::reset();
+	}
+
 	/*! \brief Refine the decomposition, available only for ParMetis distribution, for Metis it is a null call
 	 *
 	 * \param dlb Dynamic load balancing object
 	 *
 	 * \return true if the re-balance has been executed, false otherwise
 	 */
-	bool rebalance(DLB & dlb)
+	bool refine(DLB & dlb)
 	{
 		// if the DLB heuristic to use is the "Unbalance Threshold" get unbalance percentage
 		if (dlb.getHeurisitc() == DLB::Heuristic::UNBALANCE_THRLD)
@@ -1065,7 +1078,7 @@ public:
 
 		if (dlb.rebalanceNeeded())
 		{
-			rebalance(dlb.getNTimeStepSinceDLB());
+			refine(dlb.getNTimeStepSinceDLB());
 
 			return true;
 		}
@@ -1552,6 +1565,16 @@ public:
 		dist.setComputationCost(gid, c + i);
 	}
 
+	/*! \brief Get the decomposition counter
+	 *
+	 * \return the decomposition counter
+	 *
+	 */
+	size_t get_ndec()
+	{
+		return dist.get_ndec();
+	}
+
 	//! friend classes
 	friend extended_type;
 

src/Decomposition/Distribution/DistParMetisDistribution.hpp

@@ -311,7 +311,7 @@ public:
 
 	/*! \brief Returns total number of neighbors of the sub-sub-domain id
 	 *
-	 * \param i id of the sub-sub-domain
+	 * \param id id of the sub-sub-domain
 	 */
 	size_t getNSubSubDomainNeighbors(size_t id)
 	{

src/Decomposition/Distribution/Distribution_unit_tests.hpp

@@ -163,7 +163,7 @@ BOOST_AUTO_TEST_CASE( Metis_distribution_test)
 	// operator= functions
 	// operator== functions
 
-	BOOST_REQUIRE_EQUAL(sizeof(MetisDistribution<3,float>),536ul);
+	BOOST_REQUIRE_EQUAL(sizeof(MetisDistribution<3,float>),472ul);
 }
 
 BOOST_AUTO_TEST_CASE( Parmetis_distribution_test)
@@ -264,7 +264,7 @@ BOOST_AUTO_TEST_CASE( Parmetis_distribution_test)
 
 	//! [refine with parmetis the decomposition]
 
-	BOOST_REQUIRE_EQUAL(sizeof(MetisDistribution<3,float>),536ul);
+	BOOST_REQUIRE_EQUAL(sizeof(MetisDistribution<3,float>),472ul);
 }
 
 BOOST_AUTO_TEST_CASE( DistParmetis_distribution_test)

src/Decomposition/Distribution/MetisDistribution.hpp

@@ -11,7 +11,7 @@
 #include "SubdomainGraphNodes.hpp"
 #include "metis_util.hpp"
 
-#define METIS_DISTRIBUTION_ERROR 100001
+#define METIS_DISTRIBUTION_ERROR_OBJECT std::runtime_error("Metis runtime error");
 
 /*! \brief Class that distribute sub-sub-domains across processors using Metis Library
  *
@@ -58,7 +58,7 @@ class MetisDistribution
 		if (id >= gp.getNVertex())
 		{
 			std::cerr << "Error " << __FILE__ ":" << __LINE__ << " such sub-sub-domain doesn't exist (id = " << id << ", " << "total size = " << gp.getNVertex() << ")\n";
-			ACTION_ON_ERROR(METIS_DISTRIBUTION_ERROR)
+			ACTION_ON_ERROR(METIS_DISTRIBUTION_ERROR_OBJECT)
 		}
 #endif
 	}
@@ -74,7 +74,7 @@ class MetisDistribution
 		if (e >= gp.getNChilds(id))
 		{
 			std::cerr << "Error " << __FILE__ ":" << __LINE__ << " for the sub-sub-domain " << id << " such neighborhood doesn't exist (e = " << e << ", " << "total size = " << gp.getNChilds(id) << ")\n";
-			ACTION_ON_ERROR(METIS_DISTRIBUTION_ERROR)
+			ACTION_ON_ERROR(METIS_DISTRIBUTION_ERROR_OBJECT)
 		}
 #endif
 	}
@@ -208,7 +208,7 @@ public:
 			check_valid(this,8);
 #endif
 		std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " MetisDistribution does not have refine functionality";
-		ACTION_ON_ERROR(METIS_DISTRIBUTION_ERROR);
+		ACTION_ON_ERROR(METIS_DISTRIBUTION_ERROR_OBJECT);
 	}
 
 	/*! \brief Function that return the position (point P1) of the sub-sub domain box in the space

src/Decomposition/Distribution/ParMetisDistribution.hpp

@@ -262,45 +262,6 @@ class ParMetisDistribution
 
 		// Update graphs with the received data
 		updateGraphs();
-
-
-		/////////////////////////////////////////
-
-
-		// Get result partition for this processor
-/*		idx_t * partition = parmetis_graph.getPartition();
-
-		//! Prepare vector of arrays to contain all partitions
-		partitions.get(p_id).resize(nl_vertex.id);
-		std::copy(partition, partition + nl_vertex.id, &partitions.get(p_id).get(0));
-
-		// Reset data structure to keep trace of new vertices distribution in processors (needed to update main graph)
-		for (size_t i = 0; i < Np; ++i)
-		{
-			v_per_proc.get(i).clear();
-		}
-
-		openfpm::vector<size_t> prc;
-		openfpm::vector<size_t> sz;
-		openfpm::vector<void *> ptr;
-
-		for (size_t i = 0; i < Np; i++)
-		{
-			if (i != v_cl.getProcessUnitID())
-			{
-				partitions.get(i).clear();
-				prc.add(i);
-				sz.add(nl_vertex.id * sizeof(idx_t));
-				ptr.add(partitions.get(p_id).getPointer());
-			}
-		}
-
-		// Exchange informations through processors
-		v_cl.sendrecvMultipleMessagesNBX(prc.size(), &sz.get(0), &prc.get(0), &ptr.get(0), message_receive, &partitions,
-		NONE);
-
-		// Update graphs with the new distributions
-		updateGraphs();*/
 	}
 
 
@@ -408,7 +369,7 @@ public:
 			parmetis_graph.reset(gp, vtxdist, m2g, verticesGotWeights);
 
 		//! Decompose
-		parmetis_graph.decompose<nm_v::proc_id>(vtxdist);
+		parmetis_graph.decompose(vtxdist);
 
 		// update after decomposition
 		postDecomposition();
@@ -428,7 +389,24 @@ public:
 		parmetis_graph.reset(gp, vtxdist, m2g, verticesGotWeights);
 
 		// Refine
-		parmetis_graph.refine<nm_v::proc_id>(vtxdist);
+		parmetis_graph.refine(vtxdist);
+
+		postDecomposition();
+	}
+
+	/*! \brief Redecompose current decomposition
+	 *
+	 * It makes a redecomposition using Parmetis taking into consideration
+	 * also migration cost
+	 *
+	 */
+	void redecompose()
+	{
+		// Reset parmetis graph and reconstruct it
+		parmetis_graph.reset(gp, vtxdist, m2g, verticesGotWeights);
+
+		// Refine
+		parmetis_graph.redecompose(vtxdist);
 
 		postDecomposition();
 	}
@@ -577,7 +555,7 @@ public:
 
 	/*! \brief Returns total number of neighbors of the sub-sub-domain id
 	 *
-	 * \param i id of the sub-sub-domain
+	 * \param id id of the sub-sub-domain
 	 */
 	size_t getNSubSubDomainNeighbors(size_t id)
 	{
@@ -626,6 +604,16 @@ public:
 
 		return *this;
 	}
+
+	/*! \brief Get the decomposition counter
+	 *
+	 * \return the decomposition counter
+	 *
+	 */
+	size_t get_ndec()
+	{
+		return parmetis_graph.get_ndec();
+	}
 };
 
 #endif /* SRC_DECOMPOSITION_PARMETISDISTRIBUTION_HPP_ */

src/Decomposition/Distribution/SpaceDistribution.hpp

@@ -335,7 +335,7 @@ public:
 
 	/*! \brief Returns total number of neighbors of the sub-sub-domain id
 	 *
-	 * \param i id of the sub-sub-domain
+	 * \param id id of the sub-sub-domain
 	 */
 	size_t getNSubSubDomainNeighbors(size_t id)
 	{

src/Decomposition/Distribution/parmetis_dist_util.hpp

@@ -96,27 +96,24 @@ struct Parmetis_dist_graph
 template<typename Graph>
 class DistParmetis
 {
-	// Graph in metis reppresentation
+	//! Graph in parmetis reppresentation
 	Parmetis_dist_graph Mg;
 
-	// Original graph
-	//	Graph & g;
-
-	// Communticator for OpenMPI
+	//! Communticator for OpenMPI
 	MPI_Comm comm = (MPI_Comm)NULL;
 
-	// VCluster
+	//! VCluster
 	Vcluster & v_cl;
 
-	// Process rank information
+	//! Process rank information
 	int p_id = 0;
 
-	// nc Number of partition
+	//! nc Number of partition
 	size_t nc = 0;
 
 	/*! \brief Construct Adjacency list
 	 *
-	 * \param g Reference graph to get informations
+	 * \param sub_g graph in which we construct the adjacency list
 	 *
 	 */
 	void constructAdjList(Graph & sub_g)
@@ -175,9 +172,9 @@ public:
 
 	/*! \brief Constructor
 	 *
-	 * Construct a metis graph from Graph_CSR
+	 * Construct a metis graph from a Graph_CSR
 	 *
-	 * \param g Graph we want to convert to decompose
+	 * \param v_cl Vcluster
 	 * \param nc number of partitions
 	 *
 	 */
@@ -362,7 +359,7 @@ public:
 	 *
 	 * \tparam i which property store the decomposition
 	 *
-	 *
+	 * \param sub_g graph to decompose
 	 *
 	 */
 	template<unsigned int i>
@@ -389,6 +386,8 @@ public:
 	 *
 	 * \tparam i which property store the refined decomposition
 	 *
+	 * \param sub_g graph to decompose
+	 *
 	 */
 
 	template<unsigned int i>
@@ -406,6 +405,8 @@ public:
 	}
 
 	/*! \brief Get graph partition vector
+	 *
+	 * \return the partition or the assignment of each sub-sub-domain
 	 *
 	 */
 	idx_t * getPartition()
@@ -414,6 +415,8 @@ public:
 	}