Release_0.8.0 candidate

CHANGELOG.md

@@ -9,11 +9,16 @@ All notable changes to this project will be documented in this file.
 - 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 video lessons for Dynamic load balancing (openfpm.mpi-cbg.de)
 - 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)
+- Added the possibility to write binary VTK files using VTK_WRITER_BINARY 0_simple_vector
+  example
+  
 
 ### Changed
 - BOOST updated to 1.63
 - Eigen updated to 3.3.7
+- Option CSV_WRITER changed to CSV_WRITER_ASCII
 
 ## [0.7.0] 15 December 2016
 

example/Vector/0_simple/main.cpp

@@ -327,7 +327,10 @@ int main(int argc, char* argv[])
 	 * With this function we output the particle position in VTK format. A VTK file
 	 * contain information about particle position and properties. Such file can be visualizaed
 	 * with program like paraview. In case this program run on several processor Each processor
-	 * generate a VTK file
+	 * generate a VTK file. VTK has two format one is the ASCII that is human readable but produce
+	 * bigger file the other is the binary that produce not-human readable files, but smaller
+	 * and more efficent files to read for Paraview. In order to create a Binary VTK file use the
+	 * option VTK_
 	 *
 	 * \snippet Vector/0_simple/main.cpp vtk
 	 *
@@ -344,6 +347,7 @@ int main(int argc, char* argv[])
 	//! \cond [vtk] \endcond
 
 	vd.write("particles");
+	vd.write("particles",VTK_WRITE_BINARY);
 
 	//! \cond [vtk] \endcond
 

example/Vector/7_SPH_dlb/main.cpp

@@ -13,15 +13,21 @@
  * decomposition to keep all the processor load and reduce idle time.
  *
  * \htmlonly
- * <a href="#" onclick="hide_show('vector-video-3')" >Video 1</a>
+ * <a href="#" onclick="hide_show('vector-video-3')" >Simulation video 1</a><br>
  * <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>
+ * <video id="vid3" 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>
  * </div>
- * <a href="#" onclick="hide_show('vector-video-4')" >Video 2</a>
+ * <a href="#" onclick="hide_show('vector-video-4')" >Simulation video 2</a><br>
  * <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>
+ * <video id="vid4" 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>
+ * </div>
+ * <a href="#" onclick="hide_show('vector-video-15')" >Simulation dynamic load balancing video 1</a><br>
+ * <div style="display:none" id="vector-video-15">
+ * <video id="vid15" width="1200" height="576" controls> <source src="http://openfpm.mpi-cbg.de/web/images/examples/7_SPH_dlb/sph_dlb.mp4" type="video/mp4"></video>
+ * </div>
+ * <a href="#" onclick="hide_show('vector-video-16')" >Simulation dynamic load balancing video 2</a><br>
+ * <div style="display:none" id="vector-video-16">
+ * <video id="vid16" width="1200" height="576" controls> <source src="http://openfpm.mpi-cbg.de/web/images/examples/7_SPH_dlb/sph_dlb2.mp4" type="video/mp4"></video>
  * </div>
  * \endhtmlonly
  *
@@ -1196,6 +1202,21 @@ int main(int argc, char* argv[])
 	 *       balanced configuration does not correspond to the evenly distributed particles to know
 	 *       more about that please follow the video tutorials
 	 *
+	 * \htmlonly
+	 * <a href="#" onclick="hide_show('vector-video-6')" >Dynamic load balancing the theory part1</a>
+	 * <div style="display:none" id="vector-video-6">
+	 * <video id="vid6" width="1200" height="576" controls> <source src="http://openfpm.mpi-cbg.de/upload/video/dlb-1.mp4" type="video/mp4"></video>
+	 * </div>
+	 * <a href="#" onclick="hide_show('vector-video-7')" >Dynamic load balancing the theory part2</a>
+	 * <div style="display:none" id="vector-video-7">
+	 * <video id="vid7" width="1200" height="576" controls> <source src="http://openfpm.mpi-cbg.de/upload/video/dlb-2.mp4" type="video/mp4"></video>
+	 * </div>
+	 * <a href="#" onclick="hide_show('vector-video-8')" >Dynamic load balancing practice part1</a>
+	 * <div style="display:none" id="vector-video-8">
+	 * <video id="vid8" width="1200" height="576" controls> <source src="http://openfpm.mpi-cbg.de/upload/video/dlb-2.mp4" type="video/mp4"></video>
+	 * </div>
+	 * \endhtmlonly
+	 *
 	 * \snippet Vector/7_SPH_dlb/main.cpp load balancing
 	 *
 	 * \htmlonly

openfpm_data @ 8104e4b4

-Subproject commit 63bfcfa657c6d9cd66eae064a115a08e4eaeb400
+Subproject commit 8104e4b491b20b7b7c74b17ec733729fa3cb5dc3

openfpm_devices @ 9d5f962e

-Subproject commit b96708b8c2ca93ef4a8754e58a28bbad506df932
+Subproject commit 9d5f962e451893510d39b9d3233087f54a510bb7

openfpm_io @ fd804149

-Subproject commit 5dfcba90e49c58fa569f02475635938e285142b1
+Subproject commit fd804149e48a4d8d5d6f0632d4368e7e76d61183

openfpm_numerics @ 5e304636

-Subproject commit bc9efd0e62982ec86bd6d53e43fb4db1b041a82c
+Subproject commit 5e304636549cf27fd266aaf3e459d4861d4ff096

src/DLB/LB_Model.hpp

@@ -33,7 +33,7 @@ struct ModelLin
 		dec.setSubSubDomainComputationCost(v, dec.getSubSubDomainComputationCost(v));
 	}
 
-	double setDistributionTol(size_t i)
+	double distributionTol()
 	{
 		return 1.01;
 	}
@@ -58,7 +58,7 @@ struct ModelSquare
 		dec.setSubSubDomainComputationCost(v, dec.getSubSubDomainComputationCost(v) * dec.getSubSubDomainComputationCost(v));
 	}
 
-	double setDistributionTol(size_t i)
+	double distributionTol()
 	{
 		return 1.01;
 	}

src/Decomposition/CartDecomposition.hpp

@@ -393,7 +393,7 @@ public:
 	}
 
 
-	/*! It calculate the internal ghost boxes
+	/*! \brief It calculate the internal ghost boxes
 	 *
 	 * Example: Processor 10 calculate
 	 * B8_0 B9_0 B9_1 and B5_0
@@ -1275,7 +1275,7 @@ public:
 
 	/*! \brief Get the domain Cells
 	 *
-	 * It performa a linearization of the domain cells using the extension provided in gs
+	 * It perform a linearization of the domain cells using the extension provided in gs
 	 *
 	 *
 	 * \param shift Cell padding

src/Decomposition/Distribution/ParMetisDistribution.hpp

@@ -615,15 +615,14 @@ public:
 		return parmetis_graph.get_ndec();
 	}
 
-	/*! \brief Set the tollerance for each partition
+	/*! \brief Set the tolerance for each partition
 	 *
-	 * \param i partition
-	 * \param tol tollerance
+	 * \param tol tolerance
 	 *
 	 */
-	void setDistTol(size_t i, double tol)
+	void setDistTol(double tol)
 	{
-		parmetis_graph.setDistTol(i,tol);
+		parmetis_graph.setDistTol(tol);
 	}
 };
 

src/Decomposition/Distribution/parmetis_util.hpp

@@ -125,6 +125,9 @@ class Parmetis
 	//! indicate how many time decompose/refine/re-decompose has been called
 	size_t n_dec;
 
+	//! Distribution tolerance
+	real_t dist_tol = 1.05;
+
 	/*! \brief Construct Adjacency list
 	 *
 	 * \param g Global graph
@@ -482,7 +485,7 @@ public:
 		for (size_t s = 0; s < (size_t) Mg.nparts[0]; s++)
 		{
 			Mg.tpwgts[s] = 1.0 / Mg.nparts[0];
-			Mg.ubvec[s] = 1.05;
+			Mg.ubvec[s] = dist_tol;
 		}
 
 		Mg.edgecut = new idx_t[1];
@@ -547,13 +550,12 @@ public:
 
 	/*! \brief Distribution tolerance
 	 *
-	 * \param i partition id
-	 * \param tol tollerance
+	 * \param tol tolerance
 	 *
 	 */
-	const void setDistTol(size_t i, real_t tol)
+	const void setDistTol(real_t tol)
 	{
-		Mg.ubvec[i] = tol;
+		dist_tol = tol;
 	}
 };
 

src/Vector/vector_dist.hpp

@@ -183,7 +183,7 @@ private:
 		g_m = p_np;
 	}
 
-	/*! \brief Checl if the parameters describe a valid vector. In case it does not report an error
+	/*! \brief Check if the parameters describe a valid vector. In case it does not report an error
 	 *
 	 * \param box Box to check
 	 *
@@ -199,6 +199,11 @@ private:
 
 	}
 
+	/*! \brief It check that the r_cut is not bugger than the ghost
+	 *
+	 * \param r_cut cut-off radius
+	 *
+	 */
 	void check_ghost_compatible_rcut(St r_cut)
 	{
 		for (size_t i = 0 ; i < dim ; i++)
@@ -329,8 +334,7 @@ public:
 	 * \param box domain where the vector of elements live
 	 * \param bc boundary conditions
 	 * \param g Ghost margins
-	 * \param opt additional options.
-	 *        * BIND_DEC_TO_GHOST Bind the decomposition to be multiple of the
+	 * \param opt additional options. BIND_DEC_TO_GHOST Bind the decomposition to be multiple of the
 	 *          ghost size. This is required if we want to use symmetric to eliminate
 	 *          ghost communications.
 	 *
@@ -1056,14 +1060,8 @@ public:
 		}
 	}
 
-	/*! \brief for each particle get the verlet list
-	 *
-	 * \param verlet output verlet list for each particle
-	 * \param r_cut cut-off radius
-	 *
-	 * \deprecated
-	 *
-	 */
+#if 0
+
 /*	void getVerletDeprecated(openfpm::vector<openfpm::vector<size_t>> & verlet, St r_cut)
 	{
 		// resize verlet to store the number of particles
@@ -1115,14 +1113,14 @@ public:
 		}
 	}*/
 
+#endif
+
 	/*! \brief Construct a cell list starting from the stored particles and reorder a vector according to the Hilberts curve
 	 *
 	 * \tparam CellL CellList type to construct
 	 *
 	 * \param m an order of a hilbert curve
 	 *
-	 *
-	 *
 	 */
 	template<typename CellL=CellList<dim,St,FAST,shift<dim,St> > > void reorder (int32_t m)
 	{
@@ -1540,13 +1538,7 @@ public:
 		for (size_t i = 0 ; i < dec.getDistribution().getNSubSubDomains(); i++)
 			md.applyModel(dec,i);
 
-		// set the ubvec
-		size_t n_part = v_cl.getProcessingUnits();
-
-		for (size_t i = 0 ; i < n_part ; i++)
-		{
-			dec.getDistribution().setDistTol(i,md.distributionTol(i));
-		}
+		dec.getDistribution().setDistTol(md.distributionTol());
 	}
 
 	/*! \brief Output particle position and properties
@@ -1557,10 +1549,10 @@ public:
 	 * \return true if the file has been written without error
 	 *
 	 */
-	inline bool write(std::string out, int opt = NO_GHOST | VTK_WRITER )
+	inline bool write(std::string out, int opt = VTK_WRITER)
 	{
 
-		if ((opt & 0xFFFF0000) == CSV_WRITER)
+		if ((opt & 0x0FFF0000) == CSV_WRITER)
 		{
 			// CSVWriter test
 			CSVWriter<openfpm::vector<Point<dim,St>>, openfpm::vector<prop> > csv_writer;
@@ -1570,8 +1562,13 @@ public:
 			// Write the CSV
 			return csv_writer.write(output,v_pos,v_prp);
 		}
-		else if ((opt & 0xFFFF0000) == VTK_WRITER)
+		else
 		{
+			file_type ft = file_type::ASCII;
+
+			if (opt & FORMAT_BINARY)
+				ft = file_type::BINARY;
+
 			// VTKWriter for a set of points
 			VTKWriter<boost::mpl::pair<openfpm::vector<Point<dim,St>>, openfpm::vector<prop>>, VECTOR_POINTS> vtk_writer;
 			vtk_writer.add(v_pos,v_prp,g_m);
@@ -1579,7 +1576,7 @@ public:
 			std::string output = std::to_string(out + "_" + std::to_string(v_cl.getProcessUnitID()) + std::to_string(".vtk"));
 
 			// Write the VTK file
-			return vtk_writer.write(output);
+			return vtk_writer.write(output,"particles",ft);
 		}
 
 		return false;
@@ -1623,7 +1620,7 @@ public:
 	 */
 	inline bool write(std::string out, size_t iteration, int opt = NO_GHOST)
 	{
-		if ((opt & 0xFFFF0000) == CSV_WRITER)
+		if ((opt & 0x0FFF0000) == CSV_WRITER)
 		{
 			// CSVWriter test
 			CSVWriter<openfpm::vector<Point<dim, St>>, openfpm::vector<prop> > csv_writer;
@@ -1635,6 +1632,11 @@ public:
 		}
 		else
 		{
+			file_type ft = file_type::ASCII;
+
+			if (opt & FORMAT_BINARY)
+				ft = file_type::BINARY;
+
 			// VTKWriter for a set of points
 			VTKWriter<boost::mpl::pair<openfpm::vector<Point<dim,St>>, openfpm::vector<prop>>, VECTOR_POINTS> vtk_writer;
 			vtk_writer.add(v_pos,v_prp,g_m);
@@ -1642,7 +1644,7 @@ public:
 			std::string output = std::to_string(out + "_" + std::to_string(v_cl.getProcessUnitID()) + "_" + std::to_string(iteration) + std::to_string(".vtk"));
 
 			// Write the VTK file
-			return vtk_writer.write(output);
+			return vtk_writer.write(output,"particles",ft);
 		}
 	}
 

src/main.cpp

@@ -55,4 +55,5 @@ int main(int argc, char* argv[])
 #include "Grid/staggered_grid_dist_unit_test.hpp"
 #include "Vector/vector_dist_MP_unit_tests.hpp"
 #include "Vector/se_class3_vector_unit_tests.hpp"
+#include "Vector/vector_dist_dlb_test.hpp"
 //#include "antoniol_test_isolation.hpp"