VTK adding folder for vtk test and documentation

Makefile.am

-SUBDIRS = src
+SUBDIRS = src vtk
 
-bin_PROGRAMS = 
\ No newline at end of file
+bin_PROGRAMS = 

configure.ac

@@ -91,6 +91,79 @@ IMMDX_LIB_METIS([],[echo "Cannot detect metis, use the --with-metis option if it
 
 INCLUDES_PATH+="-I. -Isrc/config/ -I../openfpm_io/src -I../openfpm_data/src -I../openfpm_devices/src -I../openfpm_vcluster/src/"
 
+###### Check for se-class1
+
+AC_MSG_CHECKING(whether to build with security enhancement class1)
+se_class1=no
+AC_ARG_ENABLE(se-class1,
+        AC_HELP_STRING(
+            [--enable-se-class1],
+            [enable security enhancement class1]
+        ),
+        se_class1="$enableval"
+)
+
+
+
+AC_MSG_RESULT($se_class1)
+if test x"$se_class1" = x"yes"; then
+        AC_DEFINE([SE_CLASS1],[],[Security enhancement class 1])
+fi
+
+
+###### Check for se-class 2
+
+AC_MSG_CHECKING(whether to build with security enhancement class 2)
+se_class2=no
+AC_ARG_ENABLE(se-class2,
+        AC_HELP_STRING(
+            [--enable-se-class2],
+            [enable security enhancement class 2]
+        ),
+        se_class2="$enableval"
+)
+
+
+AC_MSG_RESULT($se_class2)
+if test x"$se_class2" = x"yes"; then
+        AC_DEFINE([SE_CLASS2],[],[Security enhancement class 2])
+fi
+
+###### Check for se-class 3
+
+AC_MSG_CHECKING(whether to build with security enhancement class 3)
+se_class3=no
+AC_ARG_ENABLE(se-class3,
+        AC_HELP_STRING(
+            [--enable-se-class3],
+            [enable security enhancement class 3]
+        ),
+        se_class3="$enableval"
+)
+
+
+
+AC_MSG_RESULT($se_class3)
+if test x"$se_class3" = x"yes"; then
+        AC_DEFINE([SE_CLASS3],[],[Security enhancement class 3])
+fi
+
+###### Check for action on error
+
+action_on_e=continue
+AC_ARG_WITH([action-on-error],
+             AS_HELP_STRING([--with-action-on-error=stop,throw,continue],
+             [specify the action to do in case of error]),
+             [action_on_e="$withval"],
+             [action_on_e=continue])
+
+if test x"$action_on_e" = x"stop"; then
+           AC_DEFINE([STOP_ON_ERROR],[],[If an error occur stop the program])
+fi
+if test x"$action_on_e" = x"throw"; then
+           AC_DEFINE([THROW_ON_ERROR],[],[when an error accur continue but avoid unsafe operation])
+fi
+
 ##### CHECK FOR BOOST ##############
 
 AX_BOOST([1.52],[],[echo "boost not found"
@@ -124,6 +197,10 @@ else
   gpu_support=no
 fi
 
+if test x$gpu_support = x"no"; then
+     CUDA_LIBS=""
+     CUDA_CFLAGS=""
+fi
 
 # Set this conditional if cuda is wanted
 
@@ -142,7 +219,7 @@ AC_SUBST(INCLUDES_PATH)
 
 # Checks for library functions.
 
-AC_CONFIG_FILES([Makefile src/Makefile])
+AC_CONFIG_FILES([Makefile src/Makefile vtk/Makefile ])
 AC_OUTPUT
 echo ""
 echo   "***********************************"
@@ -162,6 +239,21 @@ if [ test x"$debuger" = x"yes" ]; then
 else
   echo "*    debug: no                    *"
 fi
+if [ test x"$se_class1" = x"yes" ]; then
+  echo "*    se-class1: yes               *"
+else
+  echo "*    se-class1: no                *"
+fi
+if [ test x"$se_class2" = x"yes" ]; then
+  echo "*    se-class2: yes               *"
+else
+  echo "*    se-class2: no                *"
+fi
+if [ test x"$se_class3" = x"yes" ]; then
+  echo "*    se-class3: yes               *"
+else
+  echo "*    se-class3: no                *"
+fi
 if [ test x"$gpu_support" = x"no" ]; then
   echo "*    gpu: no                      *"
 else

openfpm_data @ c145364a

-Subproject commit 20abc8eed3bca0ffc5055c7c8fad6c95a484ffc1
+Subproject commit c145364a145d40bd39819f3e8d44054d16e59352

openfpm_io @ a94658c3

-Subproject commit d3a6ccf23ab183d35d77317aba70193ac0ca0bc7
+Subproject commit a94658c3e4fc0f68fd261e7df39cd2a353bd4682

src/Decomposition/CartDecomposition.hpp

@@ -9,6 +9,8 @@
 #define CARTDECOMPOSITION_HPP
 
 #include "config.h"
+#include "VCluster.hpp"
+#include "Graph/CartesianGraphFactory.hpp"
 #include "Decomposition.hpp"
 #include "Vector/map_vector.hpp"
 #include <vector>
@@ -28,6 +30,17 @@
 #include "ie_ghost.hpp"
 #include "nn_processor.hpp"
 
+#define CARTDEC_ERROR 2000lu
+
+// Macro that decide what to do in case of error
+#ifdef STOP_ON_ERROR
+#define ACTION_ON_ERROR() exit(1);
+#elif defined(THROW_ON_ERROR)
+#define ACTION_ON_ERROR() throw CARTDEC_ERROR;
+#else
+#define ACTION_ON_ERROR()
+#endif
+
 /**
  * \brief This class decompose a space into subspaces
  *
@@ -116,14 +129,20 @@ private:
 	//! Cell-list that store the geometrical information of the local internal ghost boxes
 	CellList<dim,T,FAST> lgeo_cell;
 
-
 	/*! \brief Constructor, it decompose and distribute the sub-domains across the processors
 	 *
      * \param v_cl Virtual cluster, used internally for communications
-	 *
+     *
 	 */
 	void CreateDecomposition(Vcluster & v_cl)
 	{
+#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
 		// Calculate the total number of box and and the spacing
 		// on each direction
 		// Get the box containing the domain
@@ -678,6 +697,7 @@ p1[0]<-----+         +----> p2[0]
 		return bbox;
 	}
 
+
 	////////////// Functions to get decomposition information ///////////////
 
 	/*! \brief Write the decomposition as VTK file

src/Makefile.am

-
 LINKLIBS = $(METIS_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS)
 
 bin_PROGRAMS = pdata
 pdata_SOURCES = main.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_data/src/Memleak_check.cpp
-pdata_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(METIS_INCLUDE) $(BOOST_CPPFLAGS)
+pdata_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) -Wno-unused-function
 pdata_CFLAGS = $(CUDA_CFLAGS)
 pdata_LDADD = $(LINKLIBS) -lmetis
 

vtk/.deps/metis_dec.Po

+# dummy

vtk/CartDecomposition_gen_vtk.cpp

+/*
+ * CartDecomposition_gen_vtk.hpp
+ *
+ *  Created on: Aug 28, 2015
+ *      Author: i-bird
+ */
+#include "Decomposition/CartDecomposition.hpp"
+
+
+int main(int argc, char ** argv)
+{
+	// Initialize the global VCluster
+	init_global_v_cluster(&argc,&argv);
+
+	// Vcluster
+	Vcluster & vcl = *global_v_cluster;
+
+	//! [Create CartDecomposition vtk gen]
+	CartDecomposition<2,float> dec(vcl);
+
+	// Physical domain
+	Box<2,float> box({0.0,0.0},{1.0,1.0});
+
+	// division on each direction
+	size_t div[2] = {20,20};
+
+	// Define ghost
+	Ghost<2,float> g(0.01);
+
+	// Decompose and write the decomposed graph
+	dec.setParameters(div,box,g);
+
+	// create a ghost border
+	dec.calculateGhostBoxes();
+
+	// Write the decomposition
+	dec.write("CartDecomposition/out_");
+
+	//! [Create CartDecomposition]
+
+	delete &vcl;
+}
+

vtk/Domain_decomposition.py

+#### import the simple module from the paraview
+from paraview.simple import *
+#### disable automatic camera reset on 'Show'
+
+paraview.simple._DisableFirstRenderCameraReset()
+
+# create a new 'Legacy VTK Reader'
+dom_boxvtk = LegacyVTKReader(FileNames=['/home/i-bird/Desktop/MOSAIC/OpenFPM_project/OpenFPM_pdata/vtk/CartDecomposition/dom_box.vtk'])
+
+# get active view
+renderView1 = GetActiveViewOrCreate('RenderView')
+
+renderView1.CameraPosition = [0.5, 0.5, 2.7320508075688776]
+renderView1.CameraFocalPoint = [0.5, 0.5, 0.0]
+renderView1.CameraParallelScale = 0.5843857695756589
+
+# show data in view
+dom_boxvtkDisplay = Show(dom_boxvtk, renderView1)
+
+WriteImage("domain.png")
+
+# change representation type
+dom_boxvtkDisplay.SetRepresentationType('Surface With Edges')
+
+WriteImage("domain_decomposed.png")
+
+# create a new 'Legacy VTK Reader'
+vtk_partitionvtk = LegacyVTKReader(FileNames=['/home/i-bird/Desktop/MOSAIC/OpenFPM_project/OpenFPM_pdata/vtk/Metis/vtk_partition.vtk'])
+
+
+idLUT = GetColorTransferFunction('id')
+idLUT.RGBPoints = [0.0, 0.231373, 0.298039, 0.752941, 1.5, 0.865003, 0.865003, 0.865003, 3.0, 0.705882, 0.0156863, 0.14902]
+idLUT.ScalarRangeInitialized = 1.0
+
+# show data in view
+vtk_partitionvtkDisplay = Show(vtk_partitionvtk, renderView1)
+# trace defaults for the display properties.
+vtk_partitionvtkDisplay.ColorArrayName = ['POINTS', 'id']
+vtk_partitionvtkDisplay.LookupTable = idLUT
+
+
+#changing interaction mode based on data extents
+renderView1.CameraPosition = [0.5, 0.5, 2.7320508075688776]
+renderView1.CameraFocalPoint = [0.5, 0.5, 0.0]
+renderView1.CameraParallelScale = 0.5843857695756589
+
+# show color bar/color legend
+vtk_partitionvtkDisplay.SetScalarBarVisibility(renderView1, False)
+
+# create a new 'Transform'
+transform1 = Transform(Input=vtk_partitionvtk)
+transform1.Transform = 'Transform'
+
+# Properties modified on transform1.Transform
+transform1.Transform.Translate = [0.025, 0.025, 0.0]
+transform1.Transform.Scale = [1.0, 1.0, 0.0]
+
+# show data in view
+transform1Display = Show(transform1, renderView1)
+
+# hide data in view
+Hide(vtk_partitionvtk, renderView1)
+
+# set scalar coloring
+ColorBy(transform1Display, ('POINTS', 'computation'))
+
+# change representation type
+transform1Display.SetRepresentationType('Points')
+
+# Properties modified on transform1Display
+transform1Display.PointSize = 5.0
+
+# set active source
+SetActiveSource(vtk_partitionvtk)
+
+# write decomposed
+WriteImage("domain_graph.png")
+
+# set scalar coloring
+ColorBy(transform1Display, ('POINTS', 'id'))
+
+# change representation type
+dom_boxvtkDisplay.SetRepresentationType('Surface')
+
+# write decomposed
+WriteImage("domain_graph_decomposed.png")
+
+# create a new 'Legacy VTK Reader'
+out_subdomains_0vtk = LegacyVTKReader(FileNames=['/home/i-bird/Desktop/MOSAIC/OpenFPM_project/OpenFPM_pdata/vtk/CartDecomposition/out_subdomains_0.vtk'])
+
+# create a new 'Legacy VTK Reader'
+out_subdomains_1vtk = LegacyVTKReader(FileNames=['/home/i-bird/Desktop/MOSAIC/OpenFPM_project/OpenFPM_pdata/vtk/CartDecomposition/out_subdomains_1.vtk'])
+
+# create a new 'Legacy VTK Reader'
+out_subdomains_2vtk = LegacyVTKReader(FileNames=['/home/i-bird/Desktop/MOSAIC/OpenFPM_project/OpenFPM_pdata/vtk/CartDecomposition/out_subdomains_2.vtk'])
+
+# create a new 'Legacy VTK Reader'
+out_subdomains_3vtk = LegacyVTKReader(FileNames=['/home/i-bird/Desktop/MOSAIC/OpenFPM_project/OpenFPM_pdata/vtk/CartDecomposition/out_subdomains_3.vtk'])
+
+# set active source
+#SetActiveSource(out_subdomains_0vtk)
+
+# get color transfer function/color map for 'data'
+#dataLUT = GetColorTransferFunction('data')
+#dataLUT.RGBPoints = [285.3226244096321, 0.231373, 0.298039, 0.752941, 312.3676762575527, 0.865003, 0.865003, 0.865003, 339.4127281054734, 0.705882, 0.0156863, 0.14902]
+#dataLUT.ScalarRangeInitialized = 1.0
+
+# show data in view
+out_subdomains_3vtkDisplay = Show(out_subdomains_3vtk, renderView1)
+# trace defaults for the display properties.
+#out_subdomains_3vtkDisplay.ColorArrayName = ['CELLS', 'data']
+#out_subdomains_3vtkDisplay.LookupTable = dataLUT
+#out_subdomains_3vtkDisplay.ScalarOpacityUnitDistance = 0.5153778246772277
+
+# show color bar/color legend
+#out_subdomains_3vtkDisplay.SetScalarBarVisibility(renderView1, True)
+
+# show data in view
+out_subdomains_1vtkDisplay = Show(out_subdomains_1vtk, renderView1)
+# trace defaults for the display properties.
+#out_subdomains_1vtkDisplay.ColorArrayName = ['CELLS', 'data']
+#out_subdomains_1vtkDisplay.LookupTable = dataLUT
+#out_subdomains_1vtkDisplay.ScalarOpacityUnitDistance = 0.5153778246772277
+
+# show color bar/color legend
+#out_subdomains_1vtkDisplay.SetScalarBarVisibility(renderView1, True)
+
+# show data in view
+out_subdomains_2vtkDisplay = Show(out_subdomains_2vtk, renderView1)
+# trace defaults for the display properties.
+#out_subdomains_2vtkDisplay.ColorArrayName = ['CELLS', 'data']
+#out_subdomains_2vtkDisplay.LookupTable = dataLUT
+#out_subdomains_2vtkDisplay.ScalarOpacityUnitDistance = 0.5153778246772277
+
+# show color bar/color legend
+#out_subdomains_2vtkDisplay.SetScalarBarVisibility(renderView1, True)
+
+# show data in view
+out_subdomains_0vtkDisplay = Show(out_subdomains_0vtk, renderView1)
+# trace defaults for the display properties.
+#out_subdomains_0vtkDisplay.ColorArrayName = ['CELLS', 'data']
+#out_subdomains_0vtkDisplay.LookupTable = dataLUT
+#out_subdomains_0vtkDisplay.ScalarOpacityUnitDistance = 0.5153778246772277
+
+# show color bar/color legend
+#out_subdomains_0vtkDisplay.SetScalarBarVisibility(renderView1, True)
+
+# get opacity transfer function/opacity map for 'data'
+#dataPWF = GetOpacityTransferFunction('data')
+#dataPWF.Points = [285.3226244096321, 0.0, 0.5, 0.0, 339.4127281054734, 1.0, 0.5, 0.0]
+#dataPWF.ScalarRangeInitialized = 1
+
+# turn off scalar coloring
+ColorBy(out_subdomains_0vtkDisplay, None)
+
+# set active source
+#SetActiveSource(out_subdomains_1vtk)
+
+# turn off scalar coloring
+ColorBy(out_subdomains_1vtkDisplay, None)
+
+# turn off scalar coloring
+ColorBy(out_subdomains_2vtkDisplay, None)
+
+# set active source
+#SetActiveSource(out_subdomains_3vtk)
+
+# turn off scalar coloring
+ColorBy(out_subdomains_3vtkDisplay, None)
+
+# change representation type
+out_subdomains_3vtkDisplay.SetRepresentationType('Surface With Edges')
+
+# change representation type
+out_subdomains_2vtkDisplay.SetRepresentationType('Surface With Edges')
+
+# change representation type
+out_subdomains_1vtkDisplay.SetRepresentationType('Surface With Edges')
+
+# change representation type
+out_subdomains_0vtkDisplay.SetRepresentationType('Surface With Edges')
+
+# change solid color
+out_subdomains_0vtkDisplay.DiffuseColor = [1.0, 0.3333333333333333, 0.0]
+
+# change solid color
+out_subdomains_1vtkDisplay.DiffuseColor = [0.6666666666666666, 1.0, 0.0]
+
+# change solid color
+out_subdomains_2vtkDisplay.DiffuseColor = [0.0, 0.3333333333333333, 1.0]
+
+# change solid color
+out_subdomains_3vtkDisplay.DiffuseColor = [1.0, 1.0, 0.0]
+
+# Properties modified on out_subdomains_0vtkDisplay
+out_subdomains_0vtkDisplay.LineWidth = 4.0
+
+# change representation type
+out_subdomains_0vtkDisplay.SetRepresentationType('Surface With Edges')
+
+# Properties modified on out_subdomains_1vtkDisplay
+out_subdomains_1vtkDisplay.LineWidth = 4.0
+
+# change representation type
+out_subdomains_1vtkDisplay.SetRepresentationType('Surface With Edges')
+
+# Properties modified on out_subdomains_2vtkDisplay
+out_subdomains_2vtkDisplay.LineWidth = 4.0
+
+# change representation type
+out_subdomains_2vtkDisplay.SetRepresentationType('Surface With Edges')
+
+# Properties modified on out_subdomains_3vtkDisplay
+out_subdomains_3vtkDisplay.LineWidth = 4.0
+
+# change representation type
+out_subdomains_3vtkDisplay.SetRepresentationType('Surface With Edges')
+
+# hide data in view
+Hide(dom_boxvtk, renderView1)
+
+WriteImage("domain_subdomain_decomposed.png")
+
+# hide data in view
+Hide(transform1, renderView1)
+
+WriteImage("domain_subdomain_decomposed_wg.png")
+
+
+#Destroy everything
+Delete(transform1)
+del transform1
+Delete(out_subdomains_3vtk)
+del out_subdomains_3vtk
+Delete(out_subdomains_2vtk)
+del out_subdomains_2vtk
+Delete(out_subdomains_1vtk)
+del out_subdomains_1vtk
+Delete(out_subdomains_0vtk)
+del out_subdomains_0vtk
+Delete(dom_boxvtk)
+del dom_boxvtk
+Delete(vtk_partitionvtk)
+del vtk_partitionvtk
\ No newline at end of file

vtk/Makefile.am

+
+LINKLIBS = $(METIS_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS)
+
+bin_PROGRAMS = cart_dec metis_dec dom_box
+cart_dec_SOURCES = CartDecomposition_gen_vtk.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_data/src/Memleak_check.cpp
+cart_dec_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function
+cart_dec_CFLAGS = $(CUDA_CFLAGS)
+cart_dec_LDADD = $(LINKLIBS) -lmetis
+
+metis_dec_SOURCES = Metis_gen_vtk.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_data/src/Memleak_check.cpp
+metis_dec_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function
+metis_dec_CFLAGS = $(CUDA_CFLAGS)
+metis_dec_LDADD = $(LINKLIBS) -lmetis
+
+dom_box_SOURCES = domain_gen_vtk.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_data/src/Memleak_check.cpp
+dom_box_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function
+dom_box_CFLAGS = $(CUDA_CFLAGS)
+dom_box_LDADD = $(LINKLIBS)
+
+.cu.o :
+	$(NVCC) $(NVCCFLAGS) -o $@ -c $<

vtk/Metis_gen_vtk.cpp

+/*
+ * Metis_gen_vtk.hpp
+ *
+ *  Created on: Aug 29, 2015
+ *      Author: i-bird
+ */
+
+#ifndef VTK_METIS_GEN_VTK_CPP_
+#define VTK_METIS_GEN_VTK_CPP_
+
+#include "Graph/CartesianGraphFactory.hpp"
+#include "Graph/map_graph.hpp"
+#include "metis_util.hpp"
+#include "SubdomainGraphNodes.hpp"
+
+int main(int argc, char ** argv)
+{
+	CartesianGraphFactory<2,Graph_CSR<nm_v,nm_e>> g_factory;
+
+	// Cartesian grid
+	size_t sz[2] = {20,20};
+
+	// Box
+	Box<2,float> box({0.0,0.0},{1.0,1.0});
+
+	// Graph to decompose
+
+	Graph_CSR<nm_v,nm_e> g = g_factory.construct<nm_e::communication,float,1,0,1>(sz,box);
+
+	// Convert the graph to metis
+
+	Metis<Graph_CSR<nm_v,nm_e>> met(g,4);
+
+	// decompose
+
+	met.decompose<nm_v::id>();
+
+	// Write the decomposition
+
+	VTKWriter<Graph_CSR<nm_v,nm_e>,GRAPH> vtk(g);
+	vtk.write("Metis/vtk_partition.vtk");
+}
+
+
+#endif /* VTK_METIS_GEN_VTK_CPP_ */

vtk/domain_gen_vtk.cpp

+/*
+ * domain_vtk_gen.cpp
+ *
+ *  Created on: Aug 30, 2015
+ *      Author: Pietro Incardona
+ */
+
+#include "Space/Shape/Box.hpp"
+#include "Vector/map_vector.hpp"
+#include "VTKWriter.hpp"
+
+int main(int argc, char ** argv)
+{
+	//! [Output a vector of boxes]
+
+	// Physical domain
+	Box<2,float> box({0.0,0.0},{1.0,1.0});
+
+	// Cell
+	Box<2,float> cell = box;
+
+	// division on each direction
+	size_t div[2] = {20,20};
+	Point<2,float> p_div({20.0,20.0});
+	cell /= p_div;
+
+	// create 20 cell on each direction
+
+	openfpm::vector<Box<2,float>> v_box;
+
+	for (size_t i = 0; i <= div[0] ; i++)
+	{
+		for (size_t j = 0 ; j <= div[1] ; j++)
+		{
+			Point<2,float> p({(float)i,(float)j});
+			Box<2,float> box = cell * p;
+
+			v_box.add(box);
+		}
+	}
+
+	// write the vector of boxes
+	VTKWriter<openfpm::vector<Box<2,float>>,VECTOR_BOX> vtk_box1;
+	vtk_box1.add(v_box);
+	vtk_box1.write("CartDecomposition/dom_box.vtk");
+
+	//! [Output a vector of boxes]
+}
+
+