From 35593873e79dbea1fdc532fb03a60980778cb009 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Wed, 23 Sep 2015 14:24:48 +0200
Subject: [PATCH] Creating and uploading examples
---
example/Grid/0_simple/Makefile | 21 ++++
example/Grid/0_simple/config.cfg | 2 +
example/Grid/0_simple/main.cpp | 155 +++++++++++++++++++++++++
example/Grid/1_stencil/Makefile | 21 ++++
example/Grid/1_stencil/config.cfg | 2 +
example/Grid/1_stencil/main.cpp | 158 ++++++++++++++++++++++++++
example/Makefile | 11 ++
example/README(YES, YOU MUST READ IT) | 6 +
example/Vector/0_simple/Makefile | 21 ++++
example/Vector/0_simple/config.cfg | 2 +
example/Vector/0_simple/main.cpp | 126 ++++++++++++++++++++
src/Grid/grid_dist_id_iterator.hpp | 39 ++++++-
src/Vector/vector_dist_unit_test.hpp | 1 -
13 files changed, 560 insertions(+), 5 deletions(-)
create mode 100644 example/Grid/0_simple/Makefile
create mode 100644 example/Grid/0_simple/config.cfg
create mode 100644 example/Grid/0_simple/main.cpp
create mode 100644 example/Grid/1_stencil/Makefile
create mode 100644 example/Grid/1_stencil/config.cfg
create mode 100644 example/Grid/1_stencil/main.cpp
create mode 100644 example/Makefile
create mode 100644 example/README(YES, YOU MUST READ IT)
create mode 100644 example/Vector/0_simple/Makefile
create mode 100644 example/Vector/0_simple/config.cfg
create mode 100644 example/Vector/0_simple/main.cpp
diff --git a/example/Grid/0_simple/Makefile b/example/Grid/0_simple/Makefile
new file mode 100644
index 00000000..f1df9ed1
--- /dev/null
+++ b/example/Grid/0_simple/Makefile
@@ -0,0 +1,21 @@
+include ../../example.mk
+
+CC=mpic++
+
+LDIR =
+
+OBJ = main.o
+
+%.o: %.cpp
+ $(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+
+grid: $(OBJ)
+ $(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
+
+all: grid
+
+.PHONY: clean all
+
+clean:
+ rm -f *.o *~ core grid
+
diff --git a/example/Grid/0_simple/config.cfg b/example/Grid/0_simple/config.cfg
new file mode 100644
index 00000000..1eecbac3
--- /dev/null
+++ b/example/Grid/0_simple/config.cfg
@@ -0,0 +1,2 @@
+[pack]
+files = main.cpp Makefile
diff --git a/example/Grid/0_simple/main.cpp b/example/Grid/0_simple/main.cpp
new file mode 100644
index 00000000..d88ee12e
--- /dev/null
+++ b/example/Grid/0_simple/main.cpp
@@ -0,0 +1,155 @@
+#include "Grid/grid_dist_id.hpp"
+#include "data_type/scalar.hpp"
+#include "Decomposition/CartDecomposition.hpp"
+
+/*
+ * ### WIKI 1 ###
+ *
+ * ## Simple example
+ *
+ * This example show several basic functionalities of the distributed grid
+ *
+ * ### WIKI END ###
+ *
+ */
+
+
+int main(int argc, char* argv[])
+{
+ //
+ // ### WIKI 2 ###
+ //
+ // Initialize the library and several objects
+ //
+ init_global_v_cluster(&argc,&argv);
+
+ //
+ // ### WIKI 3 ###
+ //
+ // Create several object needed later, in particular
+ // * A 3D box that define the domain
+ // * an array of 3 unsigned integer that define the size of the grid on each dimension
+ // * A Ghost object that will define the extension of the ghost part for each sub-domain in physical units
+
+ Box<3,float> domain({0.0,0.0,0.0},{1.0,1.0,1.0});
+ size_t sz[3];
+ sz[0] = 100;
+ sz[1] = 100;
+ sz[2] = 100;
+
+ // Ghost
+ Ghost<3,float> g(0.01);
+
+ //
+ // ### WIKI 4 ###
+ //
+ // Create a distributed grid in 3D (1° template parameter) defined in R^3 with float precision (2° template parameter)
+ // using a CartesianDecomposition strategy (3° parameter) (the parameter 1° and 2° inside CartDecomposition must match 1° and 2°
+ // of grid_dist_id)
+ //
+ // Constructor parameters:
+ //
+ // * sz: size of the grid on each dimension
+ // * domain: where the grid is defined
+ // * g: ghost extension
+ //
+ grid_dist_id<3, float, scalar<float[3]>, CartDecomposition<3,float>> g_dist(sz,domain,g);
+
+ // ### WIKI 5 ###
+ //
+ // Get an iterator that go throught the point of the domain (No ghost)
+ //
+ auto dom = g_dist.getDomainIterator();
+
+ // ### WIKI END ###
+
+ size_t count = 0;
+
+ // Iterate over all the points
+ while (dom.isNext())
+ {
+ //
+ // ### WIKI 6 ###
+ //
+ // Get the local grid key, the local grid key store internaly the sub-domain id (each sub-domain contain a grid)
+ // and the local grid point id identified by 2 integers in 2D 3 integer in 3D and so on. These two dinstinc element are
+ // available with key.getSub() and key.getKey()
+ //
+ auto key = dom.get();
+
+ //
+ // ### WIKI 7 ###
+ //
+ // Here we convert the local grid position, into global position, key_g contain 3 integers that identify the position
+ // of the grid point in global coordinates
+ //
+ //
+ auto key_g = g_dist.getGKey(key);
+
+ //
+ // ### WIKI 8 ###
+ //
+ // we write on the grid point of position (i,j,k) the value i*i + j*j + k*k on the component [0] of the vector
+ g_dist.template get<0>(key)[0] = key_g.get(0)*key_g.get(0) + key_g.get(1)*key_g.get(1) + key_g.get(2)*key_g.get(2);
+
+ // ### WIKI END ###
+
+ // Count the points
+ count++;
+
+ //
+ // ### WIKI 9 ###
+ //
+ // next point
+ ++dom;
+
+ // ### WIKI END ###
+ }
+
+ //
+ // ### WIKI 10 ###
+ //
+ // Each sub-domain has an extended part, that is materially contained from another processor that in general is not synchronized
+ // ghost_get<0> synchronize the property 0 (the vector) in the ghost part
+ //
+ //
+ g_dist.template ghost_get<0>();
+
+ //
+ // ### WIKI 11 ###
+ //
+ // count contain the number of points the local processor contain, if we are interested to count the total number across the processor
+ // we can use the function add, to sum across processors. First we have to get an instance of Vcluster, queue an operation of add with
+ // the variable count and finaly execute. All the operation are asynchronous, execute work like a barrier and ensure that all the
+ // queued operations are executed
+ //
+ Vcluster & vcl = g_dist.getVC();
+
+ vcl.sum(count);
+ vcl.execute();
+
+ // only master output
+ if (vcl.getProcessUnitID() == 0)
+ std::cout << "Number of points: " << count << "\n";
+
+ //
+ // ### WIKI 12 ###
+ //
+ // Finally we want a nice output to visualize the information stored by the distributed grid
+ //
+ g_dist.write("output");
+
+ //
+ // ### WIKI 13 ###
+ //
+ // For debugging porpouse and demostration we output the decomposition
+ //
+ g_dist.getDecomposition().write("dec/out");
+
+ //
+ // ### WIKI 14 ###
+ //
+ // Deinitialize the library
+ //
+ delete(global_v_cluster);
+}
diff --git a/example/Grid/1_stencil/Makefile b/example/Grid/1_stencil/Makefile
new file mode 100644
index 00000000..9e3796e0
--- /dev/null
+++ b/example/Grid/1_stencil/Makefile
@@ -0,0 +1,21 @@
+include ../../example.mk
+
+CC=mpic++
+
+LDIR =
+
+OBJ = main.o
+
+%.o: %.cpp
+ $(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+
+stencil: $(OBJ)
+ $(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
+
+all: stencil
+
+.PHONY: clean all
+
+clean:
+ rm -f *.o *~ core stencil
+
diff --git a/example/Grid/1_stencil/config.cfg b/example/Grid/1_stencil/config.cfg
new file mode 100644
index 00000000..1eecbac3
--- /dev/null
+++ b/example/Grid/1_stencil/config.cfg
@@ -0,0 +1,2 @@
+[pack]
+files = main.cpp Makefile
diff --git a/example/Grid/1_stencil/main.cpp b/example/Grid/1_stencil/main.cpp
new file mode 100644
index 00000000..1a08184c
--- /dev/null
+++ b/example/Grid/1_stencil/main.cpp
@@ -0,0 +1,158 @@
+#include "Grid/grid_dist_id.hpp"
+#include "data_type/scalar.hpp"
+#include "Decomposition/CartDecomposition.hpp"
+
+/*
+ * ### WIKI 1 ###
+ *
+ * ## Simple example
+ *
+ * This example show how to move grid_key in order to create a laplacian stencil,
+ * be carefull, the function move are convenient, we suggest to not use in case speed
+ * of a speed critical part of the code
+ *
+ * ### WIKI END ###
+ *
+ */
+
+/*
+ *
+ * ### WIKI 2 ###
+ *
+ * Define some convenient constant
+ *
+ */
+constexpr size_t x = 0;
+constexpr size_t y = 1;
+constexpr size_t z = 2;
+
+int main(int argc, char* argv[])
+{
+ //
+ // ### WIKI 3 ###
+ //
+ // Initialize the library and several objects
+ //
+ init_global_v_cluster(&argc,&argv);
+
+ //
+ // ### WIKI 4 ###
+ //
+ // Create several object needed later, in particular
+ // * A 3D box that define the domain
+ // * an array of 3 unsigned integer that define the size of the grid on each dimension
+ // * A Ghost object that will define the extension of the ghost part for each sub-domain in physical units
+
+ Box<3,float> domain({0.0,0.0,0.0},{1.0,1.0,1.0});
+ size_t sz[3];
+ sz[0] = 100;
+ sz[1] = 100;
+ sz[2] = 100;
+
+ // Ghost
+ Ghost<3,float> g(0.03);
+
+ //
+ // ### WIKI 4 ###
+ //
+ // Create a distributed grid in 3D (1° template parameter) defined in R^3 with float precision (2° template parameter)
+ // using a CartesianDecomposition strategy (3° parameter) (the parameter 1° and 2° inside CartDecomposition must match 1° and 2°
+ // of grid_dist_id)
+ //
+ // Constructor parameters:
+ //
+ // * sz: size of the grid on each dimension
+ // * domain: where the grid is defined
+ // * g: ghost extension
+ //
+ grid_dist_id<3, float, scalar<float[3]>, CartDecomposition<3,float>> g_dist(sz,domain,g);
+
+ // ### WIKI 5 ###
+ //
+ // Get an iterator that go throught the point of the domain (No ghost)
+ //
+ auto dom = g_dist.getDomainIterator();
+
+ // ### WIKI END ###
+
+ while (dom.isNext())
+ {
+ //
+ // ### WIKI 6 ###
+ //
+ // Get the local grid key, the local grid key store internaly the sub-domain id (each sub-domain contain a grid)
+ // and the local grid point id identified by 2 integers in 2D 3 integer in 3D and so on. These two dinstinc element are
+ // available with key.getSub() and key.getKey()
+ //
+ auto key = dom.get();
+
+ //
+ // ### WIKI 7 ###
+ //
+ // Here we convert the local grid position, into global position, key_g contain 3 integers that identify the position
+ // of the grid point in global coordinates
+ //
+ //
+ auto key_g = g_dist.getGKey(key);
+
+ //
+ // ### WIKI 8 ###
+ //
+ // we write on the grid point of position (i,j,k) the value i*i + j*j + k*k on the component [0] of the vector
+ g_dist.template get<0>(key)[0] = key_g.get(0)*key_g.get(0) + key_g.get(1)*key_g.get(1) + key_g.get(2)*key_g.get(2);
+
+ //
+ // ### WIKI 9 ###
+ //
+ // next point
+
+ ++dom;
+
+ // ### WIKI END ###
+ }
+
+ //
+ // ### WIKI 10 ###
+ //
+ // Each sub-domain has an extended part, that is materially contained from another processor that in general is not synchronized
+ // ghost_get<0> synchronize the property 0 (the vector) in the ghost part
+ //
+ //
+ g_dist.template ghost_get<0>();
+
+ //
+ // ### WIKI 11 ###
+ //
+ // Get again another iterator, iterate across all the domain points, calculating a Laplace stencil
+ //
+ //
+ dom = g_dist.getDomainIterator();
+
+ while (dom.isNext())
+ {
+ auto key = dom.get();
+
+ // Laplace stencil
+ g_dist.template get<0>(key)[1] = g_dist.template get<0>(key.move(x,1))[0] + g_dist.template get<0>(key.move(x,-1))[0] +
+ g_dist.template get<0>(key.move(y,1))[0] + g_dist.template get<0>(key.move(y,-1))[0] +
+ g_dist.template get<0>(key.move(z,1))[0] + g_dist.template get<0>(key.move(z,-1))[0] -
+ 6*g_dist.template get<0>(key)[0];
+
+
+ ++dom;
+ }
+
+ //
+ // ### WIKI 12 ###
+ //
+ // Finally we want a nice output to visualize the information stored by the distributed grid
+ //
+ g_dist.write("output");
+
+ //
+ // ### WIKI 14 ###
+ //
+ // Deinitialize the library
+ //
+ delete(global_v_cluster);
+}
diff --git a/example/Makefile b/example/Makefile
new file mode 100644
index 00000000..63062d5b
--- /dev/null
+++ b/example/Makefile
@@ -0,0 +1,11 @@
+SUBDIRS := $(wildcard */.)
+
+all clean:
+ for dir in $(SUBDIRS); do \
+ $(MAKE) -C $$dir $@; \
+ done
+
+clean: $(SUBDIRS)
+
+.PHONY: all clean $(SUBDIRS)
+
diff --git a/example/README(YES, YOU MUST READ IT) b/example/README(YES, YOU MUST READ IT)
new file mode 100644
index 00000000..eb7f6aaa
--- /dev/null
+++ b/example/README(YES, YOU MUST READ IT)
@@ -0,0 +1,6 @@
+This Package contain the examples. In order to compile the examples go in the root folder where you installed
+OpenFPM (example /usr/local/OpenFPM_install) and copy from there the file example.mk
+
+compile the examples with
+
+make
diff --git a/example/Vector/0_simple/Makefile b/example/Vector/0_simple/Makefile
new file mode 100644
index 00000000..4ee13178
--- /dev/null
+++ b/example/Vector/0_simple/Makefile
@@ -0,0 +1,21 @@
+include ../../example.mk
+
+CC=mpic++
+
+LDIR =
+
+OBJ = main.o
+
+%.o: %.cpp
+ $(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+
+vector: $(OBJ)
+ $(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
+
+all: vector
+
+.PHONY: clean all
+
+clean:
+ rm -f *.o *~ core vector
+
diff --git a/example/Vector/0_simple/config.cfg b/example/Vector/0_simple/config.cfg
new file mode 100644
index 00000000..1eecbac3
--- /dev/null
+++ b/example/Vector/0_simple/config.cfg
@@ -0,0 +1,2 @@
+[pack]
+files = main.cpp Makefile
diff --git a/example/Vector/0_simple/main.cpp b/example/Vector/0_simple/main.cpp
new file mode 100644
index 00000000..17d0ddc1
--- /dev/null
+++ b/example/Vector/0_simple/main.cpp
@@ -0,0 +1,126 @@
+#include "Vector/vector_dist.hpp"
+#include "Decomposition/CartDecomposition.hpp"
+#include "Point_test.hpp"
+
+/*
+ * ### WIKI 1 ###
+ *
+ * ## Simple example
+ *
+ * This example show several basic functionalities of the distributed vector
+ *
+ * ### WIKI END ###
+ *
+ */
+
+
+int main(int argc, char* argv[])
+{
+ //
+ // ### WIKI 2 ###
+ //
+ // Here we Initialize the library, than we create a uniform random generator between 0 and 1 to to generate particles
+ // randomly in the domain, we create a Box that define our domain
+ //
+ init_global_v_cluster(&argc,&argv);
+ Vcluster & v_cl = *global_v_cluster;
+
+ typedef Point<2,float> s;
+
+ // set the seed
+ // create the random generator engine
+ std::srand(v_cl.getProcessUnitID());
+ std::default_random_engine eg;
+ std::uniform_real_distribution<float> ud(0.0f, 1.0f);
+
+ Box<2,float> box({0.0,0.0},{1.0,1.0});
+
+ //
+ // ### WIKI 3 ###
+ //
+ // Here we are creating a distributed vector defined by the following parameters
+ //
+ // * Dimensionality of the space where the objects live 2D (1° template parameters)
+ // * Type of the space, float (2° template parameters)
+ // * Information stored by each object (3* template parameters), in this case a Point_test store 4 scalars
+ // 1 vector and an asymmetric tensor of rank 2
+ // * Strategy used to decompose the space
+ //
+ // Constructor instead require:
+ //
+ // * Number of particles 4096 in this case
+ // * Domain where is defined this structure
+ //
+ // The following construct a vector where each processor has 4096 / N_proc (N_proc = number of processor)
+ // objects with an undefined position in space. This non-space decomposition is also called data-driven
+ // decomposition
+ //
+ vector_dist<2,float, Point_test<float>, CartDecomposition<2,float> > vd(4096,box);
+
+ //
+ // ### WIKI 5 ###
+ //
+ // Get an iterator that go throught the objects, in an undefined position state and define its position
+ //
+ auto it = vd.getIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ vd.template getPos<s::x>(key)[0] = ud(eg);
+ vd.template getPos<s::x>(key)[1] = ud(eg);
+
+ ++it;
+ }
+
+ //
+ // ### WIKI 6 ###
+ //
+ // Once we define the position, we distribute them according to the default decomposition
+ // The default decomposition is created even before assigning the position to the object
+ // (This will probably change in future)
+ //
+ vd.map();
+
+ //
+ // ### WIKI 7 ###
+ //
+ // We get the object that store the decomposition, than we iterate again across all the objects, we count them
+ // and we confirm that all the particles are local
+ //
+ size_t cnt = 0;
+ auto & ct = vd.getDecomposition();
+ it = vd.getIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+
+ if (ct.isLocal(vd.template getPos<s::x>(key)) == false)
+ std::cerr << "Error particle is not local" << "\n";
+
+ cnt++;
+
+ ++it;
+ }
+
+ //
+ // ### WIKI 8 ###
+ //
+ // cnt contain the number of object the local processor contain, if we are interested to count the total number across the processor
+ // we can use the function add, to sum across processors. First we have to get an instance of Vcluster, queue an operation of add with
+ // the variable count and finaly execute. All the operations are asynchronous, execute work like a barrier and ensure that all the
+ // queued operations are executed
+ //
+ v_cl.sum(cnt);
+ v_cl.execute();
+
+ //
+ // ### WIKI 14 ###
+ //
+ // Deinitialize the library
+ //
+ delete(global_v_cluster);
+}
diff --git a/src/Grid/grid_dist_id_iterator.hpp b/src/Grid/grid_dist_id_iterator.hpp
index 11721e22..f7b64159 100644
--- a/src/Grid/grid_dist_id_iterator.hpp
+++ b/src/Grid/grid_dist_id_iterator.hpp
@@ -88,7 +88,7 @@ class grid_dist_iterator<dim,device_grid,FREE>
Vcluster_object_array<device_grid> & gList;
//! Extension of each grid: domain and ghost + domain
- const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext;
+ openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext;
//! Actual iterator
grid_key_dx_iterator_sub<dim> a_it;
@@ -113,12 +113,28 @@ class grid_dist_iterator<dim,device_grid,FREE>
public:
- /*! \brief Constructor of the distributed grid
+ /*! \brief Copy operator=
+ *
+ * \param tmp iterator to copy
+ *
+ */
+ grid_dist_iterator<dim,device_grid,FREE> & operator=(const grid_dist_iterator<dim,device_grid,FREE> & tmp)
+ {
+ g_c = tmp.g_c;
+ gList = tmp.gList;
+ gdb_ext = tmp.gdb_ext;
+ a_it.reinitialize(tmp.a_it);
+ m = tmp.m;
+
+ return *this;
+ }
+
+ /*! \brief Constructor of the distributed grid iterator
*
* \param gk std::vector of the local grid
*
*/
- grid_dist_iterator(Vcluster_object_array<device_grid> & gk, const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
+ grid_dist_iterator(Vcluster_object_array<device_grid> & gk, openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
:g_c(0),gList(gk),gdb_ext(gdb_ext),m(0)
{
// Initialize the current iterator
@@ -224,7 +240,22 @@ class grid_dist_iterator<dim,device_grid,FIXED>
public:
- /*! \brief Constructor of the distributed grid
+ /*! \brief Copy operator=
+ *
+ * \param tmp iterator to copy
+ *
+ */
+ grid_dist_iterator<dim,device_grid,FIXED> & operator=(const grid_dist_iterator<dim,device_grid,FIXED> & tmp)
+ {
+ g_c = tmp.g_c;
+ gList = tmp.gList;
+ gdb_ext = tmp.gdb_ext;
+ a_it.reinitialize(tmp.a_it);
+
+ return *this;
+ }
+
+ /*! \brief Constructor of the distributed grid iterator
*
* \param gk std::vector of the local grid
*
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index de114a56..2f1b974e 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -271,7 +271,6 @@ BOOST_AUTO_TEST_CASE( vector_dist_iterator_test_use_3d )
long int big_step = k / 30;
big_step = (big_step == 0)?1:big_step;
- long int small_step = 1;
print_test_v( "Testing 3D vector k<=",k);
--
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