From 7857bce369c4bfe77e98de997c93da9104a0e5c8 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Sat, 3 Jun 2017 13:17:35 +0200
Subject: [PATCH] Release 0.9.0
---
CHANGELOG.md | 4 +-
example/Grid/3_gray_scott/main.cpp | 6 +-
example/Grid/3_gray_scott_3d/main.cpp | 22 +-
.../0_2D_incompressible/main_petsc.cpp | 6 +-
example/Vector/1_celllist/main.cpp | 2 +-
example/Vector/3_molecular_dynamic/main.cpp | 84 +--
.../4_multiphase_celllist_verlet/main.cpp | 11 +-
example/Vector/4_reorder/energy_force.hpp | 4 +-
example/Vector/4_reorder/main_comp_ord.cpp | 4 +-
.../5_molecular_dynamic_sym_crs/main.cpp | 4 +-
example/Vector/7_SPH_dlb_opt/main.cpp | 9 +-
openfpm_data | 2 +-
openfpm_devices | 2 +-
openfpm_io | 2 +-
openfpm_vcluster | 2 +-
src/Decomposition/CartDecomposition.hpp | 12 +-
src/Decomposition/common.hpp | 2 +-
src/Decomposition/ie_ghost.hpp | 48 +-
src/Decomposition/ie_loc_ghost.hpp | 63 +-
src/Grid/grid_dist_id.hpp | 296 ++------
src/Grid/grid_dist_id_comm.hpp | 679 ++++++++++++++----
src/Grid/grid_dist_id_unit_test.cpp | 131 ++++
src/Grid/grid_dist_key.hpp | 19 +
src/Grid/grid_dist_util.hpp | 10 +-
src/Makefile.am | 2 +-
src/Vector/se_class3_vector.hpp | 53 +-
src/Vector/vector_dist.hpp | 129 +++-
src/Vector/vector_dist_cell_list_tests.hpp | 110 +++
src/Vector/vector_dist_key.hpp | 6 +
29 files changed, 1170 insertions(+), 554 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2d2795d5..df303bd7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,8 +20,10 @@ All notable changes to this project will be documented in this file.
- In case of miss compilation ignore system wide installation
- Bug in VTK writer binary in case of vectors
- Bug in VTK writer binary: long int are not supported removing output
+- Bug in the constructor with stencil bigger than one
-
+### Changed
+- CellList types has changed
## [0.8.0] 28 February 2016
diff --git a/example/Grid/3_gray_scott/main.cpp b/example/Grid/3_gray_scott/main.cpp
index 932a15a3..3bb0eff8 100644
--- a/example/Grid/3_gray_scott/main.cpp
+++ b/example/Grid/3_gray_scott/main.cpp
@@ -10,10 +10,10 @@
* This example show the usage of periodic grid with ghost part given in grid units to solve
* the following system of equations
*
- * \f$\frac{\partial u}{\partial t} = D_u \nabla u -uv^2 + F(1-u)\f$
+ * \f$\frac{\partial u}{\partial t} = D_u \nabla u - uv^2 + F(1-u)\f$
*
*
- * \f$\frac{\partial v}{\partial t} = D_v \nabla v -uv^2 - (F + k)v\f$
+ * \f$\frac{\partial v}{\partial t} = D_v \nabla v + uv^2 - (F + k)v\f$
*
* ## Constants and functions ##
*
@@ -201,7 +201,7 @@ int main(int argc, char* argv[])
grid_dist_id<2, double, aggregate<double,double>> Old(sz,domain,g,bc);
// New grid with the decomposition of the old grid
- grid_dist_id<2, double, aggregate<double,double>> New(Old.getDecomposition(),sz,domain,g);
+ grid_dist_id<2, double, aggregate<double,double>> New(Old.getDecomposition(),sz,g);
// spacing of the grid on x and y
diff --git a/example/Grid/3_gray_scott_3d/main.cpp b/example/Grid/3_gray_scott_3d/main.cpp
index 73ea1646..91ec575f 100644
--- a/example/Grid/3_gray_scott_3d/main.cpp
+++ b/example/Grid/3_gray_scott_3d/main.cpp
@@ -46,8 +46,16 @@ void init(grid_dist_id<3,double,aggregate<double,double> > & Old, grid_dist_id<3
++it;
}
- grid_key_dx<3> start({(long int)std::floor(Old.size(0)*1.55f/domain.getHigh(0)),(long int)std::floor(Old.size(1)*1.55f/domain.getHigh(1)),(long int)std::floor(Old.size(1)*1.55f/domain.getHigh(2))});
- grid_key_dx<3> stop ({(long int)std::ceil (Old.size(0)*1.85f/domain.getHigh(0)),(long int)std::ceil (Old.size(1)*1.85f/domain.getHigh(1)),(long int)std::floor(Old.size(1)*1.85f/domain.getHigh(1))});
+ long int x_start = Old.size(0)*1.55f/domain.getHigh(0);
+ long int y_start = Old.size(1)*1.55f/domain.getHigh(1);
+ long int z_start = Old.size(1)*1.55f/domain.getHigh(2);
+
+ long int x_stop = Old.size(0)*1.85f/domain.getHigh(0);
+ long int y_stop = Old.size(1)*1.85f/domain.getHigh(1);
+ long int z_stop = Old.size(1)*1.85f/domain.getHigh(2);
+
+ grid_key_dx<3> start({x_start,y_start,z_start});
+ grid_key_dx<3> stop ({x_stop,y_stop,z_stop});
auto it_init = Old.getSubDomainIterator(start,stop);
while (it_init.isNext())
@@ -72,7 +80,7 @@ int main(int argc, char* argv[])
Box<3,double> domain({0.0,0.0},{2.5,2.5,2.5});
// grid size
- size_t sz[3] = {128,128,128};
+ size_t sz[3] = {128,128,128};
// Define periodicity of the grid
periodicity<3> bc = {PERIODIC,PERIODIC,PERIODIC};
@@ -90,11 +98,11 @@ int main(int argc, char* argv[])
double dv = 1*1e-5;
// Number of timesteps
- size_t timeSteps = 17000;
+ size_t timeSteps = 5000;
// K and F (Physical constant in the equation)
- double K = 0.065;
- double F = 0.034;
+ double K = 0.014;
+ double F = 0.053;
//! \cond [init lib] \endcond
@@ -186,7 +194,7 @@ int main(int argc, char* argv[])
// visualization
if (i % 60 == 0)
{
- Old.write("output",count,VTK_WRITER | FORMAT_BINARY);
+ Old.write_frame("output",count,VTK_WRITER | FORMAT_BINARY);
count++;
}
}
diff --git a/example/Numerics/Stoke_flow/0_2D_incompressible/main_petsc.cpp b/example/Numerics/Stoke_flow/0_2D_incompressible/main_petsc.cpp
index 27b9cbf7..6f5ae88b 100644
--- a/example/Numerics/Stoke_flow/0_2D_incompressible/main_petsc.cpp
+++ b/example/Numerics/Stoke_flow/0_2D_incompressible/main_petsc.cpp
@@ -404,7 +404,7 @@ int main(int argc, char* argv[])
*
* Once we have the solution we copy it on the grid
*
- * \snippet Numerics/Stoke_flow/0_2D_incompressible/main_eigen.cpp copy write
+ * \snippet Numerics/Stoke_flow/0_2D_incompressible/main_petsc.cpp copy write
*
*/
@@ -424,7 +424,7 @@ int main(int argc, char* argv[])
*
* At the very end of the program we have always to de-initialize the library
*
- * \snippet Numerics/Stoke_flow/0_2D_incompressible/main_eigen.cpp fin lib
+ * \snippet Numerics/Stoke_flow/0_2D_incompressible/main_petsc.cpp fin lib
*
*/
@@ -440,7 +440,7 @@ int main(int argc, char* argv[])
*
* # Full code # {#num_sk_inc_2D_ps_code}
*
- * \include Numerics/Stoke_flow/0_2D_incompressible/main_eigen.cpp
+ * \include Numerics/Stoke_flow/0_2D_incompressible/main_petsc.cpp
*
*/
}
diff --git a/example/Vector/1_celllist/main.cpp b/example/Vector/1_celllist/main.cpp
index 28c4a6fe..c244c468 100644
--- a/example/Vector/1_celllist/main.cpp
+++ b/example/Vector/1_celllist/main.cpp
@@ -247,7 +247,7 @@ int main(int argc, char* argv[])
Point<3,float> xp = vd.getPos(p);
// Get an iterator of all the particles neighborhood of p
- auto Np = NN.getIterator(NN.getCell(vd.getPos(p)));
+ auto Np = NN.getNNIterator(NN.getCell(vd.getPos(p)));
// For each particle near p
while (Np.isNext())
diff --git a/example/Vector/3_molecular_dynamic/main.cpp b/example/Vector/3_molecular_dynamic/main.cpp
index 8d70b8c9..7a2e86db 100644
--- a/example/Vector/3_molecular_dynamic/main.cpp
+++ b/example/Vector/3_molecular_dynamic/main.cpp
@@ -6,8 +6,6 @@
*/
#include "Vector/vector_dist.hpp"
-#include "Decomposition/CartDecomposition.hpp"
-#include "data_type/aggregate.hpp"
#include "Plot/GoogleChart.hpp"
#include "Plot/util.hpp"
#include "timer.hpp"
@@ -19,7 +17,10 @@
*
* # Molecular Dynamic with Lennard-Jones potential # {#e3_md}
*
- * This example show a simple Lennard-Jones molecular dynamic simulation in a stable regime
+ * This example show a simple Lennard-Jones molecular dynamic simulation in a stable regime.
+ * Particle feel each other by the potential.
+ *
+ * \f$ V(x_p,x_q) = 4( (\frac{\sigma}{r})^{12} - (\frac{\sigma}{r})^6 ) \f$
*
* ## Constants ##
*
@@ -55,7 +56,7 @@ constexpr int force = 1;
//! \cond [calc forces] \endcond
-void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6, double r_cut2)
+template<typename CellList> void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList & NN, double sigma12, double sigma6, double r_cut2)
{
//! \cond [calc forces] \endcond
@@ -81,12 +82,12 @@ void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, Ce
/*!
*
- * \page Vector_3_md Vector 3 molecular dynamic with cell-list
+ * \page Vector_3_md_dyn Vector 3 molecular dynamic with cell-list
*
* Get an iterator over the particles and get its position. For each particle p iterate in its neighborhood q
* and calculate the force based on the Lennard-Jhones potential given by
*
- * \f$ F(x_p,x_q) = 24(\frac{2}{r^{13}} - \frac{1}{r^{7}}) r \f$
+ * \f$ F(x_p,x_q) = 24( \frac{2 \sigma^{12}}{r^{13}} - \frac{\sigma^6}{r^{7}}) \hat{r} \f$
*
* \see \ref e0_s_assign_pos
*
@@ -108,7 +109,7 @@ void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, Ce
// Get the position xp of the particle
Point<3,double> xp = vd.getPos(p);
- // Reset the forice counter
+ // Reset the force counter
vd.template getProp<force>(p)[0] = 0.0;
vd.template getProp<force>(p)[1] = 0.0;
vd.template getProp<force>(p)[2] = 0.0;
@@ -175,7 +176,7 @@ void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, Ce
//! \cond [calc energy] \endcond
-double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6, double r_cut2)
+template<typename CellList> double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList & NN, double sigma12, double sigma6, double r_cut2)
{
double rc = r_cut2;
double shift = 2.0 * ( sigma12 / (rc*rc*rc*rc*rc*rc) - sigma6 / ( rc*rc*rc) );
@@ -208,7 +209,7 @@ double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd,
* First we get an iterator over the particles and get its position. For each particle p iterate in its neighborhood q
* and calculate the energy based on the Lennard-Jhones potential given by
*
- * \f$ V(x_p,x_q) = 4(\frac{1}{r^{12}} - \frac{1}{r^{6}}) r \f$
+ * \f$ V(x_p,x_q) = 4(\frac{1}{r^{12}} - \frac{1}{r^{6}}) \f$
*
* \see \ref e0_s_assign_pos
*
@@ -284,43 +285,24 @@ int main(int argc, char* argv[])
*
* ## Initialization ## {#e3_md_init}
*
- * After we defined the two main function calc forces and calc energy, we define
- * important parameters of the simulation, time step integration,
+ * After we defined the two main function calc forces and calc energy, we Initialize
+ * the library, we create a Box that define our domain, boundary conditions and ghost.
+ * Than we define important parameters of the simulation, time step integration,
* size of the box, and cut-off radius of the interaction. We also define 2 vectors
* x and y (they are like std::vector) used for statistic
*
+ * \see \ref e0_s_init
+ *
* \snippet Vector/3_molecular_dynamic/main.cpp constants run
*
*/
//! \cond [constants run] \endcond
- double dt = 0.0005;
+ openfpm_init(&argc,&argv);
+
double sigma = 0.1;
double r_cut = 3.0*sigma;
- double sigma12 = pow(sigma,12);
- double sigma6 = pow(sigma,6);
-
- openfpm::vector<double> x;
- openfpm::vector<openfpm::vector<double>> y;
-
- //! \cond [constants run] \endcond
-
- /*!
- * \page Vector_3_md_dyn Vector 3 molecular dynamic with cell-list
- *
- * Here we Initialize the library, we create a Box that define our domain, boundary conditions and ghost
- *
- * \see \ref e0_s_init
- *
- * \snippet Vector/3_molecular_dynamic/main.cpp init
- *
- */
-
- //! \cond [init] \endcond
-
- openfpm_init(&argc,&argv);
- Vcluster & v_cl = create_vcluster();
// we will use it do place particles on a 10x10x10 Grid like
size_t sz[3] = {10,10,10};
@@ -334,7 +316,14 @@ int main(int argc, char* argv[])
// ghost, big enough to contain the interaction radius
Ghost<3,float> ghost(r_cut);
- //! \cond [init] \endcond
+ double dt = 0.0005;
+ double sigma12 = pow(sigma,12);
+ double sigma6 = pow(sigma,6);
+
+ openfpm::vector<double> x;
+ openfpm::vector<openfpm::vector<double>> y;
+
+ //! \cond [constants run] \endcond
/*!
* \page Vector_3_md_dyn Vector 3 molecular dynamic with cell-list
@@ -370,18 +359,24 @@ int main(int argc, char* argv[])
//! \cond [vect grid] \endcond
+ // We create the grid iterator
auto it = vd.getGridIterator(sz);
while (it.isNext())
{
+ // Create a new particle
vd.add();
+ // key contain (i,j,k) index of the grid
auto key = it.get();
+ // The index of the grid can be accessed with key.get(0) == i, key.get(1) == j ...
+ // We use getLastPos to set the position of the last particle added
vd.getLastPos()[0] = key.get(0) * it.getSpacing(0);
vd.getLastPos()[1] = key.get(1) * it.getSpacing(1);
vd.getLastPos()[2] = key.get(2) * it.getSpacing(2);
+ // We use getLastProp to set the property value of the last particle we added
vd.template getLastProp<velocity>()[0] = 0.0;
vd.template getLastProp<velocity>()[1] = 0.0;
vd.template getLastProp<velocity>()[2] = 0.0;
@@ -404,8 +399,8 @@ int main(int argc, char* argv[])
*
* The verlet integration stepping look like this
*
- * \f[ \vec{v}(t_{n+1/2}) = \vec{v}_p(t_n) + \frac{1}{2} \delta t \vec{a}(t_n) \f]
- * \f[ \vec{x}(t_{n}) = \vec{x}_p(t_n) + \delta t \vec{v}(t_n+1/2) \f]
+ * \f[ \vec{v}(t_{n}+1/2) = \vec{v}_p(t_n) + \frac{1}{2} \delta t \vec{a}(t_n) \f]
+ * \f[ \vec{x}(t_{n}+1) = \vec{x}_p(t_n) + \delta t \vec{v}(t_n+1/2) \f]
*
* calculate the forces from \f$ \vec{a} (t_{n}) \f$ finally
*
@@ -465,7 +460,7 @@ int main(int argc, char* argv[])
++it3;
}
- // Because we mooved the particles in space we have to map them and re-sync the ghost
+ // Because we moved the particles in space we have to map them and re-sync the ghost
vd.map();
vd.template ghost_get<>();
@@ -488,7 +483,7 @@ int main(int argc, char* argv[])
++it4;
}
- // After every iteration collect some statistic about the confoguration
+ // After every iteration collect some statistic about the configuration
if (i % 100 == 0)
{
// We write the particle position for visualization (Without ghost)
@@ -554,6 +549,15 @@ int main(int argc, char* argv[])
// width of the line
options.lineWidth = 1.0;
+ // Resolution in x
+ options.width = 1280;
+
+ // Resolution in y
+ options.heigh = 720;
+
+ // Add zoom capability
+ options.more = GC_ZOOM;
+
// Object that draw the X Y graph
GoogleChart cg;
diff --git a/example/Vector/4_multiphase_celllist_verlet/main.cpp b/example/Vector/4_multiphase_celllist_verlet/main.cpp
index de4093d5..cfa51c31 100644
--- a/example/Vector/4_multiphase_celllist_verlet/main.cpp
+++ b/example/Vector/4_multiphase_celllist_verlet/main.cpp
@@ -149,6 +149,8 @@ int main(int argc, char* argv[])
//! \cond [create multi-phase verlet] \endcond
+ {
+
// Get the cell list of the phase1
auto CL_phase1 = phases.get(1).getCellList(r_cut);
@@ -204,6 +206,8 @@ int main(int argc, char* argv[])
++it;
}
+ }
+
//! \cond [count part from phase0 to 1] \endcond
/*!
@@ -311,13 +315,14 @@ int main(int argc, char* argv[])
*
*/
+ {
//! \cond [compute sym multi-phase two phase] \endcond
// Get the cell list of the phase1
- CL_phase1 = phases.get(1).getCellListSym(r_cut);
+ auto CL_phase1 = phases.get(1).getCellListSym(r_cut);
// This function create a Verlet-list between phases 0 and 1
- NN_ver01 = createVerletSym(phases.get(0),phases.get(1),CL_phase1,r_cut);
+ auto NN_ver01 = createVerletSym(phases.get(0),phases.get(1),CL_phase1,r_cut);
// Get an iterator over the real and ghost particles
it = phases.get(0).getDomainAndGhostIterator();
@@ -371,6 +376,8 @@ int main(int argc, char* argv[])
phases.get(0).ghost_put<add_,0>();
phases.get(1).ghost_put<add_,0>();
+ }
+
//! \cond [compute sym multi-phase two phase] \endcond
/*!
diff --git a/example/Vector/4_reorder/energy_force.hpp b/example/Vector/4_reorder/energy_force.hpp
index 5836b0fc..2108b811 100644
--- a/example/Vector/4_reorder/energy_force.hpp
+++ b/example/Vector/4_reorder/energy_force.hpp
@@ -12,7 +12,7 @@ constexpr int velocity = 0;
constexpr int force = 1;
-void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6)
+template<typename CellList> void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList & NN, double sigma12, double sigma6)
{
// update the Cell-list
vd.updateCellList(NN);
@@ -73,7 +73,7 @@ void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, Ce
}
-double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6)
+template<typename CellList> double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList & NN, double sigma12, double sigma6)
{
double E = 0.0;
diff --git a/example/Vector/4_reorder/main_comp_ord.cpp b/example/Vector/4_reorder/main_comp_ord.cpp
index 9a9a1abf..77f915a4 100644
--- a/example/Vector/4_reorder/main_comp_ord.cpp
+++ b/example/Vector/4_reorder/main_comp_ord.cpp
@@ -45,7 +45,7 @@ constexpr int force = 1;
//! \cond [calc forces] \endcond
-void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList_hilb<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6)
+template<typename CellList> void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList & NN, double sigma12, double sigma6)
{
//! \cond [calc forces] \endcond
@@ -140,7 +140,7 @@ void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, Ce
//! \cond [calc energy all] \endcond
-double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList_hilb<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6)
+template<typename CellList> double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList & NN, double sigma12, double sigma6)
{
double E = 0.0;
diff --git a/example/Vector/5_molecular_dynamic_sym_crs/main.cpp b/example/Vector/5_molecular_dynamic_sym_crs/main.cpp
index fe6bec6b..a8eb5615 100644
--- a/example/Vector/5_molecular_dynamic_sym_crs/main.cpp
+++ b/example/Vector/5_molecular_dynamic_sym_crs/main.cpp
@@ -148,7 +148,7 @@ void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, Ve
//! \cond [real and ghost] \endcond
// Get an iterator over particles
- auto it2 = vd.getParticleIteratorCRS(NN.getInternalCellList());
+ auto it2 = vd.getParticleIteratorCRS(NN);
//! \cond [real and ghost] \endcond
@@ -250,7 +250,7 @@ double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd,
double shift = 4.0 * ( sigma12 / (rc*rc*rc*rc*rc*rc) - sigma6 / ( rc*rc*rc) );
// Get an iterator over particles
- auto it2 = vd.getParticleIteratorCRS(NN.getInternalCellList());
+ auto it2 = vd.getParticleIteratorCRS(NN);
// For each particle ...
while (it2.isNext())
diff --git a/example/Vector/7_SPH_dlb_opt/main.cpp b/example/Vector/7_SPH_dlb_opt/main.cpp
index cbb40805..6c54fbd9 100644
--- a/example/Vector/7_SPH_dlb_opt/main.cpp
+++ b/example/Vector/7_SPH_dlb_opt/main.cpp
@@ -912,7 +912,7 @@ int main(int argc, char* argv[])
cbar = coeff_sound * sqrt(gravity * h_swl);
// for each particle inside the fluid box ...
-/* while (fluid_it.isNext())
+ while (fluid_it.isNext())
{
// ... add a particle ...
vd.add();
@@ -946,8 +946,7 @@ int main(int argc, char* argv[])
// next fluid particle
++fluid_it;
- }*/
-
+ }
// Recipient
Box<3,double> recipient1({0.0,0.0,0.0},{1.6+dp/2.0,0.67+dp/2.0,0.4+dp/2.0});
@@ -1010,10 +1009,6 @@ int main(int argc, char* argv[])
vd.map();
- vd.write("Recipient");
-
- return 0;
-
// Now that we fill the vector with particles
ModelCustom md;
diff --git a/openfpm_data b/openfpm_data
index 3a732c98..2c313203 160000
--- a/openfpm_data
+++ b/openfpm_data
@@ -1 +1 @@
-Subproject commit 3a732c98d6404fd81529c25af4fbf33f8ca3de9c
+Subproject commit 2c31320305af04b0621d2a10818354d064ec1bbf
diff --git a/openfpm_devices b/openfpm_devices
index add2acfe..9817279e 160000
--- a/openfpm_devices
+++ b/openfpm_devices
@@ -1 +1 @@
-Subproject commit add2acfe9623e6045da1e41adbab6dc57ef50e5f
+Subproject commit 9817279ee3ac36b435d2178e994ab314a01aab30
diff --git a/openfpm_io b/openfpm_io
index a6bd0b79..9b0500dd 160000
--- a/openfpm_io
+++ b/openfpm_io
@@ -1 +1 @@
-Subproject commit a6bd0b797704f6faba662a10f5b101c218257490
+Subproject commit 9b0500dd1347d9f3d2898f2a9206220eea7907d5
diff --git a/openfpm_vcluster b/openfpm_vcluster
index 1856e665..7030e7f7 160000
--- a/openfpm_vcluster
+++ b/openfpm_vcluster
@@ -1 +1 @@
-Subproject commit 1856e665949ecca8dbcf68e08984aace853aad8d
+Subproject commit 7030e7f76e5d80a297e4cc9b2d4f3ad98beb8d0f
diff --git a/src/Decomposition/CartDecomposition.hpp b/src/Decomposition/CartDecomposition.hpp
index c097931d..728292d0 100755
--- a/src/Decomposition/CartDecomposition.hpp
+++ b/src/Decomposition/CartDecomposition.hpp
@@ -135,7 +135,7 @@ protected:
//! Structure that store the cartesian grid information
grid_sm<dim, void> gr_dist;
- //! Structure that decompose your structure into cell without creating them
+ //! Structure that decompose the space into cells without creating them
//! useful to convert positions to CellId or sub-domain id in this case
CellDecomposer_sm<dim, T, shift<dim,T>> cd;
@@ -1724,6 +1724,16 @@ public:
return dist.get_ndec();
}
+ /*! \brief Get the cell decomposer of the decomposition
+ *
+ * \return the cell decomposer
+ *
+ */
+ const CellDecomposer_sm<dim, T, shift<dim,T>> & getCellDecomposer()
+ {
+ return cd;
+ }
+
//! friend classes
friend extended_type;
diff --git a/src/Decomposition/common.hpp b/src/Decomposition/common.hpp
index 36575f12..f9cdfeb6 100755
--- a/src/Decomposition/common.hpp
+++ b/src/Decomposition/common.hpp
@@ -114,7 +114,7 @@ struct lBox_dom
{
//! Intersection between the local sub-domain enlarged by the ghost and the contiguous processor
//! sub-domains (External ghost)
- openfpm::vector_std< Box_sub<dim,T> > ebx;
+ openfpm::vector_std< Box_sub_k<dim,T> > ebx;
//! Intersection between the contiguous processor sub-domain enlarged by the ghost with the
//! local sub-domain (Internal ghost)
diff --git a/src/Decomposition/ie_ghost.hpp b/src/Decomposition/ie_ghost.hpp
index cf748514..a7b14d91 100755
--- a/src/Decomposition/ie_ghost.hpp
+++ b/src/Decomposition/ie_ghost.hpp
@@ -991,7 +991,7 @@ public:
return true;
}
- /*! \brief Check if the ie_loc_ghosts contain the same information
+ /*! \brief Check if the ie_ghosts contain the same information
*
* \param ig Element to check
*
@@ -1065,52 +1065,6 @@ public:
*/
bool is_equal_ng(ie_ghost<dim,T> & ig)
{
- Box<dim,T> bt;
-
- if (getNEGhostBox() != ig.getNEGhostBox())
- return false;
-
- if (getNIGhostBox() != ig.getNIGhostBox())
- return false;
-
- for (size_t i = 0 ; i < proc_int_box.size() ; i++)
- {
- if (getProcessorNIGhost(i) != ig.getProcessorNIGhost(i))
- return false;
- for (size_t j = 0 ; j < getProcessorNIGhost(i) ; j++)
- {
- if (getProcessorIGhostBox(i,j).Intersect(ig.getProcessorIGhostBox(i,j),bt) == false)
- return false;
- if (getProcessorIGhostId(i,j) != ig.getProcessorIGhostId(i,j))
- return false;
- if (getProcessorIGhostSub(i,j) != ig.getProcessorIGhostSub(i,j))
- return false;
- }
- if (getIGhostBox(i).Intersect(ig.getIGhostBox(i),bt) == false)
- return false;
- if (getIGhostBoxProcessor(i) != ig.getIGhostBoxProcessor(i))
- return false;
- }
-
- for (size_t i = 0 ; i < proc_int_box.size() ; i++)
- {
- if (getProcessorNEGhost(i) != ig.getProcessorNEGhost(i))
- return false;
- for (size_t j = 0 ; j < getProcessorNEGhost(i) ; j++)
- {
- if (getProcessorEGhostBox(i,j).Intersect(ig.getProcessorEGhostBox(i,j),bt) == false)
- return false;
- if (getProcessorEGhostId(i,j) != ig.getProcessorEGhostId(i,j))
- return false;
- if (getProcessorEGhostSub(i,j) != ig.getProcessorEGhostSub(i,j))
- return false;
- }
- if (getEGhostBox(i).Intersect(ig.getEGhostBox(i),bt) == false)
- return false;
- if (getEGhostBoxProcessor(i) != ig.getEGhostBoxProcessor(i))
- return false;
- }
-
return true;
}
diff --git a/src/Decomposition/ie_loc_ghost.hpp b/src/Decomposition/ie_loc_ghost.hpp
index 1d9bd570..727b1dca 100755
--- a/src/Decomposition/ie_loc_ghost.hpp
+++ b/src/Decomposition/ie_loc_ghost.hpp
@@ -70,7 +70,7 @@ class ie_loc_ghost
if (intersect == true)
{
- Box_sub<dim,T> b;
+ Box_sub_k<dim,T> b;
b.sub = rj;
b.bx = bi;
b.cmb = sub_domains_prc.get(j).cmb;
@@ -84,6 +84,7 @@ class ie_loc_ghost
if (loc_ghost_box.get(rj).ibx.get(k).sub == i && loc_ghost_box.get(rj).ibx.get(k).cmb == sub_domains_prc.get(j).cmb.operator-())
{
loc_ghost_box.get(rj).ibx.get(k).k = loc_ghost_box.get(i).ebx.size()-1;
+ loc_ghost_box.get(i).ebx.last().k = k;
break;
}
}
@@ -346,9 +347,11 @@ public:
return loc_ghost_box.get(id).ibx.size();
}
- /*! \brief For the sub-domain i intersected with the sub-domain j enlarged, the associated
- * external ghost box is located in getLocalEGhostBox(j,k) with
- * getLocalIGhostSub(j,k) == i, this function return k
+ /*! \brief For the sub-domain i intersected with a surrounding sub-domain enlarged. Produce a internal ghost box from
+ * the prospecive of i and an associated external ghost box from the prospective of j.
+ * In order to retrieve the information about the external ghost box we have to use getLocalEGhostBox(x,k).
+ * where k is the value returned by getLocalIGhostE(i,j) and x is the value returned by
+ * getLocalIGhostSub(i,j)
*
* \param i
* \param j
@@ -460,10 +463,10 @@ public:
return loc_ghost_box.get(i).ebx.get(j).cmb;
}
- /*! \brief Considering that sub-domain has N internal local ghost box identified
+ /*! \brief Considering that sub-domains has N internal local ghost box identified
* with the 0 <= k < N that come from the intersection of 2 sub-domains i and j
- * where j is enlarged, given the sub-domain i and the id k to identify the local internal ghost,
- * it return the id k of the other sub-domain that produced the intersection
+ * where j is enlarged, given the sub-domain i and the id k of the internal box,
+ * it return the id of the other sub-domain that produced the intersection
*
* \param i sub-domain
* \param k id
@@ -475,7 +478,7 @@ public:
return loc_ghost_box.get(i).ibx.get(k).sub;
}
- /*! \brief Considering that sub-domain has N external local ghost box identified
+ /*! \brief Considering that sub-domains has N external local ghost box identified
* with the 0 <= k < N that come from the intersection of 2 sub-domains i and j
* where i is enlarged, given the sub-domain i and the id k of the external box,
* it return the id of the other sub-domain that produced the intersection
@@ -562,7 +565,16 @@ public:
{
if (loc_ghost_box.get(i).ibx.get(j).k == -1)
{
- std::cout << "No ibx link" << "\n";
+ std::cout << __FILE__ << ":" << __LINE__ << " Error: inconsistent decomposition no ibx link" << "\n";
+ return false;
+ }
+
+ size_t k = loc_ghost_box.get(i).ibx.get(j).k;
+ size_t sub = loc_ghost_box.get(i).ibx.get(j).sub;
+
+ if (loc_ghost_box.get(sub).ebx.get(k).k != (long int)j)
+ {
+ std::cout << __FILE__ << ":" << __LINE__ << " Error: inconsistent link between an external ghost box and an internal ghost box" << "\n";
return false;
}
}
@@ -627,39 +639,6 @@ public:
*/
bool is_equal_ng(ie_loc_ghost<dim,T> & ilg)
{
- Box<dim,T> bt;
-
- if (ilg.loc_ghost_box.size() != loc_ghost_box.size())
- return false;
-
- // Explore all the subdomains
- for (size_t i = 0 ; i < loc_ghost_box.size() ; i++)
- {
- if (getLocalNIGhost(i) != ilg.getLocalNIGhost(i))
- return false;
-
- if (getLocalNEGhost(i) != ilg.getLocalNEGhost(i))
- return false;
-
- for (size_t j = 0 ; j < getLocalNIGhost(i) ; j++)
- {
- if (getLocalIGhostE(i,j) != ilg.getLocalIGhostE(i,j))
- return false;
- if (getLocalIGhostBox(i,j).Intersect(ilg.getLocalIGhostBox(i,j),bt) == false)
- return false;
- if (getLocalIGhostSub(i,j) != ilg.getLocalIGhostSub(i,j))
- return false;
- }
- for (size_t j = 0 ; j < getLocalNEGhost(i) ; j++)
- {
- if (getLocalEGhostBox(i,j).Intersect(ilg.getLocalEGhostBox(i,j),bt) == false)
- return false;
- if (getLocalEGhostSub(i,j) != ilg.getLocalEGhostSub(i,j))
- return false;
- }
-
- }
-
return true;
}
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index 13239393..88cb2af8 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -376,73 +376,14 @@ class grid_dist_id : public grid_dist_id_comm<dim,St,T,Decomposition,Memory,devi
pib.bid.get(s).sub = dec.getLocalEGhostSub(k,s);
pib.bid.get(s).cmb = loc_ig_box.get(i).bid.get(j).cmb;
pib.bid.get(s).cmb.sign_flip();
+ pib.bid.get(s).k = j;
+ pib.bid.get(s).initialized = true;
}
}
init_local_e_g_box = true;
}
- /*! \brief Sync the local ghost part
- *
- * \tparam prp... properties to sync
- *
- */
- template<int... prp> void ghost_get_local()
- {
- //! For all the sub-domains
- for (size_t i = 0 ; i < loc_ig_box.size() ; i++)
- {
- //! For all the internal ghost boxes of each sub-domain
- for (size_t j = 0 ; j < loc_ig_box.get(i).bid.size() ; j++)
- {
- Box<dim,size_t> bx_src = loc_ig_box.get(i).bid.get(j).box;
- // convert into local
- bx_src -= gdb_ext.get(i).origin;
-
- // sub domain connected with external box
- size_t sub_id_dst = loc_ig_box.get(i).bid.get(j).sub;
-
- // local internal ghost box connected
- size_t k = loc_ig_box.get(i).bid.get(j).k;
-
- Box<dim,size_t> bx_dst = loc_eg_box.get(sub_id_dst).bid.get(k).box;
-
- // convert into local
- bx_dst -= gdb_ext.get(sub_id_dst).origin;
-
- // create 2 sub grid iterator
-
- if (bx_dst.isValid() == false)
- continue;
-
- grid_key_dx_iterator_sub<dim> sub_src(loc_grid.get(i).getGrid(),bx_src.getKP1(),bx_src.getKP2());
- grid_key_dx_iterator_sub<dim> sub_dst(loc_grid.get(sub_id_dst).getGrid(),bx_dst.getKP1(),bx_dst.getKP2());
-
-#ifdef SE_CLASS1
-
- if (loc_eg_box.get(sub_id_dst).bid.get(k).sub != i)
- std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " source and destination are not correctly linked" << "\n";
-
- if (sub_src.getVolume() != sub_dst.getVolume())
- std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " source and destination does not match in size" << "\n";
-
-#endif
-
- const auto & gs = loc_grid.get(i);
- auto & gd = loc_grid.get(sub_id_dst);
-
- while (sub_src.isNext())
- {
- // Option 1
- gd.set(sub_dst.get(),gs,sub_src.get());
-
- ++sub_src;
- ++sub_dst;
- }
- }
- }
- }
-
/*! \brief Check the grid has a valid size
*
* \param g_sz size of the grid
@@ -625,8 +566,8 @@ protected:
// set the ghost
for (size_t i = 0 ; i < dim ; i++)
{
- gc.setLow(i,-sp.getHigh(i));
- gc.setHigh(i,sp.getHigh(i));
+ gc.setLow(i,gd.getLow(i)*(sp.getHigh(i)));
+ gc.setHigh(i,gd.getHigh(i)*(sp.getHigh(i)));
}
return gc;
@@ -1018,6 +959,8 @@ public:
return total;
}
+
+
/*! \brief It return the informations about the local grids
*
* \return The information about the local grids
@@ -1065,14 +1008,10 @@ public:
if (v_cl.getProcessUnitID() == 0)
{
for (size_t i = 1; i < v_cl.getProcessingUnits(); i++)
- {
v_cl.send(i,0,gdb_ext_global);
- }
}
else
- {
v_cl.recv(0,0,gdb_ext_global);
- }
v_cl.execute();
}
@@ -1208,6 +1147,33 @@ public:
return false;
}
+ /*! \brief Get the reference of the selected element
+ *
+ * \tparam p property to get (is an integer)
+ * \param v1 grid_key that identify the element in the grid
+ *
+ * \return the selected element
+ *
+ */
+ template <unsigned int p>inline auto getProp(const grid_dist_key_dx<dim> & v1) const -> decltype(this->template get<p>(v1))
+ {
+ return this->template get<p>(v1);
+ }
+
+ /*! \brief Get the reference of the selected element
+ *
+ * \tparam p property to get (is an integer)
+ * \param v1 grid_key that identify the element in the grid
+ *
+ * \return the selected element
+ *
+ */
+ template <unsigned int p>inline auto getProp(const grid_dist_key_dx<dim> & v1) -> decltype(this->template get<p>(v1))
+ {
+ return this->template get<p>(v1);
+ }
+
+
/*! \brief Get the reference of the selected element
*
* \tparam p property to get (is an integer)
@@ -1240,12 +1206,6 @@ public:
return loc_grid.get(v1.getSub()).template get<p>(v1.getKey());
}
- //! Memory for the ghost sending buffer
- Memory g_send_prp_mem;
-
- //! Memory for the ghost sending buffer
- Memory g_recv_prp_mem;
-
//! Flag that indicate if the external ghost box has been initialized
bool init_e_g_box = false;
@@ -1278,9 +1238,6 @@ public:
check_valid(this,8);
#endif
- // Sending property object
- typedef object<typename object_creator<typename T::type,prp...>::type> prp_object;
-
// Convert the ghost internal boxes into grid unit boxes
create_ig_box();
@@ -1293,164 +1250,45 @@ public:
// Convert the local external ghost boxes into grid unit boxes
create_local_eg_box();
+ grid_dist_id_comm<dim,St,T,Decomposition,Memory,device_grid>::template ghost_get_<prp...>(ig_box,
+ eg_box,
+ loc_ig_box,
+ loc_eg_box,
+ gdb_ext,
+ loc_grid,
+ g_id_to_external_ghost_box);
+ }
- size_t req = 0;
-
- // Create a packing request vector
- for ( size_t i = 0 ; i < ig_box.size() ; i++ )
- {
- // for each ghost box
- for (size_t j = 0 ; j < ig_box.get(i).bid.size() ; j++)
- {
- // And linked sub-domain
- size_t sub_id = ig_box.get(i).bid.get(j).sub;
- // Internal ghost box
- Box<dim,long int> g_ig_box = ig_box.get(i).bid.get(j).box;
-
- if (g_ig_box.isValid() == false)
- continue;
-
- g_ig_box -= gdb_ext.get(sub_id).origin.template convertPoint<size_t>();
-
- // Pack a size_t for the internal ghost id
- Packer<size_t,HeapMemory>::packRequest(req);
- // Create a sub grid iterator spanning the internal ghost layer
- grid_key_dx_iterator_sub<dim> sub_it(loc_grid.get(sub_id).getGrid(),g_ig_box.getKP1(),g_ig_box.getKP2());
- // and pack the internal ghost grid
- Packer<device_grid,HeapMemory>::template packRequest<prp...>(loc_grid.get(sub_id),sub_it,req);
- }
- }
-
- // resize the property buffer memory
- g_send_prp_mem.resize(req);
-
- // Create an object of preallocated memory for properties
- ExtPreAlloc<Memory> & prAlloc_prp = *(new ExtPreAlloc<Memory>(req,g_send_prp_mem));
-
- prAlloc_prp.incRef();
-
- // Pack information
- Pack_stat sts;
-
- // Pack the information for each processor and send it
- for ( size_t i = 0 ; i < ig_box.size() ; i++ )
- {
-
- sts.mark();
- void * pointer = prAlloc_prp.getPointerEnd();
-
- // for each ghost box
- for (size_t j = 0 ; j < ig_box.get(i).bid.size() ; j++)
- {
- // we pack only if it is valid
- if (ig_box.get(i).bid.get(j).box.isValid() == false)
- continue;
-
- // And linked sub-domain
- size_t sub_id = ig_box.get(i).bid.get(j).sub;
- // Internal ghost box
- Box<dim,size_t> g_ig_box = ig_box.get(i).bid.get(j).box;
- g_ig_box -= gdb_ext.get(sub_id).origin.template convertPoint<size_t>();
- // Ghost box global id
- size_t g_id = ig_box.get(i).bid.get(j).g_id;
-
- // Pack a size_t for the internal ghost id
- Packer<size_t,HeapMemory>::pack(prAlloc_prp,g_id,sts);
- // Create a sub grid iterator spanning the internal ghost layer
- grid_key_dx_iterator_sub<dim> sub_it(loc_grid.get(sub_id).getGrid(),g_ig_box.getKP1(),g_ig_box.getKP2());
- // and pack the internal ghost grid
- Packer<device_grid,HeapMemory>::template pack<prp...>(prAlloc_prp,loc_grid.get(sub_id),sub_it,sts);
- }
- // send the request
-
- void * pointer2 = prAlloc_prp.getPointerEnd();
-
- v_cl.send(ig_box.get(i).prc,0,pointer,(char *)pointer2 - (char *)pointer);
- }
-
- // Calculate the total information to receive from each processors
- std::vector<size_t> prp_recv;
-
- //! Receive the information from each processors
- for ( size_t i = 0 ; i < eg_box.size() ; i++ )
- {
- prp_recv.push_back(0);
-
- // for each external ghost box
- for (size_t j = 0 ; j < eg_box.get(i).bid.size() ; j++)
- {
- // External ghost box
- Box<dim,size_t> g_eg_box = eg_box.get(i).bid.get(j).g_e_box;
- prp_recv[prp_recv.size()-1] += g_eg_box.getVolumeKey() * sizeof(prp_object) + sizeof(size_t);
- }
- }
-
- size_t tot_recv = ExtPreAlloc<Memory>::calculateMem(prp_recv);
-
- //! Resize the receiving buffer
- g_recv_prp_mem.resize(tot_recv);
-
- // Create an object of preallocated memory for properties
- ExtPreAlloc<Memory> & prRecv_prp = *(new ExtPreAlloc<Memory>(tot_recv,g_recv_prp_mem));
- prRecv_prp.incRef();
-
- // queue the receives
- for ( size_t i = 0 ; i < eg_box.size() ; i++ )
- {
- prRecv_prp.allocate(prp_recv[i]);
- v_cl.recv(eg_box.get(i).prc,0,prRecv_prp.getPointer(),prp_recv[i]);
- }
-
- // Before wait for the communication to complete we sync the local ghost
- // in order to overlap with communication
-
- ghost_get_local<prp...>();
-
- // wait to receive communication
- v_cl.execute();
-
- Unpack_stat ps;
-
- // Unpack the object
- for ( size_t i = 0 ; i < eg_box.size() ; i++ )
- {
- // for each external ghost box
- for (size_t j = 0 ; j < eg_box.get(i).bid.size() ; j++)
- {
- // Unpack the ghost box global-id
-
- size_t g_id;
- Unpacker<size_t,HeapMemory>::unpack(prRecv_prp,g_id,ps);
-
- size_t l_id = 0;
- // convert the global id into local id
- auto key = g_id_to_external_ghost_box.find(g_id);
- if (key != g_id_to_external_ghost_box.end()) // FOUND
- l_id = key->second;
- else
- {
- // NOT FOUND
-
- // It must be always found, if not it mean that the processor has no-idea of
- // what is stored and conseguently do not know how to unpack, print a critical error
- // and return
+ /*! \brief It synchronize the ghost parts
+ *
+ * \tparam prp... Properties to synchronize
+ *
+ */
+ template<template<typename,typename> class op,int... prp> void ghost_put()
+ {
+#ifdef SE_CLASS2
+ check_valid(this,8);
+#endif
- std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " Critical, cannot unpack object, because received data cannot be interpreted\n";
+ // Convert the ghost internal boxes into grid unit boxes
+ create_ig_box();
- return;
- }
+ // Convert the ghost external boxes into grid unit boxes
+ create_eg_box();
- // Get the external ghost box associated with the packed information
- Box<dim,size_t> box = eg_box.get(i).bid.get(l_id).l_e_box;
- size_t sub_id = eg_box.get(i).bid.get(l_id).sub;
+ // Convert the local ghost internal boxes into grid unit boxes
+ create_local_ig_box();
- // sub-grid where to unpack
- grid_key_dx_iterator_sub<dim> sub2(loc_grid.get(sub_id).getGrid(),box.getKP1(),box.getKP2());
+ // Convert the local external ghost boxes into grid unit boxes
+ create_local_eg_box();
- // Unpack
- Unpacker<device_grid,HeapMemory>::template unpack<prp...>(prRecv_prp,sub2,loc_grid.get(sub_id),ps);
- }
- }
+ grid_dist_id_comm<dim,St,T,Decomposition,Memory,device_grid>::template ghost_put_<op,prp...>(ig_box,
+ eg_box,
+ loc_ig_box,
+ loc_eg_box,
+ gdb_ext,
+ loc_grid,
+ g_id_to_internal_ghost_box);
}
/*! \brief Copy the give grid into this grid
@@ -1560,7 +1398,7 @@ public:
* \return true id the write succeed
*
*/
- bool write(std::string output, size_t i, size_t opt = VTK_WRITER | FORMAT_ASCII)
+ bool write_frame(std::string output, size_t i, size_t opt = VTK_WRITER | FORMAT_ASCII)
{
#ifdef SE_CLASS2
check_valid(this,8);
diff --git a/src/Grid/grid_dist_id_comm.hpp b/src/Grid/grid_dist_id_comm.hpp
index d4309776..210164b1 100644
--- a/src/Grid/grid_dist_id_comm.hpp
+++ b/src/Grid/grid_dist_id_comm.hpp
@@ -12,6 +12,95 @@
#include "data_type/scalar.hpp"
+template<bool result,typename T, typename device_grid, typename Memory>
+struct grid_unpack_selector_with_prp
+{
+ template<template<typename,typename> class op, int ... prp> static void call_unpack(ExtPreAlloc<Memory> & recv_buf, grid_key_dx_iterator_sub<device_grid::dims> & sub2, device_grid & dg, Unpack_stat & ps)
+ {
+ std::cerr << __FILE__ << ":" << __LINE__ << " Error: complex properties on grids are not supported yet" << std::endl;
+ }
+};
+
+//
+template<typename T, typename device_grid, typename Memory>
+struct grid_unpack_selector_with_prp<true,T,device_grid,Memory>
+{
+ template<template<typename,typename> class op, unsigned int ... prp> static void call_unpack(ExtPreAlloc<Memory> & recv_buf, grid_key_dx_iterator_sub<device_grid::dims> & sub2, device_grid & gd, Unpack_stat & ps)
+ {
+ PtrMemory * ptr1;
+
+ size_t sz[device_grid::dims];
+
+ for (size_t i = 0 ; i < device_grid::dims ; i++)
+ sz[i] = sub2.getStop().get(i) - sub2.getStart().get(i) + 1;
+
+ size_t tot = 1;
+
+ for (size_t i = 0 ; i < device_grid::dims ; i++)
+ tot *= sz[i];
+
+ tot *= sizeof(T);
+
+#ifdef SE_CLASS1
+
+ if (ps.getOffset() + tot > recv_buf.size())
+ std::cerr << __FILE__ << ":" << __LINE__ << " Error: overflow in the receiving buffer for ghost_put" << std::endl;
+
+#endif
+
+ // add the received particles to the vector
+ ptr1 = new PtrMemory(((char *)recv_buf.getPointerBase()+ps.getOffset()),tot);
+
+ // create vector representation to a piece of memory already allocated
+ grid_cpu<device_grid::dims,T,PtrMemory,typename memory_traits_lin<T>::type> gs;
+
+ gs.setMemory(*ptr1);
+
+ // resize with the number of elements
+ gs.resize(sz);
+
+ // Merge the information
+
+ auto it_src = gs.getIterator();
+
+ while (sub2.isNext())
+ {
+ object_s_di_op<op,decltype(gs.get_o(it_src.get())),decltype(gd.get_o(sub2.get())),OBJ_ENCAP,prp...>(gs.get_o(it_src.get()),gd.get_o(sub2.get()));
+
+ ++sub2;
+ ++it_src;
+ }
+
+ ps.addOffset(tot);
+ }
+};
+
+
+template<typename device_grid, typename Memory, typename T>
+struct grid_call_serialize_variadic {};
+
+template<typename device_grid, typename Memory , int ... prp>
+struct grid_call_serialize_variadic<device_grid, Memory, index_tuple<prp...>>
+{
+ template<template<typename,typename> class op, typename T> inline static void call_unpack(ExtPreAlloc<Memory> & recv_buf, grid_key_dx_iterator_sub<device_grid::dims> & sub2, device_grid & dg, Unpack_stat & ps)
+ {
+ const bool result = has_pack_gen<typename T::type>::value == false;
+
+ grid_unpack_selector_with_prp<result,T,device_grid,Memory>::template call_unpack<op,prp...>(recv_buf,sub2,dg,ps);
+ }
+};
+
+//! There is max_prop inside
+template<template<typename,typename> class op, typename T, typename device_grid, typename Memory>
+struct grid_unpack_with_prp
+{
+ template<unsigned int ... prp> static void unpacking(ExtPreAlloc<Memory> & recv_buf, grid_key_dx_iterator_sub<device_grid::dims> & sub2, device_grid & dg, Unpack_stat & ps)
+ {
+ typedef index_tuple<prp...> ind_prop_to_pack;
+ grid_call_serialize_variadic<device_grid,Memory,ind_prop_to_pack>::template call_unpack<op,T>(recv_buf, sub2, dg, ps);
+ }
+};
+
/*! \brief This class is an helper for the communication of grid_dist_id
*
* \tparam dim Dimensionality of the grid
@@ -46,6 +135,146 @@ class grid_dist_id_comm
//! second id is the processor id
openfpm::vector<openfpm::vector<aggregate<device_grid,SpaceBox<dim,long int>>>> m_oGrid;
+ //! Memory for the ghost sending buffer
+ Memory g_send_prp_mem;
+
+ //! Memory for the ghost sending buffer
+ Memory g_recv_prp_mem;
+
+
+ /*! \brief Sync the local ghost part
+ *
+ * \tparam prp... properties to sync
+ *
+ */
+ template<int... prp> void ghost_get_local(const openfpm::vector<i_lbox_grid<dim>> & loc_ig_box,
+ const openfpm::vector<e_lbox_grid<dim>> & loc_eg_box,
+ const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext,
+ openfpm::vector<device_grid> & loc_grid,
+ std::unordered_map<size_t,size_t> & g_id_to_external_ghost_box)
+ {
+ //! For all the sub-domains
+ for (size_t i = 0 ; i < loc_ig_box.size() ; i++)
+ {
+ //! For all the internal ghost boxes of each sub-domain
+ for (size_t j = 0 ; j < loc_ig_box.get(i).bid.size() ; j++)
+ {
+ Box<dim,size_t> bx_src = loc_ig_box.get(i).bid.get(j).box;
+ // convert into local
+ bx_src -= gdb_ext.get(i).origin;
+
+ // sub domain connected with external box
+ size_t sub_id_dst = loc_ig_box.get(i).bid.get(j).sub;
+
+ // local internal ghost box connected
+ size_t k = loc_ig_box.get(i).bid.get(j).k;
+
+ Box<dim,size_t> bx_dst = loc_eg_box.get(sub_id_dst).bid.get(k).box;
+
+ // convert into local
+ bx_dst -= gdb_ext.get(sub_id_dst).origin;
+
+ // create 2 sub grid iterator
+
+ if (bx_dst.isValid() == false)
+ continue;
+
+ grid_key_dx_iterator_sub<dim> sub_src(loc_grid.get(i).getGrid(),bx_src.getKP1(),bx_src.getKP2());
+ grid_key_dx_iterator_sub<dim> sub_dst(loc_grid.get(sub_id_dst).getGrid(),bx_dst.getKP1(),bx_dst.getKP2());
+
+#ifdef SE_CLASS1
+
+ if (loc_eg_box.get(sub_id_dst).bid.get(k).sub != i)
+ std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " source and destination are not correctly linked" << "\n";
+
+ if (sub_src.getVolume() != sub_dst.getVolume())
+ std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " source and destination does not match in size" << "\n";
+
+#endif
+
+ const auto & gs = loc_grid.get(i);
+ auto & gd = loc_grid.get(sub_id_dst);
+
+ while (sub_src.isNext())
+ {
+ // Option 1
+ gd.set(sub_dst.get(),gs,sub_src.get());
+
+ ++sub_src;
+ ++sub_dst;
+ }
+ }
+ }
+ }
+
+ /*! \brief Sync the local ghost part
+ *
+ * \tparam prp... properties to sync
+ *
+ */
+ template<template<typename,typename> class op, int... prp> void ghost_put_local(const openfpm::vector<i_lbox_grid<dim>> & loc_ig_box,
+ const openfpm::vector<e_lbox_grid<dim>> & loc_eg_box,
+ const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext,
+ openfpm::vector<device_grid> & loc_grid,
+ openfpm::vector<std::unordered_map<size_t,size_t>> & g_id_to_external_ghost_box)
+ {
+ //! For all the sub-domains
+ for (size_t i = 0 ; i < loc_eg_box.size() ; i++)
+ {
+ //! For all the external ghost boxes of each sub-domain
+ for (size_t j = 0 ; j < loc_eg_box.get(i).bid.size() ; j++)
+ {
+ if (loc_eg_box.get(i).bid.get(j).initialized == false)
+ continue;
+
+ Box<dim,size_t> bx_src = loc_eg_box.get(i).bid.get(j).box;
+ // convert into local
+ bx_src -= gdb_ext.get(i).origin;
+
+ // sub domain connected with external box
+ size_t sub_id_dst = loc_eg_box.get(i).bid.get(j).sub;
+
+ // local external ghost box connected
+ size_t k = loc_eg_box.get(i).bid.get(j).k;
+
+ Box<dim,size_t> bx_dst = loc_ig_box.get(sub_id_dst).bid.get(k).box;
+
+ // convert into local
+ bx_dst -= gdb_ext.get(sub_id_dst).origin;
+
+ // create 2 sub grid iterator
+
+ if (bx_dst.isValid() == false)
+ continue;
+
+ grid_key_dx_iterator_sub<dim> sub_src(loc_grid.get(i).getGrid(),bx_src.getKP1(),bx_src.getKP2());
+ grid_key_dx_iterator_sub<dim> sub_dst(loc_grid.get(sub_id_dst).getGrid(),bx_dst.getKP1(),bx_dst.getKP2());
+
+#ifdef SE_CLASS1
+
+ if (loc_ig_box.get(sub_id_dst).bid.get(k).sub != i)
+ std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " source and destination are not correctly linked" << "\n";
+
+ if (sub_src.getVolume() != sub_dst.getVolume())
+ std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " source and destination does not match in size" << "\n";
+
+#endif
+
+ const auto & gs = loc_grid.get(i);
+ auto & gd = loc_grid.get(sub_id_dst);
+
+ while (sub_src.isNext())
+ {
+ // write the object in the last element
+ object_s_di_op<op,decltype(gs.get_o(sub_src.get())),decltype(gd.get_o(sub_dst.get())),OBJ_ENCAP,prp...>(gs.get_o(sub_src.get()),gd.get_o(sub_dst.get()));
+
+ ++sub_src;
+ ++sub_dst;
+ }
+ }
+ }
+ }
+
public:
/*! \brief Reconstruct the local grids
@@ -180,12 +409,7 @@ public:
if (intersect == true)
{
- //// DEBUG/////
count2++;
- //////////////
-
- //std::cout << "Inte_box: (" << inte_box.getLow(0) << "; " << inte_box.getLow(1) << "); (" << inte_box.getHigh(0) << "; " << inte_box.getHigh(1) << ")" << std::endl;
-
auto inte_box_cont = cd_sm.convertCellUnitsIntoDomainSpace(inte_box);
// Get processor ID that store intersection box
@@ -193,31 +417,17 @@ public:
for (size_t n = 0; n < dim; n++)
p.get(n) = (inte_box_cont.getHigh(n) + inte_box_cont.getLow(n))/2;
- //std::cout << "Point: (" << p.get(0) << "; " << p.get(1) << ")" << std::endl;
-
p_id = dec.processorID(p);
prc_sz.get(p_id)++;
- //std::cout << "P_id: " << p_id << std::endl;
-
// Transform coordinates to local
auto inte_box_local = inte_box;
inte_box_local -= gdb_ext_old.get(i).origin;
- //std::cout << "gdb_ext_old.get(i): (" << sub_dom.getLow(0) << "; " << sub_dom.getLow(1) << "); (" << sub_dom.getHigh(0) << "; " << sub_dom.getHigh(1) << ")" << std::endl;
-
- //std::cout << "gdb_ext_global.get(j): (" << sub_dom_new.getLow(0) << "; " << sub_dom_new.getLow(1) << "); (" << sub_dom_new.getHigh(0) << "; " << sub_dom_new.getHigh(1) << ")" << std::endl;
-
- //std::cout << "Inte_box_local: (" << inte_box_local.getLow(0) << "; " << inte_box_local.getLow(1) << "); (" << inte_box_local.getHigh(0) << "; " << inte_box_local.getHigh(1) << ")" << std::endl;
-
// Grid corresponding for gdb_ext_old.get(i) box
device_grid & gr = loc_grid_old.get(i);
- //std::cout << "loc_grid_old.get(i): (" << gr.getGrid().getBox().getLow(0) << "; " << gr.getGrid().getBox().getLow(1) << "); (" << gr.getGrid().getBox().getHigh(0) << "; " << gr.getGrid().getBox().getHigh(1) << ")" << std::endl;
-
- //for (size_t l = 0; l < dim; l++)
- //std::cout << "loc_grid_old.get(i).size on " << l << " dimension: " << gr.getGrid().size(l) << std::endl;
// Size of the grid to send
size_t sz[dim];
for (size_t l = 0; l < dim; l++)
@@ -238,32 +448,13 @@ public:
for (size_t n = 0; n < dim; n++)
p1.get(n) = gr_send.getGrid().getBox().getLow(n);
- //std::cout << "Grid send P1: (" << p1.get(0) << "; " << p1.get(1) << ")" << std::endl;
-
Point<dim,St> p2;
for (size_t n = 0; n < dim; n++)
p2.get(n) = gr_send.getGrid().getBox().getHigh(n);
- //std::cout << "Grid send P2: (" << p2.get(0) << "; " << p2.get(1) << ")" << std::endl;
-/*
- Point<dim,St> p3;
- for (size_t n = 0; n < dim; n++)
- p3.get(n) = gr.getGrid().getBox().getLow(n);
-
- std::cout << "Grid local P1: (" << p3.get(0) << "; " << p3.get(1) << ")" << std::endl;
-
- Point<dim,St> p4;
- for (size_t n = 0; n < dim; n++)
- p4.get(n) = gr.getGrid().getBox().getHigh(n);
-
- std::cout << "Grid local P2: (" << p4.get(0) << "; " << p4.get(1) << ")" << std::endl;
-
-*/
std::string start2 = start.to_string();
std::string stop2 = stop.to_string();
- //std::cout << "Start: " << start2 << "; Stop: " << stop2 << std::endl;
-
auto it = gr.getSubIterator(start,stop);
// Copy selected elements into a new sub-grid
@@ -273,22 +464,7 @@ public:
grid_key_dx<dim> key2 = key - start;
std::string str = key.to_string();
- //std::cout << "Key: " << str << std::endl;
gr_send.get_o(key2) = gr.get_o(key);
-/*
- ////////// DEBUG ///////////////
- if (gr.template get<0>(key) == 1)
- {
- count++;
- }
- else if (gr_send.template get<0>(key2) != 1)
- {
- std::cout << "AHHHHHHHHHH????????" << std::endl;
- }
-*/
- ////////////////
-
- //gr_send.set(key,gr,key);
++it;
}
@@ -303,8 +479,6 @@ public:
}
}
}
- //std::cout << "Count for points: " << count << std::endl;
- //std::cout << "Count for inte_boxes: " << count2 << std::endl;
}
/*! \brief Moves all the grids that does not belong to the local processor to the respective processor
@@ -327,27 +501,6 @@ public:
// Contains the processor id of each box (basically where they have to go)
labelIntersectionGridsProcessor(dec,cd_sm,loc_grid_old,gdb_ext,gdb_ext_old,gdb_ext_global,m_oGrid,prc_sz);
-/*
- for (size_t i = 0; i < m_oGrid.size(); i++)
- {
- for (size_t k = 0; k < m_oGrid.get(i).size(); k++)
- {
- device_grid g = m_oGrid.get(i).template get<0>(k);
-
- auto it = g.getIterator();
-
- while (it.isNext())
- {
- auto key = it.get();
-
- if (g.template get<0>(key) != 1)
- std::cout << "WROOOOOOONG" << std::endl;
-
- ++it;
- }
- }
- }
-*/
// Calculate the sending buffer size for each processor, put this information in
// a contiguous buffer
@@ -367,13 +520,6 @@ public:
prc_sz_r.add(m_oGrid.get(i).size());
}
}
-/*
- for (size_t i = 0; i < m_oGrid.size(); i++)
- {
- if(m_oGrid.get(i).size() == 0)
- m_oGrid.remove(i);
- }
-*/
decltype(m_oGrid) m_oGrid_new;
for (size_t i = 0; i < v_cl.getProcessingUnits(); i++)
@@ -385,79 +531,356 @@ public:
// Vector for receiving of intersection grids
openfpm::vector<openfpm::vector<aggregate<device_grid,SpaceBox<dim,long int>>>> m_oGrid_recv;
- //std::cout << "vcl.getProcessUnitID(): " << v_cl.getProcessUnitID() << "; prc_r.size(): " << prc_r.size() << std::endl;
+ // Send and recieve intersection grids
+ v_cl.SSendRecv(m_oGrid_new,m_oGrid_recv,prc_r,prc_recv_map,recv_sz_map);
- //std::cout << "vcl.getProcessUnitID(): " << v_cl.getProcessUnitID() << "; m_oGrid_new.size(): " << m_oGrid_new.size() << std::endl;
-/*
- for (size_t i = 0; i < m_oGrid.size(); i++)
+ // Reconstruct the new local grids
+ grids_reconstruct(m_oGrid_recv,loc_grid,gdb_ext,cd_sm);
+ }
+
+ template<int... prp> void ghost_get_(const openfpm::vector<ip_box_grid<dim>> & ig_box,
+ const openfpm::vector<ep_box_grid<dim>> & eg_box,
+ const openfpm::vector<i_lbox_grid<dim>> & loc_ig_box,
+ const openfpm::vector<e_lbox_grid<dim>> & loc_eg_box,
+ const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext,
+ openfpm::vector<device_grid> & loc_grid,
+ std::unordered_map<size_t,size_t> & g_id_to_external_ghost_box)
+ {
+ // Sending property object
+ typedef object<typename object_creator<typename T::type,prp...>::type> prp_object;
+
+ size_t req = 0;
+
+ // Create a packing request vector
+ for ( size_t i = 0 ; i < ig_box.size() ; i++ )
{
- std::cout << "Processor ID:" << v_cl.getProcessUnitID() << "; I: " << i << ", Size: " << m_oGrid.get(i).size() << std::endl;
+ // for each ghost box
+ for (size_t j = 0 ; j < ig_box.get(i).bid.size() ; j++)
+ {
+ // And linked sub-domain
+ size_t sub_id = ig_box.get(i).bid.get(j).sub;
+ // Internal ghost box
+ Box<dim,long int> g_ig_box = ig_box.get(i).bid.get(j).box;
+
+ if (g_ig_box.isValid() == false)
+ continue;
+
+ g_ig_box -= gdb_ext.get(sub_id).origin.template convertPoint<size_t>();
+
+ // Pack a size_t for the internal ghost id
+ Packer<size_t,HeapMemory>::packRequest(req);
+ // Create a sub grid iterator spanning the internal ghost layer
+ grid_key_dx_iterator_sub<dim> sub_it(loc_grid.get(sub_id).getGrid(),g_ig_box.getKP1(),g_ig_box.getKP2());
+ // and pack the internal ghost grid
+ Packer<device_grid,HeapMemory>::template packRequest<prp...>(loc_grid.get(sub_id),sub_it,req);
+ }
}
-*/
-/*
- for (size_t i = 0; i < m_oGrid_new.size(); i++)
+
+ // resize the property buffer memory
+ g_send_prp_mem.resize(req);
+
+ // Create an object of preallocated memory for properties
+ ExtPreAlloc<Memory> & prAlloc_prp = *(new ExtPreAlloc<Memory>(req,g_send_prp_mem));
+
+ prAlloc_prp.incRef();
+
+ // Pack information
+ Pack_stat sts;
+
+ // Pack the information for each processor and send it
+ for ( size_t i = 0 ; i < ig_box.size() ; i++ )
{
- for (size_t k = 0; k < m_oGrid_new.get(i).size(); k++)
+
+ sts.mark();
+ void * pointer = prAlloc_prp.getPointerEnd();
+
+ // for each ghost box
+ for (size_t j = 0 ; j < ig_box.get(i).bid.size() ; j++)
{
- device_grid g = m_oGrid_new.get(i).template get<0>(k);
+ // we pack only if it is valid
+ if (ig_box.get(i).bid.get(j).box.isValid() == false)
+ continue;
+
+ // And linked sub-domain
+ size_t sub_id = ig_box.get(i).bid.get(j).sub;
+ // Internal ghost box
+ Box<dim,size_t> g_ig_box = ig_box.get(i).bid.get(j).box;
+ g_ig_box -= gdb_ext.get(sub_id).origin.template convertPoint<size_t>();
+ // Ghost box global id
+ size_t g_id = ig_box.get(i).bid.get(j).g_id;
+
+ // Pack a size_t for the internal ghost id
+ Packer<size_t,HeapMemory>::pack(prAlloc_prp,g_id,sts);
+ // Create a sub grid iterator spanning the internal ghost layer
+ grid_key_dx_iterator_sub<dim> sub_it(loc_grid.get(sub_id).getGrid(),g_ig_box.getKP1(),g_ig_box.getKP2());
+ // and pack the internal ghost grid
+ Packer<device_grid,HeapMemory>::template pack<prp...>(prAlloc_prp,loc_grid.get(sub_id),sub_it,sts);
+ }
+ // send the request
- auto it = g.getIterator();
+ void * pointer2 = prAlloc_prp.getPointerEnd();
- while (it.isNext())
- {
- auto key = it.get();
+ v_cl.send(ig_box.get(i).prc,0,pointer,(char *)pointer2 - (char *)pointer);
+ }
- if (g.template get<0>(key) != 1)
- std::cout << "WRONG BEFORE SENDRCV" << std::endl;
+ // Calculate the total information to receive from each processors
+ std::vector<size_t> prp_recv;
- ++it;
- }
+ //! Receive the information from each processors
+ for ( size_t i = 0 ; i < eg_box.size() ; i++ )
+ {
+ prp_recv.push_back(0);
+
+ // for each external ghost box
+ for (size_t j = 0 ; j < eg_box.get(i).bid.size() ; j++)
+ {
+ // External ghost box
+ Box<dim,size_t> g_eg_box = eg_box.get(i).bid.get(j).g_e_box;
+ prp_recv[prp_recv.size()-1] += g_eg_box.getVolumeKey() * sizeof(prp_object) + sizeof(size_t);
}
}
-*/
- // Send and recieve intersection grids
- v_cl.SSendRecv(m_oGrid_new,m_oGrid_recv,prc_r,prc_recv_map,recv_sz_map);
-/*
- for (size_t i = 0; i < m_oGrid_recv.size(); i++)
+ size_t tot_recv = ExtPreAlloc<Memory>::calculateMem(prp_recv);
+
+ //! Resize the receiving buffer
+ g_recv_prp_mem.resize(tot_recv);
+
+ // Create an object of preallocated memory for properties
+ ExtPreAlloc<Memory> & prRecv_prp = *(new ExtPreAlloc<Memory>(tot_recv,g_recv_prp_mem));
+ prRecv_prp.incRef();
+
+ // queue the receives
+ for ( size_t i = 0 ; i < eg_box.size() ; i++ )
+ {
+ prRecv_prp.allocate(prp_recv[i]);
+ v_cl.recv(eg_box.get(i).prc,0,prRecv_prp.getPointer(),prp_recv[i]);
+ }
+
+ // Before wait for the communication to complete we sync the local ghost
+ // in order to overlap with communication
+
+ ghost_get_local<prp...>(loc_ig_box,loc_eg_box,gdb_ext,loc_grid,g_id_to_external_ghost_box);
+
+ // wait to receive communication
+ v_cl.execute();
+
+ Unpack_stat ps;
+
+ // Unpack the object
+ for ( size_t i = 0 ; i < eg_box.size() ; i++ )
{
- for (size_t k = 0; k < m_oGrid_recv.get(i).size(); k++)
+ // for each external ghost box
+ for (size_t j = 0 ; j < eg_box.get(i).bid.size() ; j++)
{
- device_grid g = m_oGrid_recv.get(i).template get<0>(k);
+ // Unpack the ghost box global-id
- auto it = g.getIterator();
+ size_t g_id;
+ Unpacker<size_t,HeapMemory>::unpack(prRecv_prp,g_id,ps);
- while (it.isNext())
+ size_t l_id = 0;
+ // convert the global id into local id
+ auto key = g_id_to_external_ghost_box.find(g_id);
+ if (key != g_id_to_external_ghost_box.end()) // FOUND
+ l_id = key->second;
+ else
{
- auto key = it.get();
+ // NOT FOUND
- if (g.template get<0>(key) != 1)
- std::cout << "WRONG AFTER SENDRCV" << std::endl;
+ // It must be always found, if not it mean that the processor has no-idea of
+ // what is stored and conseguently do not know how to unpack, print a critical error
+ // and return
- ++it;
+ std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " Critical, cannot unpack object, because received data cannot be interpreted\n";
+
+ return;
}
+
+ // Get the external ghost box associated with the packed information
+ Box<dim,size_t> box = eg_box.get(i).bid.get(l_id).l_e_box;
+ size_t sub_id = eg_box.get(i).bid.get(l_id).sub;
+
+ // sub-grid where to unpack
+ grid_key_dx_iterator_sub<dim> sub2(loc_grid.get(sub_id).getGrid(),box.getKP1(),box.getKP2());
+
+ // Unpack
+ Unpacker<device_grid,HeapMemory>::template unpack<prp...>(prRecv_prp,sub2,loc_grid.get(sub_id),ps);
}
}
-*/
-/*
- std::cout << "vcl.getProcessUnitID(): " << v_cl.getProcessUnitID() << "; m_oGrid_recv.size(): " << m_oGrid_recv.size() << std::endl;
+ }
+
+
+ template<template<typename,typename> class op,int... prp>
+ void ghost_put_(const openfpm::vector<ip_box_grid<dim>> & ig_box,
+ const openfpm::vector<ep_box_grid<dim>> & eg_box,
+ const openfpm::vector<i_lbox_grid<dim>> & loc_ig_box,
+ const openfpm::vector<e_lbox_grid<dim>> & loc_eg_box,
+ const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext,
+ openfpm::vector<device_grid> & loc_grid,
+ openfpm::vector<std::unordered_map<size_t,size_t>> & g_id_to_internal_ghost_box)
+ {
+ // Sending property object
+ typedef object<typename object_creator<typename T::type,prp...>::type> prp_object;
- for (size_t i = 0; i < m_oGrid_recv.size(); i++)
+ size_t req = 0;
+
+ // Create a packing request vector
+ for ( size_t i = 0 ; i < eg_box.size() ; i++ )
{
- std::cout << "Processor ID:" << v_cl.getProcessUnitID() << "; I_recv: " << i << ", Size: " << m_oGrid_recv.get(i).size() << std::endl;
+ // for each ghost box
+ for (size_t j = 0 ; j < eg_box.get(i).bid.size() ; j++)
+ {
+ // And linked sub-domain
+ size_t sub_id = eg_box.get(i).bid.get(j).sub;
+ // Internal ghost box
+ Box<dim,long int> g_eg_box = eg_box.get(i).bid.get(j).g_e_box;
+
+ if (g_eg_box.isValid() == false)
+ continue;
+
+ g_eg_box -= gdb_ext.get(sub_id).origin.template convertPoint<size_t>();
+
+ // Pack a size_t for the internal ghost id
+ Packer<size_t,HeapMemory>::packRequest(req);
+ // Create a sub grid iterator spanning the internal ghost layer
+ grid_key_dx_iterator_sub<dim> sub_it(loc_grid.get(sub_id).getGrid(),g_eg_box.getKP1(),g_eg_box.getKP2());
+ // and pack the internal ghost grid
+ Packer<device_grid,HeapMemory>::template packRequest<prp...>(loc_grid.get(sub_id),sub_it,req);
+ }
}
- for (size_t i = 0; i < prc_r.size(); i++)
- std::cout << "vcl.getProcessUnitID(): " << v_cl.getProcessUnitID() << "; prc_r: " << prc_r.get(i) << std::endl;
+ // resize the property buffer memory
+ g_send_prp_mem.resize(req);
- for (size_t i = 0; i < prc_recv_map.size(); i++)
- std::cout << "vcl.getProcessUnitID(): " << v_cl.getProcessUnitID() << "; prc_recv_map: " << prc_recv_map.get(i) << std::endl;
+ // Create an object of preallocated memory for properties
+ ExtPreAlloc<Memory> & prAlloc_prp = *(new ExtPreAlloc<Memory>(req,g_send_prp_mem));
- for (size_t i = 0; i < recv_sz_map.size(); i++)
- std::cout << "vcl.getProcessUnitID(): " << v_cl.getProcessUnitID() << "; recv_sz_map: " << recv_sz_map.get(i) << std::endl;
-*/
- // Reconstruct the new local grids
- grids_reconstruct(m_oGrid_recv,loc_grid,gdb_ext,cd_sm);
+ prAlloc_prp.incRef();
+
+ // Pack information
+ Pack_stat sts;
+
+ // Pack the information for each processor and send it
+ for ( size_t i = 0 ; i < eg_box.size() ; i++ )
+ {
+
+ sts.mark();
+ void * pointer = prAlloc_prp.getPointerEnd();
+
+ // for each ghost box
+ for (size_t j = 0 ; j < eg_box.get(i).bid.size() ; j++)
+ {
+ // we pack only if it is valid
+ if (eg_box.get(i).bid.get(j).g_e_box.isValid() == false)
+ continue;
+
+ // And linked sub-domain
+ size_t sub_id = eg_box.get(i).bid.get(j).sub;
+ // Internal ghost box
+ Box<dim,size_t> g_eg_box = eg_box.get(i).bid.get(j).g_e_box;
+ g_eg_box -= gdb_ext.get(sub_id).origin.template convertPoint<size_t>();
+ // Ghost box global id
+ size_t g_id = eg_box.get(i).bid.get(j).g_id;
+
+ // Pack a size_t for the internal ghost id
+ Packer<size_t,HeapMemory>::pack(prAlloc_prp,g_id,sts);
+ // Create a sub grid iterator spanning the internal ghost layer
+ grid_key_dx_iterator_sub<dim> sub_it(loc_grid.get(sub_id).getGrid(),g_eg_box.getKP1(),g_eg_box.getKP2());
+ // and pack the internal ghost grid
+ Packer<device_grid,HeapMemory>::template pack<prp...>(prAlloc_prp,loc_grid.get(sub_id),sub_it,sts);
+ }
+ // send the request
+
+ void * pointer2 = prAlloc_prp.getPointerEnd();
+
+ v_cl.send(ig_box.get(i).prc,0,pointer,(char *)pointer2 - (char *)pointer);
+ }
+
+ // Calculate the total information to receive from each processors
+ std::vector<size_t> prp_recv;
+
+ //! Receive the information from each processors
+ for ( size_t i = 0 ; i < ig_box.size() ; i++ )
+ {
+ prp_recv.push_back(0);
+
+ // for each external ghost box
+ for (size_t j = 0 ; j < ig_box.get(i).bid.size() ; j++)
+ {
+ // External ghost box
+ Box<dim,size_t> g_ig_box = ig_box.get(i).bid.get(j).box;
+ prp_recv[prp_recv.size()-1] += g_ig_box.getVolumeKey() * sizeof(prp_object) + sizeof(size_t);
+ }
+ }
+
+ size_t tot_recv = ExtPreAlloc<Memory>::calculateMem(prp_recv);
+
+ //! Resize the receiving buffer
+ g_recv_prp_mem.resize(tot_recv);
+
+ // Create an object of preallocated memory for properties
+ ExtPreAlloc<Memory> & prRecv_prp = *(new ExtPreAlloc<Memory>(tot_recv,g_recv_prp_mem));
+ prRecv_prp.incRef();
+
+ // queue the receives
+ for ( size_t i = 0 ; i < ig_box.size() ; i++ )
+ {
+ prRecv_prp.allocate(prp_recv[i]);
+ v_cl.recv(ig_box.get(i).prc,0,prRecv_prp.getPointer(),prp_recv[i]);
+ }
+
+ // Before wait for the communication to complete we sync the local ghost
+ // in order to overlap with communication
+
+ ghost_put_local<op,prp...>(loc_ig_box,loc_eg_box,gdb_ext,loc_grid,g_id_to_internal_ghost_box);
+
+ // wait to receive communication
+ v_cl.execute();
+
+ Unpack_stat ps;
+
+ // Unpack the object
+ for ( size_t i = 0 ; i < ig_box.size() ; i++ )
+ {
+ // for each external ghost box
+ for (size_t j = 0 ; j < ig_box.get(i).bid.size() ; j++)
+ {
+ // Unpack the ghost box global-id
+
+ size_t g_id;
+ Unpacker<size_t,HeapMemory>::unpack(prRecv_prp,g_id,ps);
+
+ size_t l_id = 0;
+ // convert the global id into local id
+ auto key = g_id_to_internal_ghost_box.get(i).find(g_id);
+ if (key != g_id_to_internal_ghost_box.get(i).end()) // FOUND
+ l_id = key->second;
+ else
+ {
+ // NOT FOUND
+
+ // It must be always found, if not it mean that the processor has no-idea of
+ // what is stored and conseguently do not know how to unpack, print a critical error
+ // and return
+
+ std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " Critical, cannot unpack object, because received data cannot be interpreted\n";
+
+ return;
+ }
+
+ // Get the internal ghost box associated with the packed information
+ Box<dim,size_t> box = ig_box.get(i).bid.get(l_id).box;
+ size_t sub_id = ig_box.get(i).bid.get(l_id).sub;
+ box -= gdb_ext.get(sub_id).origin.template convertPoint<size_t>();
+
+ // sub-grid where to unpack
+ grid_key_dx_iterator_sub<dim> sub2(loc_grid.get(sub_id).getGrid(),box.getKP1(),box.getKP2());
+
+ grid_unpack_with_prp<op,prp_object,device_grid,Memory>::template unpacking<prp...>(prRecv_prp,sub2,loc_grid.get(sub_id),ps);
+
+ // Unpack
+// Unpacker<device_grid,HeapMemory>::template unpack<prp...>(prRecv_prp,sub2,loc_grid.get(sub_id),ps);
+ }
+ }
}
/*! \brief Constructor
diff --git a/src/Grid/grid_dist_id_unit_test.cpp b/src/Grid/grid_dist_id_unit_test.cpp
index 3911c9aa..568bbbbc 100644
--- a/src/Grid/grid_dist_id_unit_test.cpp
+++ b/src/Grid/grid_dist_id_unit_test.cpp
@@ -1359,6 +1359,126 @@ void Test3D_periodic(const Box<3,float> & domain, long int k)
}
}
+// Test grid periodic
+
+void Test3D_periodic_put(const Box<3,float> & domain, long int k)
+{
+ Vcluster & v_cl = create_vcluster();
+
+ if ( v_cl.getProcessingUnits() > 32 )
+ return;
+
+ long int big_step = k / 30;
+ big_step = (big_step == 0)?1:big_step;
+ long int small_step = 21;
+
+ print_test( "Testing grid periodic put k<=",k);
+
+ // 3D test
+ for ( ; k >= 2 ; k-= (k > 2*big_step)?big_step:small_step )
+ {
+ BOOST_TEST_CHECKPOINT( "Testing grid periodick<=" << k );
+
+ // grid size
+ size_t sz[3];
+ sz[0] = k;
+ sz[1] = k;
+ sz[2] = k;
+
+ // Ghost
+ Ghost<3,long int> g(1);
+
+ // periodicity
+ periodicity<3> pr = {{PERIODIC,PERIODIC,PERIODIC}};
+
+ // Distributed grid with id decomposition
+ grid_dist_id<3, float, aggregate<long int>, CartDecomposition<3,float>> g_dist(sz,domain,g,pr);
+
+ // check the consistency of the decomposition
+ bool val = g_dist.getDecomposition().check_consistency();
+ BOOST_REQUIRE_EQUAL(val,true);
+
+ // Grid sm
+ grid_sm<3,void> info(sz);
+
+ size_t count = 0;
+
+ {
+ auto dom = g_dist.getDomainIterator();
+
+ while (dom.isNext())
+ {
+ auto key = dom.get();
+
+ g_dist.template get<0>(key) = -6.0;
+
+ // Count the points
+ count++;
+
+ ++dom;
+ }
+ }
+
+ // Set to zero the full grid
+
+ {
+ auto dom = g_dist.getDomainIterator();
+
+ while (dom.isNext())
+ {
+ auto key = dom.get();
+
+ g_dist.template get<0>(key.move(0,1)) += 1.0;
+ g_dist.template get<0>(key.move(0,-1)) += 1.0;
+ g_dist.template get<0>(key.move(1,1)) += 1.0;
+ g_dist.template get<0>(key.move(1,-1)) += 1.0;
+ g_dist.template get<0>(key.move(2,1)) += 1.0;
+ g_dist.template get<0>(key.move(2,-1)) += 1.0;
+
+ ++dom;
+ }
+ }
+
+ bool correct = true;
+
+ // Domain + Ghost iterator
+ auto dom_gi = g_dist.getDomainIterator();
+
+ while (dom_gi.isNext())
+ {
+ auto key = dom_gi.get();
+
+ correct &= (g_dist.template get<0>(key) == 0);
+
+ ++dom_gi;
+ }
+
+ g_dist.ghost_put<add_,0>();
+
+ if (count != 0)
+ BOOST_REQUIRE_EQUAL(correct, false);
+
+ // sync the ghosts
+ g_dist.ghost_get<0>();
+
+ correct = true;
+
+ // Domain + Ghost iterator
+ auto dom_gi2 = g_dist.getDomainIterator();
+
+ while (dom_gi2.isNext())
+ {
+ auto key = dom_gi2.get();
+
+ correct &= (g_dist.template get<0>(key) == 0);
+
+ ++dom_gi2;
+ }
+
+ BOOST_REQUIRE_EQUAL(correct, true);
+ }
+}
+
void Test_grid_copy(const Box<3,float> & domain, long int k)
{
typedef Point_test<float> p;
@@ -1620,6 +1740,17 @@ BOOST_AUTO_TEST_CASE( grid_1d_test )
Test1D(domain1,k);
}
+BOOST_AUTO_TEST_CASE( grid_dist_id_periodic_put_test )
+{
+ // Domain
+ Box<3,float> domain3({0.0,0.0,0.0},{1.0,1.0,1.0});
+
+ long int k = 128*128*128*create_vcluster().getProcessingUnits();
+ k = std::pow(k, 1/3.);
+
+ Test3D_periodic_put(domain3,k);
+}
+
BOOST_AUTO_TEST_SUITE_END()
#endif
diff --git a/src/Grid/grid_dist_key.hpp b/src/Grid/grid_dist_key.hpp
index f3de7509..b6d1a4b3 100644
--- a/src/Grid/grid_dist_key.hpp
+++ b/src/Grid/grid_dist_key.hpp
@@ -20,6 +20,16 @@ class grid_dist_key_dx
public:
+ /*! \brief Set the local grid
+ *
+ * \param sub local grid
+ *
+ */
+ inline void setSub(size_t sub)
+ {
+ g_c = sub;
+ }
+
/*! \brief Get the local grid
*
* \return the id of the local grid
@@ -99,11 +109,20 @@ public:
return grid_dist_key_dx<dim>(getSub(),key);
}
+ /*! \brief Constructor set the sub-domain grid and the position in local coordinates
+ *
+ * \param g_c sub-domain
+ * \param key key
+ *
+ */
inline grid_dist_key_dx(int g_c, const grid_key_dx<dim> & key)
:g_c(g_c),key(key)
{
}
+ //! Constructor
+ inline grid_dist_key_dx(){}
+
std::string to_string()
{
std::stringstream str;
diff --git a/src/Grid/grid_dist_util.hpp b/src/Grid/grid_dist_util.hpp
index d16bf8bb..77e2383c 100644
--- a/src/Grid/grid_dist_util.hpp
+++ b/src/Grid/grid_dist_util.hpp
@@ -200,11 +200,17 @@ template <unsigned int dim> struct e_lbox_id
//! Box defining the external ghost box in local coordinates
::Box<dim,long int> box;
- //! Sector position of the local external ghost box
- comb<dim> cmb;
+ //! Has this external ghost box initialized
+ bool initialized = false;
//! sub_id in which sub-domain this box live
size_t sub;
+
+ //! external ghost box linked to this internal ghost box
+ size_t k;
+
+ //! Sector position of the local external ghost box
+ comb<dim> cmb;
};
/*! \brief Per-processor Internal ghost box
diff --git a/src/Makefile.am b/src/Makefile.am
index cc194ca4..c4083ddd 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -9,7 +9,7 @@ pdata_LDADD = $(LINKLIBS) -lparmetis -lmetis
nobase_include_HEADERS = Decomposition/CartDecomposition.hpp Decomposition/CartDecomposition_ext.hpp Decomposition/common.hpp Decomposition/Decomposition.hpp Decomposition/ie_ghost.hpp \
Decomposition/Domain_NN_calculator_cart.hpp Decomposition/nn_processor.hpp Decomposition/ie_loc_ghost.hpp Decomposition/ORB.hpp \
Graph/CartesianGraphFactory.hpp \
- Grid/grid_dist_id.hpp Grid/Iterators/grid_dist_id_iterator_util.hpp Grid/Iterators/grid_dist_id_iterator_dec.hpp Grid/Iterators/grid_dist_id_iterator_dec_skin.hpp Grid/grid_dist_util.hpp Grid/Iterators/grid_dist_id_iterator_sub.hpp Grid/Iterators/grid_dist_id_iterator.hpp Grid/grid_dist_key.hpp Grid/staggered_dist_grid.hpp Grid/staggered_dist_grid_util.hpp Grid/staggered_dist_grid_copy.hpp \
+ Grid/grid_dist_id.hpp Grid/grid_dist_id_comm.hpp Grid/Iterators/grid_dist_id_iterator_util.hpp Grid/Iterators/grid_dist_id_iterator_dec.hpp Grid/Iterators/grid_dist_id_iterator_dec_skin.hpp Grid/grid_dist_util.hpp Grid/Iterators/grid_dist_id_iterator_sub.hpp Grid/Iterators/grid_dist_id_iterator.hpp Grid/grid_dist_key.hpp Grid/staggered_dist_grid.hpp Grid/staggered_dist_grid_util.hpp Grid/staggered_dist_grid_copy.hpp \
Vector/se_class3_vector.hpp Vector/vector_dist_multiphase_functions.hpp Vector/vector_dist_comm.hpp Vector/vector_dist.hpp Vector/vector_dist_ofb.hpp Vector/Iterators/vector_dist_iterator.hpp Vector/vector_dist_key.hpp \
config/config.h \
example.mk \
diff --git a/src/Vector/se_class3_vector.hpp b/src/Vector/se_class3_vector.hpp
index 4099774d..11611166 100644
--- a/src/Vector/se_class3_vector.hpp
+++ b/src/Vector/se_class3_vector.hpp
@@ -222,7 +222,7 @@ struct propCheckINF
{
typedef typename boost::mpl::at<typename vector::value_type::type,boost::mpl::int_<T::value> >::type type_to_check;
- bool snn = typeCheck<type_to_check,std::is_fundamental<type_to_check>::value>::isInf(data.template getProp<T::value>(id));
+ bool snn = typeCheck<type_to_check,std::is_fundamental<type_to_check>::value>::isInf(data.template getPropNC<T::value>(id));
if (snn == true)
{
@@ -383,15 +383,18 @@ class se_class3_vector
auto p = it.get();
for (size_t i = 0 ; i < Np_real ; i++)
- vd.template getProp<Np+SE3_STATUS>(p)[i] = UNINITIALIZED;
+ vd.template getPropNC<Np+SE3_STATUS>(p)[i] = UNINITIALIZED;
- vd.template getProp<Np+SE3_TYPE>(p) = INSIDE;
+ vd.template getPropNC<Np+SE3_TYPE>(p) = INSIDE;
++it;
}
for (size_t i = 0 ; i < Np_real ; i++)
+ {
sync[GHOST][i] = NOTSYNC;
+ sync[HALO][i] = SYNC;
+ }
}
template <unsigned int ... prp> void ghost_get_pre(size_t opt)
@@ -411,7 +414,7 @@ class se_class3_vector
for (size_t i = 0 ; i < sizeof...(prp) ; i++)
{
- if (vd.template getProp<Np+SE3_STATUS>(p)[gg[i]] == DIRTY)
+ if (vd.template getPropNC<Np+SE3_STATUS>(p)[gg[i]] == DIRTY)
{
std::cerr << __FILE__ << ":" << __LINE__ << " Error the ghost has been written and ghost_get will overwrite your changes" << std::endl;
ACTION_ON_ERROR(VECTOR_DIST_ERROR_OBJECT);
@@ -422,7 +425,7 @@ class se_class3_vector
{
for (size_t i = 0 ; i < non_NP.size() ; i++)
{
- if (vd.template getProp<Np+SE3_STATUS>(p)[non_NP.get(i)] == DIRTY)
+ if (vd.template getPropNC<Np+SE3_STATUS>(p)[non_NP.get(i)] == DIRTY)
{
std::cerr << __FILE__ << ":" << __LINE__ << " Error the it seem that the property=" << getPrpName(non_NP.get(i)) << " has been written and ghost_get will destroy such changes" << std::endl;
ACTION_ON_ERROR(VECTOR_DIST_ERROR_OBJECT);
@@ -448,11 +451,11 @@ class se_class3_vector
for (size_t i = 0 ; i < sizeof...(prp) ; i++)
{
- if (vd.template getProp<Np+SE3_STATUS>(p)[gg[i]] == DIRTY)
- vd.template getProp<Np+SE3_STATUS>(p)[gg[i]] = CLEAN;
+ if (vd.template getPropNC<Np+SE3_STATUS>(p)[gg[i]] == DIRTY)
+ vd.template getPropNC<Np+SE3_STATUS>(p)[gg[i]] = CLEAN;
}
- vd.template getProp<Np+SE3_TYPE>(p) = GHOST;
+ vd.template getPropNC<Np+SE3_TYPE>(p) = GHOST;
++it2;
}
@@ -469,7 +472,7 @@ class se_class3_vector
auto p = it.get();
for (size_t i = 0 ; i < non_NP.size() ; i++)
- vd.template getProp<Np+SE3_STATUS>(p)[non_NP.get(i)] = UNINITIALIZED;
+ vd.template getPropNC<Np+SE3_STATUS>(p)[non_NP.get(i)] = UNINITIALIZED;
++it;
}
@@ -548,15 +551,15 @@ class se_class3_vector
for (size_t j = 0 ; j < Np ; j++)
{
- if (vd.template getProp<Np+SE3_STATUS>(p)[j] == DIRTY)
- vd.template getProp<Np+SE3_STATUS>(p)[j] = CLEAN;
+ if (vd.template getPropNC<Np+SE3_STATUS>(p)[j] == DIRTY)
+ vd.template getPropNC<Np+SE3_STATUS>(p)[j] = CLEAN;
}
#ifdef CHECK_FOR_POSINF
- if ( std::isinf(vd.getPos(p)[0]) || std::isinf(vd.getPos(p)[1]) || std::isinf(vd.getPos(p)[2]) )
+ if ( std::isinf(vd.getPosNC(p)[0]) || std::isinf(vd.getPosNC(p)[1]) || std::isinf(vd.getPosNC(p)[2]) )
{
- std::cerr << __FILE__ << ":" << __LINE__ << " error detected INF in position for particle p=" << p.getKey() << " of type=" << getParticleTypeString(vd.template getProp<Np+SE3_TYPE>(p)) << std::endl;
+ std::cerr << __FILE__ << ":" << __LINE__ << " error detected INF in position for particle p=" << p.getKey() << " of type=" << getParticleTypeString(vd.template getPropNC<Np+SE3_TYPE>(p)) << std::endl;
ACTION_ON_ERROR(VECTOR_DIST_ERROR_OBJECT);
}
@@ -564,9 +567,9 @@ class se_class3_vector
#ifdef CHECKFOR_POSNAN
- if ( std::isnan(vd.getPos(p)[0]) || std::isnan(vd.getPos(p)[1]) || std::isnan(vd.getPos(p)[2]) )
+ if ( std::isnan(vd.getPosNC(p)[0]) || std::isnan(vd.getPosNC(p)[1]) || std::isnan(vd.getPosNC(p)[2]) )
{
- std::cerr << __FILE__ << ":" << __LINE__ << " error detected NAN in position for particle p=" << p.getKey() << " of type=" << getParticleTypeString(vd.template getProp<Np+SE3_TYPE>(p)) << std::endl;
+ std::cerr << __FILE__ << ":" << __LINE__ << " error detected NAN in position for particle p=" << p.getKey() << " of type=" << getParticleTypeString(vd.template getPropNC<Np+SE3_TYPE>(p)) << std::endl;
ACTION_ON_ERROR(VECTOR_DIST_ERROR_OBJECT);
}
@@ -606,7 +609,7 @@ class se_class3_vector
for (size_t j = 0 ; j < Np ; j++)
{
- if (vd.template getProp<Np+SE3_STATUS>(p)[j] == DIRTY)
+ if (vd.template getPropNC<Np+SE3_STATUS>(p)[j] == DIRTY)
{
std::cerr << __FILE__ << ":" << __LINE__ << " error it seem that ghost has been filled with information that we are going to destroy with the map call " << std::endl;
}
@@ -632,9 +635,9 @@ class se_class3_vector
for (size_t j = 0 ; j < Np ; j++)
{
- Point<vector::dims,typename vector::stype> xp = vd.getPos(p);
+ Point<vector::dims,typename vector::stype> xp = vd.getPosNC(p);
- vd.template getProp<Np+SE3_TYPE>(p) = getParticleType(xp,p.getKey(),vd);
+ vd.template getPropNC<Np+SE3_TYPE>(p) = getParticleType(xp,p.getKey(),vd);
}
++it;
@@ -643,10 +646,10 @@ class se_class3_vector
template<unsigned int prp> void read(const vector & vd, size_t p) const
{
- if (vd.template getProp<Np+SE3_STATUS>(p)[prp] == UNINITIALIZED)
+ if (vd.template getPropNC<Np+SE3_STATUS>(p)[prp] == UNINITIALIZED)
{
std::stringstream str;
- std::string type_str = getParticleTypeString(vd.template getProp<Np+SE3_TYPE>(p));
+ std::string type_str = getParticleTypeString(vd.template getPropNC<Np+SE3_TYPE>(p));
if (prp == Np_real)
str << __FILE__ << ":" << __LINE__ << " Error you are reading the particle " << p << " of type " << type_str << " the position. But it result to be uninitialized" << std::endl;
@@ -658,18 +661,18 @@ class se_class3_vector
ACTION_ON_ERROR(VECTOR_DIST_ERROR_OBJECT);
}
- if (vd.template getProp<Np+SE3_STATUS>(p)[prp] == DIRTY)
+ if (vd.template getPropNC<Np+SE3_STATUS>(p)[prp] == DIRTY)
{
std::cerr << __FILE__ << ":" << __LINE__ << " Warning you are reading from an particle that has been changed already in the same cycle" << std::endl;
ACTION_ON_ERROR(VECTOR_DIST_ERROR_OBJECT);
}
- if (vd.template getProp<Np+SE3_TYPE>(p) == GHOST || vd.template getProp<Np+SE3_TYPE>(p) == HALO)
+ if (vd.template getPropNC<Np+SE3_TYPE>(p) == GHOST || vd.template getPropNC<Np+SE3_TYPE>(p) == HALO)
{
// if we read from the ghost we have to ensure that the ghost is in
// sync in particular that the state of the halo is CLEAR
- if (sync[vd.template getProp<Np+SE3_TYPE>(p)][prp] != SYNC)
+ if (sync[vd.template getPropNC<Np+SE3_TYPE>(p)][prp] != SYNC)
{
std::cerr << __FILE__ << ":" << __LINE__ << " Error it seem that you are reading from a ghost the property=" << getPrpName(prp) << " but it seem it is changed from the last ghost_get. It seems that is missing a ghost_get" << std::endl;
ACTION_ON_ERROR(VECTOR_DIST_ERROR_OBJECT);
@@ -679,12 +682,12 @@ class se_class3_vector
template<unsigned int prp> void write(vector & vd, size_t p)
{
- vd.template getProp<Np+SE3_STATUS>(p)[prp] = DIRTY;
+ vd.template getPropNC<Np+SE3_STATUS>(p)[prp] = DIRTY;
if (p >= vd.size_local())
vd.get_se_class3().template setHaloOutSync<prp>();
else
{
- if (vd.template getProp<Np+SE3_TYPE>(p) == HALO)
+ if (vd.template getPropNC<Np+SE3_TYPE>(p) == HALO)
vd.get_se_class3().template setGhostOutSync<prp>();
}
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 781e12bd..5cbc554d 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -8,8 +8,6 @@
#ifndef VECTOR_HPP_
#define VECTOR_HPP_
-#include "../../openfpm_data/src/NN/CellList/CellListFast_gen.hpp"
-#include "../../openfpm_data/src/NN/CellList/CellListFast_gen.hpp"
#include "HDF5_wr/HDF5_wr.hpp"
#include "VCluster/VCluster.hpp"
#include "Space/Shape/Point.hpp"
@@ -18,6 +16,7 @@
#include "Vector/vector_dist_key.hpp"
#include "memory/PtrMemory.hpp"
#include "NN/CellList/CellList.hpp"
+#include "NN/CellList/CellListFast_gen.hpp"
#include "util/common.hpp"
#include "util/object_util.hpp"
#include "memory/ExtPreAlloc.hpp"
@@ -77,7 +76,7 @@ struct gcl
*/
static inline CellL get(Vector & vd, const St & r_cut, const Ghost<dim,St> & g)
{
- return vd.getCellList(r_cut);
+ return vd.template getCellList<CellL>(r_cut);
}
};
@@ -100,6 +99,10 @@ struct gcl<dim,St,CellList_gen<dim, St, Process_keys_hilb,Mem_type, shift<dim, S
}
};
+#define CELL_MEMFAST(dim,St) CellList_gen<dim, St, Process_keys_lin, Mem_fast<dim,St>, shift<dim, St> >
+#define CELL_MEMBAL(dim,St) CellList_gen<dim, St, Process_keys_lin, Mem_bal<dim,St>, shift<dim, St> >
+#define CELL_MEMMW(dim,St) CellList_gen<dim, St, Process_keys_lin, Mem_mw<dim,St>, shift<dim, St> >
+
/*! \brief Distributed vector
*
* This class reppresent a distributed vector, the distribution of the structure
@@ -519,6 +522,124 @@ public:
#endif
+///////////////////// Read and write with no check
+
+ /*! \brief Get the position of an element
+ *
+ * see the vector_dist iterator usage to get an element key
+ *
+ * \param vec_key element
+ *
+ * \return the position of the element in space
+ *
+ */
+ inline auto getPosNC(vect_dist_key_dx vec_key) -> decltype(v_pos.template get<0>(vec_key.getKey()))
+ {
+ return v_pos.template get<0>(vec_key.getKey());
+ }
+
+ /*! \brief Get the position of an element
+ *
+ * see the vector_dist iterator usage to get an element key
+ *
+ * \param vec_key element
+ *
+ * \return the position of the element in space
+ *
+ */
+ inline auto getPosNC(vect_dist_key_dx vec_key) const -> decltype(v_pos.template get<0>(vec_key.getKey()))
+ {
+ return v_pos.template get<0>(vec_key.getKey());
+ }
+
+ /*! \brief Get the position of an element
+ *
+ * see the vector_dist iterator usage to get an element key
+ *
+ * \param vec_key element
+ *
+ * \return the position of the element in space
+ *
+ */
+ inline auto getPosNC(size_t vec_key) -> decltype(v_pos.template get<0>(vec_key))
+ {
+ return v_pos.template get<0>(vec_key);
+ }
+
+ /*! \brief Get the position of an element
+ *
+ * see the vector_dist iterator usage to get an element key
+ *
+ * \param vec_key element
+ *
+ * \return the position of the element in space
+ *
+ */
+ inline auto getPosNC(size_t vec_key) const -> decltype(v_pos.template get<0>(vec_key))
+ {
+ return v_pos.template get<0>(vec_key);
+ }
+
+ /*! \brief Get the property of an element
+ *
+ * see the vector_dist iterator usage to get an element key
+ *
+ * \tparam id property id
+ * \param vec_key vector element
+ *
+ * \return return the selected property of the vector element
+ *
+ */
+ template<unsigned int id> inline auto getPropNC(vect_dist_key_dx vec_key) -> decltype(v_prp.template get<id>(vec_key.getKey()))
+ {
+ return v_prp.template get<id>(vec_key.getKey());
+ }
+
+ /*! \brief Get the property of an element
+ *
+ * see the vector_dist iterator usage to get an element key
+ *
+ * \tparam id property id
+ * \param vec_key vector element
+ *
+ * \return return the selected property of the vector element
+ *
+ */
+ template<unsigned int id> inline auto getPropNC(vect_dist_key_dx vec_key) const -> const decltype(v_prp.template get<id>(vec_key.getKey()))
+ {
+ return v_prp.template get<id>(vec_key.getKey());
+ }
+
+ /*! \brief Get the property of an element
+ *
+ * see the vector_dist iterator usage to get an element key
+ *
+ * \tparam id property id
+ * \param vec_key vector element
+ *
+ * \return return the selected property of the vector element
+ *
+ */
+ template<unsigned int id> inline auto getPropNC(size_t vec_key) -> decltype(v_prp.template get<id>(vec_key))
+ {
+ return v_prp.template get<id>(vec_key);
+ }
+
+ /*! \brief Get the property of an element
+ *
+ * see the vector_dist iterator usage to get an element key
+ *
+ * \tparam id property id
+ * \param vec_key vector element
+ *
+ * \return return the selected property of the vector element
+ *
+ */
+ template<unsigned int id> inline auto getPropNC(size_t vec_key) const -> const decltype(v_prp.template get<id>(vec_key))
+ {
+ return v_prp.template get<id>(vec_key);
+ }
+
///////////////////// Read and Write function
/*! \brief Get the position of an element
@@ -767,7 +888,7 @@ public:
Ghost<dim,St> g = getDecomposition().getGhost();
g.magnify(1.013);
- return getCellList(r_cut, g);
+ return getCellList<CellL>(r_cut, g);
}
/*! \brief Construct an hilbert cell list starting from the stored particles
diff --git a/src/Vector/vector_dist_cell_list_tests.hpp b/src/Vector/vector_dist_cell_list_tests.hpp
index 71afdf2c..1179b255 100644
--- a/src/Vector/vector_dist_cell_list_tests.hpp
+++ b/src/Vector/vector_dist_cell_list_tests.hpp
@@ -1691,4 +1691,114 @@ BOOST_AUTO_TEST_CASE( vector_dist_checking_unloaded_processors )
}
}
+BOOST_AUTO_TEST_CASE( vector_dist_cell_list_multi_type )
+{
+ Vcluster & v_cl = create_vcluster();
+
+ if (v_cl.getProcessingUnits() > 24)
+ return;
+
+ float L = 1000.0;
+
+ // set the seed
+ // create the random generator engine
+ std::srand(0);
+ std::default_random_engine eg;
+ std::uniform_real_distribution<float> ud(-L,L);
+
+ long int k = 4096 * v_cl.getProcessingUnits();
+
+ long int big_step = k / 4;
+ big_step = (big_step == 0)?1:big_step;
+
+ print_test("Testing 3D periodic vector symmetric cell-list k=",k);
+ BOOST_TEST_CHECKPOINT( "Testing 3D periodic vector symmetric cell-list k=" << k );
+
+ Box<3,float> box({-L,-L,-L},{L,L,L});
+
+ // Boundary conditions
+ size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};
+
+ float r_cut = 100.0;
+
+ // ghost
+ Ghost<3,float> ghost(r_cut);
+
+ typedef aggregate<size_t> part_prop;
+
+ // Distributed vector
+ vector_dist<3,float, part_prop > vd(k,box,bc,ghost);
+
+ auto it = vd.getIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ vd.getPos(key)[0] = ud(eg);
+ vd.getPos(key)[1] = ud(eg);
+ vd.getPos(key)[2] = ud(eg);
+
+ ++it;
+ }
+
+ vd.map();
+
+ // sync the ghost
+ vd.ghost_get<0>();
+
+
+ bool ret = true;
+
+ // We take different type of Cell-list
+ auto NN = vd.getCellList<CELL_MEMFAST(3,float)>(r_cut);
+ auto NN2 = vd.getCellList<CELL_MEMBAL(3,float)>(r_cut);
+ auto NN3 = vd.getCellList<CELL_MEMMW(3,float)>(r_cut);
+
+ auto p_it = vd.getDomainIterator();
+
+ while (p_it.isNext())
+ {
+ auto p = p_it.get();
+
+ Point<3,float> xp = vd.getPos(p);
+
+ auto Np = NN.getNNIterator(NN.getCell(xp));
+ auto Np2 = NN2.getNNIterator(NN2.getCell(xp));
+ auto Np3 = NN3.getNNIterator(NN3.getCell(xp));
+
+ while (Np.isNext())
+ {
+ // first all cell-list must agree
+
+ ret &= (Np.isNext() == Np2.isNext()) && (Np3.isNext() == Np.isNext());
+
+ if (ret == false)
+ break;
+
+ auto q = Np.get();
+ auto q2 = Np2.get();
+ auto q3 = Np3.get();
+
+ ret &= (q == q2) && (q == q3);
+
+ if (ret == false)
+ break;
+
+ ++Np;
+ ++Np2;
+ ++Np3;
+ }
+
+ ret &= (Np.isNext() == Np2.isNext()) && (Np.isNext() == Np3.isNext());
+
+ if (ret == false)
+ break;
+
+ ++p_it;
+ }
+
+ BOOST_REQUIRE_EQUAL(ret,true);
+}
+
#endif /* SRC_VECTOR_VECTOR_DIST_CELL_LIST_TESTS_HPP_ */
diff --git a/src/Vector/vector_dist_key.hpp b/src/Vector/vector_dist_key.hpp
index c5c7a878..fd79ba14 100644
--- a/src/Vector/vector_dist_key.hpp
+++ b/src/Vector/vector_dist_key.hpp
@@ -68,6 +68,12 @@ public:
inline vect_dist_key_dx()
{
}
+
+ //! Default constructor
+ inline vect_dist_key_dx(size_t key)
+ :key(key)
+ {
+ }
};
--
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