From 36080771a1d717283e5fd5506f3303a0c148a4c7 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Wed, 5 Oct 2016 18:05:27 +0200
Subject: [PATCH] Ghost put working and general with serialization
---
src/Decomposition/ie_ghost.hpp | 41 +++-
src/Vector/vector_dist_cell_list_tests.hpp | 249 ++++++---------------
src/Vector/vector_dist_comm.hpp | 21 ++
src/Vector/vector_dist_unit_test.hpp | 27 ++-
4 files changed, 148 insertions(+), 190 deletions(-)
diff --git a/src/Decomposition/ie_ghost.hpp b/src/Decomposition/ie_ghost.hpp
index 8b1bbe5fb..e6d65ffc4 100755
--- a/src/Decomposition/ie_ghost.hpp
+++ b/src/Decomposition/ie_ghost.hpp
@@ -31,11 +31,10 @@ class ie_ghost
//! It store the same information of box_nn_processor_int organized by processor id
openfpm::vector< Box_dom<dim,T> > proc_int_box;
- // External ghost boxes for this processor, indicated with G8_0 G9_0 ...
+ //! External ghost boxes for this processor
openfpm::vector<p_box<dim,T> > vb_ext;
- // Internal ghost boxes for this processor domain, indicated with B8_0 B9_0 ..... in the figure
- // below as a linear vector
+ //! Internal ghost boxes for this processor domain
openfpm::vector<p_box<dim,T> > vb_int;
//! Cell-list that store the geometrical information of the internal ghost boxes
@@ -44,8 +43,10 @@ class ie_ghost
//! shift vectors
openfpm::vector<Point<dim,T>> shifts;
- // Temporal buffers to return information for ghost_processorID
+ //! Temporal buffers to return temporal information for ghost_processorID
openfpm::vector<std::pair<size_t,size_t>> ids_p;
+
+ //! Temporal buffers to return temporal information
openfpm::vector<size_t> ids;
@@ -188,6 +189,9 @@ protected:
* The geo cell list structure exist to speed up the labelling the points if they fall on some
* internal ghost
*
+ * \param domain where the cell list is defined
+ * \param div number of division of the cell list
+ *
*/
void Initialize_geo_cell(const Box<dim,T> & domain, const size_t (&div)[dim])
{
@@ -200,7 +204,11 @@ protected:
* For each sub-domain of the local processor it store the intersection between the enlarged
* sub-domain of the calling processor with the adjacent processors sub-domains (External ghost box)
*
+ * \param v_cl Virtual cluster
* \param ghost margins
+ * \param subdomains vector of local sundomains
+ * \param box_nn_processor it will store for each sub-domain the near processors
+ * \param nn_prcs contain the sub-domains of the near processors
*
* \note Are the G8_0 G9_0 G9_1 G5_0 boxes in calculateGhostBoxes
* \see calculateGhostBoxes
@@ -296,8 +304,8 @@ protected:
* \param v_cl Virtual cluster
* \param ghost margins
* \param sub_domains
- * \param box_nn_processors sub-domains of the adjacent processors
- * \param nn_prcs structure that store the adjacent processor information
+ * \param box_nn_processors sub-domains of the near processors
+ * \param nn_prcs structure that store the near processor sub-domains
* \param geo_cell Cell list that store the subdomain information
*
* \note Are the B8_0 B9_0 B9_1 B5_0 boxes in calculateGhostBoxes
@@ -508,6 +516,8 @@ public:
* This function return the set of shift vectors that determine such shift, for example
* in the example above the shift at position 5 will be (0,-1.0)
*
+ * \return the shift vectors
+ *
*/
const openfpm::vector<Point<dim,T>> & getShiftVectors()
{
@@ -667,6 +677,8 @@ public:
}
/*! \brief Given the internal ghost box id, it return the internal ghost box
+ *
+ * \param b_id internal ghost box id
*
* \return the internal ghost box
*
@@ -679,6 +691,8 @@ public:
/*! \brief Given the internal ghost box id, it return the near processor at witch belong
* or the near processor that produced this internal ghost box
*
+ * \param internal ghost box id
+ *
* \return the processor id of the ghost box
*
*/
@@ -698,6 +712,8 @@ public:
}
/*! \brief Given the external ghost box id, it return the external ghost box
+ *
+ * \param b_id external ghost box id
*
* \return the external ghost box
*
@@ -710,6 +726,8 @@ public:
/*! \brief Given the external ghost box id, it return the near processor at witch belong
* or the near processor that produced this external ghost box
*
+ * \param b_id external ghost box id
+ *
* \return the processor id of the external ghost box
*
*/
@@ -721,6 +739,7 @@ public:
/*! /brief Given a point it return the set of boxes in which the point fall
*
* \param p Point to check
+ *
* \return An iterator with the id's of the internal boxes in which the point fall
*
*/
@@ -757,6 +776,8 @@ public:
*
* \param return the processor ids (not the rank, the id in the near processor list)
*
+ * \return a vector of pairs containinf the requested infromation
+ *
*/
template <typename id1, typename id2> inline const openfpm::vector<std::pair<size_t,size_t>> ghost_processorID_pair(Point<dim,T> & p, const int opt = MULTIPLE)
{
@@ -806,6 +827,8 @@ public:
*
* \param return the processor ids
*
+ * \return a vector containing the requested information
+ *
*/
template <typename id> inline const openfpm::vector<size_t> ghost_processorID(Point<dim,T> & p, const int opt = MULTIPLE)
{
@@ -842,10 +865,12 @@ public:
/*! \brief Given a position it return if the position belong to any neighborhood processor ghost
* (Internal ghost)
*
- * \tparam id type of if to get box_id processor_id lc_processor_id
+ * \tparam id1 first index type to get box_id processor_id lc_processor_id
+ * \tparam id2 second index type to get box_id processor_id lc_processor_id
+ *
* \param p Particle position
*
- * \param return the processor ids
+ * \return a vector of pair containing the requested information
*
*/
template<typename id1, typename id2, typename Mem> inline const openfpm::vector<std::pair<size_t,size_t>> ghost_processorID_pair(const encapc<1,Point<dim,T>,Mem> & p, const int opt = MULTIPLE)
diff --git a/src/Vector/vector_dist_cell_list_tests.hpp b/src/Vector/vector_dist_cell_list_tests.hpp
index abbd0e5c7..3826bbb9b 100644
--- a/src/Vector/vector_dist_cell_list_tests.hpp
+++ b/src/Vector/vector_dist_cell_list_tests.hpp
@@ -332,171 +332,6 @@ BOOST_AUTO_TEST_CASE( vector_dist_cl_random_vs_reorder_forces_test )
}
}
-/*
-BOOST_AUTO_TEST_CASE( vector_dist_sym_cell_list_test )
-{
- long int k = 4096*create_vcluster().getProcessingUnits();
-
- long int big_step = k / 30;
- big_step = (big_step == 0)?1:big_step;
- long int small_step = 21;
-
- if (create_vcluster().getProcessingUnits() > 48)
- return;
-
- print_test( "Testing vector symmetric cell-list k<=",k);
-
- // 3D test
- for ( ; k > 8*big_step ; k-= (k > 2*big_step)?big_step:small_step )
- {
- double r_cut = 0.1;
-
- // domain
- Box<3,double> box({0.0,0.0,0.0},{1.0,1.0,1.0});
-
- // Boundary conditions
- size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};
-
- // ghost, big enough to contain the interaction radius
- Ghost<3,float> ghost(r_cut);
-
- vector_dist<3,double, aggregate<double> > vd(k,box,bc,ghost);
-
- {
- auto it = vd.getDomainIterator();
-
- while (it.isNext())
- {
- auto p = it.get();
-
- vd.getPos(p)[0] = (double)rand()/RAND_MAX;
- vd.getPos(p)[1] = (double)rand()/RAND_MAX;
- vd.getPos(p)[2] = (double)rand()/RAND_MAX;
-
- ++it;
- }
- }
-
- vd.map();
- vd.ghost_get<>();
-
- // Get the Cell list structure
- auto NN = vd.getCellList(r_cut);
-
- // Get an iterator over particles
- auto it2 = vd.getDomainAndGhostIterator();
-
- openfpm::vector<openfpm::vector<size_t>> idx;
- idx.resize(vd.size_local_with_ghost());
-
- /////////// SYMMETRIC CASE CELL-LIST ////////
-
- // For each particle ...
- while (it2.isNext())
- {
- // ... p
- auto p = it2.get();
-
- // Get the position of the particle p
- Point<3,double> xp = vd.getPos(p);
-
- // Get an iterator over the neighborhood of the particle p symmetric
- auto NpSym = NN.template getNNIteratorSym<NO_CHECK>(NN.getCell(vd.getPos(p)),p.getKey());
-
- // For each neighborhood of the particle p
- while (NpSym.isNext())
- {
- // Neighborhood particle q
- auto q = NpSym.get();
-
- // if p == q skip this particle
- if (q == p.getKey() ) {++NpSym; continue;};
-
- // Get position of the particle q
- Point<3,double> xq = vd.getPos(q);
-
- // take the normalized direction
- double rn = norm2(xp - xq);
-
- // potential energy (using pow is slower)
- vd.getProp<0>(p) += rn;
- vd.getProp<0>(q) += rn;
-
- idx.get(p.getKey()).add(q);
- idx.get(q).add(p.getKey());
-
-
- // Next neighborhood
- ++NpSym;
- }
-
- // Next Particle
- ++it2;
- }
-
- /////////////// NON SYMMETRIC CASE ////////////////////////
-
- openfpm::vector<openfpm::vector<size_t>> idx2;
- idx2.resize(vd.size_local());
-
- auto it = vd.getDomainIterator();
-
- // For each particle ...
- while (it.isNext())
- {
- // ... p
- auto p = it.get();
-
- // Get the position of the particle p
- Point<3,double> xp = vd.getPos(p);
-
- // Get an iterator over the neighborhood of the particle p
- auto Np = NN.template getNNIterator<NO_CHECK>(NN.getCell(vd.getPos(p)));
-
- double Ep = 0.0;
-
- // For each neighborhood of the particle p
- while (Np.isNext())
- {
- // Neighborhood particle q
- auto q = Np.get();
-
- // if p == q skip this particle
- if (q == p.getKey()) {++Np; continue;};
-
- // Get position of the particle q
- Point<3,double> xq = vd.getPos(q);
-
- // take the normalized direction
- double rn = norm2(xp - xq);
-
- idx2.get(p.getKey()).add(q);
-
- // potential energy (using pow is slower)
- Ep += rn;
-
- // Next neighborhood
- ++Np;
- }
-
- idx.get(p.getKey()).sort();
- idx2.get(p.getKey()).sort();
-
- bool ret = true;
-
- for (size_t i = 0 ; i < idx.get(p.getKey()).size() ; i++)
- ret &= idx.get(p.getKey()).get(i) == idx2.get(p.getKey()).get(i);
-
- BOOST_REQUIRE_EQUAL(ret,true);
-
- BOOST_REQUIRE_CLOSE(Ep,vd.getProp<0>(p),0.01);
-
- // Next Particle
- ++it;
- }
- }
-}*/
-
BOOST_AUTO_TEST_CASE( vector_dist_symmetric_cell_list )
{
Vcluster & v_cl = create_vcluster();
@@ -504,11 +339,13 @@ BOOST_AUTO_TEST_CASE( vector_dist_symmetric_cell_list )
if (v_cl.getProcessingUnits() > 24)
return;
+ float L = 1000.0;
+
// set the seed
// create the random generator engine
- std::srand(v_cl.getProcessUnitID());
+ std::srand(0);
std::default_random_engine eg;
- std::uniform_real_distribution<float> ud(0.0f, 1.0f);
+ std::uniform_real_distribution<float> ud(-L,L);
long int k = 4096 * v_cl.getProcessingUnits();
@@ -518,20 +355,33 @@ BOOST_AUTO_TEST_CASE( vector_dist_symmetric_cell_list )
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({0.0,0.0,0.0},{1.0,1.0,1.0});
+ Box<3,float> box({-L,-L,-L},{L,L,L});
// Boundary conditions
size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};
- float r_cut = 0.1;
+ float r_cut = 100.0;
// ghost
Ghost<3,float> ghost(r_cut);
- typedef aggregate<size_t,size_t> part_prop;
+ // Point and global id
+ struct point_and_gid
+ {
+ size_t id;
+ Point<3,float> xq;
+
+ bool operator<(const struct point_and_gid & pag)
+ {
+ return (id < pag.id);
+ }
+ };
+
+ typedef aggregate<size_t,size_t,size_t,openfpm::vector<point_and_gid>,openfpm::vector<point_and_gid>> part_prop;
// Distributed vector
vector_dist<3,float, part_prop > vd(k,box,bc,ghost);
+ size_t start = vd.init_size_accum(k);
auto it = vd.getIterator();
@@ -545,7 +395,9 @@ BOOST_AUTO_TEST_CASE( vector_dist_symmetric_cell_list )
// Fill some properties randomly
- vd.getProp<0>(key) = 0.0;
+ vd.getProp<0>(key) = 0;
+ vd.getProp<1>(key) = 0;
+ vd.getProp<2>(key) = key.getKey() + start;
++it;
}
@@ -553,10 +405,9 @@ BOOST_AUTO_TEST_CASE( vector_dist_symmetric_cell_list )
vd.map();
// sync the ghost
- vd.ghost_get<0>();
-
- auto NN = vd.getCellList(0.1);
+ vd.ghost_get<0,2>();
+ auto NN = vd.getCellList(r_cut);
auto p_it = vd.getDomainIterator();
while (p_it.isNext())
@@ -571,6 +422,12 @@ BOOST_AUTO_TEST_CASE( vector_dist_symmetric_cell_list )
{
auto q = Np.get();
+ if (p.getKey() == q)
+ {
+ ++Np;
+ continue;
+ }
+
// repulsive
Point<3,float> xq = vd.getPos(q);
@@ -581,7 +438,12 @@ BOOST_AUTO_TEST_CASE( vector_dist_symmetric_cell_list )
// Particle should be inside 2 * r_cut range
if (distance < r_cut )
+ {
vd.getProp<0>(p)++;
+ vd.getProp<3>(p).add();
+ vd.getProp<3>(p).last().xq = xq;
+ vd.getProp<3>(p).last().id = vd.getProp<2>(q);
+ }
++Np;
}
@@ -591,7 +453,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_symmetric_cell_list )
// We now try symmetric Cell-list
- auto NN2 = vd.getCellListSym(0.1);
+ auto NN2 = vd.getCellListSym(r_cut);
auto p_it2 = vd.getDomainIterator();
@@ -607,6 +469,12 @@ BOOST_AUTO_TEST_CASE( vector_dist_symmetric_cell_list )
{
auto q = Np.get();
+ if (p.getKey() == q)
+ {
+ ++Np;
+ continue;
+ }
+
// repulsive
Point<3,float> xq = vd.getPos(q);
@@ -620,6 +488,14 @@ BOOST_AUTO_TEST_CASE( vector_dist_symmetric_cell_list )
{
vd.getProp<1>(p)++;
vd.getProp<1>(q)++;
+
+ vd.getProp<4>(p).add();
+ vd.getProp<4>(q).add();
+
+ vd.getProp<4>(p).last().xq = xq;
+ vd.getProp<4>(q).last().xq = xp;
+ vd.getProp<4>(p).last().id = vd.getProp<2>(q);
+ vd.getProp<4>(q).last().id = vd.getProp<2>(p);
}
++Np;
@@ -629,6 +505,29 @@ BOOST_AUTO_TEST_CASE( vector_dist_symmetric_cell_list )
}
vd.ghost_put<add_,1>();
+ vd.ghost_put<merge_,4>();
+
+ auto p_it3 = vd.getDomainIterator();
+
+ bool ret = true;
+ while (p_it3.isNext())
+ {
+ auto p = p_it3.get();
+
+ ret &= vd.getProp<1>(p) == vd.getProp<0>(p);
+
+ vd.getProp<3>(p).sort();
+ vd.getProp<4>(p).sort();
+
+ ret &= vd.getProp<3>(p).size() == vd.getProp<4>(p).size();
+
+ for (size_t i = 0 ; i < vd.getProp<3>(p).size() ; i++)
+ ret &= vd.getProp<3>(p).get(i).id == vd.getProp<4>(p).get(i).id;
+
+ ++p_it3;
+ }
+
+ BOOST_REQUIRE_EQUAL(ret,true);
}
BOOST_AUTO_TEST_CASE( vector_dist_sym_verlet_list_test )
diff --git a/src/Vector/vector_dist_comm.hpp b/src/Vector/vector_dist_comm.hpp
index 0aae55388..6a42f4c46 100644
--- a/src/Vector/vector_dist_comm.hpp
+++ b/src/Vector/vector_dist_comm.hpp
@@ -1047,6 +1047,27 @@ public:
// Send and receive ghost particle information
op_ssend_recv_merge<op> opm(g_opart);
v_cl.SSendRecvP_op<op_ssend_recv_merge<op>,send_vector,decltype(v_prp),prp...>(g_send_prp,v_prp,prc_recv_get,opm,prc_recv_put,recv_sz_put);
+
+ // process also the local replicated particles
+
+ size_t i2 = 0;
+
+ #ifdef SE_CLASS1
+
+ if (v_prp.size() - lg_m != o_part_loc.size())
+ std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " v_prp.size() - lg_m = " << v_prp.size() - lg_m << " != " << o_part_loc.size() << std::endl;
+
+ #endif
+
+ for (size_t i = lg_m ; i < v_prp.size() ; i++)
+ {
+ auto dst = v_prp.get(o_part_loc.template get<0>(i2));
+ auto src = v_prp.get(i);
+ copy_cpu_encap_encap_op_prp<op,decltype(v_prp.get(0)),decltype(v_prp.get(0)),prp...> cp(src,dst);
+
+ boost::mpl::for_each_ref< boost::mpl::range_c<int,0,sizeof...(prp)> >(cp);
+ i2++;
+ }
}
};
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index e76667dd2..90bd56628 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -1618,13 +1618,16 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost_put )
// 3D test
for ( ; k >= 2 ; k-= (k > 2*big_step)?big_step:small_step )
{
+ float r_cut = 1.3 / k;
+ float r_g = 1.5 / k;
+
Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
// Boundary conditions
size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};
// ghost
- Ghost<3,float> ghost(1.3/(k));
+ Ghost<3,float> ghost(r_g);
typedef aggregate<float> part_prop;
@@ -1656,7 +1659,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost_put )
vd.ghost_get<0>();
{
- auto NN = vd.getCellList(1.3/k);
+ auto NN = vd.getCellList(r_cut);
float a = 1.0f*k*k;
// run trough all the particles + ghost
@@ -1680,8 +1683,8 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost_put )
float dist = xp.distance(xq);
- if (dist < 1.0/k)
- vd.getProp<0>(q) += a*(-dist*dist+1.0/k/k);
+ if (dist < r_cut)
+ vd.getProp<0>(q) += a*(-dist*dist+r_cut*r_cut);
++Np;
}
@@ -1712,8 +1715,18 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost_put )
BOOST_REQUIRE_EQUAL(ret,true);
}
+ auto itp = vd.getDomainAndGhostIterator();
+ while (itp.isNext())
+ {
+ auto key = itp.get();
+
+ vd.getProp<0>(key) = 0.0;
+
+ ++itp;
+ }
+
{
- auto NN = vd.getCellList(1.3/k);
+ auto NN = vd.getCellList(r_cut);
float a = 1.0f*k*k;
// run trough all the particles + ghost
@@ -1737,8 +1750,8 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost_put )
float dist = xp.distance(xq);
- if (dist < 1.0/k)
- vd.getProp<0>(q) += a*(-dist*dist+1.0/k/k);
+ if (dist < r_cut)
+ vd.getProp<0>(q) += a*(-dist*dist+r_cut*r_cut);
++Np;
}
--
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