From 1214b212de48035277e93f1745f462af58b305aa Mon Sep 17 00:00:00 2001
From: Pietro Incardona <i-bird@localhost.localdomain>
Date: Wed, 13 Jan 2016 20:12:36 -0500
Subject: [PATCH] Added CellList in vector distributed
---
src/Decomposition/CartDecomposition.hpp | 12 ++
src/Decomposition/ie_ghost.hpp | 4 +-
src/Decomposition/ie_loc_ghost.hpp | 13 ++
src/Grid/grid_dist_id.hpp | 2 +-
src/Grid/grid_dist_id_unit_test.hpp | 4 +-
src/Vector/vector_dist.hpp | 36 ++++-
src/Vector/vector_dist_unit_test.hpp | 169 +++++++++++++++++++++++-
7 files changed, 221 insertions(+), 19 deletions(-)
diff --git a/src/Decomposition/CartDecomposition.hpp b/src/Decomposition/CartDecomposition.hpp
index 64416216..898e17e1 100644
--- a/src/Decomposition/CartDecomposition.hpp
+++ b/src/Decomposition/CartDecomposition.hpp
@@ -682,6 +682,9 @@ p1[0]<-----+ +----> p2[0]
cart.ss_box = ss_box;
cart.ghost = g;
+ for (size_t i = 0 ; i < dim ; i++)
+ cart.bc[i] = bc[i];
+
(static_cast<nn_prcs<dim,T> &>(cart)).create(box_nn_processor, sub_domains);
(static_cast<nn_prcs<dim,T> &>(cart)).applyBC(domain,ghost,bc);
@@ -720,6 +723,9 @@ p1[0]<-----+ +----> p2[0]
cart.bbox = bbox;
cart.ss_box = ss_box;
+ for (size_t i = 0 ; i < dim ; i++)
+ cart.bc[i] = this->bc[i];
+
return cart;
}
@@ -750,6 +756,9 @@ p1[0]<-----+ +----> p2[0]
bbox = cart.bbox;
ss_box = cart.ss_box;
+ for (size_t i = 0 ; i < dim ; i++)
+ bc[i] = cart.bc[i];
+
return *this;
}
@@ -780,6 +789,9 @@ p1[0]<-----+ +----> p2[0]
cart.bbox = bbox;
cart.ss_box = ss_box;
+ for (size_t i = 0 ; i < dim ; i++)
+ cart.bc[i] = bc[i];
+
return *this;
}
diff --git a/src/Decomposition/ie_ghost.hpp b/src/Decomposition/ie_ghost.hpp
index 333e12e1..b865944a 100644
--- a/src/Decomposition/ie_ghost.hpp
+++ b/src/Decomposition/ie_ghost.hpp
@@ -951,7 +951,7 @@ public:
if (getNIGhostBox() != ig.getNIGhostBox())
return false;
- for (size_t i = 0 ; i < getNIGhostBox() ; i++)
+ for (size_t i = 0 ; i < proc_int_box.size() ; i++)
{
if (getProcessorNIGhost(i) != ig.getProcessorNIGhost(i))
return false;
@@ -970,7 +970,7 @@ public:
return false;
}
- for (size_t i = 0 ; i < getNEGhostBox() ; i++)
+ for (size_t i = 0 ; i < proc_int_box.size() ; i++)
{
if (getProcessorNEGhost(i) != ig.getProcessorNEGhost(i))
return false;
diff --git a/src/Decomposition/ie_loc_ghost.hpp b/src/Decomposition/ie_loc_ghost.hpp
index 1b3c53ad..2669fc8b 100644
--- a/src/Decomposition/ie_loc_ghost.hpp
+++ b/src/Decomposition/ie_loc_ghost.hpp
@@ -39,6 +39,9 @@ class ie_loc_ghost
*/
void create_loc_ghost_ebox(Ghost<dim,T> & ghost, openfpm::vector<SpaceBox<dim,T>> & sub_domains, openfpm::vector<Box_loc_sub<dim,T>> & sub_domains_prc)
{
+ comb<dim> zero;
+ zero.zero();
+
loc_ghost_box.resize(sub_domains.size());
// For each sub-domain
@@ -54,6 +57,9 @@ class ie_loc_ghost
{
size_t rj = sub_domains_prc.get(j).sub;
+ if (rj == i && sub_domains_prc.get(j).cmb == zero)
+ continue;
+
::Box<dim,T> bi;
bool intersect = sub_with_ghost.Intersect(sub_domains_prc.get(j).bx,bi);
@@ -88,6 +94,9 @@ class ie_loc_ghost
*/
void create_loc_ghost_ibox(Ghost<dim,T> & ghost, openfpm::vector<SpaceBox<dim,T>> & sub_domains, openfpm::vector<Box_loc_sub<dim,T>> & sub_domains_prc)
{
+ comb<dim> zero;
+ zero.zero();
+
loc_ghost_box.resize(sub_domains.size());
// For each sub-domain
@@ -98,6 +107,10 @@ class ie_loc_ghost
{
SpaceBox<dim,T> sub_with_ghost = sub_domains_prc.get(j).bx;
size_t rj = sub_domains_prc.get(j).sub;
+
+ if (rj == i && sub_domains_prc.get(j).cmb == zero)
+ continue;
+
// enlarge the sub-domain with the ghost
sub_with_ghost.enlarge(ghost);
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index ccd8eec4..0379c9a1 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -562,7 +562,7 @@ public:
*/
size_t size(size_t i) const
{
- return ginfo_v.size();
+ return ginfo_v.size(i);
}
static inline Ghost<dim,float> convert_ghost(const Ghost<dim,long int> & gd,const CellDecomposer_sm<dim,St> & cd_sm)
diff --git a/src/Grid/grid_dist_id_unit_test.hpp b/src/Grid/grid_dist_id_unit_test.hpp
index d4f84fd8..ce59a1d9 100644
--- a/src/Grid/grid_dist_id_unit_test.hpp
+++ b/src/Grid/grid_dist_id_unit_test.hpp
@@ -271,8 +271,8 @@ void Test2D(const Box<2,float> & domain, long int k)
grid_key_dx<2> start = dom2.getStart();
grid_key_dx<2> stop = dom2.getStop();
- BOOST_REQUIRE_EQUAL(stop.get(0),g_dist.size(0));
- BOOST_REQUIRE_EQUAL(stop.get(1),g_dist.size(1));
+ BOOST_REQUIRE_EQUAL(stop.get(0),g_dist.size(0)-1);
+ BOOST_REQUIRE_EQUAL(stop.get(1),g_dist.size(1)-1);
BOOST_REQUIRE_EQUAL(start.get(0),0);
BOOST_REQUIRE_EQUAL(start.get(1),0);
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 5cb96f0d..85e0b013 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -162,18 +162,25 @@ private:
size_t p_id = 0;
// Check if the particle is inside the domain
-// if (dec.getDomain().isInside(v_pos.get(key)) == true)
+ if (dec.getDomain().isInside(v_pos.get(key)) == true)
p_id = dec.processorIDBC(v_pos.get(key));
-// else
-// p_id = obp::out(key,v_cl.getProcessUnitID());
+ else
+ p_id = obp::out(key,v_cl.getProcessUnitID());
// Particle to move
if (p_id != v_cl.getProcessUnitID())
{
- prc_sz.get(p_id)++;
- lbl_p.get(p_id).add(key);
- opart.add(key);
+ if (p_id != -1)
+ {
+ prc_sz.get(p_id)++;
+ lbl_p.get(p_id).add(key);
+ opart.add(key);
+ }
+ else
+ {
+ opart.add(key);
+ }
}
// Add processors and add size
@@ -922,10 +929,25 @@ public:
* \tparam CellL CellList type to construct
*
*/
- template<typename CellL=CellList<dim,St,FAST>> CellL getCellList()
+ template<typename CellL=CellList<dim,St,FAST>> CellL getCellList(St r_cut)
{
CellL cell_list;
+ // calculate the parameters of the cell list
+
+ // get the processor bounding box
+ Box<dim,St> pbox = dec.getProcessorBounds();
+ Box<dim,St> pbox_dom = pbox;
+ pbox_dom -= pbox_dom.getP1();
+
+ size_t div[dim];
+ // Calculate the division array
+
+ for (size_t i = 0 ; i < dim ; i++)
+ div[i] = (pbox.getP2().get(i) - pbox.getP1().get(i))/ r_cut;
+
+ cell_list.Initialize(pbox_dom,div,pbox.getP1());
+
// for each particle add the particle to the cell list
auto it = getDomainIterator();
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index 9d810f51..f0e2b3cb 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -508,7 +508,10 @@ BOOST_AUTO_TEST_CASE( vector_dist_periodic_test_use_2d )
// Ghost must populated because we synchronized them
if (k > 524288)
+ {
BOOST_REQUIRE(nl_cnt != 0);
+ BOOST_REQUIRE(l_cnt > nl_cnt);
+ }
// Sum all the particles inside the domain
v_cl.sum(l_cnt);
@@ -529,7 +532,9 @@ BOOST_AUTO_TEST_CASE( vector_dist_periodic_test_use_2d )
// Ghost must be populated
if (k > 524288)
+ {
BOOST_REQUIRE(nl_cnt != 0);
+ }
}
}
@@ -613,7 +618,10 @@ BOOST_AUTO_TEST_CASE( vector_dist_periodic_test_use_3d )
// Ghost must populated because we synchronized them
if (k > 524288)
+ {
BOOST_REQUIRE(nl_cnt != 0);
+ BOOST_REQUIRE(l_cnt > nl_cnt);
+ }
// Sum all the particles inside the domain
v_cl.sum(l_cnt);
@@ -632,7 +640,9 @@ BOOST_AUTO_TEST_CASE( vector_dist_periodic_test_use_3d )
// Ghost must be populated
if (k > 524288)
+ {
BOOST_REQUIRE(nl_cnt != 0);
+ }
}
}
@@ -824,7 +834,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_not_periodic_map )
BOOST_AUTO_TEST_CASE( vector_dist_out_of_bound_policy )
{
-/* Vcluster & v_cl = *global_v_cluster;
+ Vcluster & v_cl = *global_v_cluster;
if (v_cl.getProcessingUnits() > 8)
return;
@@ -849,14 +859,26 @@ BOOST_AUTO_TEST_CASE( vector_dist_out_of_bound_policy )
auto it = vd.getIterator();
+ size_t cnt = 0;
+
while (it.isNext())
{
auto key = it.get();
- vd.template getPos<s::x>(key)[0] = -0.06;
- vd.template getPos<s::x>(key)[1] = -0.06;
- vd.template getPos<s::x>(key)[2] = -0.06;
+ if (cnt < 1)
+ {
+ vd.template getPos<s::x>(key)[0] = -0.06;
+ vd.template getPos<s::x>(key)[1] = -0.06;
+ vd.template getPos<s::x>(key)[2] = -0.06;
+ }
+ else
+ {
+ vd.template getPos<s::x>(key)[0] = 0.06;
+ vd.template getPos<s::x>(key)[1] = 0.06;
+ vd.template getPos<s::x>(key)[2] = 0.06;
+ }
+ cnt++;
++it;
}
@@ -864,12 +886,145 @@ BOOST_AUTO_TEST_CASE( vector_dist_out_of_bound_policy )
// Particles out of the boundary are killed
- size_t cnt = vd.size_local();
+ size_t cnt_l = vd.size_local();
- v_cl.sum(cnt);
+ v_cl.sum(cnt_l);
v_cl.execute();
- BOOST_REQUIRE_EQUAL(cnt,0);*/
+ BOOST_REQUIRE_EQUAL(cnt_l,100-v_cl.getProcessingUnits());
+}
+
+BOOST_AUTO_TEST_CASE( vector_dist_periodic_test_interacting_particles )
+{
+
+ typedef Point<3,float> s;
+
+ Vcluster & v_cl = *global_v_cluster;
+
+ if (v_cl.getProcessingUnits() > 8)
+ return;
+
+ // set the seed
+ // create the random generator engine
+ std::srand(v_cl.getProcessUnitID());
+ std::default_random_engine eg;
+ std::uniform_real_distribution<float> ud(0.0f, 1.0f);
+
+ size_t nsz[] = {0,32,4};
+ nsz[0] = 4096 * v_cl.getProcessingUnits();
+
+ // 3D test
+ for (size_t i = 0 ; i < 3 ; i++ )
+ {
+ size_t k = nsz[i];
+
+ BOOST_TEST_CHECKPOINT( "Testing 3D random walk vector k=" << 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};
+
+ // factor
+ float factor = pow(global_v_cluster->getProcessingUnits()/2.0f,1.0f/3.0f);
+
+ // interaction radius
+ float r_cut = 0.01 / factor;
+
+ // ghost
+ Ghost<3,float> ghost(r_cut);
+
+ // Distributed vector
+ vector_dist<3,float, Point_test<float>, CartDecomposition<3,float> > vd(k,box,bc,ghost);
+
+ auto it = vd.getIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ vd.template getPos<s::x>(key)[0] = ud(eg);
+ vd.template getPos<s::x>(key)[1] = ud(eg);
+ vd.template getPos<s::x>(key)[2] = ud(eg);
+
+ ++it;
+ }
+
+ vd.map();
+
+ // 4 step random walk
+
+ for (size_t j = 0 ; j < 4 ; j++)
+ {
+ auto it = vd.getDomainIterator();
+
+ // Move the particles
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ vd.template getPos<s::x>(key)[0] += 0.02 * ud(eg);
+ vd.template getPos<s::x>(key)[1] += 0.02 * ud(eg);
+ vd.template getPos<s::x>(key)[2] += 0.02 * ud(eg);
+
+ ++it;
+ }
+
+ vd.map();
+
+ vd.ghost_get<0>();
+
+ // get the cell list with a cutoff radius
+
+ auto NN = vd.getCellList(0.01 / factor);
+
+ // iterate across the domain particle
+
+ auto it2 = vd.getDomainIterator();
+
+ while (it2.isNext())
+ {
+ auto p = it2.get();
+
+ Point<3,float> xp = vd.getPos<0>(p);
+
+ // reset the force
+
+ vd.getProp<4>(p)[0] = 0;
+ vd.getProp<4>(p)[1] = 0;
+ vd.getProp<4>(p)[2] = 0;
+
+ auto Np = NN.getIterator(NN.getCell(vd.getPos<0>(p)));
+
+ while (Np.isNext())
+ {
+ auto q = Np.get();
+
+ // repulsive
+
+ Point<3,float> xq = vd.getPos<0>(q);
+ Point<3,float> f = (xp - xq);
+
+ float distance = f.norm();
+
+ // Particle should be in the r_cut and
+ // 2 * r_cut range
+
+
+
+ ++Np;
+ }
+
+ ++it2;
+ }
+
+ // Count the local particles and check that the total number is consistent
+ size_t cnt = total_n_part_lc(vd,bc);
+
+ BOOST_REQUIRE_EQUAL((size_t)k,cnt);
+ }
+ }
}
BOOST_AUTO_TEST_SUITE_END()
--
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