From dd99a004d044d53e8b33231eb7503b29e14505ea Mon Sep 17 00:00:00 2001
From: Yaroslav <beorn.90@gmail.com>
Date: Wed, 20 Apr 2016 16:14:28 +0200
Subject: [PATCH] Benchmark with mooving particles
---
openfpm_data | 2 +-
openfpm_io | 2 +-
openfpm_vcluster | 2 +-
src/Makefile.am | 4 +-
src/Vector/vector_dist.hpp | 132 +++++++++++++++++++++++++++
src/Vector/vector_dist_iterator.hpp | 9 ++
src/Vector/vector_dist_unit_test.hpp | 80 +++++++++++++++-
src/main.cpp | 3 +
8 files changed, 228 insertions(+), 6 deletions(-)
diff --git a/openfpm_data b/openfpm_data
index 8168a90cc..21d50e7f0 160000
--- a/openfpm_data
+++ b/openfpm_data
@@ -1 +1 @@
-Subproject commit 8168a90ccd39ef504ba8699d6d0ed9aed46a3f31
+Subproject commit 21d50e7f0f796ceb5699dcf6939183572aba2ba0
diff --git a/openfpm_io b/openfpm_io
index 523332938..d07c3c784 160000
--- a/openfpm_io
+++ b/openfpm_io
@@ -1 +1 @@
-Subproject commit 523332938de0a47a1ca1d652a8e171cf9b8a6f5b
+Subproject commit d07c3c7848e446437526d0bbda0843c18ab6a925
diff --git a/openfpm_vcluster b/openfpm_vcluster
index be8c849c9..02c935545 160000
--- a/openfpm_vcluster
+++ b/openfpm_vcluster
@@ -1 +1 @@
-Subproject commit be8c849c9189fe90e1533125f2544258671d0916
+Subproject commit 02c935545524000d318f0b84578af704896eeee4
diff --git a/src/Makefile.am b/src/Makefile.am
index a79faae31..f3fd81586 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -2,9 +2,9 @@ LINKLIBS = $(METIS_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOS
noinst_PROGRAMS = pdata
pdata_SOURCES = main.cpp lib/pdata.cpp test_multiple_o.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_devices/src/Memleak_check.cpp
-pdata_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) -Wno-unused-local-typedefs
+pdata_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) -I/usr/local/libhilbert/include -Wno-unused-local-typedefs
pdata_CFLAGS = $(CUDA_CFLAGS)
-pdata_LDADD = $(LINKLIBS) -lmetis
+pdata_LDADD = $(LINKLIBS) -lmetis -L/usr/local/libhilbert/lib -lhilbert
nobase_include_HEADERS = Decomposition/CartDecomposition.hpp Decomposition/common.hpp Decomposition/Decomposition.hpp Decomposition/ie_ghost.hpp \
Decomposition/nn_processor.hpp Decomposition/ie_loc_ghost.hpp Decomposition/ORB.hpp \
Graph/CartesianGraphFactory.hpp \
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index d06a21d5a..775c7b44e 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -22,6 +22,7 @@
#include "CSVWriter/CSVWriter.hpp"
#include "Decomposition/common.hpp"
#include "Grid/grid_dist_id_iterator_dec.hpp"
+#include "Grid/grid_key_dx_iterator_hilbert.hpp"
#include "Vector/vector_dist_ofb.hpp"
#define V_SUB_UNIT_FACTOR 64
@@ -133,6 +134,21 @@ private:
openfpm::vector<prop,PreAllocHeapMemory<2>,openfpm::grow_policy_identity> prp;
};
+ /*! \brief Operator= is not permitted
+ *
+ *
+ */
+/* vector_dist<dim,St,prop,Decomposition,Memory> & operator=(const vector_dist<dim,St,prop,Decomposition,Memory> &)
+ {
+ return *this;
+ }*/
+
+ /*! Copy constructor not permitted
+ *
+ *
+ */
+// vector_dist(const vector_dist<dim,St,prop,Decomposition,Memory> &) {}
+
/*! \brief Label particles for mappings
*
* \param lbl_p Particle labeled
@@ -1126,6 +1142,122 @@ public:
}
}
+ /*! \brief Construct a cell list starting from the stored particles and reorder a vector according to the Hilberts curve
+ *
+ * \tparam CellL CellList type to construct
+ *
+ * \param m an order of a hilbert curve
+ *
+ *
+ *
+ */
+ template<typename CellL=CellList<dim,St,FAST,shift<dim,St> > > void reorder (int32_t m)
+ {
+ reorder(m,dec.getGhost());
+ }
+
+
+ /*! \brief Construct a cell list starting from the stored particles and reorder a vector according to the Hilberts curve
+ *
+ *
+ *It differs from the reorder(m) for an additional parameter, in case the
+ * domain + ghost is not big enough to contain additional padding particles, a Cell list
+ * with bigger space can be created
+ * (padding particles in general are particles added by the user out of the domains)
+ *
+ * \param m order of a curve
+ * \param enlarge In case of padding particles the cell list must be enlarged, like a ghost this parameter say how much must be enlarged
+ *
+ */
+ template<typename CellL=CellList<dim,St,FAST,shift<dim,St> > > void reorder(int32_t m, const Ghost<dim,St> & enlarge)
+ {
+ // reset the ghost part
+ v_pos.resize(g_m);
+ v_prp.resize(g_m);
+
+
+ CellL cell_list;
+
+ // calculate the parameters of the cell list
+
+ // get the processor bounding box
+ Box<dim,St> pbox = dec.getProcessorBounds();
+ // extend by the ghost
+ pbox.enlarge(enlarge);
+
+ Box<dim,St> cell_box;
+
+ size_t div[dim];
+
+ // Calculate the division array and the cell box
+ for (size_t i = 0 ; i < dim ; i++)
+ {
+ div[i] = 1 << m;
+
+ cell_box.setLow(i,0.0);
+ cell_box.setHigh(i,pbox.getP2().get(i) - pbox.getP1().get(i));
+ }
+
+ cell_list.Initialize(cell_box,div,pbox.getP1());
+
+ // for each particle add the particle to the cell list
+
+ auto it = getIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ cell_list.add(this->template getPos<0>(key),key.getKey());
+
+ ++it;
+ }
+
+ // Use cell_list to reorder v_pos
+
+ //destination vector
+ openfpm::vector<Point<dim,St>> v_pos_dest;
+ openfpm::vector<prop> v_prp_dest;
+
+ v_pos_dest.resize(v_pos.size());
+ v_prp_dest.resize(v_prp.size());
+
+ //hilberts curve iterator
+ grid_key_dx_iterator_hilbert<dim> h_it(m);
+
+ //Index for v_pos_dest
+ size_t count = 0;
+
+ grid_key_dx<dim> ksum;
+
+ for (size_t i = 0; i < dim ; i++)
+ ksum.set_d(i,cell_list.getPadding(i));
+
+ while (h_it.isNext())
+ {
+ auto key = h_it.get();
+ key += ksum;
+
+ size_t lin = cell_list.getGrid().LinId(key);
+
+ // for each particle in the Cell "lin"
+ for (size_t i = 0; i < cell_list.getNelements(lin); i++)
+ {
+ //reorder
+ auto v = cell_list.get(lin,i);
+ v_pos_dest.get(count) = v_pos.get(v);
+ v_prp_dest.get(count) = v_prp.get(v);
+
+ count++;
+ }
+ ++h_it;
+ }
+
+ v_pos.swap(v_pos_dest);
+ v_prp.swap(v_prp_dest);
+
+ }
+
/*! \brief It return the number of particles contained by the previous processors
*
* \Warning It only work with the initial decomposition
diff --git a/src/Vector/vector_dist_iterator.hpp b/src/Vector/vector_dist_iterator.hpp
index 795e4290b..4b8ee861f 100644
--- a/src/Vector/vector_dist_iterator.hpp
+++ b/src/Vector/vector_dist_iterator.hpp
@@ -74,6 +74,15 @@ class vector_dist_iterator
{
return vect_dist_key_dx(v_it);
}
+
+ /*! \brief Reset the iterator
+ *
+ *
+ */
+ void reset()
+ {
+ v_it = 0;
+ }
};
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index 8a5c813cb..93faeb798 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -10,6 +10,7 @@
#include <random>
#include "Vector/vector_dist.hpp"
+#include "data_type/aggregate.hpp"
/*! \brief Count the total number of particles
*
@@ -270,7 +271,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
void print_test_v(std::string test, size_t sz)
{
if (global_v_cluster->getProcessUnitID() == 0)
- std::cout << test << " " << sz << "\n";
+ std::cout << "\n" << test << " " << sz << "\n";
}
long int decrement(long int k, long int step)
@@ -1031,6 +1032,8 @@ BOOST_AUTO_TEST_CASE( vector_dist_periodic_test_interacting_particles )
size_t cnt = total_n_part_lc(vd,bc);
BOOST_REQUIRE_EQUAL((size_t)k,cnt);
+
+
}
}
}
@@ -1155,6 +1158,81 @@ BOOST_AUTO_TEST_CASE( vector_dist_cell_verlet_test )
}
}
+BOOST_AUTO_TEST_CASE( vector_dist_hilbert_timer_test )
+{
+ typedef Point<2,float> s;
+
+ Vcluster & v_cl = *global_v_cluster;
+
+ // 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);
+
+ long int k = 524288 * v_cl.getProcessingUnits();
+
+ long int big_step = k / 4;
+ big_step = (big_step == 0)?1:big_step;
+
+ print_test_v( "Testing 2D vector with hilbert curve reordering k<=",k);
+
+ // 2D test
+ for ( ; k >= 2 ; k-= decrement(k,big_step) )
+ {
+ BOOST_TEST_CHECKPOINT( "Testing 2D vector with hilbert curve reordering k=" << k );
+
+ //! [Create a vector of random elements on each processor 2D]
+
+ Box<2,float> box({0.0,0.0},{1.0,1.0});
+
+ // Boundary conditions
+ size_t bc[2]={NON_PERIODIC,NON_PERIODIC};
+
+ vector_dist<2,float, Point_test<float>, CartDecomposition<2,float> > vd(k,box,bc,Ghost<2,float>(0.0));
+
+ auto it = vd.getIterator();
+
+ while (it.isNext())
+ {
+ auto key = it.get();
+
+ vd.template getPos<s::x>(key)[0] = ud(eg);
+ vd.template getPos<s::x>(key)[1] = ud(eg);
+
+ ++it;
+ }
+
+ vd.map();
+
+ timer t;
+ t.start();
+
+ //! [Create a vector of random elements on each processor 2D]
+
+ auto NN1 = vd.getCellList(0.01);
+
+ //An order of a curve
+ int32_t m = 6;
+
+ //Reorder a vector
+ vd.reorder(m);
+
+ auto NN2 = vd.getCellList(0.01);
+
+ for (size_t i = 0 ; i < NN1.getGrid().size() ; i++)
+ {
+ size_t n1 = NN1.getNelements(i);
+ size_t n2 = NN2.getNelements(i);
+
+ BOOST_REQUIRE_EQUAL(n1,n2);
+ }
+
+ t.stop();
+ std::cout << " t: " << t.getwct() << "\n";
+ }
+}
+
BOOST_AUTO_TEST_SUITE_END()
#endif /* VECTOR_DIST_UNIT_TEST_HPP_ */
diff --git a/src/main.cpp b/src/main.cpp
index 0d2c73fe0..f884796da 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -26,5 +26,8 @@
#include "dec_optimizer_unit_test.hpp"
#include "Grid/grid_dist_id_unit_test.hpp"
#include "Vector/vector_dist_unit_test.hpp"
+//#ifdef PERFORMANCE_TEST
+#include "pdata_performance.hpp"
+//#endif
//#include "Decomposition/nn_processor_unit_test.hpp"
--
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