diff --git a/src/.deps/pdata-HeapMemory.Po b/src/.deps/pdata-HeapMemory.Po
index 42e2989ad7e6df81a5a55313471c01d127dc00f0..fdc68bd49c847939d37f93ea44387a05f0279fac 100644
--- a/src/.deps/pdata-HeapMemory.Po
+++ b/src/.deps/pdata-HeapMemory.Po
@@ -74,9 +74,10 @@ pdata-HeapMemory.o: ../../OpenFPM_devices/src/memory/HeapMemory.cpp \
/usr/include/sys/types.h /usr/include/sys/select.h \
/usr/include/bits/select.h /usr/include/bits/sigset.h \
/usr/include/sys/sysmacros.h /usr/include/alloca.h \
- /usr/include/bits/stdlib-float.h /usr/include/c++/4.9.2/cstdio \
- /usr/include/libio.h /usr/include/_G_config.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdlib-bsearch.h /usr/include/bits/stdlib-float.h \
+ /usr/include/c++/4.9.2/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \
+ /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
/usr/include/c++/4.9.2/cerrno /usr/include/errno.h \
/usr/include/bits/errno.h /usr/include/linux/errno.h \
/usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
@@ -301,6 +302,8 @@ pdata-HeapMemory.o: ../../OpenFPM_devices/src/memory/HeapMemory.cpp \
/usr/include/alloca.h:
+/usr/include/bits/stdlib-bsearch.h:
+
/usr/include/bits/stdlib-float.h:
/usr/include/c++/4.9.2/cstdio:
@@ -313,6 +316,8 @@ pdata-HeapMemory.o: ../../OpenFPM_devices/src/memory/HeapMemory.cpp \
/usr/include/bits/sys_errlist.h:
+/usr/include/bits/stdio.h:
+
/usr/include/c++/4.9.2/cerrno:
/usr/include/errno.h:
diff --git a/src/.deps/pdata-Memleak_check.Po b/src/.deps/pdata-Memleak_check.Po
index 6e9955e576862a4e28f4c0d6599b948c25fd017f..b83f8742ae12520c754559aeb9658d08933cff10 100644
--- a/src/.deps/pdata-Memleak_check.Po
+++ b/src/.deps/pdata-Memleak_check.Po
@@ -71,9 +71,10 @@ pdata-Memleak_check.o: ../../OpenFPM_data/src/Memleak_check.cpp \
/usr/include/sys/types.h /usr/include/sys/select.h \
/usr/include/bits/select.h /usr/include/bits/sigset.h \
/usr/include/sys/sysmacros.h /usr/include/alloca.h \
- /usr/include/bits/stdlib-float.h /usr/include/c++/4.9.2/cstdio \
- /usr/include/libio.h /usr/include/_G_config.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdlib-bsearch.h /usr/include/bits/stdlib-float.h \
+ /usr/include/c++/4.9.2/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \
+ /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
/usr/include/c++/4.9.2/cerrno /usr/include/errno.h \
/usr/include/bits/errno.h /usr/include/linux/errno.h \
/usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
@@ -302,6 +303,8 @@ pdata-Memleak_check.o: ../../OpenFPM_data/src/Memleak_check.cpp \
/usr/include/alloca.h:
+/usr/include/bits/stdlib-bsearch.h:
+
/usr/include/bits/stdlib-float.h:
/usr/include/c++/4.9.2/cstdio:
@@ -314,6 +317,8 @@ pdata-Memleak_check.o: ../../OpenFPM_data/src/Memleak_check.cpp \
/usr/include/bits/sys_errlist.h:
+/usr/include/bits/stdio.h:
+
/usr/include/c++/4.9.2/cerrno:
/usr/include/errno.h:
diff --git a/src/.deps/pdata-VCluster.Po b/src/.deps/pdata-VCluster.Po
index d5efeff1085c337d501f34e4572da0ccaa1aebee..57771c2608f19a1afb3cd86eac91d3e7405519fd 100644
--- a/src/.deps/pdata-VCluster.Po
+++ b/src/.deps/pdata-VCluster.Po
@@ -78,9 +78,10 @@ pdata-VCluster.o: ../../OpenFPM_vcluster/src/VCluster.cpp \
/usr/include/sys/types.h /usr/include/sys/select.h \
/usr/include/bits/select.h /usr/include/bits/sigset.h \
/usr/include/sys/sysmacros.h /usr/include/alloca.h \
- /usr/include/bits/stdlib-float.h /usr/include/c++/4.9.2/cstdio \
- /usr/include/libio.h /usr/include/_G_config.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdlib-bsearch.h /usr/include/bits/stdlib-float.h \
+ /usr/include/c++/4.9.2/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \
+ /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
/usr/include/c++/4.9.2/cerrno /usr/include/errno.h \
/usr/include/bits/errno.h /usr/include/linux/errno.h \
/usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
@@ -789,7 +790,8 @@ pdata-VCluster.o: ../../OpenFPM_vcluster/src/VCluster.cpp \
/usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
/usr/include/bits/inf.h /usr/include/bits/nan.h \
/usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/c++/4.9.2/sstream /usr/include/c++/4.9.2/bits/sstream.tcc \
+ /usr/include/bits/mathinline.h /usr/include/c++/4.9.2/sstream \
+ /usr/include/c++/4.9.2/bits/sstream.tcc \
/usr/include/boost/type_traits/is_compound.hpp \
/usr/include/boost/type_traits/is_copy_constructible.hpp \
/usr/include/boost/noncopyable.hpp \
@@ -998,11 +1000,6 @@ pdata-VCluster.o: ../../OpenFPM_vcluster/src/VCluster.cpp \
../../OpenFPM_vcluster/src/MPI_wrapper/MPI_IallreduceW.hpp \
../../OpenFPM_vcluster/src/MPI_wrapper/MPI_IrecvW.hpp \
../../OpenFPM_vcluster/src/MPI_wrapper/MPI_IsendW.hpp \
- ../../OpenFPM_data/src/util/check_no_pointers.hpp \
- ../../OpenFPM_data/src/util/common.hpp \
- ../../OpenFPM_data/src/util/util_debug.hpp \
- /usr/include/c++/4.9.2/cxxabi.h \
- /usr/include/c++/4.9.2/x86_64-redhat-linux/bits/cxxabi_tweaks.h \
../../OpenFPM_vcluster/src/util/Vcluster_log.hpp \
/usr/include/c++/4.9.2/fstream /usr/include/c++/4.9.2/bits/codecvt.h \
/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/basic_file.h \
@@ -1226,6 +1223,8 @@ pdata-VCluster.o: ../../OpenFPM_vcluster/src/VCluster.cpp \
/usr/include/alloca.h:
+/usr/include/bits/stdlib-bsearch.h:
+
/usr/include/bits/stdlib-float.h:
/usr/include/c++/4.9.2/cstdio:
@@ -1238,6 +1237,8 @@ pdata-VCluster.o: ../../OpenFPM_vcluster/src/VCluster.cpp \
/usr/include/bits/sys_errlist.h:
+/usr/include/bits/stdio.h:
+
/usr/include/c++/4.9.2/cerrno:
/usr/include/errno.h:
@@ -2738,6 +2739,8 @@ pdata-VCluster.o: ../../OpenFPM_vcluster/src/VCluster.cpp \
/usr/include/bits/mathcalls.h:
+/usr/include/bits/mathinline.h:
+
/usr/include/c++/4.9.2/sstream:
/usr/include/c++/4.9.2/bits/sstream.tcc:
@@ -3184,16 +3187,6 @@ pdata-VCluster.o: ../../OpenFPM_vcluster/src/VCluster.cpp \
../../OpenFPM_vcluster/src/MPI_wrapper/MPI_IsendW.hpp:
-../../OpenFPM_data/src/util/check_no_pointers.hpp:
-
-../../OpenFPM_data/src/util/common.hpp:
-
-../../OpenFPM_data/src/util/util_debug.hpp:
-
-/usr/include/c++/4.9.2/cxxabi.h:
-
-/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/cxxabi_tweaks.h:
-
../../OpenFPM_vcluster/src/util/Vcluster_log.hpp:
/usr/include/c++/4.9.2/fstream:
diff --git a/src/.deps/pdata-main.Po b/src/.deps/pdata-main.Po
index 8e142faf7f771ed582eb6d382401e16ce832c1df..9e9db061c5ee3ac8fb935bdf13bcaca219fa7471 100644
--- a/src/.deps/pdata-main.Po
+++ b/src/.deps/pdata-main.Po
@@ -70,9 +70,10 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
/usr/include/sys/types.h /usr/include/sys/select.h \
/usr/include/bits/select.h /usr/include/bits/sigset.h \
/usr/include/sys/sysmacros.h /usr/include/alloca.h \
- /usr/include/bits/stdlib-float.h /usr/include/c++/4.9.2/cstdio \
- /usr/include/libio.h /usr/include/_G_config.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdlib-bsearch.h /usr/include/bits/stdlib-float.h \
+ /usr/include/c++/4.9.2/cstdio /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \
+ /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
/usr/include/c++/4.9.2/cerrno /usr/include/errno.h \
/usr/include/bits/errno.h /usr/include/linux/errno.h \
/usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
@@ -737,7 +738,8 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
/usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
/usr/include/bits/inf.h /usr/include/bits/nan.h \
/usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/c++/4.9.2/sstream /usr/include/c++/4.9.2/bits/sstream.tcc \
+ /usr/include/bits/mathinline.h /usr/include/c++/4.9.2/sstream \
+ /usr/include/c++/4.9.2/bits/sstream.tcc \
/usr/include/boost/type_traits/is_compound.hpp \
/usr/include/boost/type_traits/is_copy_constructible.hpp \
/usr/include/boost/noncopyable.hpp \
@@ -1111,6 +1113,7 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
/usr/include/boost/math/tools/user.hpp \
/usr/include/boost/detail/fenv.hpp /usr/include/c++/4.9.2/fenv.h \
/usr/include/fenv.h /usr/include/bits/fenv.h \
+ /usr/include/bits/fenvinline.h \
/usr/include/boost/math/special_functions/math_fwd.hpp \
/usr/include/boost/math/special_functions/detail/round_fwd.hpp \
/usr/include/boost/math/tools/promotion.hpp \
@@ -1306,11 +1309,6 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
../../OpenFPM_vcluster/src/MPI_wrapper/MPI_IallreduceW.hpp \
../../OpenFPM_vcluster/src/MPI_wrapper/MPI_IrecvW.hpp \
../../OpenFPM_vcluster/src/MPI_wrapper/MPI_IsendW.hpp \
- ../../OpenFPM_data/src/util/check_no_pointers.hpp \
- ../../OpenFPM_data/src/util/common.hpp \
- ../../OpenFPM_data/src/util/util_debug.hpp \
- /usr/include/c++/4.9.2/cxxabi.h \
- /usr/include/c++/4.9.2/x86_64-redhat-linux/bits/cxxabi_tweaks.h \
../../OpenFPM_vcluster/src/util/Vcluster_log.hpp \
../../OpenFPM_data/src/timer.hpp \
../../OpenFPM_data/src/Space/SpaceBox.hpp \
@@ -1324,7 +1322,10 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
../../OpenFPM_data/src/util/object_util.hpp \
../../OpenFPM_data/src/util/object_creator.hpp \
../../OpenFPM_data/src/util/util_debug.hpp \
+ /usr/include/c++/4.9.2/cxxabi.h \
+ /usr/include/c++/4.9.2/x86_64-redhat-linux/bits/cxxabi_tweaks.h \
../../OpenFPM_data/src/util/check_no_pointers.hpp \
+ ../../OpenFPM_data/src/util/common.hpp \
../../OpenFPM_data/src/util/object_s_di.hpp \
../../OpenFPM_data/src/util/object_si_d.hpp \
../../OpenFPM_devices/src/memory/ExtPreAlloc.hpp \
@@ -1399,6 +1400,7 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
../../OpenFPM_vcluster/src/Packer.hpp \
../../OpenFPM_data/src/Grid/util.hpp \
../../OpenFPM_data/src/Vector/util.hpp \
+ ../../OpenFPM_data/src/util/util_debug.hpp \
../../OpenFPM_vcluster/src/Pack_stat.hpp \
../../OpenFPM_vcluster/src/Pack_selector.hpp \
../../OpenFPM_vcluster/src/Unpacker.hpp \
@@ -1418,7 +1420,8 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
../../OpenFPM_data/src/NN/CellList/CellListBal.hpp \
../../OpenFPM_data/src/NN/CellList/CellListMem.hpp \
../../OpenFPM_data/src/Space/Ghost.hpp ../../OpenFPM_IO/src/util.hpp \
- unit_test_init_cleanup.hpp Decomposition/ORB_unit_test.hpp \
+ unit_test_init_cleanup.hpp Decomposition/CartDecomposition_unit_test.hpp \
+ Decomposition/CartDecomposition.hpp Decomposition/ORB_unit_test.hpp \
Decomposition/ORB.hpp ../../OpenFPM_data/src/data_type/scalar.hpp \
Graph/CartesianGraphFactory_unit_test.hpp \
Graph/CartesianGraphFactory.hpp metis_util_unit_test.hpp metis_util.hpp \
@@ -1430,9 +1433,7 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
../../OpenFPM_devices/src/memory/PreAllocHeapMemory.hpp \
../../OpenFPM_devices/src/memory/HeapMemory.hpp \
../../OpenFPM_IO/src/CSVWriter.hpp \
- ../../OpenFPM_IO/src/csv_multiarray.hpp \
- Decomposition/CartDecomposition_unit_test.hpp \
- Decomposition/CartDecomposition.hpp
+ ../../OpenFPM_IO/src/csv_multiarray.hpp
/usr/include/stdc-predef.h:
@@ -1628,6 +1629,8 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
/usr/include/alloca.h:
+/usr/include/bits/stdlib-bsearch.h:
+
/usr/include/bits/stdlib-float.h:
/usr/include/c++/4.9.2/cstdio:
@@ -1640,6 +1643,8 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
/usr/include/bits/sys_errlist.h:
+/usr/include/bits/stdio.h:
+
/usr/include/c++/4.9.2/cerrno:
/usr/include/errno.h:
@@ -3052,6 +3057,8 @@ Graph/CartesianGraphFactory.hpp:
/usr/include/bits/mathcalls.h:
+/usr/include/bits/mathinline.h:
+
/usr/include/c++/4.9.2/sstream:
/usr/include/c++/4.9.2/bits/sstream.tcc:
@@ -3884,6 +3891,8 @@ Graph/CartesianGraphFactory.hpp:
/usr/include/bits/fenv.h:
+/usr/include/bits/fenvinline.h:
+
/usr/include/boost/math/special_functions/math_fwd.hpp:
/usr/include/boost/math/special_functions/detail/round_fwd.hpp:
@@ -4314,16 +4323,6 @@ Grid/grid_dist_id.hpp:
../../OpenFPM_vcluster/src/MPI_wrapper/MPI_IsendW.hpp:
-../../OpenFPM_data/src/util/check_no_pointers.hpp:
-
-../../OpenFPM_data/src/util/common.hpp:
-
-../../OpenFPM_data/src/util/util_debug.hpp:
-
-/usr/include/c++/4.9.2/cxxabi.h:
-
-/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/cxxabi_tweaks.h:
-
../../OpenFPM_vcluster/src/util/Vcluster_log.hpp:
../../OpenFPM_data/src/timer.hpp:
@@ -4352,8 +4351,14 @@ Grid/grid_dist_key.hpp:
../../OpenFPM_data/src/util/util_debug.hpp:
+/usr/include/c++/4.9.2/cxxabi.h:
+
+/usr/include/c++/4.9.2/x86_64-redhat-linux/bits/cxxabi_tweaks.h:
+
../../OpenFPM_data/src/util/check_no_pointers.hpp:
+../../OpenFPM_data/src/util/common.hpp:
+
../../OpenFPM_data/src/util/object_s_di.hpp:
../../OpenFPM_data/src/util/object_si_d.hpp:
@@ -4502,6 +4507,8 @@ Grid/grid_dist_key.hpp:
../../OpenFPM_data/src/Vector/util.hpp:
+../../OpenFPM_data/src/util/util_debug.hpp:
+
../../OpenFPM_vcluster/src/Pack_stat.hpp:
../../OpenFPM_vcluster/src/Pack_selector.hpp:
@@ -4552,6 +4559,10 @@ dec_optimizer.hpp:
unit_test_init_cleanup.hpp:
+Decomposition/CartDecomposition_unit_test.hpp:
+
+Decomposition/CartDecomposition.hpp:
+
Decomposition/ORB_unit_test.hpp:
Decomposition/ORB.hpp:
@@ -4591,7 +4602,3 @@ Vector/vector_dist_key.hpp:
../../OpenFPM_IO/src/CSVWriter.hpp:
../../OpenFPM_IO/src/csv_multiarray.hpp:
-
-Decomposition/CartDecomposition_unit_test.hpp:
-
-Decomposition/CartDecomposition.hpp:
diff --git a/src/Decomposition/CartDecomposition.hpp b/src/Decomposition/CartDecomposition.hpp
index 2a3df1105bf4412aeb41ff0986a502ec0aa48abc..3a52b44a85aa56c88169414de1317fd9cb450956 100644
--- a/src/Decomposition/CartDecomposition.hpp
+++ b/src/Decomposition/CartDecomposition.hpp
@@ -104,6 +104,23 @@ class CartDecomposition
}
};
+ //! Particular case for internal ghost boxes, in contain the internal local ghost box
+ struct Box_sub_k : Box<dim,T>
+ {
+ // Domain id
+ size_t sub;
+
+ //! k \see getLocalGhostIBoxE
+ long int k;
+
+ Box_sub_k operator=(const Box<dim,T> & box)
+ {
+ ::Box<dim,T>::operator=(box);
+
+ return *this;
+ }
+ };
+
struct Box_dom
{
// Intersection between the local sub-domain enlarged by the ghost and the contiguous processor
@@ -115,6 +132,18 @@ class CartDecomposition
openfpm::vector_std< Box_sub> ibx;
};
+ //! Case for local ghost box
+ 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 > ebx;
+
+ // Intersection between the contiguous processor sub-domain enlarged by the ghost with the
+ // local sub-domain (Internal ghost)
+ openfpm::vector_std< Box_sub_k> ibx;
+ };
+
public:
//! Type of the domain we are going to decompose
@@ -154,7 +183,7 @@ private:
std::unordered_map<size_t, N_box> nn_processor_subdomains;
//! it contain the internal ghosts of the local processor
- openfpm::vector<Box_dom> loc_ghost_box;
+ openfpm::vector<lBox_dom> loc_ghost_box;
//! Structure that contain for each sub-domain box the processor id
//! exist for efficient global communication
@@ -176,10 +205,12 @@ private:
//! Runtime virtual cluster machine
Vcluster & v_cl;
- //! Cell-list that store the geometrical information about the intersection between the local sub-domain
- //! and the near processor sub-domains
+ //! Cell-list that store the geometrical information of the internal ghost boxes
CellList<dim,T,FAST> geo_cell;
+ //! Cell-list that store the geometrical information of the local internal ghost boxes
+ CellList<dim,T,FAST> lgeo_cell;
+
/*! \brief Create internally the decomposition
*
@@ -332,8 +363,12 @@ private:
// Initialize the geo_cell structure
geo_cell.Initialize(domain,div,orig);
+ lgeo_cell.Initialize(domain,div,orig);
}
+ // Save the ghost boundaries
+ Ghost<dim,T> ghost;
+
/*! \brief Create the external local ghost boxes
*
* \param ghost margin to enlarge
@@ -341,13 +376,18 @@ private:
*/
void create_loc_ghost_ebox(Ghost<dim,T> & ghost)
{
+ // Save the ghost
+ this->ghost = ghost;
+
loc_ghost_box.resize(sub_domains.size());
// For each sub-domain
for (size_t i = 0 ; i < sub_domains.size() ; i++)
{
- // add a local ghost box
- loc_ghost_box.add();
+ SpaceBox<dim,T> sub_with_ghost = sub_domains.get(i);
+
+ // enlarge the sub-domain with the ghost
+ sub_with_ghost.enlarge(ghost);
// intersect with the other local sub-domains
for (size_t j = 0 ; j < sub_domains.size() ; j++)
@@ -355,10 +395,6 @@ private:
if (i == j)
continue;
- SpaceBox<dim,T> sub_with_ghost = sub_domains.get(j);
- // enlarge the sub-domain with the ghost
- sub_with_ghost.enlarge(ghost);
-
::Box<dim,T> bi;
bool intersect = sub_with_ghost.Intersect(::SpaceBox<dim,T>(sub_domains.get(j)),bi);
@@ -369,7 +405,18 @@ private:
b.sub = j;
b = bi;
- loc_ghost_box.get(i).ibx.add(b);
+ // local external ghost box
+ loc_ghost_box.get(i).ebx.add(b);
+
+ // search this box in the internal box of the sub-domain j
+ for (size_t k = 0; k < loc_ghost_box.get(j).ibx.size() ; k++)
+ {
+ if (loc_ghost_box.get(j).ibx.get(k).sub == i)
+ {
+ loc_ghost_box.get(j).ibx.get(k).k = loc_ghost_box.get(i).ebx.size()-1;
+ break;
+ }
+ }
}
}
}
@@ -387,29 +434,26 @@ private:
// For each sub-domain
for (size_t i = 0 ; i < sub_domains.size() ; i++)
{
- SpaceBox<dim,T> sub_with_ghost = sub_domains.get(i);
-
- // enlarge the sub-domain with the ghost
- sub_with_ghost.enlarge(ghost);
-
- // add a local ghost box
- loc_ghost_box.add();
-
// intersect with the others local sub-domains
for (size_t j = 0 ; j < sub_domains.size() ; j++)
{
if (i == j)
continue;
+ SpaceBox<dim,T> sub_with_ghost = sub_domains.get(j);
+ // enlarge the sub-domain with the ghost
+ sub_with_ghost.enlarge(ghost);
+
::Box<dim,T> bi;
- bool intersect = sub_with_ghost.Intersect(::SpaceBox<dim,T>(sub_domains.get(j)),bi);
+ bool intersect = sub_with_ghost.Intersect(::SpaceBox<dim,T>(sub_domains.get(i)),bi);
if (intersect == true)
{
- Box_sub b;
+ Box_sub_k b;
b.sub = j;
b = bi;
+ b.k = -1;
loc_ghost_box.get(i).ibx.add(b);
}
@@ -612,11 +656,12 @@ private:
Box_sub sb;
sb = b_int.box;
sb.sub = i;
+
pr_box_int.ibx.add(sb);
// update the geo_cell list
- // get the boxes this box span
+ // get the cells this box span
const grid_key_dx<dim> p1 = geo_cell.getCellGrid(b_int.box.getP1());
const grid_key_dx<dim> p2 = geo_cell.getCellGrid(b_int.box.getP2());
@@ -706,23 +751,6 @@ public:
bbox.zero();
}
- /*! \brief Cartesian decomposition constructor, it divide the space in boxes
- *
- * \param dec is a vector that store how to divide on each dimension
- * \param domain is the domain to divide
- * \param v_cl are information of the cluster runtime machine
- *
- */
- CartDecomposition(std::vector<size_t> dec, Domain<dim,T> domain, Vcluster & v_cl)
- :gr(dec),cd(domain,dec,0),domain(domain),v_cl(v_cl)
- {
- // Reset the box to zero
- bbox.zero();
-
- // Create the decomposition
- CreateDecomposition(v_cl);
- }
-
//! Cartesian decomposition destructor
~CartDecomposition()
{}
@@ -993,7 +1021,7 @@ p1[0]<-----+ +----> p2[0]
*
*
*/
- void calculateGhostBoxes(Ghost<dim,T> & ghost)
+ void calculateGhostBoxes()
{
#ifdef DEBUG
// the ghost margins are assumed to be smaller
@@ -1036,8 +1064,9 @@ p1[0]<-----+ +----> p2[0]
// create the internal structures that store ghost information
create_box_nn_processor_ext(ghost);
create_box_nn_processor_int(ghost);
- create_loc_ghost_ebox(ghost);
+ // ebox must come after ibox (in this case)
create_loc_ghost_ibox(ghost);
+ create_loc_ghost_ebox(ghost);
}
/*! \brief processorID return in which processor the particle should go
@@ -1077,30 +1106,14 @@ p1[0]<-----+ +----> p2[0]
/*! \brief Set the parameter of the decomposition
*
- * \param div_ std::vector storing into how many domain to decompose on each dimension
- * \param domain_ domain to decompose
- *
- */
- void setParameters(std::vector<size_t> div_, Domain<dim,T> domain_)
- {
- // Set the decomposition parameters
-
- div = div_;
- domain = domain_;
-
- //! Create the decomposition
-
- CreateDecomposition(v_cl);
- }
-
- /*! \brief Set the parameter of the decomposition
- *
- * \param div_ std::vector storing into how many domain to decompose on each dimension
+ * \param div_ storing into how many domain to decompose on each dimension
* \param domain_ domain to decompose
*
*/
- void setParameters(const size_t (& div_)[dim], Domain<dim,T> domain_)
+ void setParameters(const size_t (& div_)[dim], Domain<dim,T> domain_, Ghost<dim,T> ghost = Ghost<dim,T>())
{
+ // set the ghost
+ this->ghost = ghost;
// Set the decomposition parameters
gr.setDimensions(div_);
@@ -1166,11 +1179,9 @@ p1[0]<-----+ +----> p2[0]
return sub_domains.get<Object>(id);
}
- /*! \brief Get the total number of Hyper-cube
+ /*! \brief Get the total number of sub-domain for the local processor
*
- * Get the total number of Hyper-cube
- *
- * \return The total number of hyper-cube
+ * \return The total number of sub-domains
*
*/
@@ -1179,37 +1190,12 @@ p1[0]<-----+ +----> p2[0]
return gr.size();
}
- /*! \brief produce an hyper-cube approximation of the space decomposition
- *
- */
-
- void hyperCube()
- {
- }
-
-
- /*! \brief Get the local grids
- *
- * Get the local grids
+ /*! \brief Get the local sub-domain
*
- * \return the local grids
+ * \param i (each local processor can have more than one sub-domain)
+ * \return the sub-domain
*
*/
-
- auto getLocalHyperCubes() -> decltype(sub_domains) &
- {
- return sub_domains;
- }
-
- /*! \brief Get the local hyper-cubes
- *
- * Get the local hyper-cubes
- *
- * \param lc is the id of the space
- * \return the local hyper-cube
- *
- */
-
SpaceBox<dim,T> getLocalHyperCube(size_t lc)
{
// Create a space box
@@ -1227,6 +1213,24 @@ p1[0]<-----+ +----> p2[0]
return sp;
}
+ /*! \brief Get the local sub-domain with ghost extension
+ *
+ * \param i (each local processor can have more than one sub-domain)
+ * \return the sub-domain
+ *
+ */
+
+ SpaceBox<dim,T> getSubDomainWithGhost(size_t lc)
+ {
+ // Create a space box
+ SpaceBox<dim,T> sp = sub_domains.get(lc);
+
+ // enlarge with ghost
+ sp.enlarge(ghost);
+
+ return sp;
+ }
+
/*! \brief Return the structure that store the physical domain
*
* Return the structure that store the physical domain
@@ -1323,7 +1327,7 @@ p1[0]<-----+ +----> p2[0]
*/
inline size_t getLocalNEGhost(size_t id)
{
- return loc_ghost_box.get(id).ibx.size();
+ return loc_ghost_box.get(id).ebx.size();
}
/*! \brief Get the number of internal local ghost box for each sub-domain
@@ -1335,7 +1339,7 @@ p1[0]<-----+ +----> p2[0]
*/
inline size_t getLocalNIGhost(size_t id)
{
- return loc_ghost_box.get(id).ebx.size();
+ return loc_ghost_box.get(id).ibx.size();
}
/*! \brief Get the j Internal ghost box for one processor
@@ -1362,7 +1366,26 @@ p1[0]<-----+ +----> p2[0]
return proc_int_box.get(id).ebx.get(j);
}
+ /*! \brief For the sub-domain i intersected with the sub-domain j enlarged, the associated
+ * external ghost box is located in getLocalIGhostBox(j,k) with
+ * getLocalIGhostSub(j,k) == i, this function return k
+ *
+ *
+ */
+ inline size_t getLocalIGhostE(size_t i, size_t j)
+ {
+ return loc_ghost_box.get(i).ibx.get(j).k;
+ }
+
/*! \brief Get the j internal local ghost box for the i sub-domain of the local processor
+ *
+ * \note For the sub-domain i intersected with the sub-domain j enlarged, the associated
+ * external ghost box is located in getLocalIGhostBox(j,k) with
+ * getLocalIGhostSub(j,k) == i
+ *
+ * To get k use getLocalIGhostE
+ *
+ * \see getLocalIGhostE
*
* \param i sub-domain
* \param j box
@@ -1371,7 +1394,7 @@ p1[0]<-----+ +----> p2[0]
*/
inline const ::Box<dim,T> & getLocalIGhostBox(size_t i, size_t j) const
{
- return loc_ghost_box.get(i).ibox.get(j).box;
+ return loc_ghost_box.get(i).ibx.get(j);
}
/*! \brief Get the j external local ghost box for the local processor
@@ -1383,7 +1406,7 @@ p1[0]<-----+ +----> p2[0]
*/
inline const ::Box<dim,T> & getLocalEGhostBox(size_t i, size_t j) const
{
- return loc_ghost_box.get(i).ebox.get(j).box;
+ return loc_ghost_box.get(i).ebx.get(j);
}
/*! \brief Considering that sub-domain has N internal local ghost box identified
@@ -1396,9 +1419,9 @@ p1[0]<-----+ +----> p2[0]
* \return the box
*
*/
- inline const ::Box<dim,T> & getLocalIGhostSub(size_t i, size_t j) const
+ inline size_t getLocalIGhostSub(size_t i, size_t j) const
{
- return loc_ghost_box.get(i).ibox.get(j).sub;
+ return loc_ghost_box.get(i).ibx.get(j).sub;
}
/*! \brief Considering that sub-domain has N external local ghost box identified
@@ -1411,9 +1434,9 @@ p1[0]<-----+ +----> p2[0]
* \return the box
*
*/
- inline const ::Box<dim,T> & getLocalEGhostSub(size_t i, size_t j) const
+ inline size_t getLocalEGhostSub(size_t i, size_t j) const
{
- return loc_ghost_box.get(i).ebox.get(j).sub;
+ return loc_ghost_box.get(i).ebx.get(j).sub;
}
/*! \brief Get the local sub-domain at witch belong the internal ghost box
@@ -1606,6 +1629,40 @@ p1[0]<-----+ +----> p2[0]
return true;
}
+
+ /*! \brief function to check the consistency of the information of the decomposition
+ *
+ * \return false if is inconsistent
+ *
+ */
+ bool check_consistency()
+ {
+ //! for each sub-domain
+ for (size_t i = 0 ; i < loc_ghost_box.size() ; i++)
+ {
+ for (size_t j = 0 ; j < loc_ghost_box.get(i).ibx.size() ; j++)
+ {
+ if (loc_ghost_box.get(i).ibx.get(j).k == -1)
+ return false;
+ }
+ }
+
+ // if we have more than one sub domain, the local internal/external ghost boxes must be different
+ // from zero
+
+ if (getNLocalHyperCube() > 1)
+ {
+ for (size_t i = 0 ; i < loc_ghost_box.size() ; i++)
+ {
+ if (loc_ghost_box.get(i).ibx.size() == 0)
+ return false;
+ if (loc_ghost_box.get(i).ebx.size() == 0)
+ return false;
+ }
+ }
+
+ return true;
+ }
};
diff --git a/src/Decomposition/CartDecomposition_unit_test.hpp b/src/Decomposition/CartDecomposition_unit_test.hpp
index d358ef7753386693e0ef5d27030695785cd23f88..490cf438810a059f19ff7743f39e939393d25ba0 100644
--- a/src/Decomposition/CartDecomposition_unit_test.hpp
+++ b/src/Decomposition/CartDecomposition_unit_test.hpp
@@ -31,13 +31,13 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_test_use)
for (int i = 0 ; i < 3 ; i++)
{div[i] = openfpm::math::round_big_2(pow(n_sub,1.0/3));}
- // Decompose
- dec.setParameters(div,box);
-
Ghost<3,float> g(0.01);
+ // Decompose
+ dec.setParameters(div,box,g);
+
// create a ghost border
- dec.calculateGhostBoxes(g);
+ dec.calculateGhostBoxes();
// For each calculated ghost box
for (size_t i = 0 ; i < dec.getNIGhostBox() ; i++)
@@ -61,14 +61,16 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_test_use)
if (found == false)
{
- int debug = 0;
- debug++;
-
const openfpm::vector<size_t> pr2 = dec.template ghost_processorID<CartDecomposition<3,float>::processor_id>(p);
}
BOOST_REQUIRE_EQUAL(found,true);
}
+
+ // Check the consistency
+
+ bool val = dec.check_consistency();
+ BOOST_REQUIRE_EQUAL(val,true);
}
BOOST_AUTO_TEST_SUITE_END()
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index 636aa555947d962ca3d64e664644d4b64931141b..b9e6f782fd6255ee0a14f3f8205237824923da09 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -267,9 +267,10 @@ class grid_dist_id
if (ib.isValid() == false)
continue;
- pib.ibx.add();
- pib.ibx.last() = ib;
- pib.ibx.last().sub = dec.getLocalIGhostSub(i,j);
+ pib.bid.add();
+ pib.bid.last().box = ib;
+ pib.bid.last().sub = dec.getLocalIGhostSub(i,j);
+ pib.bid.last().k = dec.getLocalIGhostE(i,j);
}
}
@@ -300,13 +301,13 @@ class grid_dist_id
::Box<dim,St> ib_dom = dec.getLocalEGhostBox(i,j);
::Box<dim,size_t> ib = cd_sm.convertDomainSpaceIntoGridUnits(ib_dom);
- // Check if ib is valid if not it mean that the internal ghost does not contain information so skip it
- if (ib.isValid() == false)
- continue;
+ // Warning even if the ib is not a valid in grid unit we are forced to keep it
+ // otherwise the value returned from dec.getLocalEGhostSub(i,j) will point to an
+ // invalid or wrong box
- pib.ebx.add();
- pib.ebx.last() = ib;
- pib.ebx.last().sub = dec.getLocalEGhostSub(i,j);
+ pib.bid.add();
+ pib.bid.last().box = ib;
+ pib.bid.last().sub = dec.getLocalEGhostSub(i,j);
}
}
@@ -326,37 +327,45 @@ class grid_dist_id
//! 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;
+ 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
- size_t sub_id = loc_ig_box.get(i).bid.get(j).sub;
+ // sub domain connected with external box
+ size_t sub_id_dst = loc_ig_box.get(i).bid.get(j).sub;
// local external ghost box connected
- size_t e_box_sub = loc_ig_box.get(i).bid.get(j).e_b;
+ size_t k = loc_ig_box.get(i).bid.get(j).k;
- Box<dim,size_t> & bx_dst = loc_eg_box.get(sub_id).bid.get(e_box_sub).box;
+ 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
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).getGrid(),bx_dst.getKP1(),bx_dst.getKP2());
+ grid_key_dx_iterator_sub<dim> sub_dst(loc_grid.get(sub_id_dst).getGrid(),bx_dst.getKP1(),bx_dst.getKP2());
#ifdef DEBUG
+ 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);
+ auto & gd = loc_grid.get(sub_id_dst);
while (sub_src.isNext())
{
// Option 1
- gd.set(sub_src.get(),gs,sub_src.get());
+ gd.set(sub_dst.get(),gs,sub_src.get());
// Option 2
- gd.get_o(sub_src.get()) = gs.get_o(sub_dst.get());
+// gd.get_o(sub_dst.get()) = gs.get_o(sub_src.get());
++sub_src;
++sub_dst;
@@ -434,13 +443,13 @@ public:
{div[i] = openfpm::math::round_big_2(pow(n_sub,1.0/dim));}
// Create the sub-domains
- dec.setParameters(div,domain);
+ dec.setParameters(div,domain,ghost);
// Create local grid
Create();
// Calculate ghost boxes
- dec.calculateGhostBoxes(ghost);
+ dec.calculateGhostBoxes();
}
/*! \brief Get the object that store the decomposition information
@@ -464,29 +473,15 @@ public:
return cd_sm;
}
- /*! \brief Create
- *
- *
- */
-
/*! \brief Create the grids on memory
*
*/
void Create()
{
- // Box used for rounding error
-// Box<dim,St> rnd_box;
-// for (size_t i = 0 ; i < dim ; i++) {rnd_box.setHigh(i,0.5); rnd_box.setLow(i,0.5);}
- // Box used for rounding in case of ghost
Box<dim,St> g_rnd_box;
for (size_t i = 0 ; i < dim ; i++) {g_rnd_box.setHigh(i,0.5); g_rnd_box.setLow(i,-0.5);}
- // ! Create an hyper-cube approximation.
- // ! In order to work on grid_dist the decomposition
- // ! has to be a set of hyper-cube
- dec.hyperCube();
-
// Get the number of local grid needed
size_t n_grid = dec.getNLocalHyperCube();
@@ -503,39 +498,25 @@ public:
// Get the local hyper-cube
SpaceBox<dim,St> sp = dec.getLocalHyperCube(i);
+ SpaceBox<dim,St> sp_g = dec.getSubDomainWithGhost(i);
- // Convert from SpaceBox<dim,float> to SpaceBox<dim,long int>
+ // Convert from SpaceBox<dim,St> to SpaceBox<dim,long int>
SpaceBox<dim,long int> sp_t = cd_sm.convertDomainSpaceIntoGridUnits(sp);
-
- // convert the ghost from space coordinate to grid units
- Ghost<dim,St> g_int = ghost;
- g_int /= cd_sm.getCellBox().getP2();
-
- // enlarge by 0.5 for rounding
- g_int.enlarge(g_rnd_box);
-
- // convert from Ghost<dim,St> to Ghost<dim,long int>
- Ghost<dim,long int> g_int_t = g_int;
+ SpaceBox<dim,long int> sp_tg = cd_sm.convertDomainSpaceIntoGridUnits(sp_g);
//! Save the origin of the local grid
- gdb_ext.last().origin = sp_t.getP1();
-
- // Center the local grid to zero
- sp_t -= sp_t.getP1();
+ gdb_ext.last().origin = sp_tg.getP1();
// save information about the local grid: domain box seen inside the domain + ghost box (see GDBoxes for a visual meaning)
// and where the GDBox start, or the origin of the local grid (+ghost) in global coordinate
gdb_ext.last().Dbox = sp_t;
- gdb_ext.last().Dbox -= g_int_t.getP1();
- // needed because the last key coordinate is size - 1 on each direction
- // The origin is the Domain box + ghost, so shift
- gdb_ext.last().origin += g_int_t.getP1();
+ gdb_ext.last().Dbox -= sp_tg.getP1();
- // Enlarge sp with the Ghost size
- sp_t.enlarge_fix_P1(g_int_t);
+ // center to zero
+ sp_tg -= sp_tg.getP1();
// Get the size of the local grid
- for (size_t i = 0 ; i < dim ; i++) {l_res[i] = (sp_t.getHigh(i) >= 0)?(sp_t.getHigh(i)+1):0;}
+ for (size_t i = 0 ; i < dim ; i++) {l_res[i] = (sp_tg.getHigh(i) >= 0)?(sp_tg.getHigh(i)+1):0;}
// Set the dimensions of the local grid
loc_grid.get(i).template resize<Memory>(l_res);
@@ -637,7 +618,7 @@ public:
size_t sub;
//! external box
- size_t e_b;
+ size_t k;
};
/*! \brief It store the information about the external ghost box
@@ -752,6 +733,12 @@ public:
// Convert the ghost external boxes into grid unit boxes
create_eg_box();
+ // Convert the local ghost internal boxes into grid unit boxes
+ create_local_ig_box();
+
+ // Convert the local external ghost boxes into grid unit boxes
+ create_local_eg_box();
+
// total number of sending vector
std::vector<size_t> pap_prp;
diff --git a/src/Grid/grid_dist_id_iterator.hpp b/src/Grid/grid_dist_id_iterator.hpp
index 7a50cebc7b8235b67301f3a65f46617f926d884c..0ae0639577d6b2dea038b263d084215ff85646ac 100644
--- a/src/Grid/grid_dist_id_iterator.hpp
+++ b/src/Grid/grid_dist_id_iterator.hpp
@@ -122,7 +122,7 @@ class grid_dist_iterator<dim,device_grid,FREE>
*
*/
- grid_dist_iterator<dim,device_grid,FREE> operator++()
+ inline grid_dist_iterator<dim,device_grid,FREE> operator++()
{
++a_it;
@@ -136,7 +136,7 @@ class grid_dist_iterator<dim,device_grid,FREE>
g_c++;
// When the grid has size 0 potentially all the other informations are garbage
- while (gList[g_c].size() == 0 ) g_c++;
+ while (g_c < gList.size() && (gList[g_c].size() == 0 || gdb_ext.get(g_c).Dbox.isValid() == false ) ) g_c++;
// get the next grid iterator
if (g_c < gList.size())
@@ -153,7 +153,7 @@ class grid_dist_iterator<dim,device_grid,FREE>
* \return true if there is the next, false otherwise
*
*/
- bool isNext()
+ inline bool isNext()
{
// If there are no other grid stop
@@ -168,7 +168,7 @@ class grid_dist_iterator<dim,device_grid,FREE>
* \return the actual key
*
*/
- grid_dist_key_dx<dim> get()
+ inline grid_dist_key_dx<dim> get()
{
return grid_dist_key_dx<dim>(g_c,a_it.get());
}
@@ -239,7 +239,7 @@ class grid_dist_iterator<dim,device_grid,FIXED>
g_c++;
// When the grid has size 0 potentially all the other informations are garbage
- while (gList[g_c].size() == 0 ) g_c++;
+ while (g_c < gList.size() && gList[g_c].size() == 0 ) g_c++;
// get the next grid iterator
if (g_c < gList.size())
diff --git a/src/Grid/grid_dist_id_unit_test.hpp b/src/Grid/grid_dist_id_unit_test.hpp
index 9be882ec715c591ab8c601313ca47fe879dc2b14..6629ff267e271e136f4528fbbd5ef2ff7e8af7c3 100644
--- a/src/Grid/grid_dist_id_unit_test.hpp
+++ b/src/Grid/grid_dist_id_unit_test.hpp
@@ -58,6 +58,10 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_domain_grid_unit_converter_test)
// get the decomposition
auto & dec = g_dist.getDecomposition();
+ // check the consistency of the decomposition
+ bool val = dec.check_consistency();
+ BOOST_REQUIRE_EQUAL(val,true);
+
// for each local volume
// Get the number of local grid needed
size_t n_grid = dec.getNLocalHyperCube();
@@ -92,6 +96,8 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
for (long int k = 1026 ; k > 1 ; k-= 33)
{
+ std::cout << "Testing: " << k << "\n";
+
// grid size
size_t sz[2];
sz[0] = k;
@@ -103,6 +109,10 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
// Distributed grid with id decomposition
grid_dist_id<2, float, scalar<float>, CartDecomposition<2,float>> g_dist(sz,domain,g);
+ // check the consistency of the decomposition
+ bool val = g_dist.getDecomposition().check_consistency();
+ BOOST_REQUIRE_EQUAL(val,true);
+
// Grid sm
grid_sm<2,void> info(sz);
@@ -142,12 +152,6 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
auto key = dom2.get();
auto key_g = g_dist.getGKey(key);
- if (key_g.get(0) == 503 && key_g.get(1) == 779)
- {
- int debug = 0;
- debug++;
- }
-
BOOST_REQUIRE_EQUAL(g_dist.template get<0>(key),info.LinId(key_g));
++dom2;
@@ -168,12 +172,6 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
// In this case the boundary condition are non periodic
if (g_dist.isInside(key_g))
{
- if (g_dist.template get<0>(key) != info.LinId(key_g))
- {
- int debug = 0;
- debug++;
- }
-
BOOST_REQUIRE_EQUAL(g_dist.template get<0>(key),info.LinId(key_g));
}
diff --git a/src/Makefile b/src/Makefile
index 9ff90164b05e220dcb359cc424bbe7e69dc6b10f..e9a648097ef05cd3bbd8ada9ad456f3f8d78dc61 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -193,7 +193,7 @@ CUDA_CFLAGS = -I -I -I/usr/local/cuda/include
CUDA_LIBS = -L -L -L/usr/local/cuda/lib64 -lcuda -lcudart
CXX = mpic++
CXXDEPMODE = depmode=gcc3
-CXXFLAGS = --std=c++11 -march=native -mtune=native -g3 -Wall -O0
+CXXFLAGS = --std=c++11 -march=native -mtune=native -Wall -O3 -g3 -funroll-loops
CYGPATH_W = echo
DEFS = -DHAVE_CONFIG_H
DEPDIR = .deps
@@ -214,7 +214,7 @@ LTLIBOBJS =
MAKEINFO = ${SHELL} /home/i-bird/Desktop/MOSAIC/OpenFPM_project/OpenFPM_pdata/missing makeinfo
MKDIR_P = /usr/bin/mkdir -p
NVCC = /usr/local/cuda/bin/nvcc
-NVCCFLAGS = -g -O0
+NVCCFLAGS = -O3
NVCC_EXIST = yes
OBJEXT = o
PACKAGE = full-package-name
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 4b1a02761605fa2bc7cfa1983fc2f070f434bda5..d52d7cda028eb7f5b17c39bf44cb6d3aec3e663c 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -77,7 +77,7 @@ public:
* \param Global number of elements
*
*/
- vector_dist(size_t np, Box box)
+ vector_dist(size_t np, Box box, Ghost<point::dims,typename point::coord_type> g = Ghost<point::dims,typename point::coord_type>())
:dec(Decomposition(*global_v_cluster)),v_cl(*global_v_cluster)
{
// Allocate unassigned particles vectors
@@ -106,7 +106,7 @@ public:
{div[i] = openfpm::math::round_big_2(pow(n_sub,1.0/point::dims));}
// Create the sub-domains
- dec.setParameters(div,box);
+ dec.setParameters(div,box,g);
// Get the bounding box containing the processor domain
const ::Box<point::dims,typename point::coord_type> & bbound = dec.getProcessorBounds();
@@ -173,9 +173,9 @@ public:
* \param g ghost
*
*/
- void setGhost(Ghost<point::dims,typename point::coord_type> & g)
+ void setGhost()
{
- dec.calculateGhostBoxes(g);
+ dec.calculateGhostBoxes();
}
//! It map the processor id with the communication request into map procedure
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index 837546e12291e09e063151dae0509febb088e5fc..d73d720eacccace1bf34fc6fae9091fd98c9970d 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -42,8 +42,11 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
grid_key_dx<2> stop(point_div * (v_cl.getProcessUnitID() + 1) - 1,g_div[0]);
auto g_sub = g_info.getSubIterator(start,stop);
+ // set the ghost based on the radius cut off (make just a little bit smaller than the spacing)
+ Ghost<2,float> g(spacing.get(0) - spacing .get(0) * 0.0001);
+
// Vector of particles
- vector_dist<Point<2,float>, Point_test<float>, Box<2,float>, CartDecomposition<2,float> > vd(g_info.size(),box);
+ vector_dist<Point<2,float>, Point_test<float>, Box<2,float>, CartDecomposition<2,float> > vd(g_info.size(),box,g);
auto it = vd.getIterator();
@@ -57,12 +60,6 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
vd.template getPos<s::x>(key_v)[0] = key.get(0) * spacing[0] + m_spacing[0];
vd.template getPos<s::x>(key_v)[1] = key.get(1) * spacing[1] + m_spacing[1];
- if (vd.template getPos<s::x>(key_v)[0] >= 1.0 || vd.template getPos<s::x>(key_v)[1] >= 1.0)
- {
- int debug = 0;
- debug++;
- }
-
++g_sub;
++it;
}
@@ -94,12 +91,6 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost )
++it;
}
- // set the ghost based on the radius cut off (make just a little bit smaller than the spacing)
- Ghost<2,float> g(spacing.get(0) - spacing .get(0) * 0.0001);
-
- // set the ghost
- vd.setGhost(g);
-
//! Output the decomposition
ct.write(".");
diff --git a/src/main.cpp b/src/main.cpp
index bdee86089aaed30fc6d36b449445bb34fbc4c7f0..fe5923ba5cde47805ad87778d49c9de02402728e 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -18,11 +18,12 @@
#include "util.hpp"
#include "unit_test_init_cleanup.hpp"
+#include "Decomposition/CartDecomposition_unit_test.hpp"
#include "Decomposition/ORB_unit_test.hpp"
#include "Graph/CartesianGraphFactory_unit_test.hpp"
#include "metis_util_unit_test.hpp"
#include "dec_optimizer_unit_test.hpp"
#include "Grid/grid_dist_id_unit_test.hpp"
#include "Vector/vector_dist_unit_test.hpp"
-#include "Decomposition/CartDecomposition_unit_test.hpp"
+