diff --git a/configure.ac b/configure.ac
index cd1ce4486715c633a72f81e09e6eedaf0e048418..08578e10db2a274fc0219f4bdb0afc21ad4c7c01 100755
--- a/configure.ac
+++ b/configure.ac
@@ -9,10 +9,7 @@ AC_CONFIG_SRCDIR([src/main.cpp])
AM_INIT_AUTOMAKE
AC_CONFIG_HEADER([src/config/config.h])
m4_ifdef([ACX_PTHREAD],,[m4_include([m4/acx_pthread.m4])])
-m4_ifdef([AX_CHECK_CL],,[m4_include([m4/ax_opencl.m4])])
-m4_ifdef([AX_BOOST_BASE],,[m4_include([m4/ax_boost_base.m4])])
-m4_ifdef([AX_BOOST_PROGRAM_OPTIONS],,[m4_include([m4/ax_boost_program_options.m4])])
-m4_ifdef([AX_BOOST_THREAD],,[m4_include([m4/ax_boost_thread.m4])])
+m4_ifdef([AX_BOOST],,[m4_include([m4/ax_boost.m4])])
m4_ifdef([ACX_MPI],,[m4_include([m4/acx_mpi.m4])])
m4_ifdef([AX_OPENMP],,[m4_include([m4/ax_openmp.m4])])
m4_ifdef([AX_CUDA],,[m4_include([m4/ax_cuda.m4])])
@@ -53,7 +50,7 @@ if test x"$debuger" = x"yes"; then
CXXFLAGS="$CXXFLAGS -g3 -Wall -O0 "
NVCCFLAGS+="$NVCCFLAGS -g -O0 "
else
- CXXFLAGS="$CXXFLAGS -Wall -O3 -g3 -flto -funroll-loops "
+ CXXFLAGS="$CXXFLAGS -Wall -O3 -g3 -funroll-loops "
NVCCFLAGS+="$NVCCFLAGS -O3 "
fi
@@ -80,6 +77,10 @@ fi
INCLUDES_PATH+="-I. -Isrc/config/ -I../../metis_install/include -I../../OpenFPM_IO/src -I../../OpenFPM_data/src -I../../OpenFPM_devices/src -I../../OpenFPM_vcluster/src/"
+##### CHECK FOR BOOST ##############
+
+AX_BOOST([1.52],[],[])
+
####### Checking for GPU support
AX_CUDA
@@ -116,10 +117,6 @@ AM_CONDITIONAL(BUILDCUDA, test ! x$NVCC = x"no")
AC_DEFINE([HAVE_MPI],[],[MPI Enabled])
-#####
-
-AX_CHECK_COMPILER_FLAGS([-Wno-unused-but-set-variable],[CXXFLAGS="$CXXFLAGS -Wno-unused-but-set-variable"],[])
-
AC_SUBST(NVCCFLAGS)
AC_SUBST(INCLUDES_PATH)
diff --git a/src/.deps/pdata-VCluster.Po b/src/.deps/pdata-VCluster.Po
index 2a569d2695f35f2ee8ae5cde33efa626a9374bf9..259e45d854988f9b650d6b28625fb755665a0947 100644
--- a/src/.deps/pdata-VCluster.Po
+++ b/src/.deps/pdata-VCluster.Po
@@ -956,6 +956,7 @@ pdata-VCluster.o: ../../OpenFPM_vcluster/src/VCluster.cpp \
../../OpenFPM_data/src/Grid/comb.hpp \
../../OpenFPM_data/src/Grid/grid_key_expression.hpp \
../../OpenFPM_data/src/Space/Shape/Point.hpp \
+ ../../OpenFPM_data/src/Grid/Encap.hpp \
../../OpenFPM_data/src/Grid/grid_key.hpp \
../../OpenFPM_data/src/Grid/Encap.hpp \
../../OpenFPM_data/src/memory_array.hpp \
@@ -3059,6 +3060,8 @@ pdata-VCluster.o: ../../OpenFPM_vcluster/src/VCluster.cpp \
../../OpenFPM_data/src/Space/Shape/Point.hpp:
+../../OpenFPM_data/src/Grid/Encap.hpp:
+
../../OpenFPM_data/src/Grid/grid_key.hpp:
../../OpenFPM_data/src/Grid/Encap.hpp:
diff --git a/src/.deps/pdata-main.Po b/src/.deps/pdata-main.Po
index 59a49a224d42709fbf8963718c63e9dea987dbc4..2f0458c8c6aef30c75317261ccd794d027839cd8 100644
--- a/src/.deps/pdata-main.Po
+++ b/src/.deps/pdata-main.Po
@@ -921,6 +921,7 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
../../OpenFPM_data/src/Grid/comb.hpp \
../../OpenFPM_data/src/Grid/grid_key_expression.hpp \
../../OpenFPM_data/src/Space/Shape/Point.hpp \
+ ../../OpenFPM_data/src/Grid/Encap.hpp \
../../OpenFPM_data/src/Grid/grid_key.hpp \
../../OpenFPM_data/src/Grid/Encap.hpp \
../../OpenFPM_data/src/memory_array.hpp \
@@ -1288,13 +1289,78 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
../../OpenFPM_data/src/Space/SpaceBox.hpp \
../../OpenFPM_data/src/Space/Shape/Point.hpp \
../../OpenFPM_data/src/Space/Shape/Box.hpp \
- ../../OpenFPM_data/src/Grid/Encap.hpp Grid/grid_dist_id_iterator.hpp \
+ ../../OpenFPM_data/src/Space/Ghost.hpp Grid/grid_dist_id_iterator.hpp \
Grid/grid_dist_key.hpp ../../OpenFPM_data/src/Point_test.hpp \
../../OpenFPM_data/src/base_type.hpp Decomposition/CartDecomposition.hpp \
Decomposition/Decomposition.hpp ../../OpenFPM_data/src/global_const.hpp \
SubdomainGraphNodes.hpp metis_util.hpp \
../../metis_install/include/metis.h /usr/include/inttypes.h \
- ../../OpenFPM_IO/src/VTKWriter.hpp dec_optimizer.hpp \
+ ../../OpenFPM_IO/src/VTKWriter.hpp \
+ ../../OpenFPM_IO/src/VTKWriter_graph.hpp \
+ ../../OpenFPM_IO/src/VTKWriter_vector_box.hpp \
+ /usr/include/boost/math/special_functions/pow.hpp \
+ /usr/include/boost/math/policies/error_handling.hpp \
+ /usr/include/boost/math/tools/precision.hpp \
+ /usr/include/boost/format.hpp \
+ /usr/include/boost/format/detail/compat_workarounds.hpp \
+ /usr/include/boost/format/detail/config_macros.hpp \
+ /usr/include/boost/format/detail/workarounds_gcc-2_95.hpp \
+ /usr/include/boost/format/detail/workarounds_stlport.hpp \
+ /usr/include/boost/format/format_fwd.hpp \
+ /usr/include/boost/format/internals_fwd.hpp \
+ /usr/include/boost/format/internals.hpp \
+ /usr/include/boost/format/alt_sstream.hpp \
+ /usr/include/boost/format/alt_sstream_impl.hpp \
+ /usr/include/boost/format/format_class.hpp \
+ /usr/include/boost/format/exceptions.hpp \
+ /usr/include/boost/format/format_implementation.hpp \
+ /usr/include/boost/format/group.hpp \
+ /usr/include/boost/format/feed_args.hpp \
+ /usr/include/boost/format/detail/msvc_disambiguater.hpp \
+ /usr/include/boost/format/parsing.hpp \
+ /usr/include/boost/format/free_funcs.hpp \
+ /usr/include/boost/format/detail/unset_macros.hpp \
+ ../../OpenFPM_IO/src/util.hpp \
+ /usr/include/boost/iostreams/device/mapped_file.hpp \
+ /usr/include/boost/iostreams/close.hpp \
+ /usr/include/boost/iostreams/categories.hpp \
+ /usr/include/boost/iostreams/flush.hpp \
+ /usr/include/boost/iostreams/detail/dispatch.hpp \
+ /usr/include/boost/iostreams/detail/select.hpp \
+ /usr/include/boost/iostreams/traits.hpp \
+ /usr/include/boost/iostreams/detail/bool_trait_def.hpp \
+ /usr/include/boost/iostreams/detail/template_params.hpp \
+ /usr/include/boost/preprocessor/control/expr_if.hpp \
+ /usr/include/boost/iostreams/detail/config/wide_streams.hpp \
+ /usr/include/boost/iostreams/detail/is_iterator_range.hpp \
+ /usr/include/boost/iostreams/detail/config/disable_warnings.hpp \
+ /usr/include/boost/iostreams/detail/config/enable_warnings.hpp \
+ /usr/include/boost/iostreams/detail/select_by_size.hpp \
+ /usr/include/boost/preprocessor/iteration/local.hpp \
+ /usr/include/boost/preprocessor/iteration/detail/local.hpp \
+ /usr/include/boost/iostreams/detail/wrap_unwrap.hpp \
+ /usr/include/boost/iostreams/detail/enable_if_stream.hpp \
+ /usr/include/boost/iostreams/traits_fwd.hpp \
+ /usr/include/boost/iostreams/detail/streambuf.hpp \
+ /usr/include/boost/iostreams/operations_fwd.hpp \
+ /usr/include/boost/iostreams/detail/adapter/non_blocking_adapter.hpp \
+ /usr/include/boost/iostreams/detail/ios.hpp \
+ /usr/include/boost/iostreams/read.hpp \
+ /usr/include/boost/iostreams/char_traits.hpp \
+ /usr/include/boost/iostreams/detail/char_traits.hpp \
+ /usr/include/boost/iostreams/seek.hpp \
+ /usr/include/boost/iostreams/positioning.hpp \
+ /usr/include/boost/iostreams/detail/config/codecvt.hpp \
+ /usr/include/boost/iostreams/detail/config/fpos.hpp \
+ /usr/include/boost/iostreams/write.hpp \
+ /usr/include/boost/iostreams/concepts.hpp \
+ /usr/include/boost/iostreams/detail/default_arg.hpp \
+ /usr/include/boost/iostreams/detail/config/auto_link.hpp \
+ /usr/include/boost/config/auto_link.hpp \
+ /usr/include/boost/iostreams/detail/config/dyn_link.hpp \
+ /usr/include/boost/iostreams/detail/path.hpp \
+ /usr/include/boost/config/abi_prefix.hpp \
+ /usr/include/boost/config/abi_suffix.hpp dec_optimizer.hpp \
../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp \
/usr/include/c++/4.8.3/unordered_map \
/usr/include/c++/4.8.3/bits/hashtable.h \
@@ -1306,9 +1372,9 @@ pdata-main.o: main.cpp /usr/include/stdc-predef.h \
../../OpenFPM_data/src/NN/CellList/CellNNIterator.hpp \
../../OpenFPM_data/src/NN/CellList/CellListBal.hpp \
../../OpenFPM_data/src/NN/CellList/CellListMem.hpp \
- ../../OpenFPM_data/src/util.hpp unit_test_init_cleanup.hpp \
- Decomposition/ORB_unit_test.hpp Decomposition/ORB.hpp \
- ../../OpenFPM_data/src/data_type/scalar.hpp \
+ ../../OpenFPM_data/src/Space/Ghost.hpp ../../OpenFPM_IO/src/util.hpp \
+ unit_test_init_cleanup.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 \
dec_optimizer_unit_test.hpp dec_optimizer.hpp \
@@ -3344,6 +3410,8 @@ Graph/CartesianGraphFactory.hpp:
../../OpenFPM_data/src/Space/Shape/Point.hpp:
+../../OpenFPM_data/src/Grid/Encap.hpp:
+
../../OpenFPM_data/src/Grid/grid_key.hpp:
../../OpenFPM_data/src/Grid/Encap.hpp:
@@ -4164,7 +4232,7 @@ Grid/grid_dist_id.hpp:
../../OpenFPM_data/src/Space/Shape/Box.hpp:
-../../OpenFPM_data/src/Grid/Encap.hpp:
+../../OpenFPM_data/src/Space/Ghost.hpp:
Grid/grid_dist_id_iterator.hpp:
@@ -4190,6 +4258,136 @@ metis_util.hpp:
../../OpenFPM_IO/src/VTKWriter.hpp:
+../../OpenFPM_IO/src/VTKWriter_graph.hpp:
+
+../../OpenFPM_IO/src/VTKWriter_vector_box.hpp:
+
+/usr/include/boost/math/special_functions/pow.hpp:
+
+/usr/include/boost/math/policies/error_handling.hpp:
+
+/usr/include/boost/math/tools/precision.hpp:
+
+/usr/include/boost/format.hpp:
+
+/usr/include/boost/format/detail/compat_workarounds.hpp:
+
+/usr/include/boost/format/detail/config_macros.hpp:
+
+/usr/include/boost/format/detail/workarounds_gcc-2_95.hpp:
+
+/usr/include/boost/format/detail/workarounds_stlport.hpp:
+
+/usr/include/boost/format/format_fwd.hpp:
+
+/usr/include/boost/format/internals_fwd.hpp:
+
+/usr/include/boost/format/internals.hpp:
+
+/usr/include/boost/format/alt_sstream.hpp:
+
+/usr/include/boost/format/alt_sstream_impl.hpp:
+
+/usr/include/boost/format/format_class.hpp:
+
+/usr/include/boost/format/exceptions.hpp:
+
+/usr/include/boost/format/format_implementation.hpp:
+
+/usr/include/boost/format/group.hpp:
+
+/usr/include/boost/format/feed_args.hpp:
+
+/usr/include/boost/format/detail/msvc_disambiguater.hpp:
+
+/usr/include/boost/format/parsing.hpp:
+
+/usr/include/boost/format/free_funcs.hpp:
+
+/usr/include/boost/format/detail/unset_macros.hpp:
+
+../../OpenFPM_IO/src/util.hpp:
+
+/usr/include/boost/iostreams/device/mapped_file.hpp:
+
+/usr/include/boost/iostreams/close.hpp:
+
+/usr/include/boost/iostreams/categories.hpp:
+
+/usr/include/boost/iostreams/flush.hpp:
+
+/usr/include/boost/iostreams/detail/dispatch.hpp:
+
+/usr/include/boost/iostreams/detail/select.hpp:
+
+/usr/include/boost/iostreams/traits.hpp:
+
+/usr/include/boost/iostreams/detail/bool_trait_def.hpp:
+
+/usr/include/boost/iostreams/detail/template_params.hpp:
+
+/usr/include/boost/preprocessor/control/expr_if.hpp:
+
+/usr/include/boost/iostreams/detail/config/wide_streams.hpp:
+
+/usr/include/boost/iostreams/detail/is_iterator_range.hpp:
+
+/usr/include/boost/iostreams/detail/config/disable_warnings.hpp:
+
+/usr/include/boost/iostreams/detail/config/enable_warnings.hpp:
+
+/usr/include/boost/iostreams/detail/select_by_size.hpp:
+
+/usr/include/boost/preprocessor/iteration/local.hpp:
+
+/usr/include/boost/preprocessor/iteration/detail/local.hpp:
+
+/usr/include/boost/iostreams/detail/wrap_unwrap.hpp:
+
+/usr/include/boost/iostreams/detail/enable_if_stream.hpp:
+
+/usr/include/boost/iostreams/traits_fwd.hpp:
+
+/usr/include/boost/iostreams/detail/streambuf.hpp:
+
+/usr/include/boost/iostreams/operations_fwd.hpp:
+
+/usr/include/boost/iostreams/detail/adapter/non_blocking_adapter.hpp:
+
+/usr/include/boost/iostreams/detail/ios.hpp:
+
+/usr/include/boost/iostreams/read.hpp:
+
+/usr/include/boost/iostreams/char_traits.hpp:
+
+/usr/include/boost/iostreams/detail/char_traits.hpp:
+
+/usr/include/boost/iostreams/seek.hpp:
+
+/usr/include/boost/iostreams/positioning.hpp:
+
+/usr/include/boost/iostreams/detail/config/codecvt.hpp:
+
+/usr/include/boost/iostreams/detail/config/fpos.hpp:
+
+/usr/include/boost/iostreams/write.hpp:
+
+/usr/include/boost/iostreams/concepts.hpp:
+
+/usr/include/boost/iostreams/detail/default_arg.hpp:
+
+/usr/include/boost/iostreams/detail/config/auto_link.hpp:
+
+/usr/include/boost/config/auto_link.hpp:
+
+/usr/include/boost/iostreams/detail/config/dyn_link.hpp:
+
+/usr/include/boost/iostreams/detail/path.hpp:
+
+/usr/include/boost/config/abi_prefix.hpp:
+
+/usr/include/boost/config/abi_suffix.hpp:
+
dec_optimizer.hpp:
../../OpenFPM_data/src/NN/CellList/CellDecomposer.hpp:
@@ -4214,7 +4412,9 @@ dec_optimizer.hpp:
../../OpenFPM_data/src/NN/CellList/CellListMem.hpp:
-../../OpenFPM_data/src/util.hpp:
+../../OpenFPM_data/src/Space/Ghost.hpp:
+
+../../OpenFPM_IO/src/util.hpp:
unit_test_init_cleanup.hpp:
diff --git a/src/Decomposition/CartDecomposition.hpp b/src/Decomposition/CartDecomposition.hpp
index ec34eb735c782d9442c6537a7269e3f22cf9f63e..8a1c01ed54c08eeea1dd635bc5fe7ae4700e809e 100644
--- a/src/Decomposition/CartDecomposition.hpp
+++ b/src/Decomposition/CartDecomposition.hpp
@@ -22,8 +22,7 @@
#include "NN/CellList/CellDecomposer.hpp"
#include <unordered_map>
#include "NN/CellList/CellList.hpp"
-
-template<unsigned int dim, typename T> using Ghost = Box<dim,T>;
+#include "Space/Ghost.hpp"
/**
* \brief This class decompose a space into subspaces
@@ -52,6 +51,15 @@ template<unsigned int dim, typename T> using Ghost = Box<dim,T>;
template<unsigned int dim, typename T, template<typename> class device_l=openfpm::device_cpu, typename Memory=HeapMemory, template<unsigned int, typename> class Domain=Box, template<typename, typename, typename, typename, unsigned int> class data_s = openfpm::vector>
class CartDecomposition
{
+ struct N_box
+ {
+ // id of the processor in the nn_processor list
+ size_t id;
+
+ // Near processor sub-domains
+ typename openfpm::vector<::Box<dim,T>> bx;
+ };
+
struct Box_proc
{
// Intersection between the local sub-domain enlarged by the ghost and the contiguous processor
@@ -89,21 +97,21 @@ private:
SpaceBox<dim,T> sub_domain;
//! the set of all local sub-domain as vector
- data_s<SpaceBox<dim,T>,device_l<SpaceBox<dim,T>>,Memory,openfpm::vector_grow_policy_default, openfpm::vect_isel<SpaceBox<dim,T>>::value > sub_domains;
+ openfpm::vector<SpaceBox<dim,T>> sub_domains;
//! List of near processors
openfpm::vector<size_t> nn_processors;
//! for each sub-domain, contain the list of the neighborhood processors
//! and for each processor contain the boxes calculated from the intersection
- //! of the sub-domain ghost with the near-by processor sub-domain ()
+ //! of the sub-domain + ghost with the near-by processor sub-domain ()
openfpm::vector< openfpm::vector< Box_proc > > box_nn_processor_int;
- //! for each box, contain the list of the neighborhood processors
+ //! for each sub-domain, contain the list of the neighborhood processors
openfpm::vector<openfpm::vector<long unsigned int> > box_nn_processor;
// for each near-processor store the sub-domain of the near processor
- std::unordered_map<size_t,typename openfpm::vector<::Box<dim,T>> > nn_processor_subdomains;
+ std::unordered_map<size_t, N_box> nn_processor_subdomains;
//! Structure that contain for each sub-domain box the processor id
//! exist for efficient global communication
@@ -144,22 +152,6 @@ private:
//! and the near processor sub-domains
CellList<dim,T,FAST> geo_cell;
- /*! \brief Enlarge the ghost domain
- *
- * \param the box
- * \param gh spacing of the margin to enlarge
- *
- */
- void enlarge(::Box<dim,T> & box, Ghost<dim,T> & gh)
- {
- typedef ::Box<dim,T> g;
-
- for (size_t j = 0 ; j < dim ; j++)
- {
- box.template getBase<g::p1>(j) = box.template getBase<g::p1>(j) - gh.template getBase<g::p1>(j);
- box.template getBase<g::p2>(j) = box.template getBase<g::p2>(j) + gh.template getBase<g::p2>(j);
- }
- }
/*! \brief Create internally the decomposition
*
@@ -170,24 +162,20 @@ private:
{
// Calculate the total number of box and and the spacing
// on each direction
-
// Get the box containing the domain
SpaceBox<dim,T> bs = domain.getBox();
for (unsigned int i = 0; i < dim ; i++)
{
// Calculate the spacing
-
spacing[i] = (bs.getHigh(i) - bs.getLow(i)) / gr.size(i);
}
// Here we use METIS
-
// Create a cartesian grid graph
CartesianGraphFactory<dim,Graph_CSR<nm_part_v,nm_part_e>> g_factory_part;
// Processor graph
-
Graph_CSR<nm_part_v,nm_part_e> gp = g_factory_part.template construct<NO_EDGE,T,dim-1>(gr.getSize(),domain);
// Get the number of processing units
@@ -200,16 +188,13 @@ private:
Metis<Graph_CSR<nm_part_v,nm_part_e>> met(gp,Np);
// decompose
-
met.decompose<nm_part_v::id>();
// fill the structure that store the processor id for each sub-domain
-
fine_s.resize(gr.size());
// Optimize the decomposition creating bigger spaces
// And reducing Ghost over-stress
-
dec_optimizer<dim,Graph_CSR<nm_part_v,nm_part_e>> d_o(gp,gr.getSize());
// set of Boxes produced by the decomposition optimizer
@@ -218,7 +203,8 @@ private:
// optimize the decomposition
d_o.template optimize<nm_part_v::sub_id,nm_part_v::id>(gp,p_id,loc_box,box_nn_processor);
- // produce the list of the contiguous processor
+ // produce the list of the contiguous processor (nn_processors) and link nn_processor_subdomains to the
+ // processor list
for (size_t i = 0 ; i < box_nn_processor.size() ; i++)
{
for (size_t j = 0 ; j < box_nn_processor.get(i).size() ; j++)
@@ -232,18 +218,65 @@ private:
auto last = std::unique(nn_processors.begin(), nn_processors.end());
nn_processors.erase(last, nn_processors.end());
+ // produce the list of the contiguous processor (nn_processors) and link nn_processor_subdomains to the
+ // processor list
+ for (size_t i = 0 ; i < box_nn_processor.size() ; i++)
+ {
+ for (size_t j = 0 ; j < box_nn_processor.get(i).size() ; j++)
+ {
+ // processor id near to this sub-domain
+ size_t proc_id = box_nn_processor.get(i).get(j);
+
+ size_t k = 0;
+ // search inside near processor list
+ for (k = 0 ; k < nn_processors.size() ; k++)
+ if (nn_processors.get(k) == proc_id) break;
+
+ nn_processor_subdomains[proc_id].id = k;
+ }
+ }
+
+ // Initialize ss_box and bbox
+ if (loc_box.size() >= 0)
+ {
+ SpaceBox<dim,T> sub_d(loc_box.get(0));
+ sub_d.mul(spacing);
+ sub_d.expand(spacing);
+
+ // add the sub-domain
+ sub_domains.add(sub_d);
+
+ ss_box = sub_d;
+ bbox = sub_d;
+ }
+
// convert into sub-domain
- for (size_t s = 0 ; s < loc_box.size() ; s++)
+ for (size_t s = 1 ; s < loc_box.size() ; s++)
{
SpaceBox<dim,T> sub_d(loc_box.get(s));
- // re-scale with spacing
- sub_d.spacing(spacing);
+ // re-scale and add spacing (the end is the starting point of the next domain + spacing)
+ sub_d.mul(spacing);
+ sub_d.expand(spacing);
// add the sub-domain
sub_domains.add(sub_d);
+
+ // Calculate the bound box
+ bbox.enclose(sub_d);
+
+ // Create the smallest box contained in all sub-domain
+ ss_box.contained(sub_d);
}
+ //++++++++++++++++++++++++++++++++++++++++ Debug output NN boxes
+ {
+ VTKWriter<openfpm::vector<::SpaceBox<dim,T>>,VECTOR_BOX> vtk_box1;
+ vtk_box1.add(sub_domains);
+ vtk_box1.write(std::string("loc_") + std::to_string(v_cl.getProcessUnitID()) + std::string(".vtk"));
+ }
+ //+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
// fill fine_s structure
// fine_s structure contain the processor id for each sub-sub-domain
// with sub-sub-domain we mean the sub-domain decomposition before
@@ -314,21 +347,28 @@ private:
* \param total message size to receive from all the processors
* \param the total number of processor want to communicate with you
* \param i processor id
+ * \param ri request id (it is an id that goes from 0 to total_p, and is unique
+ * every time message_alloc is called)
* \param ptr a pointer to the vector_dist structure
*
* \return the pointer where to store the message
*
*/
- static void * message_alloc(size_t msg_i ,size_t total_msg, size_t total_p, size_t i, void * ptr)
+ static void * message_alloc(size_t msg_i ,size_t total_msg, size_t total_p, size_t i, size_t ri, void * ptr)
{
// cast the pointer
CartDecomposition<dim,T,device_l,Memory,Domain,data_s> * cd = static_cast< CartDecomposition<dim,T,device_l,Memory,Domain,data_s> *>(ptr);
+ if (cd->v_cl.getProcessUnitID() == 0)
+ {
+ std::cout << "Receiving from " << i << " msg size: " << msg_i << "\n";
+ }
+
// Resize the memory
- cd->nn_processor_subdomains[i].resize(msg_i);
+ cd->nn_processor_subdomains[i].bx.resize(msg_i);
// Return the receive pointer
- return cd->nn_processor_subdomains[i].getPointer();
+ return cd->nn_processor_subdomains[i].bx.getPointer();
}
public:
@@ -341,6 +381,9 @@ public:
CartDecomposition(CartDecomposition<dim,T,device_l,Memory,Domain,data_s> && cd)
:sub_domain(cd.sub_domain),gr(cd.gr),cd(cd.cd),domain(cd.domain),v_cl(cd.v_cl)
{
+ // Reset the box to zero
+ bbox.zero();
+
//! Subspace selected
//! access_key in case of grid is just the set of the index to access the grid
id_sub.swap(cd.id_sub);
@@ -362,7 +405,10 @@ public:
*/
CartDecomposition(Vcluster & v_cl)
:id_sub(0),v_cl(v_cl)
- {}
+ {
+ // Reset the box to zero
+ bbox.zero();
+ }
/*! \brief Cartesian decomposition constructor, it divide the space in boxes
*
@@ -372,10 +418,12 @@ public:
*
*/
CartDecomposition(std::vector<size_t> dec, Domain<dim,T> domain, Vcluster & v_cl)
- :id_sub(0),gr(dec),cd(domain,dec),domain(domain),v_cl(v_cl)
+ :id_sub(0),gr(dec),cd(domain,dec,0),domain(domain),v_cl(v_cl)
{
- // Create the decomposition
+ // Reset the box to zero
+ bbox.zero();
+ // Create the decomposition
CreateDecomposition(v_cl);
}
@@ -383,6 +431,72 @@ public:
~CartDecomposition()
{}
+ openfpm::vector<size_t> ids;
+
+ /*! \brief Given a position it return if the position belong to any neighborhood processor ghost
+ *
+ * \param p Particle position
+ *
+ * \param return the processor ids
+ *
+ */
+ const openfpm::vector<size_t> ghost_processorID(Point<dim,T> & p)
+ {
+ ids.clear();
+
+ // Check with geo-cell if a particle is inside one Cell caotaining boxes
+
+ auto cell_it = geo_cell.getCellIterator(p);
+
+ // For each element in the cell, check if the point is inside the box
+ // if it is store the processor id
+ while (cell_it.isNext())
+ {
+ size_t bid = cell_it.get();
+
+ if (vb_int.get(bid).box.isInside(p) == true)
+ {
+ ids.add(vb_int.get(bid).proc);
+ }
+ }
+
+ return ids;
+ }
+
+ /*! \brief Given a position it return if the position belong to any neighborhood processor ghost
+ *
+ * \param p Particle position
+ *
+ * \param return the processor ids
+ *
+ */
+ template<typename Mem> inline const openfpm::vector<size_t> ghost_processorID(const encapc<1,Point<dim,T>,Mem> & p)
+ {
+ ids.clear();
+
+ // Check with geo-cell if a particle is inside one Cell containing boxes
+
+ auto cell_it = geo_cell.getCellIterator(p);
+
+ // For each element in the cell, check if the point is inside the box
+ // if it is, store the processor id
+ while (cell_it.isNext())
+ {
+ size_t bid = cell_it.get();
+
+ if (vb_int.get(bid).box.isInside(p) == true)
+ {
+ ids.add(vb_int.get(bid).proc);
+ }
+ }
+
+ return ids;
+ }
+
+ // Internal boxes for this processor domain, indicated with B8_0 B9_0 ..... in the figure
+ // below as a linear vector
+ openfpm::vector<::Box<dim,T>> vb_int;
+
/*! It calculate the ghost boxes and internal boxes
*
* Example: Processor 10 calculate
@@ -466,29 +580,24 @@ p1[0]<-----+ +----> p2[0]
*/
void calculateGhostBoxes(Ghost<dim,T> & ghost)
{
- typedef Ghost<dim,T> g;
-
#ifdef DEBUG
// the ghost margins are assumed to be smaller
// than one sub-domain
for (size_t i = 0 ; i < dim ; i++)
{
- if (ghost.template getBase<g::p1>() >= domain.template getBase<g::p1>() / gr.size(i) )
+ if (ghost.template getLow(i) >= domain.template getHigh(i) / gr.size(i) || ghost.template getHigh(i) >= domain.template getHigh(i) / gr.size(i))
{
std::cerr << "Error: Ghost are bigger that one domain" << "\n";
}
}
#endif
- // create a buffer with the sub-domain of this processors, the informations ( the box )
- // of sub-domain contiguous to the processor A are sent to the processor A and
+ // create a buffer with the sub-domains of this processor, the informations ( the boxes )
+ // of the sub-domains contiguous to the processor A are sent to the processor A and
// the information of the contiguous sub-domains in the near processors are received
//
- openfpm::vector< openfpm::vector< ::Box<dim,T>> > boxes(nn_processors.size());
-
- // create the sub-domain buffer information to send
- openfpm::vector< size_t > prc;
+ openfpm::vector< openfpm::vector< ::SpaceBox<dim,T>> > boxes(nn_processors.size());
for (size_t b = 0 ; b < box_nn_processor.size() ; b++)
{
@@ -496,24 +605,61 @@ p1[0]<-----+ +----> p2[0]
{
size_t prc = box_nn_processor.get(b).get(p);
- boxes.add(sub_domains.get(b));
+ // id of the processor in the processor list
+ // [value between 0 and the number of the near processors]
+ size_t id = nn_processor_subdomains[prc].id;
+
+ boxes.get(id).add(sub_domains.get(b));
}
}
+ //++++++++++++++++++++++++++++++++++++++++ Debug output NN boxes
+ {
+ for (size_t b = 0 ; b < boxes.size() ; b++)
+ {
+ VTKWriter<openfpm::vector<::SpaceBox<dim,T>>,VECTOR_BOX> vtk_box1;
+ vtk_box1.add(boxes.get(b));
+ vtk_box1.write(std::string("Processor_") + std::to_string(v_cl.getProcessUnitID()) + "_" + std::to_string(nn_processors.get(b)) + std::string(".vtk"));
+ }
+ }
+
+ //+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
// Intersect all the local sub-domains with the sub-domains of the contiguous processors
// Get the sub-domains of the near processors
- v_cl.sendrecvMultipleMessages(boxes,prc,CartDecomposition<dim,T,device_l,Memory,Domain,data_s>::message_alloc, this ,NEED_ALL_SIZE);
+ v_cl.sendrecvMultipleMessages(nn_processors,boxes,CartDecomposition<dim,T,device_l,Memory,Domain,data_s>::message_alloc, this ,NEED_ALL_SIZE);
+
+ // ++++++++++++++++++++++++++++++++++++++++++ Check received boxes
+
+ {
+ VTKWriter<openfpm::vector<::Box<dim,T>>,VECTOR_BOX> vtk_box1;
+ for (size_t p = 0 ; p < nn_processors.size() ; p++)
+ {
+ size_t prc = nn_processors.get(p);
+
+ if (v_cl.getProcessUnitID() == 0)
+ std::cout << "Received from " << prc << " n_boxes: " << nn_processor_subdomains[prc].bx.size() << "\n";
- box_nn_processor_int.resize(box_nn_processor.size());
+ vtk_box1.add(nn_processor_subdomains[prc].bx);
+ }
+ vtk_box1.write(std::string("rb_Processor_") + std::to_string(v_cl.getProcessUnitID()) + std::string(".vtk"));
+ }
+
+ // +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+ box_nn_processor_int.resize(sub_domains.size());
// For each sub-domain
for (size_t i = 0 ; i < sub_domains.size() ; i++)
{
- ::Box<dim,size_t> sub_with_ghost = sub_domains.get(i);
+ SpaceBox<dim,T> sub_with_ghost = sub_domains.get(i);
// enlarge the sub-domain with the ghost
- enlarge(sub_with_ghost,ghost);
+ sub_with_ghost.enlarge(ghost);
+
+ // resize based on the number of contiguous processors
+ box_nn_processor_int.get(i).resize(box_nn_processor.get(i).size());
// For each processor contiguous to this sub-domain
for (size_t j = 0 ; j < box_nn_processor.get(i).size() ; j++)
@@ -522,7 +668,7 @@ p1[0]<-----+ +----> p2[0]
size_t p_id = box_nn_processor.get(i).get(j);
// get the set of sub-domains of the contiguous processor p_id
- openfpm::vector< ::Box<dim,T> > & p_box = nn_processor_subdomains[p_id];
+ openfpm::vector< ::Box<dim,T> > & p_box = nn_processor_subdomains[p_id].bx;
// near processor sub-domain intersections
openfpm::vector< ::Box<dim,T> > & p_box_int = box_nn_processor_int.get(i).get(j).bx;
@@ -530,9 +676,9 @@ p1[0]<-----+ +----> p2[0]
// for each near processor sub-domain intersect with the enlarged local sub-domain and store it
for (size_t b = 0 ; b < p_box.size() ; b++)
{
- bool intersect;
+ ::Box<dim,T> bi;
- ::Box<dim,T> bi = sub_with_ghost.Intersect(p_box.get(b),intersect);
+ bool intersect = sub_with_ghost.Intersect(::Box<dim,T>(p_box.get(b)),bi);
if (intersect == true)
p_box_int.add(bi);
@@ -546,37 +692,39 @@ p1[0]<-----+ +----> p2[0]
size_t p_id = box_nn_processor.get(i).get(j);
// get the set of sub-domains of the contiguous processor p_id
- openfpm::vector< ::Box<dim,T> > & nn_p_box = nn_processor_subdomains[p_id];
+ openfpm::vector< ::Box<dim,T> > & nn_p_box = nn_processor_subdomains[p_id].bx;
// near processor sub-domain intersections
- openfpm::vector< ::Box<dim,T> > & p_box_int = box_nn_processor_int.get(i).get(j).bbx;
+ openfpm::vector< ::Box<dim,T> > & p_box_int = box_nn_processor_int.get(i).get(j).nbx;
// For each near processor sub-domains enlarge and intersect with the local sub-domain and store the result
for (size_t k = 0 ; k < nn_p_box.size() ; k++)
{
- // enlarge the local sub-domain
+ // enlarge the near-processor sub-domain
::Box<dim,T> n_sub = nn_p_box.get(k);
+ // local sub-domain
+ ::SpaceBox<dim,T> l_sub = sub_domains.get(i);
+
// Create a margin of ghost size around the near processor sub-domain
- elarge(n_sub,ghost);
+ n_sub.enlarge(ghost);
// Intersect with the local sub-domain
- bool intersect;
- ::Box<dim,T> b_int = n_sub.Intersect(n_sub,intersect);
+ ::Box<dim,T> b_int;
+ bool intersect = n_sub.Intersect(l_sub,b_int);
// store if it intersect
if (intersect == true)
{
- typedef ::Box<dim,T> b;
-
p_box_int.add(b_int);
+ vb_int.add(b_int);
// update the geo_cell list
// get the boxes this box span
- grid_key<dim> p1 = geo_cell.getCell(b_int.template get<b::p1>() );
- grid_key<dim> p2 = geo_cell.getCell(b_int.template get<b::p2>() );
+ const grid_key_dx<dim> p1 = geo_cell.getCellGrid(b_int.getP1());
+ const grid_key_dx<dim> p2 = geo_cell.getCellGrid(b_int.getP2());
// Get the grid and the sub-iterator
auto & gi = geo_cell.getGrid();
@@ -585,13 +733,31 @@ p1[0]<-----+ +----> p2[0]
// add the box-id to the cell list
while (g_sub.isNext())
{
- auto & key = g_sub.get();
- geo_cell.add(gi.LinId(key),p_box_int.size()-1);
+ auto key = g_sub.get();
+ geo_cell.addCell(gi.LinId(key),vb_int.size()-1);
++g_sub;
}
}
}
}
+
+
+ // ++++++++++++++++++++++++++++++++++++++++ Debug +++++++++++++++++++++++++++++
+
+ {
+ VTKWriter<openfpm::vector<::Box<dim,T>>,VECTOR_BOX> vtk_box1;
+ for (size_t p = 0 ; p < box_nn_processor_int.size() ; p++)
+ {
+ for (size_t s = 0 ; s < box_nn_processor_int.get(p).size() ; s++)
+ {
+ vtk_box1.add(box_nn_processor_int.get(p).get(s).nbx);
+ }
+ }
+ vtk_box1.write(std::string("inte_Processor_") + std::to_string(v_cl.getProcessUnitID()) + std::string(".vtk"));
+ }
+
+ // ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
}
}
@@ -606,6 +772,19 @@ p1[0]<-----+ +----> p2[0]
return fine_s.get(cd.getCell(p));
}
+ // Smallest subdivision on each direction
+ ::Box<dim,T> ss_box;
+
+ /*! \brief Get the smallest subdivision of the domain on each direction
+ *
+ * \return a box p1 is set to zero
+ *
+ */
+ const ::Box<dim,T> & getSmallestSubdivision()
+ {
+ return ss_box;
+ }
+
/*! \brief processorID return in which processor the particle should go
*
* \return processorID
@@ -647,7 +826,7 @@ p1[0]<-----+ +----> p2[0]
gr.setDimensions(div_);
domain = domain_;
- cd.setDimensions(domain,div_);
+ cd.setDimensions(domain,div_,0);
//! Create the decomposition
@@ -888,6 +1067,68 @@ p1[0]<-----+ +----> p2[0]
{
return bbox;
}
+
+ /*! \brief if the point fall into the ghost of some near processor it return the processors id's in which
+ * it fall
+ *
+ * \param p Point
+ * \return iterator of the processors id's
+ *
+ */
+ inline auto labelPoint(Point<dim,T> & p) -> decltype(geo_cell.getIterator(geo_cell.getCell(p)))
+ {
+ return geo_cell.getIterator(geo_cell.getCell(p));
+ }
+
+ /*! \brief if the point fall into the ghost of some near processor it return the processor number in which
+ * it fall
+ *
+ * \param p Point
+ * \return number of processors
+ *
+ */
+ inline size_t labelPointNp(Point<dim,T> & p)
+ {
+ return geo_cell.getNelements(geo_cell.getCell(p));
+ }
+
+ /*! \brief It return the label point cell
+ *
+ * The labeling of a point p is regulated by a Cell list, give a point it give a cell-id
+ *
+ * \param p Point
+ * \return cell-id
+ *
+ */
+ inline size_t labelPointCell(Point<dim,T> & p)
+ {
+ return geo_cell.getCell(p);
+ }
+
+ /*! \brief Fill the ghost buffer
+ *
+ * \tparam one or more properties to get
+ *
+ */
+/* template<unsigned int ...i> void ghost_get()
+ {
+ // first check if a local particle must be sent to another processor
+ for (size_t i = 0 ; i < ; i++)
+ {
+
+ }
+ }*/
+
+ /*! \brief Fill the ghost buffer
+ *
+ * \tparam one or more properties to get
+ *
+ */
+/* template<unsigned int ...i> void ghost_put()
+ {
+
+ }*/
+
};
diff --git a/src/Decomposition/CartDecomposition_unit_test.hpp b/src/Decomposition/CartDecomposition_unit_test.hpp
index 668adc11eb02970ad576a72d473e5614a1601805..0fd1c9f388f22f7691d044d675e09939313ce1f5 100644
--- a/src/Decomposition/CartDecomposition_unit_test.hpp
+++ b/src/Decomposition/CartDecomposition_unit_test.hpp
@@ -33,6 +33,13 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_test_use)
// Decompose
dec.setParameters(div,box);
+
+ Ghost<3,float> g(0.01);
+
+ // create a ghost border
+ dec.calculateGhostBoxes(g);
+
+ //
}
BOOST_AUTO_TEST_SUITE_END()
diff --git a/src/Graph/CartesianGraphFactory.hpp b/src/Graph/CartesianGraphFactory.hpp
index f667d06aad14a68d5c3c276c073c7cabd82a5def..5d2a72b631348d1fbd9c05d987be332276b54ef2 100644
--- a/src/Graph/CartesianGraphFactory.hpp
+++ b/src/Graph/CartesianGraphFactory.hpp
@@ -353,14 +353,15 @@ public:
*
* Each vertex is a subspace (Hyper-cube) of dimension dim, each vertex is
* connected with an edge if two vertex (Hyper-cube) share a element of dimension grater than
- * dim_c
+ * dim_c. One property can be used to store the contact size or the d-dimensional
+ * surface in common between two connected hyper-cube.
*
* \param sz Vector that store the size of the grid on each dimension
* \param dom Box enclosing the physical domain
*
- * \tparam se Indicate which properties fill with the element weight. The
- * element weight is the point, line , surface, d dimensional object
- * in contact (in common between two hyper-cube). NO_EDGE indicate
+ * \tparam se Indicate which properties fill with the contact size. The
+ * contact size is the point, line , surface, d-dimensional object size
+ * in contact (in common) between two hyper-cube. NO_EDGE indicate
* no property will store this information
* \tparam T type of the domain like (int real complex ... )
* \tparam dim_c Connectivity dimension
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index 899a268e4c1c795ec866106263f3ea1f40e8f9b0..5a786ab0e2d07e635c4239683385ebbb9621d235 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -54,7 +54,7 @@ class grid_dist_id
/*! \brief Get the grid size
*
- * Get the grid size, given a domain, the resolution on it and another spaceBox
+ * Given a domain, the resolution of the grid on it and another spaceBox contained in the domain
* it give the size on all directions of the local grid
*
* \param sp SpaceBox enclosing the local grid
@@ -92,7 +92,7 @@ class grid_dist_id
for (size_t d = 0 ; d < dim ; d++)
{
// push the size of the local grid
- v_size[d] = sp.getHigh(d) - sp.getLow(d) + 1;
+ v_size[d] = sp.getHigh(d) - sp.getLow(d);
}
}
@@ -175,11 +175,9 @@ public:
dec.hyperCube();
// Get the number of local grid needed
-
size_t n_grid = dec.getNLocalHyperCube();
// create local grids for each hyper-cube
-
loc_grid = v_cl.allocate<device_grid>(n_grid);
// Size of the grid on each dimension
@@ -322,7 +320,7 @@ class grid_dist_id<1,T,Decomposition,Memory,device_grid>
for (size_t d = 0 ; d < 1 ; d++)
{
// push the size of the local grid
- v_size[d] = sp.getHigh(d) - sp.getLow(d) + 1;
+ v_size[d] = sp.getHigh(d) - sp.getLow(d);
}
}
diff --git a/src/Grid/grid_dist_id_unit_test.hpp b/src/Grid/grid_dist_id_unit_test.hpp
index 43c7293c0b0dcb12b750331cb00ed2d721013388..7718e1d0b149dee76da8ad76b610be13f2fc6263 100644
--- a/src/Grid/grid_dist_id_unit_test.hpp
+++ b/src/Grid/grid_dist_id_unit_test.hpp
@@ -58,6 +58,16 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
++dom;
}
+ // Get the virtual cluster machine
+ Vcluster & vcl = g_dist.getVC();
+
+ // reduce
+ vcl.reduce(count);
+ vcl.execute();
+
+ // Check
+ BOOST_REQUIRE_EQUAL(count,1024*1024);
+
size_t count_check = 0;
dom = g_dist.getDomainIterator();
@@ -71,16 +81,6 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_iterator_test_use)
++dom;
}
- // Get the virtual cluster machine
- Vcluster & vcl = g_dist.getVC();
-
- // reduce
- vcl.reduce(count);
- vcl.execute();
-
- // Check
- BOOST_REQUIRE_EQUAL(count,1024*1024);
-
/* auto g_it = g_dist.getIteratorBulk();
auto g_it_halo = g_dist.getHalo();
diff --git a/src/Makefile b/src/Makefile
index 95e81349f24d6be0cf4a60fbca5c9bba46748a56..68aa50d3e4d61da92d2f3f020abc0f6e30059c11 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -84,13 +84,10 @@ subdir = src
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/m4/ax_check_compiler_flags.m4 \
- $(top_srcdir)/m4/acx_pthread.m4 $(top_srcdir)/m4/ax_opencl.m4 \
- $(top_srcdir)/m4/ax_boost_base.m4 \
- $(top_srcdir)/m4/ax_boost_program_options.m4 \
- $(top_srcdir)/m4/ax_boost_thread.m4 \
- $(top_srcdir)/m4/acx_mpi.m4 $(top_srcdir)/m4/ax_openmp.m4 \
- $(top_srcdir)/m4/ax_cuda.m4 $(top_srcdir)/configure.ac
+am__aclocal_m4_deps = $(top_srcdir)/m4/acx_pthread.m4 \
+ $(top_srcdir)/m4/ax_boost.m4 $(top_srcdir)/m4/acx_mpi.m4 \
+ $(top_srcdir)/m4/ax_openmp.m4 $(top_srcdir)/m4/ax_cuda.m4 \
+ $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
mkinstalldirs = $(install_sh) -d
@@ -104,7 +101,8 @@ am_pdata_OBJECTS = pdata-main.$(OBJEXT) pdata-HeapMemory.$(OBJEXT) \
pdata-Memleak_check.$(OBJEXT)
pdata_OBJECTS = $(am_pdata_OBJECTS)
am__DEPENDENCIES_1 =
-am__DEPENDENCIES_2 = $(am__DEPENDENCIES_1)
+am__DEPENDENCIES_2 = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
pdata_DEPENDENCIES = $(am__DEPENDENCIES_2)
pdata_LINK = $(CXXLD) $(pdata_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \
$(LDFLAGS) -o $@
@@ -175,6 +173,18 @@ AUTOCONF = ${SHELL} /home/i-bird/Desktop/MOSAIC/OpenFPM_project/OpenFPM_pdata/mi
AUTOHEADER = ${SHELL} /home/i-bird/Desktop/MOSAIC/OpenFPM_project/OpenFPM_pdata/missing autoheader
AUTOMAKE = ${SHELL} /home/i-bird/Desktop/MOSAIC/OpenFPM_project/OpenFPM_pdata/missing automake-1.13
AWK = gawk
+BOOST_CPPFLAGS = -pthread -I/usr/include
+BOOST_DATE_TIME_LIB = -lboost_date_time
+BOOST_FILESYSTEM_LIB = -lboost_filesystem
+BOOST_IOSTREAMS_LIB = -lboost_iostreams
+BOOST_LDFLAGS = -L/usr/lib
+BOOST_PROGRAM_OPTIONS_LIB = -lboost_program_options
+BOOST_REGEX_LIB = -lboost_regex
+BOOST_SERIALIZATION_LIB = -lboost_serialization
+BOOST_SIGNALS_LIB = -lboost_signals
+BOOST_THREAD_LIB = -lboost_thread
+BOOST_UNIT_TEST_FRAMEWORK_LIB = -lboost_unit_test_framework
+BOOST_WSERIALIZATION_LIB = -lboost_wserialization
CC = gcc
CCDEPMODE = depmode=gcc3
CFLAGS = -g -O2
@@ -183,7 +193,7 @@ CUDA_CFLAGS = -I -I -I/usr/local/cuda-5.5/include
CUDA_LIBS = -L -L -L/usr/local/cuda-5.5/lib64 -lcuda -lcudart
CXX = mpic++
CXXDEPMODE = depmode=gcc3
-CXXFLAGS = --std=c++11 -march=native -mtune=native -Wall -O3 -g3 -flto -funroll-loops -Wno-unused-but-set-variable
+CXXFLAGS = --std=c++11 -march=native -mtune=native -g3 -Wall -O0
CYGPATH_W = echo
DEFS = -DHAVE_CONFIG_H
DEPDIR = .deps
@@ -204,7 +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-5.5/bin/nvcc
-NVCCFLAGS = -O3
+NVCCFLAGS = -g -O0
NVCC_EXIST = yes
OBJEXT = o
PACKAGE = full-package-name
@@ -274,7 +284,7 @@ target_vendor = unknown
top_build_prefix = ../
top_builddir = ..
top_srcdir = ..
-LINKLIBS = $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(CUDA_LIBS) $(BOOST_THREAD_LIB)
+LINKLIBS = $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS)
pdata_SOURCES = main.cpp ../../OpenFPM_devices/src/memory/HeapMemory.cpp ../../OpenFPM_devices/src/memory/PtrMemory.cpp ../../OpenFPM_vcluster/src/VCluster.cpp ../../OpenFPM_data/src/Memleak_check.cpp
pdata_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH)
pdata_CFLAGS = $(CUDA_CFLAGS)
diff --git a/src/Makefile.am b/src/Makefile.am
old mode 100755
new mode 100644
index 0b3679871bb8bbab62d7561681df3420880fbd41..a0fa9da119c9658bed3d914fb66f08a95042c449
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,5 +1,5 @@
-LINKLIBS = $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(CUDA_LIBS) $(BOOST_THREAD_LIB)
+LINKLIBS = $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS)
bin_PROGRAMS = pdata
pdata_SOURCES = main.cpp ../../OpenFPM_devices/src/memory/HeapMemory.cpp ../../OpenFPM_devices/src/memory/PtrMemory.cpp ../../OpenFPM_vcluster/src/VCluster.cpp ../../OpenFPM_data/src/Memleak_check.cpp
diff --git a/src/Makefile.in b/src/Makefile.in
index a8cfb9ca289a1ac33e6705c0093608b1307c7f27..0d7175e1ee0d7415f255c6d8e5500e05f5acf868 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -84,13 +84,10 @@ subdir = src
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/depcomp
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/m4/ax_check_compiler_flags.m4 \
- $(top_srcdir)/m4/acx_pthread.m4 $(top_srcdir)/m4/ax_opencl.m4 \
- $(top_srcdir)/m4/ax_boost_base.m4 \
- $(top_srcdir)/m4/ax_boost_program_options.m4 \
- $(top_srcdir)/m4/ax_boost_thread.m4 \
- $(top_srcdir)/m4/acx_mpi.m4 $(top_srcdir)/m4/ax_openmp.m4 \
- $(top_srcdir)/m4/ax_cuda.m4 $(top_srcdir)/configure.ac
+am__aclocal_m4_deps = $(top_srcdir)/m4/acx_pthread.m4 \
+ $(top_srcdir)/m4/ax_boost.m4 $(top_srcdir)/m4/acx_mpi.m4 \
+ $(top_srcdir)/m4/ax_openmp.m4 $(top_srcdir)/m4/ax_cuda.m4 \
+ $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
mkinstalldirs = $(install_sh) -d
@@ -104,7 +101,8 @@ am_pdata_OBJECTS = pdata-main.$(OBJEXT) pdata-HeapMemory.$(OBJEXT) \
pdata-Memleak_check.$(OBJEXT)
pdata_OBJECTS = $(am_pdata_OBJECTS)
am__DEPENDENCIES_1 =
-am__DEPENDENCIES_2 = $(am__DEPENDENCIES_1)
+am__DEPENDENCIES_2 = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
pdata_DEPENDENCIES = $(am__DEPENDENCIES_2)
pdata_LINK = $(CXXLD) $(pdata_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \
$(LDFLAGS) -o $@
@@ -175,6 +173,18 @@ AUTOCONF = @AUTOCONF@
AUTOHEADER = @AUTOHEADER@
AUTOMAKE = @AUTOMAKE@
AWK = @AWK@
+BOOST_CPPFLAGS = @BOOST_CPPFLAGS@
+BOOST_DATE_TIME_LIB = @BOOST_DATE_TIME_LIB@
+BOOST_FILESYSTEM_LIB = @BOOST_FILESYSTEM_LIB@
+BOOST_IOSTREAMS_LIB = @BOOST_IOSTREAMS_LIB@
+BOOST_LDFLAGS = @BOOST_LDFLAGS@
+BOOST_PROGRAM_OPTIONS_LIB = @BOOST_PROGRAM_OPTIONS_LIB@
+BOOST_REGEX_LIB = @BOOST_REGEX_LIB@
+BOOST_SERIALIZATION_LIB = @BOOST_SERIALIZATION_LIB@
+BOOST_SIGNALS_LIB = @BOOST_SIGNALS_LIB@
+BOOST_THREAD_LIB = @BOOST_THREAD_LIB@
+BOOST_UNIT_TEST_FRAMEWORK_LIB = @BOOST_UNIT_TEST_FRAMEWORK_LIB@
+BOOST_WSERIALIZATION_LIB = @BOOST_WSERIALIZATION_LIB@
CC = @CC@
CCDEPMODE = @CCDEPMODE@
CFLAGS = @CFLAGS@
@@ -274,7 +284,7 @@ target_vendor = @target_vendor@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
-LINKLIBS = $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(CUDA_LIBS) $(BOOST_THREAD_LIB)
+LINKLIBS = $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS)
pdata_SOURCES = main.cpp ../../OpenFPM_devices/src/memory/HeapMemory.cpp ../../OpenFPM_devices/src/memory/PtrMemory.cpp ../../OpenFPM_vcluster/src/VCluster.cpp ../../OpenFPM_data/src/Memleak_check.cpp
pdata_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH)
pdata_CFLAGS = $(CUDA_CFLAGS)
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 4fa9f1bdb7f3209129bf423f4623c79c90abeaf2..d990938a08da8239ddeff4b9bb17f78452c32743 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -17,6 +17,8 @@
#include "memory/PtrMemory.hpp"
#include "NN/CellList/CellList.hpp"
#include "common.hpp"
+#include "util/vector_creator.hpp"
+#include "memory/ExtPreAlloc.hpp"
#define NO_ID false
#define ID true
@@ -24,6 +26,25 @@
#define GET 1
#define PUT 2
+#define INTERNAL 0
+#define NO_POSITION 1
+
+/*! \brief This is a container for the sending buffers
+ *
+ * It is used in ghost_get to create a particular object with the properties selected
+ *
+ * \tparam Is a boost::fusion::vector with the properties selected
+ *
+ *
+ */
+template<typename v>
+class buff_com
+{
+ typedef v type;
+
+ const int max_prop = boost::fusion::result_of::size<v>::value;
+};
+
/*! \brief Distributed vector
*
*/
@@ -91,19 +112,16 @@ public:
// Create the sub-domains
dec.setParameters(div,box);
- // Get the bounding box containing the processor domain +- one sub-domain spacing
- ::Box<point::dims,typename point::coord_type> & bbound = dec.getProcessorBounds();
+ // Get the bounding box containing the processor domain
+ const ::Box<point::dims,typename point::coord_type> & bbound = dec.getProcessorBounds();
- // the smallest sub-division of the domain on each dimension
- typename point::coord_type smallest_doms[point::dims];
+ const ::Box<point::dims,typename point::coord_type> & smallest_unit = dec.getSmallestSubdivision();
// convert spacing divisions
size_t n_g[point::dims];
for (size_t i = 0 ; i < point::dims ; i++)
- {
- n_g[i] = box.template getBase<b::p2>(i) / smallest_doms[i];
- }
+ n_g[i] = (bbound.getHigh(i) - bbound.getLow(i)) / smallest_unit.getHigh(i);
point p;
p.zero();
@@ -112,6 +130,16 @@ public:
geo_cell.Initialize(box,n_g,p,8);
}
+ /*! \brief return the local size of the vector
+ *
+ * \return local size
+ *
+ */
+ size_t size_local()
+ {
+ v_pos.get(0).size();
+ }
+
/*! \brief Get position of an object
*
* \param vec_key vector element
@@ -144,6 +172,16 @@ public:
openfpm::vector<prop,openfpm::device_cpu<prop>,PreAllocHeapMemory<2>,openfpm::grow_policy_identity> prp;
};
+ /*! \brief set the ghost
+ *
+ * \param g ghost
+ *
+ */
+ void setGhost(Ghost<point::dims,typename point::coord_type> & g)
+ {
+ dec.calculateGhostBoxes(g);
+ }
+
/*! \brief It communicate the particle to the respective processor
*
*/
@@ -256,12 +294,10 @@ public:
prc_cnt.get(lbl)++;
// Add processors and add size
-
++it;
}
// Create the set of pointers
-
openfpm::vector<void *> ptr(prc_r.size());
for (size_t i = 0 ; i < prc_r.size() ; i++)
{
@@ -269,8 +305,7 @@ public:
}
// convert the particle number to buffer size
-
- for (size_t i = 0 ; i < v_cl.getProcessingUnits() ; i++)
+ for (size_t i = 0 ; i < prc_sz_r.size() ; i++)
{
prc_sz_r.get(i) = prc_sz_r.get(i)*(sizeof(prop) + sizeof(point));
}
@@ -328,72 +363,133 @@ public:
v_prp.get(0).remove(opart,o_p_id);
}
- // ghost particles sending buffer
- openfpm::vector<HeapMemory> ghost_send_hp;
+ // outgoing particles-id
+ openfpm::vector<openfpm::vector<size_t>> opart;
// Each entry contain the size of the ghost sending buffer
- std::unordered_map<size_t,size_t> ghost_prc_sz;
+ openfpm::vector<size_t> ghost_prc_sz;
// ghost particle labels
openfpm::vector<size_t> ghost_lbl_p;
+ // Memory for the ghost sending buffer
+ Memory g_prp_mem;
+
+ // Memory for the ghost
+ Memory g_pos_mem;
+
/*! \brief It synchronize getting the ghost particles
*
* \prp Properties to get
* \opt options
- * NO_RELABEL: If the particles does not move avoid to relabel
+ * NO_RELABEL: If the particles does not move avoid to relabel and send particle position
*
*/
- template<unsigned int N> void ghost_get(const size_t prp[N], size_t opt)
+ template<int... prp> void ghost_get(size_t opt = NONE)
{
- // outgoing particles-id
- openfpm::vector<size_t> opart;
-
+ // Create the ghost buffer
ghost_prc_sz.clear();
+ ghost_lbl_p.clear();
+ ghost_lbl_p.resize(v_pos.get(INTERNAL).size());
// Label the internal (assigned) particles
- auto it = v_pos.get(0).getIterator();
+ auto it = v_pos.get(INTERNAL).getIterator();
// Label all the particles with the processor id, where they should go
while (it.isNext())
{
auto key = it.get();
- size_t p_id = dec.ghost_processorID(v_pos.get(0).get(key));
+ size_t p_id = dec.ghost_processorID(v_pos.get(INTERNAL).get(key));
ghost_lbl_p.get(key) = p_id;
// It has to communicate
if (p_id != v_cl.getProcessUnitID())
{
+ size_t id = dec.ProcToID(p_id);
+
// add particle to communicate
- ghost_prc_sz[p_id]++;
+ ghost_prc_sz.get(id)++;
- opart.add(key);
+
+ opart.get(id).add(key);
}
++it;
}
- // Create memory allocator for the send buffers
- size_t i = 0;
- ghost_send_hp.resize(ghost_prc_sz.size());
+ // Total number of elements
+ size_t n_ele = 0;
+
+ // sequence of pre-allocation pattern
+ openfpm::vector<size_t> pap;
+
+ // Calculate the total size required for the sending buffer
+ for ( size_t i = 0 ; i < ghost_prc_sz.size() ; i++ )
+ {
+ pap.add(ghost_prc_sz.get(i)*sizeof(vector_creator<Point_test<float>::type,prp...>::type));
+ n_ele += ghost_prc_sz.get(i);
+ }
+
+ // resize the property buffer memory
+ g_prp_mem.resize(n_ele * sizeof(typename vector_creator<Point_test<float>::type,prp...>::type));
+ // resize the position buffer memory
+ if (opt != NO_POSITION) g_pos_mem.resize(n_ele * sizeof(point));
+
+ // Create an object of preallocated memory
+ ExtPreAlloc<Memory> prAlloc(pap,g_prp_mem);
- for ( auto it = ghost_prc_sz.begin(); it != ghost_prc_sz.end(); ++it )
+ // definition of a property object based on the property selected
+ typedef typename vector_creator<Point_test<float>::type,prp...>::type property_object;
+
+ // definition of the send vector for each processor
+ typedef openfpm::vector<property_object,openfpm::device_cpu<prop>,ExtPreAlloc<Memory>> send_vector;
+
+ // create a vector of send vector (ExtPreAlloc warrant that all the created vector are contiguous)
+ openfpm::vector<send_vector> g_send;
+
+ // create a number of send buffer equal to the near processors
+ g_send.resize(ghost_prc_sz.size());
+ for (size_t i = 0 ; i < g_send.size() ; i++)
+ {
+ // set the preallocated memory to ensure contiguity
+ g_send.get(i).setMemory(prAlloc);
+
+ // resize the sending vector (No allocation is produced)
+ g_send.get(i).resize(ghost_prc_sz.get(i));
+ }
+
+ // Fill the send buffer
+ for ( size_t i = 0 ; i < opart.size() ; i++ )
{
- // we are sending only some properties, so calculate the size of the sending buffer
- size_t element_size = ele_size<N,typename prop::type>(prp);
+ for (size_t j = 0 ; j < opart.get(i).size() ; j++)
+ {
+ g_send.get(i).get(j) = v_prp.get(INTERNAL).get(opart.get(i).get(j));
+ }
+ }
+
+ // Create the buffer for particle position
- ghost_send_hp.get(i).resize(it->second * element_size);
+ // definition of the send vector for each processor
+ typedef openfpm::vector<property_object,openfpm::device_cpu<point>,ExtPreAlloc<Memory>> send_pos_vector;
- i++;
+ openfpm::vector<point> g_pos_send;
+ if (opt != NO_POSITION)
+ {
+ // Fill the send buffer
+ for ( size_t i = 0 ; i < opart.size() ; i++ )
+ {
+ for (size_t j = 0 ; j < opart.get(i).size() ; j++)
+ {
+ g_send.get(i).get(j) = v_pos.get(INTERNAL).get(opart.get(i).get(j));
+ }
+ }
}
- //
+ // Send receive the particles information
- // ca
- // send and receive the properties of the particles
// add the received particles to the vector
}
@@ -413,17 +509,19 @@ public:
* \param total message size to receive from all the processors
* \param the total number of processor want to communicate with you
* \param i processor id
+ * \param ri request id (it is an id that goes from 0 to total_p, and is unique
+ * every time message_alloc is called)
* \param ptr a pointer to the vector_dist structure
*
* \return the pointer where to store the message
*
*/
- static void * message_alloc(size_t msg_i ,size_t total_msg, size_t total_p, size_t i, void * ptr)
+ static void * message_alloc(size_t msg_i ,size_t total_msg, size_t total_p, size_t i, size_t ri, void * ptr)
{
// cast the pointer
vector_dist<point,prop,Box,Decomposition,Memory,with_id> * vd = static_cast<vector_dist<point,prop,Box,Decomposition,Memory,with_id> *>(ptr);
- // Resize the memory and
+ // Resize the receive buffer, and the size of each message buffer
vd->hp_recv.resize(total_msg);
vd->v_proc.resize(total_p);
@@ -434,7 +532,7 @@ public:
vd->recv_cnt += msg_i;
// Save the processor message size
- vd->v_proc.get(i) = msg_i;
+ vd->v_proc.get(ri) = msg_i;
return recv_ptr;
}
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index 748940c02f2e2f0ec7649131c89e9266e4fdc621..1c3eb3fbb6483afbb9bab107db29be79af2ba917 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -55,6 +55,16 @@ BOOST_AUTO_TEST_CASE( vector_dist_iterator_test_use )
++it;
}
+
+ // set the ghost based on the radius cut off
+ Ghost<2,float> g(0.01);
+
+ vd.setGhost(g);
+
+ // do a ghost get
+
+ typedef Point_test<float> p;
+ vd.template ghost_get<p::s,p::v>();
}
BOOST_AUTO_TEST_SUITE_END()
diff --git a/src/dec_optimizer.hpp b/src/dec_optimizer.hpp
index b6c21c96cded626a0d98ad98ae0d9593c2794607..c1998384b0f92da26b4841d6a7dcd8172f5e28c9 100644
--- a/src/dec_optimizer.hpp
+++ b/src/dec_optimizer.hpp
@@ -176,9 +176,6 @@ private:
*/
template<unsigned int p_sub, unsigned int p_id> void add_to_queue(openfpm::vector<size_t> & domains, openfpm::vector<wavefront<dim>> & v_w, Graph & graph, std::vector<comb<dim>> & w_comb, long int pr_id, openfpm::vector< openfpm::vector<size_t> > & box_nn_processor)
{
- // it contain a list of the near processor to the box
- box_nn_processor.add();
-
// create a new queue
openfpm::vector<size_t> domains_new;
@@ -289,7 +286,7 @@ private:
// direction of expansion
- size_t domain_id = graph.vertex(gh.LinId(start_p)).template get<p_id>();
+ size_t domain_id = graph.vertex(start_p).template get<p_id>();
bool can_expand = true;
// while is possible to expand
@@ -600,7 +597,7 @@ public:
box_nn_processor.add();
// Create the biggest box containing the domain
- expand_from_point<p_sub,p_id>(gh.LinId(v_q.get(0)),graph,box,v_w,w_comb);
+ expand_from_point<p_sub,p_id>(v_q.get(0),graph,box,v_w,w_comb);
// Add the created box to the list of boxes
lb.add(box);
diff --git a/src/dec_optimizer_unit_test.hpp b/src/dec_optimizer_unit_test.hpp
index e17f6f7a523e97a27c8fddf70a570e3c30f00e02..bcfbc4a8e428724643a7acd9c239fa6443707193 100644
--- a/src/dec_optimizer_unit_test.hpp
+++ b/src/dec_optimizer_unit_test.hpp
@@ -2,7 +2,7 @@
* dec_optimize.hpp
*
* Created on: Jan 16, 2015
- * Author: i-bird
+ * Author: Pietro Incardona
*/
#ifndef DEC_OPTIMIZE_HPP_
@@ -32,34 +32,28 @@ BOOST_AUTO_TEST_CASE( dec_optimizer_test_use)
Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
// Graph to decompose
-
Graph_CSR<nm_v,nm_e> g = g_factory.construct<nm_e::communication,float,2,0,1,2>(sz,box);
// Processor graph
-
Graph_CSR<nm_part_v,nm_part_e> gp = g_factory_part.construct<NO_EDGE,float,2>(sz,box);
// Convert the graph to metis
-
Metis<Graph_CSR<nm_v,nm_e>> met(g,16);
// decompose
-
met.decompose<nm_part_v::id>(gp);
met.decompose<nm_v::id>();
// optimize
-
dec_optimizer<3,Graph_CSR<nm_v,nm_e>> d_o(g,sz);
grid_key_dx<3> keyZero(0,0,0);
d_o.optimize<nm_v::sub_id,nm_v::id>(keyZero,g);
// Write the VTK file
-
- VTKWriter<Graph_CSR<nm_part_v,nm_part_e>> vtk(gp);
+ VTKWriter<Graph_CSR<nm_part_v,nm_part_e>,GRAPH> vtk(gp);
vtk.write("vtk_partition.vtk");
- VTKWriter<Graph_CSR<nm_v,nm_e>> vtk2(g);
+ VTKWriter<Graph_CSR<nm_v,nm_e>,GRAPH> vtk2(g);
vtk2.write("vtk_partition2.vtk");
}
diff --git a/src/main.cpp b/src/main.cpp
old mode 100755
new mode 100644
index fe80dc22a50f03e316e7f7467be967f758e0cd74..cb799f429a7c6701b823e7c86b009ab904f4a773
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -8,6 +8,13 @@
#define BOOST_TEST_MODULE "C++ test module for OpenFPM_pdata project"
#include <boost/test/included/unit_test.hpp>
+/*struct MPIFixture {
+ MPIFixture() { MPI_Init(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);}
+ ~MPIFixture() { MPI_Finalize(); }
+};
+
+BOOST_GLOBAL_FIXTURE(MPIFixture);*/
+
#include "Grid/grid_dist_id.hpp"
#include "Point_test.hpp"
#include "Decomposition/CartDecomposition.hpp"
diff --git a/src/metis_util_unit_test.hpp b/src/metis_util_unit_test.hpp
index 7638a2063405e0a4e31d50303dec03a5a261281e..f63d2097fd29c693660d53eda56c2dd287839de1 100644
--- a/src/metis_util_unit_test.hpp
+++ b/src/metis_util_unit_test.hpp
@@ -50,13 +50,6 @@ BOOST_AUTO_TEST_CASE( Metis_test_use)
met.decompose<nm_part_v::id>(gp);
met.decompose<nm_v::id>();
-
- // Write the VTK file
-
- VTKWriter<Graph_CSR<nm_part_v,nm_part_e>> vtk(gp);
- vtk.write("vtk_partition.vtk");
- VTKWriter<Graph_CSR<nm_v,nm_e>> vtk2(g);
- vtk2.write("vtk_partition2.vtk");
}
BOOST_AUTO_TEST_SUITE_END()