diff --git a/CHANGELOG.md b/CHANGELOG.md
index c04b0b9bca0253646874ca0acf04d5dd8b46ff20..54f0e06a995be1881ecfb4a5faa00bb3d713ed79 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,19 @@
# Change Log
All notable changes to this project will be documented in this file.
+## [0.2.0] - 2015-02-17
+### Added
+- PSE 1D example with multiple precision
+- Plot example for GoogleChart plotting
+- Distributed data structure now support 128bit floating point precision (on Beta)
+- OpenFPM support for Microsoft Windows (Cygwin) compilation
+
+### Fixed
+- Detection 32 bit system and report as an error
+
+### Changed
+- Nothing to report
+
## [0.1.0] - 2015-02-05
### Added
- PSE 1D example
diff --git a/Makefile.am b/Makefile.am
index 2a675a02ee48361d4af1c61b67be361fa39e71af..a6fbc5374b3fd1f026c8d0ad28d5b5b393c69a7d 100755
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,3 +1,3 @@
-SUBDIRS = src vtk openfpm_data openfpm_io openfpm_devices openfpm_vcluster
+SUBDIRS = src vtk openfpm_data openfpm_io openfpm_devices openfpm_vcluster openfpm_numerics
bin_PROGRAMS =
diff --git a/configure.ac b/configure.ac
index 9945dfa989743a65af10646fd488da7e8fc87812..295e144b2f6fab33ac60d939b2644bf5f737ba1a 100755
--- a/configure.ac
+++ b/configure.ac
@@ -40,7 +40,17 @@ m4_ifdef([AX_EIGEN],,[m4_include([m4/ax_eigen.m4])])
m4_ifdef([AX_LIB_HDF5],,[m4_include([m4/ax_lib_hdf5.m4])]])
m4_ifdef([AX_H5PART],,[m4_include([m4/ax_h5part.m4])])
-CXXFLAGS+=" --std=c++11 "
+case $host_os in
+ *cygwin*)
+ # Do something specific for cygwin
+ CXXFLAGS+=" --std=gnu++11 "
+ ;;
+ *)
+ #Default Case
+ CXXFLAGS+=" --std=c++11 "
+ ;;
+esac
+
NVCCFLAGS=" "
INCLUDES_PATH=" "
diff --git a/example/Numerics/PSE/0_Derivative_approx_1D/main.cpp b/example/Numerics/PSE/0_Derivative_approx_1D/main.cpp
index 3fd936b4b71a1900c620fba3e2ed7deb6bc443d1..cd16f24ea75324682efd284c1c71134d53c9cba4 100644
--- a/example/Numerics/PSE/0_Derivative_approx_1D/main.cpp
+++ b/example/Numerics/PSE/0_Derivative_approx_1D/main.cpp
@@ -11,7 +11,7 @@
#include "Vector/vector_dist.hpp"
#include "Decomposition/CartDecomposition.hpp"
-#include "Kernels.hpp"
+#include "PSE/Kernels.hpp"
#include "data_type/aggregate.hpp"
#include <cmath>
@@ -63,10 +63,10 @@ int main(int argc, char* argv[])
//
// Number of particles
- const size_t Npart = 1000;
+ const size_t Npart = 125;
// Number of padding particles (At least)
- const size_t Npad = 20;
+ const size_t Npad = 40;
// The domain
Box<1,double> box({0.0},{4.0});
@@ -212,7 +212,7 @@ int main(int argc, char* argv[])
// get and construct the Cell list
Ghost<1,double> gp(enlarge);
- auto cl = vd.getCellList(8*eps,gp);
+ auto cl = vd.getCellList(12*eps,gp);
// Maximum infinity norm
double linf = 0.0;
diff --git a/example/SE/0_classes/Makefile b/example/SE/0_classes/Makefile
index 172ffbd665222f8f35a17e1b68d2d628a8f07208..3cd88b493e5e1adc65ccc44010a4aee0c9036fab 100644
--- a/example/SE/0_classes/Makefile
+++ b/example/SE/0_classes/Makefile
@@ -7,7 +7,7 @@ LDIR =
OBJ = main.o
%.o: %.cpp
- $(CC) -O0 -g3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+ $(CC) -O3 -g3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
se_classes: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
diff --git a/m4/ax_suitesparse.m4 b/m4/ax_suitesparse.m4
index f4ff1309ede91dd1ebee35dd1e8d19960d1f9969..ea32ce0ed11348b27b1d17511ceed7c7f564e849 100644
--- a/m4/ax_suitesparse.m4
+++ b/m4/ax_suitesparse.m4
@@ -87,10 +87,11 @@ esac
# First, check SUITESPARSE_LIBS environment variable
if test "x$SUITESPARSE_LIBS" != x; then
- save_LIBS="$LIBS"; LIBS="$SUITESPARSE_LIBS -lumfpack -lsuitesparseconfig -lm $RT_LIB"
+ save_LIBS="$LIBS"; LIBS="$SUITESPARSE_LIBS -lumfpack -lamd -lbtf -lcamd -lccolamd -lcholmod -lcolamd -lcxsparse -lklu -ldl -lrbio -lspqr -lsuitesparseconfig -lm $RT_LIB"
AC_MSG_CHECKING([for umf_l_malloc])
AC_TRY_LINK_FUNC(umf_l_malloc, [ax_suitesparse_ok=yes
- SUITESPARSE_LIB="$SUITESPARSE_LIBS -lamd -lbtf -lcamd -lccolamd -lcholmod -lcolamd -lcxsparse -lklu -ldl -lrbio -lspqr -lsuitesparseconfig -lumfpack"], [SUITRSPARSE_LIBS=""])
+ SUITESPARSE_LIBS="$SUITESPARSE_LIBS -lumfpack -lamd -lbtf -lcamd -lccolamd -lcholmod -lcolamd -lcxsparse -lklu -ldl -lrbio -lspqr -lsuitesparseconfig"
+ ], [SUITRSPARSE_LIBS=""])
AC_MSG_RESULT($ax_suitesparse_ok)
LIBS="$save_LIBS"
if test $ax_suitesparse_ok = no; then
@@ -100,12 +101,18 @@ if test "x$SUITESPARSE_LIBS" != x; then
CFLAGS=$SUITESPARSE_INCLUDE
AC_CHECK_HEADER(umfpack.h,[],[SUITESPARSE_INCLUDE=""
ax_suitesparse_ok=no])
+
CFLAGS="$old_CFLAGS"
else
- AC_CHECK_LIB(umfpack,umf_l_alloc,[SUITESPARSE_LIB="$SUITESPARSE_LIB -lamd -lbtf -lcamd -lccolamd -lcholmod -lcolamd -lcxsparse -lklu -ldl -lrbio -lspqr -lsuitesparseconfig -lumfpack"],[SUITESPARSE_LIB=""])
+ AC_CHECK_LIB(umfpack,umf_l_alloc,[SUITESPARSE_LIBS="$SUITESPARSE_LIBS -lumfpack -lamd -lbtf -lcamd -lccolamd -lcholmod -lcolamd -lcxsparse -lklu -ldl -lrbio -lspqr -lsuitesparseconfig"],[
+ SUITESPARSE_LIBS=""
+ ax_suitesparse_ok=no
+ ])
old_CFLAGS="$CFLAGS"
AC_CHECK_HEADER(umfpack.h,[],[SUITESPARSE_INCLUDE=""
ax_suitesparse_ok=no])
+
+
CFLAGS="$old_CFLAGS"
fi
diff --git a/script/discover_os b/script/discover_os
index 722665c7a1443e232862d748320d40962cfda035..4abdd2de3e9737ab0f71a87527572c74bfe07539 100755
--- a/script/discover_os
+++ b/script/discover_os
@@ -15,8 +15,6 @@ platform=unknown
platform=osx
elif [[ "$OSTYPE" == "cygwin" ]]; then
echo -e "We are on\033[1;34m CYGWIN \033[0m"
- echo "This platform is not supported"
- exit 1
elif [[ "$OSTYPE" == "msys" ]]; then
echo -e "We are on\033[1;34m Microsoft Window \033[0m"
echo "This platform is not supported"
diff --git a/script/install_MPI.sh b/script/install_MPI.sh
index e48c7275321c74b2b65260d6f8594d89e0aa5ce6..bc829f3bb4c336082513a2ae9427661ac234ddf0 100755
--- a/script/install_MPI.sh
+++ b/script/install_MPI.sh
@@ -10,6 +10,20 @@ fi
wget http://ppmcore.mpi-cbg.de/upload/openmpi-1.8.7.tar.bz2
tar -xvf openmpi-1.8.7.tar.bz2
cd openmpi-1.8.7
+
+#
+# --disable-mca-dso \
+# --disable-sysv-shmem \
+# --enable-cxx-exceptions \
+# --with-threads=posix \
+# --without-cs-fs \
+# --with-mpi-param_check=always \
+# --enable-contrib-no-build=vt,libompitrace \
+#
+#--enable-mca-no-build=paffinity,installdirs-windows,timer-windows,shmem-sysv
+#
+#
+
sh ./configure --prefix=$1/MPI --enable-opal-multi-threads --enable-mpi-f90 $2 $3
make -j 4
mkdir $1/MPI
diff --git a/src/Decomposition/CartDecomposition.hpp b/src/Decomposition/CartDecomposition.hpp
index 2751dedf41fa10cb04854f9f4936c4c14e1116f5..217cfc1e36a03961a4cbc6c915a09b1b720024e3 100644
--- a/src/Decomposition/CartDecomposition.hpp
+++ b/src/Decomposition/CartDecomposition.hpp
@@ -351,6 +351,122 @@ private:
}
}
+
+ /*! \brief It copy the sub-domains into another CartesianDecomposition object extending them
+ *
+ * \see duplicate (in case of extended domain)
+ *
+ * \param cart Cartesian decomposition object
+ * \param box Extended domain
+ *
+ */
+ void extend_subdomains(CartDecomposition<dim,T> & cart, const ::Box<dim,T> & ext_dom) const
+ {
+ // Box
+ typedef ::Box<dim,T> b;
+
+ cart.bbox = ext_dom;
+ cart.ss_box = ext_dom;
+
+ for (size_t i = 0 ; i < sub_domains.size() ; i++)
+ {
+ ::Box<dim,T> box;
+
+ // Calculate the extended box
+ for (size_t j = 0 ; j < dim ; j++)
+ {
+ if (sub_domains.template get<b::p1>(i)[j] == domain.getLow(j))
+ box.setLow(j,ext_dom.getLow(j));
+ else
+ box.setLow(j,sub_domains.template get<b::p1>(i)[j]);
+
+ if (sub_domains.template get<b::p2>(i)[j] == domain.getHigh(j))
+ box.setHigh(j,ext_dom.getHigh(j));
+ else
+ box.setHigh(j,sub_domains.template get<b::p2>(i)[j]);
+ }
+
+ // add the subdomain
+ cart.sub_domains.add(box);
+
+ // Calculate the bound box
+ cart.bbox.enclose(box);
+
+ // Create the smallest box contained in all sub-domain
+ cart.ss_box.contained(box);
+ }
+ }
+
+ /*! \brief Extend the fines for the new Cartesian decomposition
+ *
+ * \param new_fines extended fine_s
+ * \param old_fines old fine_s
+ *
+ */
+ void extend_fines(CartDecomposition<dim,T> & cart) const
+ {
+ // Extension, first we calculate the extensions of the new domain compared
+ // to the old one in cell units (each cell unit is a sub-sub-domain)
+ ::Box<dim,size_t> ext;
+ // Extension of the new fines structure
+ ::Box<dim,size_t> n_fines_ext;
+ // Extension of the old fines structure
+ ::Box<dim,size_t> o_fines_ext;
+
+ size_t sz_new[dim];
+ size_t sz_old[dim];
+
+ for (size_t i = 0; i < dim ; i++)
+ {
+ size_t p1 = (domain.getLow(i) - this->domain.getLow(i)) / cd.getCellBox().getHigh(i) + 1;
+ size_t p2 = (domain.getLow(i) - this->domain.getLow(i)) / cd.getCellBox().getHigh(i) + 1;
+
+ ext.setLow(i,p1);
+ ext.setHigh(i,p2);
+ sz_new[i] = p1+p2+cd.getGrid().size(i);
+ sz_old[i] = cd.getGrid().size(i);
+ }
+
+ grid_sm<dim,void> info_new(sz_new);
+ grid_sm<dim,void> info_old(sz_old);
+
+ // resize the new fines
+ cart.fine_s.resize(info_new.size());
+
+ // we create an iterator that iterate across the full new fines
+ grid_key_dx_iterator<dim> fines_t(info_new);
+
+ while (fines_t.isNext())
+ {
+ auto key = fines_t.get();
+
+ // new_fines is bigger than old_fines structure
+ // out of bound key must be adjusted
+ // The adjustment produce a natural extension
+ // a representation can be seen in the figure of
+ // CartDecomposition duplicate function with extended domains
+
+ grid_key_dx<dim> key_old;
+ for (size_t i = 0 ; i < dim ; i++)
+ {
+ key_old.set_d(i,(long int)key.get(i) - ext.getLow(i));
+ if (key_old.get(i) < 0)
+ key_old.set_d(i,0);
+ else if(key_old.get(i) >= (long int)info_old.size(i) )
+ key_old.set_d(i,info_old.size(i)-1);
+ }
+
+ cart.fine_s.get(info_new.LinId(key)) = fine_s.get(info_old.LinId(key_old));
+
+ ++fines_t;
+ }
+
+ cart.gr.setDimensions(sz_new);
+
+ // the new extended CellDecomposer must be consistent with the old cellDecomposer.
+ cart.cd.setDimensions(cd,ext);
+ }
+
public:
static constexpr int dims = dim;
@@ -699,6 +815,83 @@ p1[0]<-----+ +----> p2[0]
return cart;
}
+ /*! \brief It create another object that contain the same decomposition information but with different ghost boxes and an extended domain
+ *
+ * The domain extension is produced extending the boxes at the border like in figure
+ *
+ * \verbatim
+ *
++--------------^--------^----------^----------+
+| | | | |
+| A | E | F | N |
+| +-----------------------------------+---->
+| | | | | | |
+| A | A | | F | | |
+| | | | | | |
+| | | E +----------+ N | N |
+<--------------+ | | | |
+| | | | | | |
+| | | | G | | |
+| | | | +---------->
+| B | B | +----------+ | |
+| | +--------+ | M | M |
+| | | | H | | |
+| | | +-----+----+---------->
+<--------------+ D | | | |
+| | | | I | L | L |
+| C | C | | | | |
+| | | | | | |
+| +-----------------------------------+ |
+| | | | |
+| C | D | I | L |
++--------------v--------v-----v---------------+
+
+ *
+ * \endverbatim
+ *
+ * \param g ghost
+ * \param domain extended domain (MUST be extended)
+ *
+ * \return a duplicated decomposition with different ghost boxes and an extended domain
+ *
+ */
+ CartDecomposition<dim,T,Memory> duplicate(const Ghost<dim,T> & g, const ::Box<dim,T> & ext_domain) const
+ {
+ CartDecomposition<dim,T,Memory> cart(v_cl);
+
+ cart.box_nn_processor = box_nn_processor;
+
+ // Calculate new sub-domains for extended domain
+ extend_subdomains(cart,ext_domain);
+
+ // Calculate fine_s structure for the extended domain
+ // update the cell decomposer and gr
+ extend_fines(cart);
+
+ // Get the old sub-sub-domain grid extension
+
+ cart.domain = ext_domain;
+
+ // spacing does not change
+ std::copy(spacing,spacing+3,cart.spacing);
+
+ //! Runtime virtual cluster
+ cart.v_cl = v_cl;
+
+ cart.ghost = g;
+
+ for (size_t i = 0 ; i < dim ; i++)
+ cart.bc[i] = bc[i];
+
+ (static_cast<nn_prcs<dim,T> &>(cart)).create(cart.box_nn_processor, cart.sub_domains);
+ (static_cast<nn_prcs<dim,T> &>(cart)).applyBC(ext_domain,ghost,bc);
+
+ cart.Initialize_geo_cell_lists();
+ cart.calculateGhostBoxes();
+
+ return cart;
+ }
+
/*! \brief It create another object that contain the same information and act in the same way
*
* \return a duplicated decomposition
diff --git a/src/Decomposition/CartDecomposition_unit_test.hpp b/src/Decomposition/CartDecomposition_unit_test.hpp
index 834cad13ed3852d97248217514601dade15f8ae9..6d880e13318e210ceaa421723d4181ce20b76bb3 100644
--- a/src/Decomposition/CartDecomposition_unit_test.hpp
+++ b/src/Decomposition/CartDecomposition_unit_test.hpp
@@ -173,6 +173,7 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_periodic_test)
}
// Check the consistency
+
bool val = dec.check_consistency();
BOOST_REQUIRE_EQUAL(val,true);
@@ -203,6 +204,141 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_periodic_test)
BOOST_REQUIRE_EQUAL(ret,true);
}
+BOOST_AUTO_TEST_CASE( CartDecomposition_extend_test)
+{
+ // Initialize the global VCluster
+ init_global_v_cluster(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);
+
+ // Vcluster
+ Vcluster & vcl = *global_v_cluster;
+
+ //! [Create CartDecomposition]
+ CartDecomposition<3,float> dec(vcl);
+
+ // Physical domain
+ Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
+ Box<3,float> bulk({0.05,0.05,0.05},{0.95,0.95,0.95});
+ Box<3,float> bulk_g({0.01,0.01,0.01},{0.95,0.95,0.95});
+ size_t div[3];
+
+ // Get the number of processor and calculate the number of sub-domain
+ // for each processor (SUB_UNIT_FACTOR=64)
+ size_t n_proc = vcl.getProcessingUnits();
+ size_t n_sub = n_proc * SUB_UNIT_FACTOR;
+
+ // Set the number of sub-sub-domains on each dimension (in a scalable way)
+ for (int i = 0 ; i < 3 ; i++)
+ {div[i] = openfpm::math::round_big_2(pow(n_sub,1.0/3));}
+
+ // Define ghost size
+ Ghost<3,float> g(0.01);
+
+ // Boundary conditions
+ size_t bc[] = {PERIODIC,PERIODIC,PERIODIC};
+
+ // Decompose
+ dec.setParameters(div,box,bc,g);
+
+ // Internally create the ghosts
+ dec.calculateGhostBoxes();
+
+ // Duplicate the decomposition extending the domain
+ Box<3,float> box_ext({-0.1,-0.1,-0.1},{1.1,1.1,1.1});
+ CartDecomposition<3,float> dec2 = dec.duplicate(g,box_ext);
+
+ // than we create a grid iterator that iterate across the
+
+ // Create a grid based iterator on the smaller decomposition
+ size_t sz[3] = {128,128,128};
+ grid_dist_id_iterator_dec<CartDecomposition<3,float>> git(dec,sz);
+
+ // iterate across the grid points and we check that the results are consistent
+ while (git.isNext())
+ {
+ auto key = git.get();
+
+ Point<3,float> p = key.toPoint();
+
+ if (bulk_g.isInside(p) == false)
+ {
+ ++git;
+ continue;
+ }
+
+ for (size_t i = 0 ; i < 3 ; i++)
+ p.get(i) = key.get(i) * git.getSpacing(i);
+
+ const openfpm::vector<size_t> & pr_pid = dec.template ghost_processorID<CartDecomposition<3,float>::processor_id>(p);
+ const openfpm::vector<size_t> & pr2_pid = dec2.template ghost_processorID<CartDecomposition<3,float>::processor_id>(p);
+
+ BOOST_REQUIRE(pr_pid == pr2_pid);
+
+ const openfpm::vector<size_t> & pr_bid = dec.template ghost_processorID<CartDecomposition<3,float>::box_id>(p);
+ const openfpm::vector<size_t> & pr2_bid = dec2.template ghost_processorID<CartDecomposition<3,float>::box_id>(p);
+
+ BOOST_REQUIRE(pr_bid == pr2_bid);
+
+ const openfpm::vector<size_t> & pr_lid = dec.template ghost_processorID<CartDecomposition<3,float>::lc_processor_id>(p);
+ const openfpm::vector<size_t> & pr2_lid = dec2.template ghost_processorID<CartDecomposition<3,float>::lc_processor_id>(p);
+
+ BOOST_REQUIRE(pr_lid == pr2_lid);
+
+ size_t n_test = 0;
+
+ // Given a point p, if the point is near the boundary
+ if (bulk.isInside(p) == false)
+ {
+ // we can move p in one direction and check that dec2 return the same result
+ for (size_t i = 0 ; i < 3 ; i++)
+ {
+ Point<3,float> q = p;
+
+ q.get(i) = p.get(i) + 0.05;
+
+ if (box.isInside(q) == false)
+ {
+ const openfpm::vector<size_t> & pr3_pid = dec2.template ghost_processorID<CartDecomposition<3,float>::processor_id>(q);
+ const openfpm::vector<size_t> & pr3_bid = dec2.template ghost_processorID<CartDecomposition<3,float>::box_id>(q);
+ const openfpm::vector<size_t> & pr3_lid = dec2.template ghost_processorID<CartDecomposition<3,float>::lc_processor_id>(q);
+ BOOST_REQUIRE(pr2_pid == pr3_pid);
+ BOOST_REQUIRE(pr2_bid == pr3_bid);
+ BOOST_REQUIRE(pr2_lid == pr3_lid);
+
+ n_test++;
+ }
+
+ q = p;
+ q.get(i) = p.get(i) - 0.05;
+
+ if (box.isInside(q) == false)
+ {
+ const openfpm::vector<size_t> & pr3_pid = dec2.template ghost_processorID<CartDecomposition<3,float>::processor_id>(q);
+ const openfpm::vector<size_t> & pr3_bid = dec2.template ghost_processorID<CartDecomposition<3,float>::box_id>(q);
+ const openfpm::vector<size_t> & pr3_lid = dec2.template ghost_processorID<CartDecomposition<3,float>::lc_processor_id>(q);
+
+ if (pr2_pid != pr3_pid)
+ {
+ const openfpm::vector<size_t> & pr3_pid = dec2.template ghost_processorID<CartDecomposition<3,float>::processor_id>(q);
+
+ int debug = 0;
+ debug++;
+ }
+
+ BOOST_REQUIRE(pr2_pid == pr3_pid);
+ BOOST_REQUIRE(pr2_bid == pr3_bid);
+ BOOST_REQUIRE(pr2_lid == pr3_lid);
+
+ n_test++;
+ }
+ }
+ }
+
+ BOOST_REQUIRE(n_test != 0);
+
+ ++git;
+ }
+}
+
BOOST_AUTO_TEST_SUITE_END()
diff --git a/src/Decomposition/ie_loc_ghost.hpp b/src/Decomposition/ie_loc_ghost.hpp
index ec2d08b6d57870766c063dfc33439879245d08fb..3772b98871b41ce2733144220f3a70bad42ba3c1 100644
--- a/src/Decomposition/ie_loc_ghost.hpp
+++ b/src/Decomposition/ie_loc_ghost.hpp
@@ -133,12 +133,11 @@ class ie_loc_ghost
}
}
- /*! \brief In case of periodic boundary conditions we have to add boxes
- * at the borders
+ /*! \brief In case of periodic boundary conditions we replicate the sub-domains at the border
*
* \param list of sub-domains
* \param domain Domain box
- * \param boundary boundary conditions
+ * \param boundary conditions
* \param ghost ghost part
*
*/
@@ -167,7 +166,7 @@ class ie_loc_ghost
case 1:
bp.setLow(k,domain.getHigh(k)+ghost.getLow(k));
bp.setHigh(k,domain.getHigh(k));
- shift.get(k) = -domain.getHigh(k);
+ shift.get(k) = -domain.getHigh(k)+domain.getLow(k);
break;
case 0:
bp.setLow(k,domain.getLow(k));
@@ -177,7 +176,7 @@ class ie_loc_ghost
case -1:
bp.setLow(k,domain.getLow(k));
bp.setHigh(k,ghost.getHigh(k));
- shift.get(k) = domain.getHigh(k);
+ shift.get(k) = domain.getHigh(k)-domain.getLow(k);
break;
}
}
@@ -527,7 +526,10 @@ public:
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)
+ {
+ std::cout << "No ibx link" << "\n";
return false;
+ }
}
}
@@ -536,9 +538,15 @@ public:
for (size_t i = 0 ; i < loc_ghost_box.size() ; i++)
{
if (loc_ghost_box.get(i).ibx.size() == 0)
+ {
+ std::cout << "Zero ibx" << "\n";
return false;
+ }
if (loc_ghost_box.get(i).ebx.size() == 0)
+ {
+ std::cout << "Zero ebx" << "\n";
return false;
+ }
}
}
diff --git a/src/Decomposition/nn_processor.hpp b/src/Decomposition/nn_processor.hpp
index a8eff91ef0367e663d7da9189beb5356afdc9552..a3fdb27a43cb0967bbf1abfa210056419e64375c 100644
--- a/src/Decomposition/nn_processor.hpp
+++ b/src/Decomposition/nn_processor.hpp
@@ -86,8 +86,7 @@ class nn_prcs
nnpst.pos.add(c);
}
- /*! \brief In case of periodic boundary conditions we have to add boxes
- * at the borders
+ /*! \brief In case of periodic boundary conditions we replicate the sub-domains at the border
*
* \param domain Domain box
* \param boundary boundary conditions
@@ -109,6 +108,7 @@ class nn_prcs
if (check_valid(cmbs[j],bc) == false)
continue;
+ // Calculate the sector box
Box<dim,T> bp;
Point<dim,T> shift;
@@ -119,7 +119,7 @@ class nn_prcs
case 1:
bp.setLow(k,domain.getHigh(k)+ghost.getLow(k));
bp.setHigh(k,domain.getHigh(k));
- shift.get(k) = -domain.getHigh(k);
+ shift.get(k) = -domain.getHigh(k)+domain.getLow(k);
break;
case 0:
bp.setLow(k,domain.getLow(k));
@@ -129,7 +129,7 @@ class nn_prcs
case -1:
bp.setLow(k,domain.getLow(k));
bp.setHigh(k,ghost.getHigh(k));
- shift.get(k) = domain.getHigh(k);
+ shift.get(k) = domain.getHigh(k)-domain.getLow(k);
break;
}
}
@@ -211,6 +211,10 @@ public:
*/
static bool inline check_valid(comb<dim> cmb,const size_t (& bc)[dim])
{
+ // the combination 0 is not valid
+ if (cmb.n_zero() == dim)
+ return false;
+
for (size_t i = 0 ; i < dim ; i++)
{
if (bc[i] == NON_PERIODIC && cmb.getComb()[i] != 0)
diff --git a/src/Grid/grid_dist_id_iterator_sub.hpp b/src/Grid/grid_dist_id_iterator_sub.hpp
index 6c985fc40d3511135062bedb3addcc1564a527e9..244fa2e589faf36f5b46cf65c43de329d0e6a780 100644
--- a/src/Grid/grid_dist_id_iterator_sub.hpp
+++ b/src/Grid/grid_dist_id_iterator_sub.hpp
@@ -131,7 +131,11 @@ class grid_dist_iterator_sub
grid_dist_iterator_sub(const grid_dist_iterator_sub<dim,device_grid> & tmp)
:g_c(tmp.g_c),gList(tmp.gList),gdb_ext(gdb_ext),start(tmp.start),stop(tmp.stop)
{
- a_it.reinitialize(tmp.a_it);
+ // get the next grid iterator
+ if (g_c < gList.size())
+ {
+ a_it.reinitialize(tmp.a_it);
+ }
}
/*! \brief Constructor of the distributed grid iterator
diff --git a/src/Grid/grid_dist_id_unit_test.hpp b/src/Grid/grid_dist_id_unit_test.hpp
index d33d76d758ae670f91b67e79303628b1c8b64b37..7c337b386709f45ffe9e92bdfc1b356e23953a77 100644
--- a/src/Grid/grid_dist_id_unit_test.hpp
+++ b/src/Grid/grid_dist_id_unit_test.hpp
@@ -3,6 +3,7 @@
#include "grid_dist_id.hpp"
#include "data_type/scalar.hpp"
+#include "data_type/aggregate.hpp"
BOOST_AUTO_TEST_SUITE( grid_dist_id_test )
@@ -587,6 +588,113 @@ void Test3D_gg(const Box<3,float> & domain, long int k, long int gk)
}
}
+/*! \brief Test when the domain is not from 0.0 to 1.0
+ *
+ *
+ */
+
+void Test3D_domain(const Box<3,float> & domain, long int k)
+{
+ long int big_step = k / 30;
+ big_step = (big_step == 0)?1:big_step;
+ long int small_step = 21;
+
+ print_test( "Testing 3D grid k<=",k);
+
+ // 3D test
+ for ( ; k >= 2 ; k-= (k > 2*big_step)?big_step:small_step )
+ {
+ BOOST_TEST_CHECKPOINT( "Testing 3D grid k=" << k );
+
+ // grid size
+ size_t sz[3];
+ sz[0] = k;
+ sz[1] = k;
+ sz[2] = k;
+
+ // factor
+ float factor = pow(global_v_cluster->getProcessingUnits()/2.0f,1.0f/3.0f);
+
+ // Ghost
+ Ghost<3,float> g(0.01 / factor);
+
+ // Distributed grid with id decomposition
+ grid_dist_id<3, float, aggregate<long int,long int>, CartDecomposition<3,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<3,void> info(sz);
+
+ // get the domain iterator
+ size_t count = 0;
+
+ auto dom = g_dist.getDomainIterator();
+
+ while (dom.isNext())
+ {
+ auto key = dom.get();
+ auto key_g = g_dist.getGKey(key);
+
+ g_dist.template get<0>(key) = count;
+ g_dist.template get<1>(key) = info.LinId(key_g);
+
+ // Count the point
+ count++;
+
+ ++dom;
+ }
+
+ size_t count2 = count;
+ openfpm::vector<size_t> pnt;
+
+ // Get the total size of the local grids on each processors
+ // and the total size
+ Vcluster & v_cl = g_dist.getVC();
+ v_cl.sum(count2);
+ v_cl.allGather(count,pnt);
+ v_cl.execute();
+ size_t s_pnt = 0;
+
+ // calculate the starting point for this processor
+ for (size_t i = 0 ; i < v_cl.getProcessUnitID() ; i++)
+ s_pnt += pnt.get(i);
+
+ // Check
+ BOOST_REQUIRE_EQUAL(count2,(size_t)k*k*k);
+
+ // sync the ghost
+ g_dist.template ghost_get<0,1>();
+
+ bool match = true;
+
+ // check that the communication is correctly completed
+
+ auto domg = g_dist.getDomainGhostIterator();
+
+ // check that the grid with the ghost past store the correct information
+ while (domg.isNext())
+ {
+ auto key = domg.get();
+ auto key_g = g_dist.getGKey(key);
+
+ // In this case the boundary condition are non periodic
+ if (g_dist.isInside(key_g))
+ {
+ match &= (g_dist.template get<1>(key) == info.LinId(key_g))?true:false;
+ }
+
+ ++domg;
+ }
+
+ BOOST_REQUIRE_EQUAL(match,true);
+ }
+}
+
+
+
void Test2D_complex(const Box<2,float> & domain, long int k)
{
typedef Point_test<float> p;
@@ -1253,6 +1361,20 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_decomposition_iterator )
Test3D_decit(domain3,k);
}
+
+BOOST_AUTO_TEST_CASE( grid_dist_id_domain_test_use)
+{
+ // Initialize the global VCluster
+ init_global_v_cluster(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);
+
+ // Domain
+ Box<3,float> domain3({0.1,0.1,0.1},{1.1,1.1,1.1});
+
+ long int k = 128*128*128*global_v_cluster->getProcessingUnits();
+ k = std::pow(k, 1/3.);
+ Test3D_domain(domain3,k);
+}
+
BOOST_AUTO_TEST_SUITE_END()
#endif
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 2090ca4c7d830e32be53c6163e4429c2a3d58108..44caa10319393c7531fe0ab7712800703bb96ecb 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -1046,7 +1046,7 @@ public:
// Calculate the division array and the cell box
for (size_t i = 0 ; i < dim ; i++)
{
- div[i] = (pbox.getP2().get(i) - pbox.getP1().get(i))/ r_cut;
+ div[i] = static_cast<size_t>((pbox.getP2().get(i) - pbox.getP1().get(i))/ r_cut);
div[i]++;
cell_box.setLow(i,0.0);
diff --git a/src/Vector/vector_dist_key.hpp b/src/Vector/vector_dist_key.hpp
index 03a0286ddd9cf0460332e6b87c538f776952cd4a..80f77580f6b0306c392ecde39a385e8b79d6b0a8 100644
--- a/src/Vector/vector_dist_key.hpp
+++ b/src/Vector/vector_dist_key.hpp
@@ -24,12 +24,22 @@ class vect_dist_key_dx
public:
+ /*! \brief set the key
+ *
+ * \return the local key
+ *
+ */
+ inline void setKey(size_t key)
+ {
+ this->key = key;
+ }
+
/*! \brief Get the key
*
* \return the local key
*
*/
- size_t getKey()
+ inline size_t getKey()
{
return key;
}
@@ -46,10 +56,14 @@ public:
return ts.str();
}
- vect_dist_key_dx(size_t key)
+ inline vect_dist_key_dx(size_t key)
:key(key)
{
}
+
+ inline vect_dist_key_dx()
+ {
+ }
};