diff --git a/CHANGELOG.md b/CHANGELOG.md
index e5b701ba6067648d3c9ee47d92b74ab20c729880..a7c64dd8d614791a26373e5639d545886e1a184c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,8 +9,9 @@ All notable changes to this project will be documented in this file.
### Fixed
- Installation PETSC installation fail in case of preinstalled MPI
+- Miss-compilation of SUITESPARSE on gcc-6.2
- vector_dist with negative domain (Now supported)
-- Grid 1D fixing
+- Grid 1D has been fixed
### Changed
diff --git a/script/install_SUITESPARSE.sh b/script/install_SUITESPARSE.sh
index 8ad698013d80686f6527944d92bb7c2bd6412815..73cba06e438587546c9544426e4deea0f1ad95d5 100755
--- a/script/install_SUITESPARSE.sh
+++ b/script/install_SUITESPARSE.sh
@@ -43,7 +43,7 @@ else
sed -i "/INSTALL_LIB\s=\s\/usr\/local\/lib/c\INSTALL_LIB = $1\/SUITESPARSE\/lib" SuiteSparse_config/SuiteSparse_config.mk
sed -i "/INSTALL_INCLUDE\s=\s\/usr\/local\/include/c\INSTALL_INCLUDE = $1\/SUITESPARSE\/include" SuiteSparse_config/SuiteSparse_config.mk
sed -i "/\sLAPACK\s=\s-llapack/c\LAPACK = " SuiteSparse_config/SuiteSparse_config.mk
- sed -i "/\sBLAS\s=\s\-lopenblas/c\BLAS = -L$1/OPENBLAS/lib -lopenblas" SuiteSparse_config/SuiteSparse_config.mk
+ sed -i "/\sBLAS\s=\s\-lopenblas/c\BLAS = -L$1/OPENBLAS/lib -lopenblas -lpthread" SuiteSparse_config/SuiteSparse_config.mk
fi
diff --git a/src/Decomposition/CartDecomposition.hpp b/src/Decomposition/CartDecomposition.hpp
index 144150979487aaa9c21ceb3bcc828a86fc6f4dc6..daf0682dab1d53a22af31494418a37a616a55d2e 100755
--- a/src/Decomposition/CartDecomposition.hpp
+++ b/src/Decomposition/CartDecomposition.hpp
@@ -75,6 +75,7 @@
* \see calculateGhostBoxes() for a visualization of internal and external ghost boxes
*
* ### Create a Cartesian decomposition object on a Box space, distribute, calculate internal and external ghost boxes
+ *
* \snippet CartDecomposition_unit_test.hpp Create CartDecomposition
*
*/
@@ -203,6 +204,7 @@ public:
/*! \brief Constructor, it decompose and distribute the sub-domains across the processors
*
* \param v_cl Virtual cluster, used internally for communications
+ * \param bc boundary conditions
*
*/
void createSubdomains(Vcluster & v_cl, const size_t (& bc)[dim])
@@ -405,30 +407,30 @@ public:
*
\verbatim
-+----------------------------------------------------+
-| |
-| Processor 8 |
-| Sub+domain 0 +-----------------------------------+
-| | |
-| | |
-++--------------+---+---------------------------+----+ Processor 9 |
- | | | B8_0 | | Subdomain 0 |
- | +------------------------------------+ |
- | | | | | |
- | | | |B9_0| |
- | | B | Local processor | | |
- | Processor 5 | 5 | Subdomain 0 | | |
- | Subdomain 0 | _ | +----------------------------------------+
- | | 0 | | | |
- | | | | | |
- | | | | | Processor 9 |
- | | | |B9_1| Subdomain 1 |
- | | | | | |
- | | | | | |
- | | | | | |
- +--------------+---+---------------------------+----+ |
- | |
- +-----------------------------------+
+ +----------------------------------------------------+
+ | |
+ | Processor 8 |
+ | Sub+domain 0 +-----------------------------------+
+ | | |
+ | | |
+ ++--------------+---+---------------------------+----+ Processor 9 |
+ | | | B8_0 | | Subdomain 0 |
+ | +------------------------------------+ |
+ | | | | | |
+ | | | |B9_0| |
+ | | B | Local processor | | |
+ | Processor 5 | 5 | Subdomain 0 | | |
+ | Subdomain 0 | _ | +----------------------------------------+
+ | | 0 | | | |
+ | | | | | |
+ | | | | | Processor 9 |
+ | | | |B9_1| Subdomain 1 |
+ | | | | | |
+ | | | | | |
+ | | | | | |
+ +--------------+---+---------------------------+----+ |
+ | |
+ +-----------------------------------+
\endverbatim
@@ -436,30 +438,32 @@ public:
and also
G8_0 G9_0 G9_1 G5_0 (External ghost boxes)
- +----------------------------------------------------+
- | Processor 8 |
- | Subdomain 0 +-----------------------------------+
- | | |
- | +---------------------------------------------+ |
- | | G8_0 | | |
-+-----+---------------+------------------------------------+ | Processor 9 |
-| | | | | Subdomain 0 |
-| | | |G9_0| |
-| | | | | |
-| | | | | |
-| | | Local processor | | |
-| Processor 5 | | Sub+domain 0 | | |
-| Subdomain 0 | | +-----------------------------------+
-| | | | | |
-| | G | | | |
-| | 5 | | | Processor 9 |
-| | | | | | Subdomain 1 |
-| | 0 | |G9_1| |
-| | | | | |
-| | | | | |
-+---------------------+------------------------------------+ | |
- | | | |
- +----------------------------------------+----+------------------------------+
+\verbatim
+
+ +----------------------------------------------------+
+ | Processor 8 |
+ | Subdomain 0 +-----------------------------------+
+ | | |
+ | +---------------------------------------------+ |
+ | | G8_0 | | |
+ +-----+---------------+------------------------------------+ | Processor 9 |
+ | | | | | Subdomain 0 |
+ | | | |G9_0| |
+ | | | | | |
+ | | | | | |
+ | | | Local processor | | |
+ | Processor 5 | | Sub+domain 0 | | |
+ | Subdomain 0 | | +-----------------------------------+
+ | | | | | |
+ | | G | | | |
+ | | 5 | | | Processor 9 |
+ | | | | | | Subdomain 1 |
+ | | 0 | |G9_1| |
+ | | | | | |
+ | | | | | |
+ +---------------------+------------------------------------+ | |
+ | | | |
+ +----------------------------------------+----+------------------------------+
\endverbatim
@@ -502,8 +506,10 @@ public:
public:
+ //! Space dimensions
static constexpr int dims = dim;
+ //! Space type
typedef T stype;
//! Increment the reference counter
@@ -641,7 +647,11 @@ public:
/*! \brief Apply boundary condition to the point
*
- * \param p Point to apply the boundary condition
+ * If the particle go out to the right, bring back the particle on the left
+ * in case of periodic, nothing in case of non periodic
+ *
+ * \param pt Point to apply the boundary condition. (it's coordinated are changed according the
+ * the explanation before)
*
*/
void applyPointBC(float (& pt)[dim]) const
@@ -655,7 +665,11 @@ public:
/*! \brief Apply boundary condition to the point
*
- * \param p Point to apply the boundary condition
+ * If the particle go out to the right, bring back the particle on the left
+ * in case of periodic, nothing in case of non periodic
+ *
+ * \param pt Point to apply the boundary conditions.(it's coordinated are changed according the
+ * the explanation before)
*
*/
void applyPointBC(Point<dim,T> & pt) const
@@ -669,7 +683,11 @@ public:
/*! \brief Apply boundary condition to the point
*
- * \param encapsulated object
+ * If the particle go out to the right, bring back the particle on the left
+ * in case of periodic, nothing in case of non periodic
+ *
+ * \param pt encapsulated point object (it's coordinated are changed according the
+ * the explanation before)
*
*/
template<typename Mem> void applyPointBC(encapc<1,Point<dim,T>,Mem> && pt) const
@@ -721,7 +739,7 @@ public:
/*! \brief It create another object that contain the same information and act in the same way
*
- * \return a duplicated decomposition
+ * \return a duplicated CartDecomposition object
*
*/
CartDecomposition<dim,T,Memory> duplicate() const
@@ -755,6 +773,8 @@ public:
*
* \param cart element to copy
*
+ * \return itself
+ *
*/
CartDecomposition<dim,T,Memory> & operator=(const CartDecomposition & cart)
{
@@ -785,6 +805,8 @@ public:
*
* \param cart element to copy
*
+ * \return itself
+ *
*/
CartDecomposition<dim,T,Memory> & operator=(CartDecomposition && cart)
{
@@ -819,6 +841,10 @@ public:
* it define in how many cell it will be divided the space for a particular required minimum
* number of sub-domain
*
+ * \param n_sub number of subdomains per processors
+ *
+ * \return grid dimension (it is one number because on the other dimensions is the same)
+ *
*/
static size_t getDefaultGrid(size_t n_sub)
{
@@ -828,6 +854,8 @@ public:
}
/*! \brief Given a point return in which processor the particle should go
+ *
+ * \param p point
*
* \return processorID
*
@@ -838,6 +866,8 @@ public:
}
/*! \brief Given a point return in which processor the particle should go
+ *
+ * \param p point
*
* \return processorID
*
@@ -848,6 +878,8 @@ public:
}
/*! \brief Given a point return in which processor the particle should go
+ *
+ * \param p point
*
* \return processorID
*
@@ -857,10 +889,12 @@ public:
return fine_s.get(cd.getCell(p));
}
- /*! \brief Given a point return in which processor the particle should go
+ /*! \brief Given a point return in which processor the point/particle should go
*
* Boundary conditions are considered
*
+ * \param p point
+ *
* \return processorID
*
*/
@@ -876,6 +910,8 @@ public:
*
* Boundary conditions are considered
*
+ * \param p point
+ *
* \return processorID
*
*/
@@ -891,6 +927,8 @@ public:
*
* Boundary consition are considered
*
+ * \param p point position
+ *
* \return processorID
*
*/
@@ -939,7 +977,7 @@ public:
*
* \param div_ storing into how many sub-sub-domains to decompose on each dimension
* \param domain_ domain to decompose
- * \param bc_ boundary conditions
+ * \param bc boundary conditions
* \param ghost Ghost size
*
*/
@@ -962,6 +1000,10 @@ public:
}
+ /*! \brief Delete the decomposition and reset the data-structure
+ *
+ *
+ */
void reset()
{
sub_domains.clear();
@@ -989,6 +1031,8 @@ public:
}
/*! \brief Refine the decomposition, available only for ParMetis distribution, for Metis it is a null call
+ *
+ * \param ts number of time step from the previous load balancing
*
*/
void rebalance(size_t ts)
@@ -1005,6 +1049,8 @@ public:
}
/*! \brief Refine the decomposition, available only for ParMetis distribution, for Metis it is a null call
+ *
+ * \param dlb Dynamic load balancing object
*
* \return true if the re-balance has been executed, false otherwise
*/
@@ -1075,9 +1121,10 @@ public:
return dist.getNSubSubDomains();
}
- /*! \brief function that set the weight of the vertex
+ /*! \brief Function that set the computational cost for a of a sub-sub domain
*
* \param id vertex id
+ * \param weight compotational cost
*
*/
inline void setSubSubDomainComputationCost(size_t id, size_t weight)
@@ -1085,9 +1132,11 @@ public:
dist.setComputationCost(id, weight);
}
- /*! \brief function that set the weight of the vertex
+ /*! \brief function that return the computation cost of the sub-sub-domain id
*
- * \param id vertex id
+ * \param id sub-sub-domain id
+ *
+ * \return the computational cost
*
*/
inline size_t getSubSubDomainComputationCost(size_t id)
@@ -1116,7 +1165,8 @@ public:
/*! \brief Get the local sub-domain
*
- * \param i (each local processor can have more than one sub-domain)
+ * \param lc (each local processor can have more than one sub-domain)
+ *
* \return the sub-domain
*
*/
@@ -1137,10 +1187,11 @@ public:
return sp;
}
- /*! \brief Get the local sub-domain with ghost extension
+ /*! \brief Get the local sub-domain enlarged with ghost extension
*
- * \param i (each local processor can have more than one sub-domain)
- * \return the sub-domain
+ * \param lc (each processor can have more than one sub-domain)
+ *
+ * \return the sub-domain extended
*
*/
SpaceBox<dim, T> getSubDomainWithGhost(size_t lc)
@@ -1182,7 +1233,7 @@ public:
*
* \warning if the particle id outside the domain the result is unreliable
*
- * \param p object position
+ * \param pos object position
*
* \return true if it is local
*
@@ -1194,11 +1245,12 @@ public:
/*! \brief Check if the particle is local considering boundary conditions
*
- * \warning if the particle id outside the domain and non periodic the result
+ * \warning if the particle id outside the domain and non periodic boundary the result
* is unreliable
*
*
* \param p object position
+ * \param bc boundary conditions
*
* \return true if it is local
*
@@ -1217,8 +1269,12 @@ public:
}
/*! \brief Check if the particle is local considering boundary conditions
+ *
+ * \warning if the particle id outside the domain and non periodic boundary the result
+ * is unreliable
*
* \param p object position
+ * \param bc boundary conditions
*
* \return true if it is local
*
@@ -1251,6 +1307,8 @@ public:
/*! \brief Return the ghost
*
*
+ * \return the ghost extension
+ *
*/
const Ghost<dim,T> & getGhost() const
{
@@ -1283,6 +1341,8 @@ public:
*
* \param output directory where to write the files
*
+ * \return true if the write succeed
+ *
*/
bool write(std::string output) const
{
@@ -1358,7 +1418,9 @@ public:
/*! \brief Check if the CartDecomposition contain the same information
*
- * \param ele Element to check
+ * \param cart Element to check with
+ *
+ * \return true if they are equal
*
*/
bool is_equal(CartDecomposition<dim,T,Memory> & cart)
@@ -1402,7 +1464,9 @@ public:
/*! \brief Check if the CartDecomposition contain the same information with the exception of the ghost part
* It is anyway required that the ghost come from the same sub-domains decomposition
*
- * \param ele Element to check
+ * \param cart Element to check with
+ *
+ * \return true if the two CartDecomposition are equal
*
*/
bool is_equal_ng(CartDecomposition<dim,T,Memory> & cart)
@@ -1463,8 +1527,7 @@ public:
dist.setComputationCost(gid, c + i);
}
- // friend classes
-
+ //! friend classes
friend extended_type;
};
diff --git a/src/Decomposition/CartDecomposition_unit_test.hpp b/src/Decomposition/CartDecomposition_unit_test.hpp
index 5871b7ee822f3540276d96090fbf0cc6cda6aefe..034188054df229d1f2cd9ab33d4baf3aa0a85b7f 100755
--- a/src/Decomposition/CartDecomposition_unit_test.hpp
+++ b/src/Decomposition/CartDecomposition_unit_test.hpp
@@ -57,7 +57,6 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_non_periodic_test)
// Vcluster
Vcluster & vcl = create_vcluster();
- //! [Create CartDecomposition]
CartDecomposition<3, float> dec(vcl);
// Physical domain
@@ -83,8 +82,6 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_non_periodic_test)
dec.setParameters(div,box,bc,g);
dec.decompose();
- //! [Create CartDecomposition]
-
// For each calculated ghost box
for (size_t i = 0; i < dec.getNIGhostBox(); i++)
{
@@ -244,7 +241,6 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_ext_non_periodic_test)
// Vcluster
Vcluster & vcl = create_vcluster();
- //! [Create CartDecomposition]
CartDecomposition<3,float> dec(vcl);
// Physical domain
diff --git a/src/Decomposition/nn_processor_unit_test.hpp b/src/Decomposition/nn_processor_unit_test.hpp
index bc904d7b952b5d963e5ab2baaafce703e4ccfd21..71297a3288d93a2e3f4e1ed1bf47410427522c42 100644
--- a/src/Decomposition/nn_processor_unit_test.hpp
+++ b/src/Decomposition/nn_processor_unit_test.hpp
@@ -93,9 +93,9 @@ BOOST_AUTO_TEST_CASE( nn_processor_np_test)
if (v_cl.getProcessUnitID() == 0)
{
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(1),1);
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(2),1);
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(3),1);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(1),1ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(2),1ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(3),1ul);
const openfpm::vector< ::Box<2,float> > & nsubs1 = nnp.getNearSubdomains(1);
const openfpm::vector< ::Box<2,float> > & nsubs2 = nnp.getNearSubdomains(2);
@@ -120,9 +120,9 @@ BOOST_AUTO_TEST_CASE( nn_processor_np_test)
}
else if (v_cl.getProcessUnitID() == 1)
{
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(0),1);
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(2),1);
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(3),1);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(0),1ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(2),1ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(3),1ul);
const openfpm::vector< ::Box<2,float> > & nsubs1 = nnp.getNearSubdomains(0);
const openfpm::vector< ::Box<2,float> > & nsubs2 = nnp.getNearSubdomains(2);
@@ -147,9 +147,9 @@ BOOST_AUTO_TEST_CASE( nn_processor_np_test)
}
else if (v_cl.getProcessUnitID() == 2)
{
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(1),1);
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(0),1);
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(3),1);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(1),1ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(0),1ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(3),1ul);
const openfpm::vector< ::Box<2,float> > & nsubs1 = nnp.getNearSubdomains(1);
const openfpm::vector< ::Box<2,float> > & nsubs2 = nnp.getNearSubdomains(0);
@@ -173,9 +173,9 @@ BOOST_AUTO_TEST_CASE( nn_processor_np_test)
}
else if (v_cl.getProcessUnitID() == 3)
{
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(0),1);
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(1),1);
- BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(2),1);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(0),1ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(1),1ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNRealSubdomains(2),1ul);
const openfpm::vector< ::Box<2,float> > & nsubs1 = nnp.getNearSubdomains(0);
const openfpm::vector< ::Box<2,float> > & nsubs2 = nnp.getNearSubdomains(1);
@@ -250,9 +250,9 @@ BOOST_AUTO_TEST_CASE( nn_processor_box_periodic_test)
if (v_cl.getProcessUnitID() == 0)
{
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(1).size(),4);
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(2).size(),4);
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(3).size(),4);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(1).size(),4ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(2).size(),4ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(3).size(),4ul);
openfpm::vector<Box<2,float>> bv;
@@ -286,9 +286,9 @@ BOOST_AUTO_TEST_CASE( nn_processor_box_periodic_test)
}
else if (v_cl.getProcessUnitID() == 1)
{
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(0).size(),4);
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(2).size(),4);
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(3).size(),4);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(0).size(),4ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(2).size(),4ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(3).size(),4ul);
openfpm::vector<Box<2,float>> bv;
@@ -322,9 +322,9 @@ BOOST_AUTO_TEST_CASE( nn_processor_box_periodic_test)
}
else if (v_cl.getProcessUnitID() == 2)
{
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(0).size(),4);
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(1).size(),4);
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(3).size(),4);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(0).size(),4ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(1).size(),4ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(3).size(),4ul);
openfpm::vector<Box<2,float>> bv;
@@ -358,9 +358,9 @@ BOOST_AUTO_TEST_CASE( nn_processor_box_periodic_test)
}
else if (v_cl.getProcessUnitID() == 3)
{
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(0).size(),4);
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(1).size(),4);
- BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(2).size(),4);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(0).size(),4ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(1).size(),4ul);
+ BOOST_REQUIRE_EQUAL(nnp.getNearSubdomains(2).size(),4ul);
openfpm::vector<Box<2,float>> bv;
diff --git a/src/Grid/grid_dist_id_iterator.hpp b/src/Grid/grid_dist_id_iterator.hpp
index 84b2cd8dbf2ee01cec32d5039277e12721278153..47b909debc5fcb75c86b8acba595eba39c97555f 100644
--- a/src/Grid/grid_dist_id_iterator.hpp
+++ b/src/Grid/grid_dist_id_iterator.hpp
@@ -116,9 +116,11 @@ class grid_dist_iterator<dim,device_grid,FREE>
/*! \brief Constructor of the distributed grid iterator
*
* \param gk std::vector of the local grid
+ * \param gdb_ext set of local subdomains
+ * \param stop end point
*
*/
- grid_dist_iterator(const openfpm::vector<device_grid> & gk, const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext, grid_key_dx<dim> stop)
+ grid_dist_iterator(const openfpm::vector<device_grid> & gk, const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext, const grid_key_dx<dim> & stop)
:g_c(0),gList(gk),gdb_ext(gdb_ext),stop(stop)
{
// Initialize the current iterator
diff --git a/src/Grid/grid_dist_id_unit_test.cpp b/src/Grid/grid_dist_id_unit_test.cpp
index d26644b153e796db8abd2f0c007abc0db0f20532..89f04a8d0a9654c87b3459e30553de3dba4a8cfa 100644
--- a/src/Grid/grid_dist_id_unit_test.cpp
+++ b/src/Grid/grid_dist_id_unit_test.cpp
@@ -390,11 +390,131 @@ void Test2D(const Box<2,float> & domain, long int k)
// In this case the boundary condition are non periodic
if (g_dist.isInside(key_g))
{
- match &= (g_dist.template get<0>(key),info.LinId(key_g));
+ match &= (g_dist.template get<0>(key) == info.LinId(key_g))?true:false;
}
++domg;
}
+
+ BOOST_REQUIRE_EQUAL(match,true);
+ }
+}
+
+
+void Test1D(const Box<1,float> & domain, long int k)
+{
+ Vcluster & v_cl = create_vcluster();
+ long int big_step = k / 30;
+ big_step = (big_step == 0)?1:big_step;
+ long int small_step = 21;
+
+ if (v_cl.getProcessingUnits() > 48)
+ return;
+
+ print_test( "Testing 1D grid k<=",k);
+
+ // 1D test
+ for ( ; k >= 2 ; k-= (k > 2*big_step)?big_step:small_step )
+ {
+ BOOST_TEST_CHECKPOINT( "Testing 1D grid k=" << k );
+
+ //! [Create and access a distributed grid]
+
+ // grid size
+ size_t sz[1];
+ sz[0] = k;
+
+ float factor = pow(create_vcluster().getProcessingUnits()/2.0f,1.0f);
+
+ // Ghost
+ Ghost<1,float> g(0.01 / factor);
+
+ // Distributed grid with id decomposition
+ grid_dist_id<1, float, scalar<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<1,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) = info.LinId(key_g);
+
+ // Count the point
+ count++;
+
+ ++dom;
+ }
+
+ //! [Create and access a distributed grid]
+
+ // Get the virtual cluster machine
+ Vcluster & vcl = g_dist.getVC();
+
+ // reduce
+ vcl.sum(count);
+ vcl.execute();
+
+ // Check
+ BOOST_REQUIRE_EQUAL(count,(size_t)k);
+
+ auto dom2 = g_dist.getDomainIterator();
+
+ grid_key_dx<1> start = dom2.getStart();
+ grid_key_dx<1> stop = dom2.getStop();
+
+ BOOST_REQUIRE_EQUAL((long int)stop.get(0),(long int)g_dist.size(0)-1);
+
+ BOOST_REQUIRE_EQUAL(start.get(0),0);
+
+ bool match = true;
+
+ // check that the grid store the correct information
+ while (dom2.isNext())
+ {
+ auto key = dom2.get();
+ auto key_g = g_dist.getGKey(key);
+
+ match &= (g_dist.template get<0>(key) == info.LinId(key_g))?true:false;
+
+ ++dom2;
+ }
+
+ BOOST_REQUIRE_EQUAL(match,true);
+
+ g_dist.template ghost_get<0>();
+
+ // 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<0>(key) == info.LinId(key_g))?true:false;
+ }
+
+ ++domg;
+ }
+
+ BOOST_REQUIRE_EQUAL(match,true);
}
}
@@ -1770,6 +1890,16 @@ BOOST_AUTO_TEST_CASE( grid_dist_id_copy )
Test_grid_copy(domain3,k);
}
+BOOST_AUTO_TEST_CASE( grid_1d_test )
+{
+ // Domain
+ Box<1,float> domain1({-1.0},{1.0});
+
+ long int k = 32*32*32*create_vcluster().getProcessingUnits();
+
+ Test1D(domain1,k);
+}
+
BOOST_AUTO_TEST_SUITE_END()
#endif
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index a59e33784e240eace172656b5fd601c65704d086..47ee46c08b63a737eebab9dc67c9c4c371b80003 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -1191,8 +1191,13 @@ BOOST_AUTO_TEST_CASE( vector_dist_cell_verlet_test )
// Boundary conditions
size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};
+ float spacing = 1.0/Ng;
+ float first_dist = spacing;
+ float second_dist = sqrt(2.0*spacing*spacing);
+ float third_dist = sqrt(3.0 * spacing*spacing);
+
// ghost
- Ghost<3,float> ghost(1.0/(Ng-2));
+ Ghost<3,float> ghost(third_dist*1.1);
// Distributed vector
vector_dist<3,float, Point_test<float>, CartDecomposition<3,float> > vd(0,box,bc,ghost);
@@ -1229,14 +1234,11 @@ BOOST_AUTO_TEST_CASE( vector_dist_cell_verlet_test )
vd.ghost_get<0>();
+ vd.write("Debug_output");
+
// calculate the distance of the first, second and third neighborhood particle
// Consider that they are on a regular grid
- float spacing = it.getSpacing(0);
- float first_dist = spacing;
- float second_dist = sqrt(2.0*spacing*spacing);
- float third_dist = sqrt(3.0 * spacing*spacing);
-
// add a 5% to dist
first_dist += first_dist * 0.05;
@@ -1249,6 +1251,8 @@ BOOST_AUTO_TEST_CASE( vector_dist_cell_verlet_test )
bool correct = true;
+ BOOST_REQUIRE_EQUAL(vd.size_local(),verlet.size());
+
// for each particle
for (size_t i = 0 ; i < verlet.size() ; i++)
{
diff --git a/src/dec_optimizer.hpp b/src/dec_optimizer.hpp
index 737377a0d3d78f55f1f1dd180fcef1b7595bae97..d7f4f18f9110314cec1b80f1fb5f5d7d6c16f24a 100644
--- a/src/dec_optimizer.hpp
+++ b/src/dec_optimizer.hpp
@@ -6,86 +6,24 @@
/*! \brief this class represent a wavefront of dimension dim
*
- * \dim Dimensionality of the wavefront (dimensionality of the space
+ * \tparam dim Dimensionality of the wavefront (dimensionality of the space
* where it live so the wavefront
* is dim-1)
*
+ * Each wavefront is identified by one starting point and one stop point.
+ * More or less a wavefront is just a box defined in the integer space
+ *
*/
-
template <unsigned int dim>
-class wavefront
+class wavefront : public Box<dim,size_t>
{
public:
- typedef boost::fusion::vector<size_t[dim],size_t[dim]> type;
-
- type data;
-
+ //! start point is the property with id 0 (first property)
static const int start = 0;
- static const int stop = 1;
- static const int max_prop = 2;
-
- /* \brief Get the key to the point 1
- *
- * \return the key to the point 1
- *
- */
-
- grid_key_dx<dim> getKP1()
- {
- // grid key to return
- grid_key_dx<dim> ret(boost::fusion::at_c<start>(data));
-
- return ret;
- }
-
- /* \brief Get the key to point 2
- *
- * \return the key to the point 2
- *
- */
-
- grid_key_dx<dim> getKP2()
- {
- // grid key to return
- grid_key_dx<dim> ret(boost::fusion::at_c<stop>(data));
-
- return ret;
- }
-
- /* \brief produce a box from an encapsulated object
- *
- * \param encap encapsulated object
- *
- */
-
- template<typename encap> static Box<dim,size_t> getBox(const encap && enc)
- {
- Box<dim,size_t> bx;
-
- // Create the object from the encapsulation
- getBox(enc,bx);
-
- return bx;
- }
-
- /* \brief produce a box from an encapsulated object
- *
- * \param encap encapsulated object
- *
- */
-
- template<typename encap> static void getBox(const encap & enc, Box<dim,size_t> & bx)
- {
- // Create the object from the encapsulation
-
- for (int i = 0 ; i < dim ; i++)
- {
- bx.setLow(i,enc.template get<wavefront::start>()[i]);
- bx.setHigh(i,enc.template get<wavefront::stop>()[i]);
- }
- }
+ //! stop point is the property with id 1 (second property)
+ static const int stop = 1;
};
/*! \brief This class take a graph representing the space decomposition and produce a
@@ -100,8 +38,7 @@ public:
template <unsigned int dim, typename Graph>
class dec_optimizer
{
- // create a grid header for helping
-
+ //! Contain information about the grid size
grid_sm<dim,void> gh;
private:
@@ -111,7 +48,6 @@ private:
* \param v_w wavefronts
* \param w_comb wavefront expansion combinations
* \param d direction of expansion
- * \param bc boundary condition
*
*/
void expand_one_wf(openfpm::vector<wavefront<dim>> & v_w, std::vector<comb<dim>> & w_comb , size_t d)
@@ -126,6 +62,9 @@ private:
/*! \brief Adjust the other wavefronts
*
+ * \param v_w array of wavefronts
+ * \param hyp Hyper cube used to adjust the wavefront
+ * \param w_comb for each wavefront indicate their position (normal to the face of the wavefront)
* \param d direction
*
*/
@@ -154,7 +93,6 @@ private:
size_t id = hyp.LinId(q_comb[j]);
// get the combination of the direction d
-
bool is_pos = hyp.isPositive(d);
// is positive, modify the stop point or the starting point
@@ -169,16 +107,14 @@ private:
}
}
- /* \brief Fill the wavefront position
+ /*! \brief Fill the wavefront position
*
* \tparam prp property to set
*
* \param graph we are processing
- * \param Box to fill
- * \param id value to fill with
+ * \param v_w array of wavefronts
*
*/
-
template<unsigned int prp> void write_wavefront(Graph & graph,openfpm::vector<wavefront<dim>> & v_w)
{
// fill the wall domain with 0
@@ -195,12 +131,12 @@ private:
}
}
- /* \brief Fill the domain
+ /*! \brief Fill the domain
*
* \tparam p_sub property to set with the sub-domain id
*
* \param graph we are processing
- * \param Box to fill
+ * \param box Box to fill
* \param ids value to fill with
*
*/
@@ -226,16 +162,17 @@ private:
}
}
- /* \brief Add the boundary domain of id p_id to the queue
+ /*! \brief Add the boundary domain of id p_id to the queue
*
- * \tparam i-property where is stored the decomposition
+ * \tparam p_sub property id where to store the sub-domain decomposition
+ * \tparam p_id property id where is stored the decomposition
*
- * \param domains vector with domains to process
+ * \param domains vector with sub-sub-domains still to process
+ * \param v_w array of wave-fronts
* \param graph we are processing
- * \param w_comb hyper-cube combinations
- * \param p_id processor id
- * \param box_nn_processor list of neighborhood processors for the box
- * \param bc Boundary conditions
+ * \param w_comb wavefront combination, it is the normal vector to the wavefront
+ * \param pr_id processor id for which we are optimizing the decomposition
+ * \param bc boundary conditions
*
*/
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, const size_t(& bc)[dim])
@@ -308,7 +245,7 @@ private:
domains.swap(domains_new);
}
- /* \brief Find the biggest hyper-cube
+ /*! \brief Find the biggest hyper-cube
*
* starting from one initial sub-domain find the biggest hyper-cube
* output the box, and fill a list of neighborhood processor
@@ -402,38 +339,41 @@ private:
// expand the intersection of the wavefronts
- std::vector<comb<dim>> q_comb = SubHyperCube<dim,dim-1>::getCombinations_R(w_comb[d],dim-2);
+ if (dim >= 2)
+ {
+ std::vector<comb<dim>> q_comb = SubHyperCube<dim,dim-1>::getCombinations_R(w_comb[d],dim-2);
- // Eliminate the w_comb[d] direction
+ // Eliminate the w_comb[d] direction
- for (size_t k = 0 ; k < q_comb.size() ; k++)
- {
- for (size_t j = 0 ; j < dim ; j++)
+ for (size_t k = 0 ; k < q_comb.size() ; k++)
{
- if (w_comb[d].c[j] != 0)
+ for (size_t j = 0 ; j < dim ; j++)
{
- q_comb[k].c[j] = 0;
+ if (w_comb[d].c[j] != 0)
+ {
+ q_comb[k].c[j] = 0;
+ }
}
}
- }
- // for all the combinations
- for (size_t j = 0 ; j < q_comb.size() ; j++)
- {
- size_t id = hyp.LinId(q_comb[j]);
+ // for all the combinations
+ for (size_t j = 0 ; j < q_comb.size() ; j++)
+ {
+ size_t id = hyp.LinId(q_comb[j]);
- // get the combination of the direction d
+ // get the combination of the direction d
- bool is_pos = hyp.isPositive(d);
+ bool is_pos = hyp.isPositive(d);
- // is positive, modify the stop point or the starting point
+ // is positive, modify the stop point or the starting point
- for (size_t s = 0 ; s < dim ; s++)
- {
- if (is_pos == true)
- {v_w.template get<wavefront<dim>::stop>(id)[s] = v_w.template get<wavefront<dim>::stop>(id)[s] + w_comb[d].c[s];}
- else
- {v_w.template get<wavefront<dim>::start>(id)[s] = v_w.template get<wavefront<dim>::start>(id)[s] + w_comb[d].c[s];}
+ for (size_t s = 0 ; s < dim ; s++)
+ {
+ if (is_pos == true)
+ {v_w.template get<wavefront<dim>::stop>(id)[s] = v_w.template get<wavefront<dim>::stop>(id)[s] + w_comb[d].c[s];}
+ else
+ {v_w.template get<wavefront<dim>::start>(id)[s] = v_w.template get<wavefront<dim>::start>(id)[s] + w_comb[d].c[s];}
+ }
}
}
}
@@ -456,8 +396,8 @@ private:
/*! \brief Initialize the wavefronts
*
- * \param starting point of the wavefront set
- * \param v_w Wavefront to initialize
+ * \param start_p starting point for the wavefront set
+ * \param v_w Wavefront array
*
*/
void InitializeWavefront(grid_key_dx<dim> & start_p, openfpm::vector<wavefront<dim>> & v_w)
@@ -479,13 +419,15 @@ private:
* search in the graph for one sub-domain labelled with processor id
* to use as seed
*
- * \tparam p_id property in the graph storing the sub-domain id
+ * \tparam p_id property id containing the decomposition
+ * \tparam p_sub property id that will contain the sub-domain decomposition
*
- * \param Graph graph
+ * \param graph Graph
* \param id processor id
*
+ * \return a valid seed key
+ *
*/
-
template<unsigned int p_id, unsigned int p_sub> grid_key_dx<dim> search_seed(Graph & graph, long int id)
{
// if no processor is selected return the first point
@@ -531,18 +473,18 @@ private:
* To the domains inside the hyper-cube one sub-id is assigned. This procedure continue until
* all the domain of one p_id has a sub-id
*
- * \tparam j property containing the decomposition
- * \tparam i property to fill with the sub-decomposition
+ * \tparam p_id property containing the decomposition
+ * \tparam p_sub property to fill with the sub-domain decomposition
*
* \param start_p seed point
* \param graph we are processing
- * \param p_id Processor id (if p_id == -1 the optimization is done for all the processors)
- * \param list of sub-domain boxes produced by the algorithm
- * \param box_nn_processor for each box it list all the neighborhood processor
+ * \param pr_id Processor id (if p_id == -1 the optimization is done for all the processors)
+ * \param lb list of sub-domain boxes produced by the algorithm
+ * \param box_nn_processor for each sub-domain it list all the neighborhood processors
* \param ghe Ghost extension in sub-sub-domain units in each direction
- * \param bc Boundary condition
- * \param init_sub_id when true p_sub property is initial set to -1 [default true]
- * \param sub_id starting sub_id enumeration [default 0]
+ * \param init_sub_id when true p_sub property is initially set to -1 [default true]
+ * \param sub_id starting sub_id to enumerate them [default 0]
+ * \param bc boundary conditions
*
* \return last assigned sub-id
*
@@ -606,10 +548,17 @@ private:
}
/*! \brief Construct the sub-domain processor list
+ *
+ * \tparam p_id property that contain the decomposition
*
* Each entry is a sub-domain, the list of numbers indicate the neighborhood processors
*
- * \brief box_nn_processor
+ * \param graph graph to process
+ * \param box_nn_processor for each sub-domain it list all the neighborhood processors
+ * \param subs vector of sub-domains
+ * \param ghe ghost extensions
+ * \param bc boundary conditions
+ * \param pr_id processor that we are processing
*
*/
template<unsigned int p_id> void construct_box_nn_processor(Graph & graph, openfpm::vector< openfpm::vector<size_t> > & box_nn_processor, const openfpm::vector<Box<dim,size_t>> & subs, const Ghost<dim,long int> & ghe, const size_t (& bc)[dim], long int pr_id)
@@ -621,6 +570,7 @@ private:
map.clear();
Box<dim,size_t> sub = subs.get(i);
sub.enlarge(ghe);
+
grid_skin_iterator_bc<dim> gsi(gh,subs.get(i),sub,bc);
while (gsi.isNext())
@@ -666,11 +616,13 @@ public:
* the boundary until the wavefronts cannot expand any more, creating a sub-domain covering more sub-sub-domain.
* This procedure continue until all the domain is covered by a sub-domains
*
- * \tparam j property containing the processor decomposition
- * \tparam i property to fill with the sub-domain-decomposition id
+ * \tparam p_id property containing the processor decomposition
+ * \tparam p_sub property to fill with the sub-domain decomposition
*
* \param start_p seed point
* \param graph we are processing
+ * \param ghe ghost size
+ * \param bc boundary conditions
*
*/
template <unsigned int p_sub, unsigned int p_id> void optimize(grid_key_dx<dim> & start_p, Graph & graph, const Ghost<dim,long int> & ghe , const size_t (& bc)[dim])
@@ -691,12 +643,14 @@ public:
* the boundary until the wavefronts cannot expand any more, creating a sub-domain covering more sub-sub-domain.
* This procedure continue until all the sub-domain of the processor p_id are covered by a sub-domains
*
- * \tparam j property containing the decomposition
- * \tparam i property to fill with the sub-domain-decomposition id
+ * \tparam p_id property containing the decomposition
+ * \tparam p_sub property to fill with the sub-domain decomposition
*
* \param graph we are processing
- * \param p_id Processor id (if p_id == -1 the optimization is done for all the processors)
- * \param list of sub-domain boxes
+ * \param pr_id Processor id (if p_id == -1 the optimization is done for all the processors)
+ * \param lb list of sub-domain boxes
+ * \param box_nn_processor for each sub-domain it list all the neighborhood processors
+ * \param ghe ghost size
*
*/
template <unsigned int p_sub, unsigned int p_id> void optimize(Graph & graph, long int pr_id, openfpm::vector<Box<dim,size_t>> & lb, openfpm::vector< openfpm::vector<size_t> > & box_nn_processor, const Ghost<dim,long int> & ghe, const size_t (& bc)[dim])