From 5ad87499bfc307770a496dad39a81f7996414d4f Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Thu, 22 Sep 2016 19:48:10 +0200
Subject: [PATCH] Latest modules
---
CHANGELOG.md | 9 +++++++-
configure.ac | 9 +++-----
.../PSE/0_Derivative_approx_1D/Makefile | 2 +-
example/Numerics/PSE/1_Diffusion_1D/Makefile | 2 +-
.../Stoke_flow/0_2D_incompressible/Makefile | 2 +-
.../Stoke_flow/1_3D_incompressible/Makefile | 2 +-
example/Vector/0_simple/Makefile | 2 +-
example/Vector/2_expressions/Makefile | 2 +-
example/Vector/3_molecular_dynamic/Makefile | 2 +-
example/Vector/4_complex_prop/Makefile | 2 +-
example/Vector/4_multiphase_celllist/Makefile | 2 +-
example/Vector/4_reorder/Makefile | 2 +-
openfpm_data | 2 +-
openfpm_numerics | 2 +-
src/Makefile.am | 2 +-
src/Vector/vector_dist.hpp | 21 +++++++++++++++++--
src/Vector/vector_dist_comm.hpp | 21 +++++++++++++++++++
17 files changed, 64 insertions(+), 22 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5042a8a4..8c03e493 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,9 +13,16 @@ All notable changes to this project will be documented in this file.
- Miss-compilation of SUITESPARSE on gcc-6.2
- vector_dist with negative domain (Now supported)
- Grid 1D has been fixed
-- One constructor of Box had arguments inverted.
+- One constructor of Box had arguments inverted.
+ PLEASE CAREFULL ON THIS BUG
+ float xmin[] = {0.0,0.0};
+ float xmax[] = {1.0,1.0};
+ // Box<2,float> box(xmax,xmin) BUG IT WAS xmax,xmin
+ Box<2,float> box(xmin,xmax) <--- NOW IT IS xmin,xmax
+ Box<2,float> box({0.0,0.0},{1.0,1.0}) <---- This constructor is not affected by the BUG
### Changed
+- On gcc the -fext-numeric-literals compilation flag is now mandatory
## [0.5.0] - 15 August 2016
diff --git a/configure.ac b/configure.ac
index bff4f8b1..45305737 100644
--- a/configure.ac
+++ b/configure.ac
@@ -175,14 +175,11 @@ my_save_cflags="$CXXFLAGS"
CXXFLAGS=-fext-numeric-literals
AC_MSG_CHECKING([whether CXX supports -fext-numeric-literals])
AC_COMPILE_IFELSE([AC_LANG_PROGRAM([])],
- [AC_MSG_RESULT([yes])],
- [
- AM_CXXFLAGS=-fext-numeric-literals
- echo "-fext-numeric-literals" > config_opt
+ [AC_MSG_RESULT([yes])
+ AM_CXXFLAGS="-fext-numeric-literals"
],
[
- AC_MSG_RESULT([no]),
- echo "" > config_opt
+ AC_MSG_RESULT([no])
]
)
AC_LANG_POP([C++])
diff --git a/example/Numerics/PSE/0_Derivative_approx_1D/Makefile b/example/Numerics/PSE/0_Derivative_approx_1D/Makefile
index 4399591a..24da6b8b 100644
--- a/example/Numerics/PSE/0_Derivative_approx_1D/Makefile
+++ b/example/Numerics/PSE/0_Derivative_approx_1D/Makefile
@@ -7,7 +7,7 @@ LDIR =
OBJ = main.o
%.o: %.cpp
- $(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+ $(CC) -fext-numeric-literals -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
pse_1d: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
diff --git a/example/Numerics/PSE/1_Diffusion_1D/Makefile b/example/Numerics/PSE/1_Diffusion_1D/Makefile
index 80cc4ffe..241b3dfd 100644
--- a/example/Numerics/PSE/1_Diffusion_1D/Makefile
+++ b/example/Numerics/PSE/1_Diffusion_1D/Makefile
@@ -7,7 +7,7 @@ LDIR =
OBJ = main.o
%.o: %.cpp
- $(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+ $(CC) -fext-numeric-literals -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
diff_1d: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
diff --git a/example/Numerics/Stoke_flow/0_2D_incompressible/Makefile b/example/Numerics/Stoke_flow/0_2D_incompressible/Makefile
index b6512e4c..3c6a733e 100644
--- a/example/Numerics/Stoke_flow/0_2D_incompressible/Makefile
+++ b/example/Numerics/Stoke_flow/0_2D_incompressible/Makefile
@@ -8,7 +8,7 @@ OBJ_EIGEN = main_eigen.o
OBJ_PETSC = main_petsc.o
%.o: %.cpp
- $(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+ $(CC) -fext-numeric-literals -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
all: stokes_2d_eigen stokes_2d_petsc
diff --git a/example/Numerics/Stoke_flow/1_3D_incompressible/Makefile b/example/Numerics/Stoke_flow/1_3D_incompressible/Makefile
index 37f93648..68f9098b 100644
--- a/example/Numerics/Stoke_flow/1_3D_incompressible/Makefile
+++ b/example/Numerics/Stoke_flow/1_3D_incompressible/Makefile
@@ -8,7 +8,7 @@ OBJ_EIGEN = main_eigen.o
OBJ_PETSC = main_petsc.o
%.o: %.cpp
- $(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+ $(CC) -fext-numeric-literals -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
all: stokes_3d_eigen stokes_3d_petsc
diff --git a/example/Vector/0_simple/Makefile b/example/Vector/0_simple/Makefile
index 646357e9..9afd8418 100644
--- a/example/Vector/0_simple/Makefile
+++ b/example/Vector/0_simple/Makefile
@@ -7,7 +7,7 @@ LDIR =
OBJ = main.o
%.o: %.cpp
- $(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+ $(CC) -fext-numeric-literals -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
vect: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
diff --git a/example/Vector/2_expressions/Makefile b/example/Vector/2_expressions/Makefile
index a7705b97..bfa50d40 100644
--- a/example/Vector/2_expressions/Makefile
+++ b/example/Vector/2_expressions/Makefile
@@ -7,7 +7,7 @@ LDIR =
OBJ = main.o
%.o: %.cpp
- $(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+ $(CC) -fext-numeric-literals -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
expr: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
diff --git a/example/Vector/3_molecular_dynamic/Makefile b/example/Vector/3_molecular_dynamic/Makefile
index 9c467c81..6d55806e 100644
--- a/example/Vector/3_molecular_dynamic/Makefile
+++ b/example/Vector/3_molecular_dynamic/Makefile
@@ -12,7 +12,7 @@ OBJ_VL_SYM = main_vl_sym.o
all: md_dyn md_dyn_expr md_dyn_vl md_dyn_vl_sym
%.o: %.cpp
- $(CC) -O3 -g -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+ $(CC) -fext-numeric-literals -O3 -g -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
md_dyn: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
diff --git a/example/Vector/4_complex_prop/Makefile b/example/Vector/4_complex_prop/Makefile
index 47ec488c..f41f44fc 100644
--- a/example/Vector/4_complex_prop/Makefile
+++ b/example/Vector/4_complex_prop/Makefile
@@ -10,7 +10,7 @@ OBJ_SER = main_ser.o
all: vect_cp vect_ser
%.o: %.cpp
- $(CC) -O0 -g -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+ $(CC) -fext-numeric-literals -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
vect_cp: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
diff --git a/example/Vector/4_multiphase_celllist/Makefile b/example/Vector/4_multiphase_celllist/Makefile
index 0acbf7c2..16168a45 100644
--- a/example/Vector/4_multiphase_celllist/Makefile
+++ b/example/Vector/4_multiphase_celllist/Makefile
@@ -7,7 +7,7 @@ LDIR =
OBJ = main.o
%.o: %.cpp
- $(CC) -O0 -g -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+ $(CC) -fext-numeric-literals -O3 -g -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
cell: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
diff --git a/example/Vector/4_reorder/Makefile b/example/Vector/4_reorder/Makefile
index c5ada0a4..0c5222d9 100644
--- a/example/Vector/4_reorder/Makefile
+++ b/example/Vector/4_reorder/Makefile
@@ -13,7 +13,7 @@ all_test: OPT += -DTEST_RUN
all_test: md_data_ord_test md_comp_ord_test
%.o: %.cpp
- $(CC) -O3 -g -c --std=c++11 $(OPT) -o $@ $< $(INCLUDE_PATH)
+ $(CC) -fext-numeric-literals -O3 -g -c --std=c++11 $(OPT) -o $@ $< $(INCLUDE_PATH)
md_data_ord: $(OBJ_DORD)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
diff --git a/openfpm_data b/openfpm_data
index fd67c262..ebf5628c 160000
--- a/openfpm_data
+++ b/openfpm_data
@@ -1 +1 @@
-Subproject commit fd67c2620e44caed20d3e3c30fad72c41cd9d48e
+Subproject commit ebf5628ca2191c298589d36973da2bbaceb4ecfe
diff --git a/openfpm_numerics b/openfpm_numerics
index a384941b..c476b51f 160000
--- a/openfpm_numerics
+++ b/openfpm_numerics
@@ -1 +1 @@
-Subproject commit a384941b412db3d3aa280caae3cb3eaa874a86c2
+Subproject commit c476b51f466d6e5ed746d7dd64a09a48b77bafdd
diff --git a/src/Makefile.am b/src/Makefile.am
index a2c3cee0..66860062 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -18,7 +18,7 @@ nobase_include_HEADERS = Decomposition/CartDecomposition.hpp Decomposition/CartD
lib_LIBRARIES = libofpm_pdata.a
libofpm_pdata_a_SOURCES = lib/pdata.cpp
-libofpm_pdata_a_CXXFLAGS = $(INCLUDES_PATH) $(BOOST_CPPFLAGS) -I/usr/local/include -Wno-unused-local-typedefs
+libofpm_pdata_a_CXXFLAGS = $(AM_CXXFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) -I/usr/local/include -Wno-unused-local-typedefs
libofpm_pdata_a_CFLAGS =
.cu.o :
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index ef47a83d..7fc66a8a 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -164,7 +164,7 @@ public:
*
*/
vector_dist(const vector_dist<dim,St,prop,Decomposition,Memory> & v)
- :vector_dist_comm<dim,St,prop,Decomposition,Memory>(v.dec),v_cl(v.v_cl)
+ :vector_dist_comm<dim,St,prop,Decomposition,Memory>(v.getDecomposition()),v_cl(v.v_cl)
{
#ifdef SE_CLASS2
check_new(this,8,VECTOR_DIST_EVENT,4);
@@ -799,6 +799,16 @@ public:
return vector_dist_comm<dim,St,prop,Decomposition,Memory>::getDecomposition();
}
+ /*! \brief Get the decomposition
+ *
+ * \return
+ *
+ */
+ inline const Decomposition & getDecomposition() const
+ {
+ return vector_dist_comm<dim,St,prop,Decomposition,Memory>::getDecomposition();
+ }
+
/*! \brief It move all the particles that does not belong to the local processor to the respective processor
*
* \tparam out of bound policy it specify what to do when the particles are detected out of bound
@@ -1022,7 +1032,14 @@ public:
*/
void getCellListParams(St r_cut, size_t (&div)[dim],Box<dim, St> & box, Ghost<dim,St> enlarge = Ghost<dim,St>(0.0))
{
- box = cl_param_calculate(div,r_cut,enlarge);
+ // get the processor bounding box
+ Box<dim, St> pbox = getDecomposition().getProcessorBounds();
+
+ // enlarge the processor bounding box by the ghost
+ Ghost<dim,St> g = getDecomposition().getGhost();
+ pbox.enlarge(g);
+
+ cl_param_calculate(pbox, div,r_cut,enlarge);
}
/*! \brief It return the id of structure in the allocation list
diff --git a/src/Vector/vector_dist_comm.hpp b/src/Vector/vector_dist_comm.hpp
index 585be039..ca70fd99 100644
--- a/src/Vector/vector_dist_comm.hpp
+++ b/src/Vector/vector_dist_comm.hpp
@@ -743,6 +743,17 @@ class vector_dist_comm
public:
+ /*! \brief Copy Constructor
+ *
+ * \param v vector to copy
+ *
+ */
+ vector_dist_comm(const vector_dist_comm<dim,St,prop,Decomposition,Memory> & v)
+ {
+ this->operator=(v);
+ }
+
+
/*! \brief Constructor
*
* \param dec Domain decompositon
@@ -999,6 +1010,16 @@ public:
return dec;
}
+ /*! \brief Get the decomposition
+ *
+ * \return
+ *
+ */
+ inline const Decomposition & getDecomposition() const
+ {
+ return dec;
+ }
+
/*! \brief Copy a vector
*
* \param vc vector to copy
--
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