From cf8f5ab106fd61e167c78b9b3f3898e000b283a3 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <i-bird@private-incardon-3.mpi-cbg.de>
Date: Mon, 7 Dec 2015 12:10:14 -0500
Subject: [PATCH] Small fixe and changes
---
configure.ac | 23 +++++++++
install | 69 +++++++++++++++++---------
openfpm_numerics | 2 +-
src/Grid/grid_dist_id.hpp | 68 +++++++++++++++++++++++--
src/Grid/grid_dist_id_iterator.hpp | 38 ++++++++++++--
src/Grid/grid_dist_id_iterator_sub.hpp | 10 ++--
src/Grid/grid_dist_id_unit_test.hpp | 9 ++++
7 files changed, 179 insertions(+), 40 deletions(-)
diff --git a/configure.ac b/configure.ac
index 00c4690fc..bfa1a6701 100755
--- a/configure.ac
+++ b/configure.ac
@@ -33,6 +33,11 @@ m4_ifdef([AX_BOOST_BASE],,[m4_include([m4/ax_boost_base.m4])])
m4_ifdef([AX_BOOST_IOSTREAMS],,[m4_include([m4/ax_boost_iostreams.m4])])
m4_ifdef([AX_BOOST_PROGRAM_OPTIONS],,[m4_include([m4/ax_boost_program_options.m4])])
m4_ifdef([AX_BOOST_UNIT_TEST_FRAMEWORK],,[m4_include([m4/ax_boost_unit_test_framework.m4])])
+m4_ifdef([AX_BLAS],,[m4_include([m4/ax_blas.m4])])
+m4_ifdef([AX_LAPACK],,[m4_include([m4/ax_lapack.m4])])
+m4_ifdef([AX_SUITESPARSE],,[m4_include([m4/ax_suitesparse.m4])])
+m4_ifdef([AX_EIGEN],,[m4_include([m4/ax_eigen.m4])])
+
CXXFLAGS+=" --std=c++11 "
NVCCFLAGS=" "
@@ -227,6 +232,24 @@ BOOST_CPPFLAGS=$(echo "$BOOST_CPPFLAGS" | sed -e 's/-I\/usr\/include[ \b]//g')
AC_SUBST(BOOST_LDFLAGS)
AC_SUBST(BOOST_CPPFLAGS)
+###### Checking for OpenBLAS
+
+AX_BLAS([],[echo "blas not found"
+ exit 204])
+
+AX_LAPACK([],[echo "lapack not found"
+ exit 204])
+
+###### Checking for SUITESPARSE
+
+AX_SUITESPARSE([],[echo "suitesparse not found"
+ exit 205])
+
+###### Checking for EIGEN
+
+AX_EIGEN([],[echo "eigen not found"
+ exit 206])
+
####### Checking for GPU support
AX_CUDA
diff --git a/install b/install
index da99cc11f..ecc631cb6 100755
--- a/install
+++ b/install
@@ -124,6 +124,10 @@ echo -e "Installing requirements into: $i_dir "
MPI_installed=0
METIS_installed=0
BOOST_installed=0
+LAPACK_installed=0
+SUITESPARSE_installed=0
+EIGEN_installed=0
+blas_options=""
conf_err=1
## MPI
@@ -140,35 +144,15 @@ else
fi
fi
-## if a new compiler has been installed reinstall all the dependencies
-
-if [ x"$compiler_opt" != x"" ]; then
- ./script/install_MPI.sh $i_dir $compiler_opt
- export PATH="$PATH:$i_dir/MPI/bin"
- configure_options="$configure_options CXX=mpic++ "
- MPI_installed=1
- ./script/install_BOOST.sh $i_dir $compiler_opt
- configure_options=" $configure_options --with-boost=$i_dir/BOOST "
- BOOST_installed=1
- ./script/install_METIS.sh $i_dir $compiler_gcc $compiler_gpp
- configure_options=" $configure_options --with-metis=$i_dir/METIS "
- METIS_installed=1
- ./script/install_SuiteSparse.sh $i_dir $compiler_opt
- configure_options=" $configure_options --with-suitesparse=$i_dir/SUITESPARSE "
- SUITESPARSE_installed=1
- ./script/install_lapack.sh $i_dir $compiler_opt
- configure_option="$configure_options --with-lapack=$i_dir/LAPACK"
- LAPACK_installed=1
-fi
echo "./configure $options $configure_options"
if [ $install_req -eq 0 ]; then
- ./configure $options $configure_options
+ ./configure $options $configure_options "$blas_options"
else
while [ $conf_err -ne 0 ]
do
- ./configure $options $configure_options
+ ./configure $options $configure_options "$blas_options"
conf_err=$?
echo "Configure script terminated with $conf_err"
@@ -208,7 +192,9 @@ else
echo "Error the installation of LAPACK failed"
exit 1
fi
- ./script/install_SUITESPARSE.sh $i_dir $compiler_opt
+ ./script/install_OPENBLAS.sh $i_dir $compiler_opt
+ LAPACK_installed=1
+ blas_options="--with-blas=-L/home/i-bird/OPENBLAS/lib/ -lopenblas"
elif [ $conf_err -eq 205 ]; then
echo "SuiteSparse not found try to install"
if [ $SUITESPARSE_installed -eq 1 ]; then
@@ -216,6 +202,17 @@ else
exit 1
fi
./script/install_SUITESPARSE.sh $i_dir $compiler_opt
+ configure_options=" $configure_options --with-suitesparse=$i_dir/SUITESPARSE "
+ SUITESPARSE_installed=1
+ elif [ $conf_err -eq 206 ]; then
+ echo "Eigen not found try to install"
+ if [ $EIGEN_installed -eq 1 ]; then
+ echo "Error the installation of Eigen failed"
+ exit 1
+ fi
+ ./script/install_EIGEN.sh $i_dir $compiler_opt
+ configure_options=" $configure_options --with-eigen=$i_dir/EIGEN "
+ EIGEN_installed=1
elif [ $conf_err -ne 0 ]; then
echo "I do not know how to recover from this error"
exit 1
@@ -249,7 +246,7 @@ fi
echo "Command used to configure"
echo ""
-echo -e "\033[1m ./configure $options $configure_options \033[0m "
+echo -e "\033[1m ./configure $options $configure_options "$blas_options" \033[0m "
echo ""
if [ $MPI_installed -eq 1 ]; then
echo -e "\033[1;34;5m --------------------------------------- \033[0m"
@@ -290,6 +287,30 @@ if [ $BOOST_installed -eq 1 ]; then
echo -e "\033[1m export DYLD_LIBRARY_PATH=\"\$DYLD_LIBRARY_PATH:$i_dir/BOOST/lib\" \033[0m"
fi
fi
+if [ $LAPACK_installed -eq 1 ]; then
+ echo ""
+ echo -e "\033[1;34;5m --------------------------------------- \033[0m"
+ echo -e "\033[1;34;5m --------------- OPENBLAS -------------- \033[0m"
+ echo -e " OPENBLAS has been installed into: \033[1m $i_dir/OPENBLAS \033[0m"
+ echo ""
+ if [ x"$platform" = x"linux" ]; then
+ echo -e "\033[1m export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:$i_dir/OPENBLAS/lib\" \033[0m "
+ else
+ echo -e "\033[1m export DYLD_LIBRARY_PATH=\"\$DYLD_LIBRARY_PATH:$i_dir/OPENBLAS/lib\" \033[0m"
+ fi
+fi
+if [ $SUITESPARSE_installed -eq 1 ]; then
+ echo ""
+ echo -e "\033[1;34;5m --------------------------------------- \033[0m"
+ echo -e "\033[1;34;5m ------------- SUITESPARSE ------------- \033[0m"
+ echo -e " SUITESPARSE has been installed into: \033[1m $i_dir/SUITESPARSE \033[0m"
+ echo ""
+ if [ x"$platform" = x"linux" ]; then
+ echo -e "\033[1m export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:$i_dir/SUITESPARSE/lib\" \033[0m "
+ else
+ echo -e "\033[1m export DYLD_LIBRARY_PATH=\"\$DYLD_LIBRARY_PATH:$i_dir/SUITESPARSE/lib\" \033[0m"
+ fi
+fi
echo ""
echo ""
if [ $conf_err -ne 0 ]; then
diff --git a/openfpm_numerics b/openfpm_numerics
index 32914d0aa..dfb8b8f7b 160000
--- a/openfpm_numerics
+++ b/openfpm_numerics
@@ -1 +1 @@
-Subproject commit 32914d0aad507eae2f82e3ac006e4bab42e9e3ed
+Subproject commit dfb8b8f7b56e455c3e1db0ff39e5d513055eb472
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index 9c859af9b..bd1e22a4b 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -484,6 +484,19 @@ public:
// Decomposition used
typedef Decomposition decomposition;
+ // value_type
+ typedef T value_type;
+
+ /*! \brief Return the total number of points in the grid
+ *
+ * \return number of points
+ *
+ */
+ size_t size() const
+ {
+ return ginfo_v.size();
+ }
+
static inline Ghost<dim,float> convert_ghost(const Ghost<dim,long int> & gd,const CellDecomposer_sm<dim,St> & cd_sm)
{
Ghost<dim,float> gc;
@@ -527,6 +540,16 @@ public:
InitializeStructures(g_sz);
}
+ /*! \brief Get the spacing of the grid in direction i
+ *
+ * \return the spacing
+ *
+ */
+ inline St spacing(size_t i) const
+ {
+ return cd_sm.getCellBox().getHigh(i);
+ }
+
/*! \brief Constrcuctor
*
* \param g_sz array with the grid size on each dimension
@@ -639,7 +662,7 @@ public:
* \return an information object about this grid
*
*/
- const grid_sm<dim,T> & getGridInfo()
+ const grid_sm<dim,T> & getGridInfo() const
{
return ginfo;
}
@@ -649,7 +672,7 @@ public:
* \return an information object about this grid
*
*/
- const grid_sm<dim,void> & getGridInfoVoid()
+ const grid_sm<dim,void> & getGridInfoVoid() const
{
return ginfo_v;
}
@@ -724,7 +747,12 @@ public:
*/
grid_dist_iterator<dim,device_grid,FREE> getDomainIterator()
{
- grid_dist_iterator<dim,device_grid,FREE> it(loc_grid,gdb_ext);
+ grid_key_dx<dim> stop(ginfo_v.getSize());
+ grid_key_dx<dim> one;
+ one.one();
+ stop = stop - one;
+
+ grid_dist_iterator<dim,device_grid,FREE> it(loc_grid,gdb_ext,stop);
return it;
}
@@ -733,7 +761,7 @@ public:
*
*
*/
- grid_dist_iterator<dim,device_grid,FIXED> getDomainGhostIterator()
+ grid_dist_iterator<dim,device_grid,FIXED> getDomainGhostIterator() const
{
grid_dist_iterator<dim,device_grid,FIXED> it(loc_grid,gdb_ext);
@@ -743,17 +771,37 @@ public:
/*! \brief It return an iterator that span the grid domain only in the specified
* part
*
+ * The key spanned are the one inside the box spanned by the start point and the end
+ * point included
+ *
* \param start point
* \param stop point
*
*/
- grid_dist_iterator_sub<dim,device_grid> getSubDomainIterator(const grid_key_dx<dim> & start, const grid_key_dx<dim> & stop)
+ grid_dist_iterator_sub<dim,device_grid> getSubDomainIterator(const grid_key_dx<dim> & start, const grid_key_dx<dim> & stop) const
{
grid_dist_iterator_sub<dim,device_grid> it(start,stop,loc_grid,gdb_ext);
return it;
}
+ /*! \brief It return an iterator that span the grid domain only in the specified
+ * part
+ *
+ * The key spanned are the one inside the box spanned by the start point and the end
+ * point included
+ *
+ * \param start point
+ * \param stop point
+ *
+ */
+ grid_dist_iterator_sub<dim,device_grid> getSubDomainIterator(const long int (& start)[dim], const long int (& stop)[dim]) const
+ {
+ grid_dist_iterator_sub<dim,device_grid> it(grid_key_dx<dim>(start),grid_key_dx<dim>(stop),loc_grid,gdb_ext);
+
+ return it;
+ }
+
//! Destructor
~grid_dist_id()
{
@@ -771,6 +819,16 @@ public:
return v_cl;
}
+ /*! \brief Indicate that this grid is not staggered
+ *
+ * \return false
+ *
+ */
+ bool is_staggered()
+ {
+ return false;
+ }
+
/*! \brief Get the reference of the selected element
*
* \param p property to get (is an integer)
diff --git a/src/Grid/grid_dist_id_iterator.hpp b/src/Grid/grid_dist_id_iterator.hpp
index f7b64159c..56ba2ea60 100644
--- a/src/Grid/grid_dist_id_iterator.hpp
+++ b/src/Grid/grid_dist_id_iterator.hpp
@@ -93,8 +93,8 @@ class grid_dist_iterator<dim,device_grid,FREE>
//! Actual iterator
grid_key_dx_iterator_sub<dim> a_it;
- //! margin of the grid iterator
- size_t m;
+ //! stop point (is the grid size)
+ grid_key_dx<dim> stop;
/*! \brief from g_c increment g_c until you find a valid grid
*
@@ -124,7 +124,7 @@ class grid_dist_iterator<dim,device_grid,FREE>
gList = tmp.gList;
gdb_ext = tmp.gdb_ext;
a_it.reinitialize(tmp.a_it);
- m = tmp.m;
+ stop = tmp.stop;
return *this;
}
@@ -134,8 +134,8 @@ class grid_dist_iterator<dim,device_grid,FREE>
* \param gk std::vector of the local grid
*
*/
- grid_dist_iterator(Vcluster_object_array<device_grid> & gk, openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
- :g_c(0),gList(gk),gdb_ext(gdb_ext),m(0)
+ grid_dist_iterator(Vcluster_object_array<device_grid> & gk, openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext, grid_key_dx<dim> stop)
+ :g_c(0),gList(gk),gdb_ext(gdb_ext),stop(stop)
{
// Initialize the current iterator
// with the first grid
@@ -196,6 +196,34 @@ class grid_dist_iterator<dim,device_grid,FREE>
{
return grid_dist_key_dx<dim>(g_c,a_it.get());
}
+
+ /*! \brief it return the stop point of the iterator
+ *
+ * The stop point of the iterator is just the grid size
+ *
+ * \return the stop point
+ *
+ */
+ inline grid_key_dx<dim> getStop() const
+ {
+ return stop;
+ }
+
+ /*! \brief it return the start point of the iterator
+ *
+ * The start point of the iterator is the point with all coordinates zeros
+ *
+ * \return the start point
+ *
+ */
+ inline grid_key_dx<dim> getStart() const
+ {
+ grid_key_dx<dim> start;
+
+ start.zero();
+
+ return start;
+ }
};
diff --git a/src/Grid/grid_dist_id_iterator_sub.hpp b/src/Grid/grid_dist_id_iterator_sub.hpp
index 11ac7cc10..4ae562c8a 100644
--- a/src/Grid/grid_dist_id_iterator_sub.hpp
+++ b/src/Grid/grid_dist_id_iterator_sub.hpp
@@ -34,10 +34,10 @@ class grid_dist_iterator_sub
size_t g_c;
//! List of the grids we are going to iterate
- Vcluster_object_array<device_grid> & gList;
+ const Vcluster_object_array<device_grid> & gList;
//! Extension of each grid: domain and ghost + domain
- openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext;
+ const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext;
//! Actual iterator
grid_key_dx_iterator_sub<dim> a_it;
@@ -144,7 +144,7 @@ class grid_dist_iterator_sub
* \param gdb_ext information about the local grids
*
*/
- grid_dist_iterator_sub(const grid_key_dx<dim> & start, const grid_key_dx<dim> & stop ,Vcluster_object_array<device_grid> & gk, openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
+ grid_dist_iterator_sub(const grid_key_dx<dim> & start, const grid_key_dx<dim> & stop ,const Vcluster_object_array<device_grid> & gk, const openfpm::vector<GBoxes<device_grid::dims>> & gdb_ext)
:g_c(0),gList(gk),gdb_ext(gdb_ext),start(start),stop(stop),m(0)
{
// Initialize the current iterator
@@ -233,7 +233,7 @@ class grid_dist_iterator_sub
* \return the starting point
*
*/
- inline grid_key_dx<dim> getStart()
+ inline grid_key_dx<dim> getStart() const
{
return start;
}
@@ -243,7 +243,7 @@ class grid_dist_iterator_sub
* \return the stop point
*
*/
- inline grid_key_dx<dim> getStop()
+ inline grid_key_dx<dim> getStop() const
{
return stop;
}
diff --git a/src/Grid/grid_dist_id_unit_test.hpp b/src/Grid/grid_dist_id_unit_test.hpp
index 2c17ed99f..27bb837e9 100644
--- a/src/Grid/grid_dist_id_unit_test.hpp
+++ b/src/Grid/grid_dist_id_unit_test.hpp
@@ -268,6 +268,15 @@ void Test2D(const Box<2,float> & domain, long int k)
auto dom2 = g_dist.getDomainIterator();
+ grid_key_dx<2> start = dom2.getStart();
+ grid_key_dx<2> stop = dom2.getStop();
+
+ BOOST_REQUIRE_EQUAL(stop.get(0),g_dist.size(0));
+ BOOST_REQUIRE_EQUAL(stop.get(1),g_dist.size(1));
+
+ BOOST_REQUIRE_EQUAL(start.get(0),0);
+ BOOST_REQUIRE_EQUAL(start.get(1),0);
+
bool match = true;
// check that the grid store the correct information
--
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