From e28bda9120c10995e2d1dd2d9576de2e317a7078 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <i-bird@private-incardon-3.mpi-cbg.de>
Date: Mon, 2 May 2016 19:02:00 +0200
Subject: [PATCH] PETSC introduction
---
configure.ac | 5 ++
src/Makefile.am | 4 +-
src/Matrix/SparseMatrix.hpp | 2 +-
src/Matrix/SparseMatrix_Eigen.hpp | 12 -----
src/Vector/Vector.hpp | 2 +-
src/Vector/Vector_eigen.hpp | 2 +-
src/Vector/Vector_unit_tests.hpp | 90 +++++++++++++++++++++++++++++++
7 files changed, 100 insertions(+), 17 deletions(-)
diff --git a/configure.ac b/configure.ac
index 03069f41..82506ffe 100755
--- a/configure.ac
+++ b/configure.ac
@@ -25,6 +25,7 @@ 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])])
m4_ifdef([AX_LIB_HDF5],,[m4_include([m4/ax_lib_hdf5.m4])]])
+m4_ifdef([AX_PETSC_LIB],,[m4/ax_petsc_lib.m4])
case $host_os in
*cygwin*)
@@ -107,6 +108,10 @@ IMMDX_LIB_METIS([],[echo "Cannot detect metis, use the --with-metis option if it
IMMDX_LIB_PARMETIS([],[echo "Cannot detect parmetis, use the --with-parmetis option if it is not installed in the default location"
exit 203])
+## Check for PETSC
+
+AX_LIB_PETSC()
+
#########
## Check for HDF5
diff --git a/src/Makefile.am b/src/Makefile.am
index 114dbb77..e1327a40 100755
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,9 +1,9 @@
-LINKLIBS = $(SUITESPARSE_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(METIS_LIB) $(PARMETIS_LIB) $(DEFAULT_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_IOSTREAMS_LIB) $(HDF5_LDFLAGS) $(HDF5_LIBS) $(LIBQUADMATH)
+LINKLIBS = $(SUITESPARSE_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(METIS_LIB) $(PARMETIS_LIB) $(DEFAULT_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_IOSTREAMS_LIB) $(HDF5_LDFLAGS) $(HDF5_LIBS) $(LIBQUADMATH) $(PETSC_LIB)
noinst_PROGRAMS = numerics
numerics_SOURCES = main.cpp ../../openfpm_vcluster/src/VCluster.cpp ../../openfpm_devices/src/memory/HeapMemory.cpp ../../openfpm_devices/src/memory/PtrMemory.cpp ../../openfpm_devices/src/Memleak_check.cpp
-numerics_CXXFLAGS = $(AM_CXXFLAGS) $(HDF5_CPPFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) $(SUITESPARSE_INCLUDE) $(METIS_INCLUDE) $(PARMETIS_INCLUDE) $(EIGEN_INCLUDE) -Wno-deprecated-declarations -Wno-unused-local-typedefs
+numerics_CXXFLAGS = $(AM_CXXFLAGS) $(HDF5_CPPFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) $(SUITESPARSE_INCLUDE) $(METIS_INCLUDE) $(PARMETIS_INCLUDE) $(EIGEN_INCLUDE) $(PETSC_INCLUDE) -Wno-deprecated-declarations -Wno-unused-local-typedefs
numerics_CFLAGS = $(CUDA_CFLAGS)
numerics_LDADD = $(LINKLIBS) -lparmetis -lmetis
nobase_include_HEADERS = PSE/Kernels.hpp PSE/Kernels_test_util.hpp
diff --git a/src/Matrix/SparseMatrix.hpp b/src/Matrix/SparseMatrix.hpp
index 3caf01bf..ca60651c 100644
--- a/src/Matrix/SparseMatrix.hpp
+++ b/src/Matrix/SparseMatrix.hpp
@@ -50,7 +50,7 @@ template<typename T, unsigned int impl> struct triplet
*
* \tparam T Type of the sparse Matrix store on each row,colums
* \tparam id_t type of id
- * \tparam impl implementation
+ * \tparam Mi implementation
*
*/
template<typename T,typename id_t ,typename Mi = Eigen::SparseMatrix<T,0,id_t>>
diff --git a/src/Matrix/SparseMatrix_Eigen.hpp b/src/Matrix/SparseMatrix_Eigen.hpp
index beb758c2..dde9edd0 100644
--- a/src/Matrix/SparseMatrix_Eigen.hpp
+++ b/src/Matrix/SparseMatrix_Eigen.hpp
@@ -139,18 +139,6 @@ public:
{
}
- /*! \brief Create a Matrix from a set of triplet
- *
- * \param N1 number of row
- * \param N2 number of colums
- * \param trpl triplet set
- *
- */
- SparseMatrix(size_t N1, size_t N2, const openfpm::vector<Eigen::Triplet<T,id_t>> & trpl)
- :mat(N1,N2)
- {
- this->trpl = trpl;
- }
/*! \brief Create an empty Matrix
*
diff --git a/src/Vector/Vector.hpp b/src/Vector/Vector.hpp
index 43469dba..21e5765d 100644
--- a/src/Vector/Vector.hpp
+++ b/src/Vector/Vector.hpp
@@ -34,6 +34,6 @@ class Vector
};
#include "Vector_eigen.hpp"
-
+#include "Vector_petsc.hpp"
#endif /* OPENFPM_NUMERICS_SRC_VECTOR_VECTOR_HPP_ */
diff --git a/src/Vector/Vector_eigen.hpp b/src/Vector/Vector_eigen.hpp
index 439f70f4..00d74672 100644
--- a/src/Vector/Vector_eigen.hpp
+++ b/src/Vector/Vector_eigen.hpp
@@ -89,7 +89,7 @@ class Vector<T,Eigen::Matrix<T, Eigen::Dynamic, 1>>
mutable openfpm::vector<size_t> sz;
- /*! \brief Here we collect the full matrix on master
+ /*! \brief Here we collect the full vector on master
*
*/
void collect() const
diff --git a/src/Vector/Vector_unit_tests.hpp b/src/Vector/Vector_unit_tests.hpp
index bc9c01f8..b3ee5d4b 100644
--- a/src/Vector/Vector_unit_tests.hpp
+++ b/src/Vector/Vector_unit_tests.hpp
@@ -130,6 +130,96 @@ BOOST_AUTO_TEST_CASE(vector_eigen_parallel)
}
+BOOST_AUTO_TEST_CASE(vector_petsc_parallel)
+{
+ Vcluster & vcl = create_vcluster();
+
+ if (vcl.getProcessingUnits() != 3)
+ return;
+
+ // 3 Processors 9x9 Matrix to invert
+
+ Vector<double,Vec> v(9);
+
+ if (vcl.getProcessUnitID() == 0)
+ {
+ // v row1
+ v.insert(0,0);
+ v.insert(1,1);
+ v.insert(2,2);
+ }
+ else if (vcl.getProcessUnitID() == 1)
+ {
+ v.insert(3,3);
+ v.insert(4,4);
+ v.insert(5,5);
+ }
+ else if (vcl.getProcessUnitID() == 2)
+ {
+ v.insert(6,6);
+ v.insert(7,7);
+ v.insert(8,8);
+ }
+
+ Vector<double,Vec> v3;
+ v3 = v;
+
+ if (vcl.getProcessUnitID() == 0)
+ {
+ // v row1
+ v(0) = 8;
+ v(1) = 7;
+ v(2) = 6;
+ }
+ else if (vcl.getProcessUnitID() == 1)
+ {
+ v(3) = 5;
+ v(4) = 4;
+ v(5) = 3;
+ }
+ else if (vcl.getProcessUnitID() == 2)
+ {
+ v(6) = 2;
+ v(7) = 1;
+ v(8) = 0;
+ }
+
+ // Master has the full vector
+
+ if (vcl.getProcessUnitID() == 0)
+ {
+ BOOST_REQUIRE_EQUAL(v(0),8);
+ BOOST_REQUIRE_EQUAL(v(1),7);
+ BOOST_REQUIRE_EQUAL(v(2),6);
+
+ BOOST_REQUIRE_EQUAL(v3(0),0);
+ BOOST_REQUIRE_EQUAL(v3(1),1);
+ BOOST_REQUIRE_EQUAL(v3(2),2);
+ }
+ else if (vcl.getProcessUnitID() == 1)
+ {
+ BOOST_REQUIRE_EQUAL(v(3),5);
+ BOOST_REQUIRE_EQUAL(v(4),4);
+ BOOST_REQUIRE_EQUAL(v(5),3);
+
+ BOOST_REQUIRE_EQUAL(v3(0),3);
+ BOOST_REQUIRE_EQUAL(v3(1),4);
+ BOOST_REQUIRE_EQUAL(v3(2),5);
+ }
+ else if (vcl.getProcessUnitID() == 2)
+ {
+ BOOST_REQUIRE_EQUAL(v(6),2);
+ BOOST_REQUIRE_EQUAL(v(7),1);
+ BOOST_REQUIRE_EQUAL(v(8),0);
+
+ BOOST_REQUIRE_EQUAL(v3(0),6);
+ BOOST_REQUIRE_EQUAL(v3(1),7);
+ BOOST_REQUIRE_EQUAL(v3(2),9);
+ }
+
+ Vec & v2 = v.getVec();
+}
+
BOOST_AUTO_TEST_SUITE_END()
--
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