Updating modules

configure.ac

@@ -39,6 +39,7 @@ 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_LIB_PETSC],,[m4/ax_petsc_lib.m4])
 
 case $host_os in
    *darwin*|*macosx*)
@@ -126,6 +127,12 @@ if test x"$with_hdf5" = x"no"; then
     exit 207
 fi
 
+##########
+
+## Check for PETSC
+
+AX_LIB_PETSC()
+
 ########
 
 ## Enable scan coverty

images/Makefile.am

 
-LINKLIBS = $(METIS_LIB) $(PARMETIS_LIB)  $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS)
+LINKLIBS = $(PETSC_LIB) $(METIS_LIB) $(PARMETIS_LIB)  $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS)
 
 noinst_PROGRAMS = cart_dec metis_dec dom_box vector_dist
 cart_dec_SOURCES = CartDecomposition_gen_vtk.cpp ../src/lib/pdata.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_devices/src/Memleak_check.cpp
-cart_dec_CXXFLAGS = $(METIS_INCLUDE) $(PARMETIS_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function -Wno-unused-local-typedefs
+cart_dec_CXXFLAGS = $(PETSC_INCLUDE) $(METIS_INCLUDE) $(PARMETIS_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function -Wno-unused-local-typedefs
 cart_dec_CFLAGS = $(CUDA_CFLAGS)
 cart_dec_LDADD = $(LINKLIBS) -lparmetis -lmetis
 
 metis_dec_SOURCES = Metis_gen_vtk.cpp ../src/lib/pdata.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_devices/src/Memleak_check.cpp
-metis_dec_CXXFLAGS = $(METIS_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function -Wno-unused-local-typedefs
+metis_dec_CXXFLAGS = $(PETSC_INCLUDE) $(METIS_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function -Wno-unused-local-typedefs
 metis_dec_CFLAGS = $(CUDA_CFLAGS)
 metis_dec_LDADD = $(LINKLIBS) -lmetis
 
 dom_box_SOURCES = domain_gen_vtk.cpp ../src/lib/pdata.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_devices/src/Memleak_check.cpp
-dom_box_CXXFLAGS = $(METIS_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function -Wno-unused-local-typedefs
+dom_box_CXXFLAGS = $(PETSC_INCLUDE) $(METIS_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function -Wno-unused-local-typedefs
 dom_box_CFLAGS = $(CUDA_CFLAGS)
 dom_box_LDADD = $(LINKLIBS)
 
 vector_dist_SOURCES = vector.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_devices/src/memory/PtrMemory.cpp
-vector_dist_CXXFLAGS = $(PARMETIS_INCLUDE) $(METIS_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(HDF5_CPPFLAGS) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function -Wno-unused-local-typedefs
+vector_dist_CXXFLAGS = $(PETSC_INCLUDE) $(PARMETIS_INCLUDE) $(METIS_INCLUDE) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(HDF5_CPPFLAGS) $(BOOST_CPPFLAGS) -I../src -Wno-unused-function -Wno-unused-local-typedefs
 vector_dist_CFLAGS = $(CUDA_CFLAGS)
 vector_dist_LDADD = $(LINKLIBS) -lparmetis -lmetis
 

openfpm_numerics @ b8c57f35

-Subproject commit 5e9466dcdbcbe8093f50d4974691f18f0719161b
+Subproject commit b8c57f35f0820831fc7c8c2169ca0e7a62946adb

src/Makefile.am

-LINKLIBS = $(METIS_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS) $(H5PART_LIB) $(HDF5_LDFLAGS)  $(HDF5_LIBS) $(PARMETIS_LIB)
+LINKLIBS = $(METIS_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS) $(PETSC_LIB) $(HDF5_LDFLAGS)  $(HDF5_LIBS) $(PARMETIS_LIB)
 
 noinst_PROGRAMS = pdata
 pdata_SOURCES = main.cpp lib/pdata.cpp test_multiple_o.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_devices/src/Memleak_check.cpp
-pdata_CXXFLAGS = $(HDF5_CPPFLAGS) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(PARMETIS_INCLUDE) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) $(H5PART_INCLUDE) -DPARALLEL_IO  -Wno-unused-local-typedefs
+pdata_CXXFLAGS = $(PETSC_INCLUDE) $(HDF5_CPPFLAGS) $(CUDA_CFLAGS) $(INCLUDES_PATH) $(PARMETIS_INCLUDE) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) $(H5PART_INCLUDE) -DPARALLEL_IO  -Wno-unused-local-typedefs
 pdata_CFLAGS = $(CUDA_CFLAGS)
 pdata_LDADD = $(LINKLIBS) -lmetis -lparmetis
 nobase_include_HEADERS = Decomposition/CartDecomposition.hpp Decomposition/CartDecomposition_ext.hpp Decomposition/common.hpp Decomposition/Decomposition.hpp  Decomposition/ie_ghost.hpp \