[petsc-users] Makefile for mixed C++ and Fortran code
Satish Balay
balay at mcs.anl.gov
Sat Jun 2 16:51:15 CDT 2018
Try the attached makefile. [with correct PETSC_DIR and PETSC_ARCH values]
If you have issues - send the complete makefiles - and complete error log..
On Sat, 2 Jun 2018, Danyang Su wrote:
> Hi Barry,
>
> For the code without PETSc, the rules used to compile the code with CGAL is
note: DLIB can probably be simlified - and a fewof the options eliminated.
> DLIB = -lstdc++ -lmetis -lm -L/usr/local/lib -rdynamic
-lstdc++ is setup by petsc
-lmetis can be a dependency of petsc - so care should be taken to have only one copy of metis
> /usr/local/lib/libmpfr.so /usr/local/lib/libgmp.so
Why are these here? Normally these are dependencies of gcc/gfortran [and PETSc configure picks up the correct ones]
> /usr/local/lib/libCGAL_ImageIO.so.11.0.1 /usr/local/lib/libCGAL.so.11.0.1
I have no idea what these are..
Satish
> /usr/local/lib/libboost_thread.so /usr/local/lib/libboost_system.so -lpthread
> -lGLU -lGL -lX11 -lXext -lz /usr/local/lib/libCGAL_ImageIO.so.11.0.1
> /usr/local/lib/libCGAL.so.11.0.1 /usr/local/lib/libboost_thread.so
> /usr/local/lib/libboost_system.so -lpthread -lGLU -lGL -lX11 -lXext -lz
> /usr/local/lib/libmpfr.so /usr/local/lib/libgmp.so
> /usr/local/lib/libboost_thread.so /usr/local/lib/libboost_system.so -lpthread
> -Wl,-rpath,/usr/local/lib
>
> FFLAGS = -O3 -I$(LIS_INC)
> CXXFLAGS = -std=c++11 -O3 -I$(LIS_INC)
>
> However, after adding these to the makefile using PETSc, I got error telling
> me that all the petsc include files cannot be found.
>
> ../../solver/solver_snes_common.F90:27:0: fatal error: petscversion.h: No such
> \
> file or directory
> #include <petscversion.h>
>
> ../../solver/solver_snes_common.F90:27:0: fatal error: petscversion.h: No such
> \
> file or directory
> #include <petscversion.h>
>
> Similar for other head files. However, If I change the file path to the the
> full path, the code cannot compiled. Does the rule I use destroy the PETSc
> relative path/
>
> The make commands I use is
>
> executable: $(SOURCES) chkopts
> -${FLINKER} $(FFLAGS) $(FPPFLAGS) $(CPPFLAGS) -o executable.out
> $(SOURCES) ${PETSC_LIB} ${LIS_LIB} ${DLIB}
> %.o:%.F90
> $(FLINKER) $(FFLAGS) $(FPPFLAGS) -c -frounding-math $< -o $@
> %.o:%.cpp
> $(CLINKER) $(CXXFLAGS) $(CPPFLAGS) -c -frounding-math $< -o $@
>
> Thanks,
>
> Danyang
>
> On 18-06-01 10:41 AM, Smith, Barry F. wrote:
> > You need to determine exactly what flags are passed to the C++ compiler
> > for your compile that works and make sure those same flags are used in
> > "PETSc version" of the makefile. You could add the flags directly to the
> > rule
> >
> >> %.o:%.cpp
> >> $(CLINKER) $(CXXFLAGS) $(CPPFLAGS) -c -frounding-math $< -o $@
> > Barry
> >
> >
> >> On Jun 1, 2018, at 12:37 PM, Danyang Su <danyang.su at gmail.com> wrote:
> >>
> >> Follow up:
> >>
> >> With following command
> >>
> >> executable: $(SOURCES) chkopts
> >> -${FLINKER} $(FFLAGS) $(FPPFLAGS) $(CPPFLAGS) -o executable.out
> >> $(SOURCES) ${PETSC_LIB}
> >>
> >> %.o:%.F90
> >> $(FLINKER) $(FFLAGS) $(FPPFLAGS) -c -frounding-math $< -o $@
> >> %.o:%.cpp
> >> $(CLINKER) $(CXXFLAGS) $(CPPFLAGS) -c -frounding-math $< -o $@
> >>
> >> The compiler return error: no match function.
> >>
> >> ../../usg/cgal_triangulation_2d.cpp: In function ‘void
> >> outputTriangulation2d(in\
> >> t, const char*, int, const char*)’:
> >> ../../usg/cgal_triangulation_2d.cpp:485:20: error: no matching function for
> >> cal\
> >> l to ‘std::basic_ofstream<char>::open(std::string&)’
> >> out.open(strfile);
> >>
> >> Thanks,
> >>
> >>
> >> Danyang
> >>
> >> On 18-06-01 10:07 AM, Danyang Su wrote:
> >>> Hi All,
> >>>
> >>> My code needs to link to an external C++ library (CGAL). The code is
> >>> written in Fortran and I have already written interface to let Fortran
> >>> call C++ function. For the sequential version without PETSc, it can be
> >>> compiled without problem using the following makefile. The parallel
> >>> version without CGAL can also be compiled successfully. However, when I
> >>> tried to use PETSc together with CGAL library, I cannot compile the code.
> >>> My questions is: How can I modify the makefile? Do I need to reconfigure
> >>> PETSc with special flags? All the makefile samples are shown below.
> >>>
> >>> #makefile for sequential version
> >>>
> >>> FC = gfortran
> >>> #FC = ifort
> >>> CXX = g++ -std=c++11
> >>>
> >>> DLIB = -lstdc++ -lm -L/usr/local/lib -rdynamic /usr/local/lib/libmpfr.so
> >>> /usr/local/lib/libgmp.so /usr/local/lib/libCGAL_ImageIO.so.11.0.1
> >>> /usr/local/lib/libCGAL.so.11.0.1 /usr/local/lib/libboost_thread.so
> >>> /usr/local/lib/libboost_system.so -lpthread -lGLU -lGL -lX11 -lXext -lz
> >>> /usr/local/lib/libCGAL_ImageIO.so.11.0.1 /usr/local/lib/libCGAL.so.11.0.1
> >>> /usr/local/lib/libboost_thread.so /usr/local/lib/libboost_system.so
> >>> -lpthread -lGLU -lGL -lX11 -lXext -lz /usr/local/lib/libmpfr.so
> >>> /usr/local/lib/libgmp.so /usr/local/lib/libboost_thread.so
> >>> /usr/local/lib/libboost_system.so -lpthread -Wl,-rpath,/usr/local/lib
> >>>
> >>> FFLAGS = -O3
> >>> CXXFLAGS = -O3
> >>>
> >>> FPPFLAGS = -DUSECGAL
> >>>
> >>> SRC =./../../
> >>>
> >>> SOURCES = $(SRC)usg/math_common.o\
> >>> $(SRC)usg/geometry_definition.o\
> >>> $(SRC)usg/cgal_common.o\
> >>>
> >>> ...
> >>>
> >>> executable: $(SOURCES)
> >>> $(FC) $(FFLAGS) $(FPPFLAGS) -o executable.out $(SOURCES) ${LIS_LIB}
> >>> $(DLIB)
> >>> %.o:%.F90
> >>> $(FC) $(FFLAGS) $(FPPFLAGS) -c -frounding-math $< -o $@
> >>> %.o:%.cpp
> >>> $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -frounding-math $< -o $@
> >>>
> >>>
> >>> #makefile for parallel version with PETSc, without CGAL
> >>>
> >>> #FC = ifort
> >>> #FC = gfortran
> >>>
> >>> DLIB = -lm
> >>>
> >>> FFLAGS = -O3
> >>>
> >>> FPPFLAGS = -DUSEPETSC
> >>>
> >>> SRC =./../../
> >>>
> >>> SOURCES = $(SRC)usg/math_common.o\
> >>> $(SRC)usg/geometry_definition.o\
> >>> $(SRC)usg/cgal_common.o\
> >>>
> >>> ...
> >>>
> >>> executable: $(SOURCES) chkopts
> >>> -${FLINKER} $(FFLAGS) $(FPPFLAGS) $(CPPFLAGS) -o executable.out
> >>> $(SOURCES) ${PETSC_LIB}
> >>>
> >>>
> >>> #makefile for parallel version with PETSc, with CGAL, CANNOT work
> >>>
> >>> #FC = ifort
> >>> #FC = gfortran
> >>>
> >>> DLIB = -lm
> >>>
> >>> FFLAGS = -O3
> >>>
> >>> FPPFLAGS = -DUSEPETSC -DUSECGAL
> >>>
> >>> SRC =./../../
> >>>
> >>> SOURCES = $(SRC)usg/math_common.o\
> >>> $(SRC)usg/geometry_definition.o\
> >>> $(SRC)usg/cgal_common.o\
> >>>
> >>> ...
> >>>
> >>> executable: $(SOURCES) chkopts
> >>> -${FLINKER} $(FFLAGS) $(FPPFLAGS) $(CPPFLAGS) -o executable.out
> >>> $(SOURCES) ${PETSC_LIB}
> >>>
> >>> %.o:%.F90
> >>> $(FC) $(FFLAGS) $(FPPFLAGS) -c -frounding-math $< -o $@
> >>> %.o:%.cpp
> >>> $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -frounding-math $< -o $@
> >>>
> >>>
> >>> Thanks,
> >>>
> >>> Danyang
> >>>
>
>
-------------- next part --------------
CFLAGS =
FFLAGS = -frounding-math
CPPFLAGS =
FPPFLAGS = -DUSECGAL
CXXFLAGS = -std=c++11
CLEANFILES = executable.out
include ${PETSC_DIR}/lib/petsc/conf/variables
include ${PETSC_DIR}/lib/petsc/conf/rules
SRC =./../../
OBJS = $(SRC)usg/math_common.o\
$(SRC)usg/geometry_definition.o\
$(SRC)usg/cgal_common.o\
DLIB = -lstdc++ -lm -L/usr/local/lib -rdynamic /usr/local/lib/libmpfr.so /usr/local/lib/libgmp.so /usr/local/lib/libCGAL_ImageIO.so.11.0.1 \
/usr/local/lib/libCGAL.so.11.0.1 /usr/local/lib/libboost_thread.so /usr/local/lib/libboost_system.so -lpthread -lGLU -lGL -lX11 -lXext -lz \
/usr/local/lib/libCGAL_ImageIO.so.11.0.1 /usr/local/lib/libCGAL.so.11.0.1 /usr/local/lib/libboost_thread.so /usr/local/lib/libboost_system.so \
-lpthread -lGLU -lGL -lX11 -lXext -lz /usr/local/lib/libmpfr.so /usr/local/lib/libgmp.so /usr/local/lib/libboost_thread.so \
/usr/local/lib/libboost_system.so -lpthread -Wl,-rpath,/usr/local/lib
executable: $(OBJS)
-$(FLINKER) -o executable.out $(OBJS) $(PETSC_LIB) $(DLIB)
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