[petsc-users] Makefile for mixed C++ and Fortran code

[Danyang Su]

Hi Satish,

Your makefile works.

Please ignore the CGAL dependency. I just modified from CGAL example and 
it needs to be further optimized with the dependency that is required 
for the algorithm I use.

Thanks,

Danyang


On 18-06-02 02:51 PM, Satish Balay wrote:
> 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
>>>>>
>>