Re: [petsc-users] Makefile for mixed C++ and Fortran code
Glad it works. Thanks for the update.
Satish
On Sun, 3 Jun 2018, Danyang Su wrote:
> 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
> >>
> >> ../../solver/solver_snes_common.F90:27:0: fatal error: petscversion.h: No
> >> such
> >> \
> >> file or directory
> >> #include
> >>
> >> 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 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::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.
Re: [petsc-users] Makefile for mixed C++ and Fortran code
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
../../solver/solver_snes_common.F90:27:0: fatal error: petscversion.h: No such
\
file or directory
#include
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 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::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 = $(SRC)usg/math_common.o\
Re: [petsc-users] Makefile for mixed C++ and Fortran code
Try the attached makefile. [with correct PETSC_DIR and PETSC_ARCH values]
If you have issues - send the complete makefiles - and complete error log..
On Sat, 2 Jun 2018, Danyang Su wrote:
> Hi Barry,
>
> For the code without PETSc, the rules used to compile the code with CGAL is
note: DLIB can probably be simlified - and a fewof the options eliminated.
> DLIB = -lstdc++ -lmetis -lm -L/usr/local/lib -rdynamic
-lstdc++ is setup by petsc
-lmetis can be a dependency of petsc - so care should be taken to have only one
copy of metis
> /usr/local/lib/libmpfr.so /usr/local/lib/libgmp.so
Why are these here? Normally these are dependencies of gcc/gfortran [and PETSc
configure picks up the correct ones]
> /usr/local/lib/libCGAL_ImageIO.so.11.0.1 /usr/local/lib/libCGAL.so.11.0.1
I have no idea what these are..
Satish
> /usr/local/lib/libboost_thread.so /usr/local/lib/libboost_system.so -lpthread
> -lGLU -lGL -lX11 -lXext -lz /usr/local/lib/libCGAL_ImageIO.so.11.0.1
> /usr/local/lib/libCGAL.so.11.0.1 /usr/local/lib/libboost_thread.so
> /usr/local/lib/libboost_system.so -lpthread -lGLU -lGL -lX11 -lXext -lz
> /usr/local/lib/libmpfr.so /usr/local/lib/libgmp.so
> /usr/local/lib/libboost_thread.so /usr/local/lib/libboost_system.so -lpthread
> -Wl,-rpath,/usr/local/lib
>
> FFLAGS = -O3 -I$(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
>
> ../../solver/solver_snes_common.F90:27:0: fatal error: petscversion.h: No such
> \
> file or directory
> #include
>
> 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 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::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
Re: [petsc-users] Makefile for mixed C++ and Fortran code
Hi Barry,
For the code without PETSc, the rules used to compile the code with CGAL is
DLIB = -lstdc++ -lmetis -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 -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
../../solver/solver_snes_common.F90:27:0: fatal error: petscversion.h:
No such \
file or directory
#include
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 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::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 =
Re: [petsc-users] Makefile for mixed C++ and Fortran code
On 18-06-01 10:29 AM, Smith, Barry F. wrote:
What happens if you add ${DLIB} to the end of the line
executable: $(SOURCES) chkopts
-${FLINKER} $(FFLAGS) $(FPPFLAGS) $(CPPFLAGS) -o executable.out $(SOURCES)
${PETSC_LIB}
Send all the output from trying this.
Barry
Thanks, Barry. Still not work after including ${DLIB}
On Jun 1, 2018, at 12:07 PM, 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 $@
Thanks,
Danyang
Re: [petsc-users] Makefile for mixed C++ and Fortran code
You need to determine exactly what flags are passed to the C++ compiler for
your compile that works and make sure those same flags are used in "PETSc
version" of the makefile. You could add the flags directly to the rule
> %.o:%.cpp
>$(CLINKER) $(CXXFLAGS) $(CPPFLAGS) -c -frounding-math $< -o $@
Barry
> On Jun 1, 2018, at 12:37 PM, Danyang Su 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::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
>>
>
Re: [petsc-users] Makefile for mixed C++ and Fortran code
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::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
Re: [petsc-users] Makefile for mixed C++ and Fortran code
What happens if you add ${DLIB} to the end of the line
> executable: $(SOURCES) chkopts
>-${FLINKER} $(FFLAGS) $(FPPFLAGS) $(CPPFLAGS) -o executable.out
> $(SOURCES) ${PETSC_LIB}
Send all the output from trying this.
Barry
> On Jun 1, 2018, at 12:07 PM, 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
>
[petsc-users] Makefile for mixed C++ and Fortran code
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
