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...@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
