[petsc-users] Error with file linking

[Satish Balay]

Attaching the modified makefile. It might need a couple of iterations
of fixing.

Hopefully its clear why it would work. Note - if not for different
flags required for different sources (opt/opt2/opt3) - you can build
all petsc/non-petsc sources with petsc makefile targets.

> In my fortran files, do I simply use petsc.h or I have to use specific *.h
> depending on what petsc commands are used?

With petsc-3.1 you just have to use petsc.h for all F77 interface stuff, and
petsc.h90 for all f90 interface stuff [like VecGetArrayF90()]

Satish

On Thu, 13 May 2010, Wee-Beng TAY wrote:

> Hi Satish,
> 
> Sorry for the confusion.
> 
> I have attached my makefile. This was used to compile and link my code before
> I used PETSc 3.1.
> 
> I have several fortran files. Some contain PETSc commands and need to use
> PETSc include files. Other do not. In the end, they all have to be linked to
> form my final code. I used to copy part of the compiling and linking command
> from "make ex1f" to compile my code:
> 
> /app1/mvapich2/current/bin/mpif90 -c  -O3
> -I/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/include
> -I/home/svu/g0306332/codes/petsc-3.1-p0/include
> -I/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/include
> -I/app1/mvapich2/1.4/include -I/app1/mvapich2/current/include
> -I/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/include
> -I/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/include
> -I/app1/mvapich2/1.4/include -I/app1/mvapich2/current/include    -o ex1f.o
> ex1f.F
> 
> /app1/mvapich2/current/bin/mpif90 -O3   -o ex1f ex1f.o
> -Wl,-rpath,/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib
> -L/home/svu/g0306332/codes/petsc-3.1-p0/atlas5-mpi-nodebug/lib -lpetsc
> -Wl,-rpath,/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/lib
> -L/home/svu/g0306332/lib/hypre-2.6.0b_atlas5/lib -lHYPRE -lmpichcxx -lstdc++
> -Wl,-rpath,/app1/intel/mkl/10.0.5.025/lib/em64t
> -L/app1/intel/mkl/10.0.5.025/lib/em64t -lmkl_lapack -lmkl -lguide -lpthread
> -L/app1/mvapich2/1.4/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -ldl -lmpich
> -lpthread -lrdmacm -libverbs -libumad -lrt -lgcc_s -lmpichf90
> -L/app1/intel/Compiler/11.0/074/lib/intel64 -lifport -lifcore -limf -lsvml -lm
> -lipgo -lirc -lirc_s -lm -lmpichcxx -lstdc++ -lmpichcxx -lstdc++ -ldl -lmpich
> -lpthread -lrdmacm -libverbs -libumad -lrt -lgcc_s -ldl
> 
> However, it doesn't seem to work now. I tried to look at chapter 14 but I
> don't really understand since I know very little about makefiles.
> 
> Can you give a rough guide for my case? I will try to read up on the manual to
> get more info.
> 
> Moreover, I am confused by the use of:
> 
> #include "finclude/petsc.h" etc.
> 
> In my fortran files, do I simply use petsc.h or I have to use specific *.h
> depending on what petsc commands are used?
> 
> Thank you very much and have a nice day!
> 
> Yours sincerely,
> 
> Wee-Beng Tay
> 
> 
> On 12/5/2010 9:55 AM, Satish Balay wrote:
> > Lets step back and deal with this primary issue.
> > 
> > Have you attempted to use makefiles in petsc format? What problems
> > have you encountered? Perhaps they are fixable.
> > 
> > The reason to use this format is to make your makefile as portable as
> > possible [and avoid such issues].
> > 
> > Satish
> > 
> > On Tue, 11 May 2010, Satish Balay wrote:
> > 
> >    
> > > Why not use petsc makefiles - and avoid these hasseles?
> > > 
> > >      
> >    
-------------- next part --------------
# PETSC_DIR and PETSC_ARCH should be set either in env or in this makeifle

CFLAGS	         =
FFLAGS	         = -r8 -132 -fPIC -g -w90 -w -w95 -c -O3  # instead of opt2 add these flags to default petsc compile target for .F/.f
CPPFLAGS         =
FPPFLAGS         =
CLEANFILES       = a.out

include ${PETSC_DIR}/conf/variables
include ${PETSC_DIR}/conf/rules

opt = -r8  -w95 -c -O3
opt3 = -w95 -c -O3

libs =/home/svu/g0306332/lib/tecio64.a /home/svu/g0306332/lib/linux64.a

OBJS = global.o grid.o flux_area.o bc.o bc_impl.o bc_semi.o set_matrix.o inter_step.o mom_disz.o poisson.o petsc_sub.o cell_data.o fractional.o ns2d_c.o

# perhaps -r8 -w95 -fPIC -g -O3 flags not needed here?
a.out : $(OBJS)
	$(FLINKER) -r8 -w95 -fPIC -g -O3 -o a.out $(OBJS) $(libs) $(PETSC_LIB)

#compiled these sources with default petsc targets
global.o : global.F
petsc_sub.o : petsc_sub.F poisson.o
ns2d_c.o : ns2d_c.f90 cell_data.o fractional.o

# sources compiled separately - as they need different opt/opt3 compiler flags.
grid.o : grid.f90 global.o
	$(FC) $(opt3) grid.f90 

flux_area.o : flux_area.f90 global.o 
	$(FC) $(opt) flux_area.f90

bc.o : bc.f90 flux_area.o
	$(FC) $(opt) bc.f90

bc_impl.o : bc_impl.f90 bc.o
	$(FC) $(opt) bc_impl.f90

bc_semi.o : bc_semi.f90 bc.o
	$(FC) $(opt) bc_semi.f90

set_matrix.o : set_matrix.f90 bc_semi.o bc_impl.o
	$(FC) $(opt) set_matrix.f90

inter_step.o : inter_step.f90 bc_impl.o
	$(FC) $(opt) inter_step.f90

mom_disz.o : mom_disz.f90 bc_impl.o bc_semi.o set_matrix.o
	$(FC) $(opt) mom_disz.f90

poisson.o : poisson.f90 set_matrix.o
	$(FC) $(opt) poisson.f90

cell_data.o : cell_data.f90 grid.o set_matrix.o
	$(FC) $(opt) cell_data.f90

fractional.o : fractional.f90 mom_disz.o petsc_sub.o inter_step.o
	$(FC) $(opt) fractional.f90