[petsc-users] Error with file linking

Wed May 12 12:56:59 CDT 2010

try the attached makefile. If you have problems copy/paste the
*complete* make session from your terminal.

Satish

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

> Hi Satish,
> 
> I tried to run it, with the -c present and absent. However, nothing happened.
> I run using "make". I also specified "export
> PETSC_DIR=/home/svu/g0306332/codes/petsc-3.1-p0/" and "export
> PETSC_ARCH=atlas5-mpi-nodebug" before that.
> 
> Did I miss out something?
> 
> Also supposed that I have the same flag for all sources. In that case, how can
> I build them?
> 
> Thank you very much and have a nice day!
> 
> Yours sincerely,
> 
> Wee-Beng Tay
> 
> 
> On 13/5/2010 1:27 AM, Satish Balay wrote:
> > 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 --------------
ALL: a.out

# PETSC_DIR and PETSC_ARCH should be set either in env or in this makeifle
PETSC_DIR=/home/svu/g0306332/codes/petsc-3.1-p0
PETSC_ARCH=atlas5-mpi-nodebug

CFLAGS	         =
FFLAGS	         = -r8 -132 -fPIC -g -w90 -w -w95 -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

a.out : $(OBJS)
	$(FLINKER) -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