My question is related to this post:
Including a compiled module in module that is wrapped with f2py (Minimum working example)?
in which the poster was trying to compile a Fortran code (Test.f90) with f2py and link that to a pre-compiled library (or in my case, object, myex44f.o). The answer enabled me to compile the Fortran code and generated the python module.
My problem is different from the above posters problem in that my object is linked to PETSc. When I try to import my f2py-generated library into python, I get the error that it cannot locate 'VecDestroy', a PETSc subroutine. My most recent attempt was:
f2py -c --fcompiler=gfortran -I. myex44f.o ../../../Codes/third_party/petsc/include/petsc/finclude/petscdef.h -m test Test.f90
Here is the code Test.f90:
subroutine test
USE petsctest
call mainsub
end subroutine test
which calls mainsub from the module petsctest:
module petsctest ! Solves the linear system J x = f
#include <petsc/finclude/petscdef.h>
contains
subroutine mainsub
use petscksp; use petscdm
Vec x,f
Mat J
DM da
KSP ksp
PetscErrorCode ierr
call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
call DMDACreate1d(MPI_COMM_WORLD,DM_BOUNDARY_NONE,8,1,1, &
& PETSC_NULL_INTEGER,da,ierr)
call DMCreateGlobalVector(da,x,ierr)
call VecDuplicate(x,f,ierr)
call DMSetMatType(da,MATAIJ,ierr)
call DMCreateMatrix(da,J,ierr)
call ComputeRHS(da,f,ierr)
call ComputeMatrix(da,J,ierr)
call KSPCreate(MPI_COMM_WORLD,ksp,ierr)
call KSPSetOperators(ksp,J,J,ierr)
call KSPSetFromOptions(ksp,ierr)
call KSPSolve(ksp,f,x,ierr)
call MatDestroy(J,ierr)
call VecDestroy(x,ierr)
call VecDestroy(f,ierr)
call KSPDestroy(ksp,ierr)
call DMDestroy(da,ierr)
call PetscFinalize(ierr)
end
The error that I get is:
import test Traceback (most recent call last): File "", line 1, in ImportError: ./test.so: undefined symbol: vecdestroy_
Does anyone have any suggestions? Thank you very much for any help you can provide me.
UPDATE:
I generated the original myex44f.o object using the makefile provided with the PETSc examples. Looking at the link line, I reasoned that I might need to link the petsc library when compiling with f2py. My current attempt is:
f2py -c --fcompiler=gfortran -m test Test.f90 -I. myex44f.o -I/home/costoich/Documents/AFPWork/Codes/third_party/petsc/include -I/home/costoich/Documents/AFPWork/Codes/third_party/petsc/arch-linux2-c-debug/include -L/home/costoich/Documents/AFPWork/Codes/third_party/petsc/arch-linux2-c-debug/lib -lpetsc
This seems to be linking correctly during the compile steps (if I just write -lpetsc without the path the compiler fails). However, when I type ldd test.so, I get:
linux-vdso.so.1 => (0x00007ffe09886000)
libpetsc.so.3.7 => not found
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007fc315be5000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc31581b000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007fc3155dc000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fc3152d3000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fc3150bc000)
/lib64/ld-linux-x86-64.so.2 (0x000055a3fad27000)
Do I need two use the link flags Wl,rpath? f2py seems to not understand these. Thank you for any comments.
RESOLVED
I found my issue. I can't get f2py to accept the -Wl,rpath options, but if I define the environment variable LD_LIBRARY_PATH=/home/costoich/Documents/AFPWork/Codes/third_party/petsc/arch-linux2-c-debug/lib everything works out. Thank you for your help.
