[petsc-users] petsc4py installation error with PETSc v 3.6.1

Wed Jul 22 18:46:20 CDT 2015

How do I use this again?

On Wednesday, July 22, 2015, Satish Balay <balay at mcs.anl.gov> wrote:

> The attached patch to petsc4py should fix the error.
>
> Satish
>
> On Wed, 22 Jul 2015, Justin Chang wrote:
>
> > Hi all,
> >
> > Just installed the latest petsc-dev, and when I tried to build petsc4py
> via
> > git clone ... and pip setup.py build  i get the following errors:
> >
> > ====
> >
> > running build
> >
> > running build_src
> >
> > cythonizing 'petsc4py.PETSc.pyx' -> 'petsc4py.PETSc.c'
> >
> > cythonizing 'libpetsc4py/libpetsc4py.pyx' -> 'libpetsc4py/libpetsc4py.c'
> >
> > running build_py
> >
> > creating build
> >
> > creating build/lib.linux-x86_64-2.7
> >
> > creating build/lib.linux-x86_64-2.7/petsc4py
> >
> > copying src/PETSc.py -> build/lib.linux-x86_64-2.7/petsc4py
> >
> > copying src/__init__.py -> build/lib.linux-x86_64-2.7/petsc4py
> >
> > copying src/__main__.py -> build/lib.linux-x86_64-2.7/petsc4py
> >
> > creating build/lib.linux-x86_64-2.7/petsc4py/lib
> >
> > copying src/lib/__init__.py -> build/lib.linux-x86_64-2.7/petsc4py/lib
> >
> > creating build/lib.linux-x86_64-2.7/petsc4py/include
> >
> > creating build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py
> >
> > copying src/include/petsc4py/numpy.h ->
> > build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py
> >
> > copying src/include/petsc4py/petsc4py.h ->
> > build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py
> >
> > copying src/include/petsc4py/petsc4py.PETSc.h ->
> > build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py
> >
> > copying src/include/petsc4py/petsc4py.PETSc_api.h ->
> > build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py
> >
> > copying src/include/petsc4py/petsc4py.i ->
> > build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py
> >
> > copying src/include/petsc4py/PETSc.pxd ->
> > build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py
> >
> > copying src/include/petsc4py/__init__.pxd ->
> > build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py
> >
> > copying src/include/petsc4py/__init__.pyx ->
> > build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py
> >
> > copying src/lib/petsc.cfg -> build/lib.linux-x86_64-2.7/petsc4py/lib
> >
> > running build_ext
> >
> > PETSC_DIR:   /home/jchang23/petsc-dev
> >
> > PETSC_ARCH:  arch-linux2-c-opt
> >
> > version:     3.6.1 development
> >
> > scalar-type: real
> >
> > precision:   double
> >
> > language:    CONLY
> >
> > compiler:    /share/apps/openmpi-1.8.3/bin/mpicc
> >
> > linker:      /share/apps/openmpi-1.8.3/bin/mpicc
> >
> > building 'PETSc' extension
> >
> > creating build/temp.linux-x86_64-2.7
> >
> > creating build/temp.linux-x86_64-2.7/arch-linux2-c-opt
> >
> > creating build/temp.linux-x86_64-2.7/arch-linux2-c-opt/src
> >
> > /share/apps/openmpi-1.8.3/bin/mpicc -pthread -fPIC -O -fPIC
> > -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
> > -DPETSC_DIR=/home/jchang23/petsc-dev -I/share/apps/openmpi-1.8.3/include
> > -I/home/jchang23/petsc-dev/arch-linux2-c-opt/include
> > -I/home/jchang23/petsc-dev/include -Isrc/include
> > -I/home/jchang23/.local/lib/python2.7/site-packages/numpy/core/include
> > -I/home/jchang23/.local/include/python2.7 -c src/PETSc.c -o
> > build/temp.linux-x86_64-2.7/arch-linux2-c-opt/src/PETSc.o
> >
> > In file included from
> >
> /home/jchang23/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
> >
> >                  from
> >
> /home/jchang23/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
> >
> >                  from
> >
> /home/jchang23/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
> >
> >                  from src/include/petsc4py/numpy.h:11,
> >
> >                  from src/petsc4py.PETSc.c:258,
> >
> >                  from src/PETSc.c:3:
> >
> >
> /home/jchang23/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
> > warning: #warning "Using deprecated NumPy API, disable it by " "#defining
> > NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
> >
> >  #warning "Using deprecated NumPy API, disable it by " \
> >
> >   ^
> >
> > In file included from src/PETSc.c:3:0:
> >
> > src/petsc4py.PETSc.c: In function
> > ‘__pyx_pf_8petsc4py_5PETSc_7Section_76createGlobalSection’:
> >
> > src/petsc4py.PETSc.c:108243:47: error: incompatible type for argument 4
> of
> > ‘PetscSectionCreateGlobalSection’
> >
> >    __pyx_t_2 =
> >
> __pyx_f_8petsc4py_5PETSc_CHKERR(PetscSectionCreateGlobalSection(__pyx_v_self->sec,
> > __pyx_v_sf->sf, PETSC_FALSE, (&__pyx_v_gsec->sec))); if
> (unlikely(__pyx_t_2
> > == -1)) {__pyx_filename = __pyx_f[32]; __pyx_lineno = 213; __pyx_clineno
> =
> > __LINE__; goto __pyx_L1_error;}
> >
> >                                                ^
> >
> > In file included from /home/jchang23/petsc-dev/include/petscvec.h:9:0,
> >
> >                  from /home/jchang23/petsc-dev/include/petscmat.h:6,
> >
> >                  from /home/jchang23/petsc-dev/include/petscdm.h:6,
> >
> >                  from /home/jchang23/petsc-dev/include/petscdmda.h:4,
> >
> >                  from /home/jchang23/petsc-dev/include/petsc.h:12,
> >
> >                  from src/petsc4py.PETSc.c:254,
> >
> >                  from src/PETSc.c:3:
> >
> > /home/jchang23/petsc-dev/include/petscis.h:334:29: note: expected
> > ‘PetscBool’ but argument is of type ‘struct _p_PetscSection **’
> >
> >  PETSC_EXTERN PetscErrorCode
> PetscSectionCreateGlobalSection(PetscSection,
> > PetscSF, PetscBool, PetscBool, PetscSection *);
> >
> >                              ^
> >
> > In file included from src/PETSc.c:3:0:
> >
> > src/petsc4py.PETSc.c:108243:47: error: too few arguments to function
> > ‘PetscSectionCreateGlobalSection’
> >
> >    __pyx_t_2 =
> >
> __pyx_f_8petsc4py_5PETSc_CHKERR(PetscSectionCreateGlobalSection(__pyx_v_self->sec,
> > __pyx_v_sf->sf, PETSC_FALSE, (&__pyx_v_gsec->sec))); if
> (unlikely(__pyx_t_2
> > == -1)) {__pyx_filename = __pyx_f[32]; __pyx_lineno = 213; __pyx_clineno
> =
> > __LINE__; goto __pyx_L1_error;}
> >
> >                                                ^
> >
> > In file included from /home/jchang23/petsc-dev/include/petscvec.h:9:0,
> >
> >                  from /home/jchang23/petsc-dev/include/petscmat.h:6,
> >
> >                  from /home/jchang23/petsc-dev/include/petscdm.h:6,
> >
> >                  from /home/jchang23/petsc-dev/include/petscdmda.h:4,
> >
> >                  from /home/jchang23/petsc-dev/include/petsc.h:12,
> >
> >                  from src/petsc4py.PETSc.c:254,
> >
> >                  from src/PETSc.c:3:
> >
> > /home/jchang23/petsc-dev/include/petscis.h:334:29: note: declared here
> >
> >  PETSC_EXTERN PetscErrorCode
> PetscSectionCreateGlobalSection(PetscSection,
> > PetscSF, PetscBool, PetscBool, PetscSection *);
> >
> > error: command '/share/apps/openmpi-1.8.3/bin/mpicc' failed with exit
> > status 1
> >
> >
> > =========
> >
> > I am guessing it's because PetscSectionCreateGlobalSection has changed in
> > this latest released. Is there a way to fix this?
> >
> > Thanks,
> >
> > Justin
> >
>
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