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

Wed Jul 22 19:44:06 CDT 2015

You can apply the patch with the 'patch' command

cd petsc4py
patch -Np1 < petsc4py.patch

Satish

On Wed, 22 Jul 2015, Justin Chang wrote:

> 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
> > >
> >
> 