[petsc-users] petsc4py installation error with PETSc v 3.6.1
Justin Chang
jychang48 at gmail.com
Wed Jul 22 18:15:18 CDT 2015
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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