Dear Lawrence,
Again, thanks for your help. That seemed to work, although I have
come up against another error deep inside the installation. Sorry
the error message is so long, I'm not sure exactly what the most
useful bit would be...
Installing firedrake/
/home/tmb15/src/firedrake/bin/pip install --no-deps
--ignore-installed firedrake/
Processing ./firedrake
Installing collected packages: firedrake
Running setup.py install for firedrake ... error
Complete output from command
/home/tmb15/src/firedrake/bin/python -u -c "import setuptools,
tokenize;__file__='/tmp/pip-3AwIsU-build/setup.py';exec(compile(getattr(tokenize,
'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
'exec'))" install --record
/tmp/pip-XNmbta-record/install-record.txt
--single-version-externally-managed --compile --install-headers
/home/tmb15/src/firedrake/include/site/python2.7/firedrake:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/firedrake
copying firedrake/output.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/halo.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/optimizer.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/version.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/ufl_expr.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/assembly_cache.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/extrusion_utils.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/plot.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/expression.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/pointeval_utils.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/exceptions.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/linear_solver.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/utility_meshes.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/parameters.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/matrix.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/constant.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/_version.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/interpolation.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/pointquery_utils.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/norms.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/petsc.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/projection.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/variational_solver.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/assemble.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/functionspace.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/functionspaceimpl.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/bcs.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/mesh.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/nullspace.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/logging.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/__init__.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/formmanipulation.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/tsfc_interface.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/assemble_expressions.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/function.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/solving.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/utils.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/checkpointing.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/parloops.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/solving_utils.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/functionspacedata.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/dmhooks.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/vector.py ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/citations.py ->
build/lib.linux-x86_64-2.7/firedrake
creating build/lib.linux-x86_64-2.7/firedrake/mg
copying firedrake/mg/interface.py ->
build/lib.linux-x86_64-2.7/firedrake/mg
copying firedrake/mg/mesh.py ->
build/lib.linux-x86_64-2.7/firedrake/mg
copying firedrake/mg/__init__.py ->
build/lib.linux-x86_64-2.7/firedrake/mg
copying firedrake/mg/utils.py ->
build/lib.linux-x86_64-2.7/firedrake/mg
copying firedrake/mg/ufl_utils.py ->
build/lib.linux-x86_64-2.7/firedrake/mg
creating build/lib.linux-x86_64-2.7/firedrake/slope_limiter
copying firedrake/slope_limiter/limiter.py ->
build/lib.linux-x86_64-2.7/firedrake/slope_limiter
copying firedrake/slope_limiter/vertex_based_limiter.py ->
build/lib.linux-x86_64-2.7/firedrake/slope_limiter
copying firedrake/slope_limiter/__init__.py ->
build/lib.linux-x86_64-2.7/firedrake/slope_limiter
creating build/lib.linux-x86_64-2.7/firedrake/matrix_free
copying firedrake/matrix_free/operators.py ->
build/lib.linux-x86_64-2.7/firedrake/matrix_free
copying firedrake/matrix_free/__init__.py ->
build/lib.linux-x86_64-2.7/firedrake/matrix_free
copying firedrake/matrix_free/preconditioners.py ->
build/lib.linux-x86_64-2.7/firedrake/matrix_free
creating build/lib.linux-x86_64-2.7/firedrake_configuration
copying firedrake_configuration/__init__.py ->
build/lib.linux-x86_64-2.7/firedrake_configuration
copying firedrake/firedrake_geometry.h ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/evaluate.h ->
build/lib.linux-x86_64-2.7/firedrake
copying firedrake/locate.c ->
build/lib.linux-x86_64-2.7/firedrake
creating build/lib.linux-x86_64-2.7/firedrake/icons
copying firedrake/icons/play.png ->
build/lib.linux-x86_64-2.7/firedrake/icons
copying firedrake/icons/plus.png ->
build/lib.linux-x86_64-2.7/firedrake/icons
copying firedrake/icons/minus.png ->
build/lib.linux-x86_64-2.7/firedrake/icons
UPDATING build/lib.linux-x86_64-2.7/firedrake/_version.py
set build/lib.linux-x86_64-2.7/firedrake/_version.py to
'0.13.0+752.g812a6f4'
running build_ext
cythoning firedrake/dmplex.pyx to firedrake/dmplex.c
warning: firedrake/dmplex.pyx:1197:4: Buffer unpacking not
optimized away.
warning: firedrake/dmplex.pyx:1197:4: Buffer unpacking not
optimized away.
warning: firedrake/dmplex.pyx:1589:4: Buffer unpacking not
optimized away.
warning: firedrake/dmplex.pyx:1589:4: Buffer unpacking not
optimized away.
warning: firedrake/dmplex.pyx:1590:4: Buffer unpacking not
optimized away.
warning: firedrake/dmplex.pyx:1590:4: Buffer unpacking not
optimized away.
building 'firedrake.dmplex' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/firedrake
mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes
-fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g
-fstack-protector-strong -Wformat -Werror=format-security -fPIC
-I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include
-I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc4py/include
-I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include
-I/usr/include/python2.7 -c firedrake/dmplex.c -o
build/temp.linux-x86_64-2.7/firedrake/dmplex.o
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from firedrake/dmplex.c:406:
/home/tmb15/src/firedrake/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
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscbag.h:4:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:5,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsys.h:241:0:
warning: "__STDC_FORMAT_MACROS" redefined
#define __STDC_FORMAT_MACROS /* required for using PRId64
from c++ */
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/numpyconfig.h:4:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_common.h:5,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:4,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from firedrake/dmplex.c:406:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/_numpyconfig.h:30:0:
note: this is the location of the previous definition
#define __STDC_FORMAT_MACROS 1
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:270:1:
warning: function declaration isn’t a prototype
[-Wstrict-prototypes]
PETSC_EXTERN PetscErrorCode DMAddBoundary(DM,
DMBoundaryConditionType, const char[], const char[], PetscInt,
PetscInt, const PetscInt *, void (*)(), PetscInt, const PetscInt
*, void *);
^
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:272:1:
warning: function declaration isn’t a prototype
[-Wstrict-prototypes]
PETSC_EXTERN PetscErrorCode DMGetBoundary(DM, PetscInt,
DMBoundaryConditionType *, const char **, const char **, PetscInt
*, PetscInt *, const PetscInt **, void (**)(), PetscInt *, const
PetscInt **, void **);
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:21:0,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscds.h:273:1:
warning: function declaration isn’t a prototype
[-Wstrict-prototypes]
PETSC_EXTERN PetscErrorCode PetscDSAddBoundary(PetscDS,
DMBoundaryConditionType, const char[], const char[], PetscInt,
PetscInt, const PetscInt *, void (*)(), PetscInt, const PetscInt
*, void *);
^
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscds.h:275:1:
warning: function declaration isn’t a prototype
[-Wstrict-prototypes]
PETSC_EXTERN PetscErrorCode PetscDSGetBoundary(PetscDS,
PetscInt, DMBoundaryConditionType *, const char **, const char **,
PetscInt *, PetscInt *, const PetscInt **, void (**)(), PetscInt
*, const PetscInt **, void **);
^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_facet_numbering’:
firedrake/dmplex.c:3940:243: warning: passing argument 3 of
‘DMPlexGetSupport’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_12 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetSupport(__pyx_v_plex->dm,
(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *,
__pyx_pybuffernd_facets.rcbuffer->pybuffer.buf, __pyx_t_17,
__pyx_pybuffernd_facets.diminfo[0].strides)),
(&__pyx_v_cells))); if (unlikely(__pyx_t_12 == -1))
__PYX_ERR(0, 57, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:66:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode DMPlexGetSupport(DM, PetscInt,
const PetscInt *[]);
^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_2closure_ordering’:
firedrake/dmplex.c:5385:126: warning: passing argument 3 of
‘DMPlexGetCone’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_9 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm,
(__pyx_v_closure[(2 * __pyx_v_ci)]),
(&__pyx_v_face_vertices))); if (unlikely(__pyx_t_9 == -1))
__PYX_ERR(0, 183, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:58:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const
PetscInt *[]);
^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_14mark_entity_classes’:
firedrake/dmplex.c:9833:128: warning: passing argument 4 of
‘PetscSFGetGraph’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_9 =
__pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_point_sf->sf,
(&__pyx_v_nroots), (&__pyx_v_nleaves),
(&__pyx_v_ilocal), (&__pyx_v_iremote))); if
(unlikely(__pyx_t_9 == -1)) __PYX_ERR(0, 629, __pyx_L1_error)
^
In file included from firedrake/dmplex.c:416:0:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt
*nroots,PetscInt *nleaves,const PetscInt **ilocal,const
PetscSFNode **iremote);
^
firedrake/dmplex.c:9833:147: warning: passing argument 5 of
‘PetscSFGetGraph’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_9 =
__pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_point_sf->sf,
(&__pyx_v_nroots), (&__pyx_v_nleaves),
(&__pyx_v_ilocal), (&__pyx_v_iremote))); if
(unlikely(__pyx_t_9 == -1)) __PYX_ERR(0, 629, __pyx_L1_error)
^
In file included from firedrake/dmplex.c:416:0:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29:
note: expected ‘const PetscSFNode ** {aka const struct
<anonymous> **}’ but argument is of type ‘PetscSFNode **
{aka struct <anonymous> **}’
PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt
*nroots,PetscInt *nleaves,const PetscInt **ilocal,const
PetscSFNode **iremote);
^
firedrake/dmplex.c:9949:85: warning: passing argument 2 of
‘ISGetIndices’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_9 =
__pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_cell_is->iset,
(&__pyx_v_cells))); if (unlikely(__pyx_t_9 == -1))
__PYX_ERR(0, 644, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscis.h:52:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode ISGetIndices(IS,const PetscInt
*[]);
^
firedrake/dmplex.c:10237:85: warning: passing argument 2 of
‘ISGetIndices’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_9 =
__pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_cell_is->iset,
(&__pyx_v_cells))); if (unlikely(__pyx_t_9 == -1))
__PYX_ERR(0, 680, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscis.h:52:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode ISGetIndices(IS,const PetscInt
*[]);
^
firedrake/dmplex.c:10558:86: warning: passing argument 2 of
‘ISGetIndices’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_9 =
__pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_facet_is->iset,
(&__pyx_v_facets))); if (unlikely(__pyx_t_9 == -1))
__PYX_ERR(0, 709, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscis.h:52:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode ISGetIndices(IS,const PetscInt
*[]);
^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_16get_entity_classes’:
firedrake/dmplex.c:11507:90: warning: passing argument 2 of
‘ISGetIndices’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_8 =
__pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_class_is->iset,
(&__pyx_v_indices))); if (unlikely(__pyx_t_8 == -1))
__PYX_ERR(0, 789, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscis.h:52:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode ISGetIndices(IS,const PetscInt
*[]);
^
firedrake/dmplex.c:11586:94: warning: passing argument 2 of
‘ISRestoreIndices’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_8 =
__pyx_f_9firedrake_6dmplex_CHKERR(ISRestoreIndices(__pyx_v_class_is->iset,
(&__pyx_v_indices))); if (unlikely(__pyx_t_8 == -1))
__PYX_ERR(0, 795, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscis.h:53:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode ISRestoreIndices(IS,const
PetscInt *[]);
^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_26plex_renumbering’:
firedrake/dmplex.c:15026:88: warning: passing argument 2 of
‘ISGetIndices’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_9 =
__pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_facet_is->iset,
(&__pyx_v_facets))); if (unlikely(__pyx_t_9 == -1))
__PYX_ERR(0, 1063, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscis.h:52:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode ISGetIndices(IS,const PetscInt
*[]);
^
firedrake/dmplex.c:15104:92: warning: passing argument 2 of
‘ISRestoreIndices’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_9 =
__pyx_f_9firedrake_6dmplex_CHKERR(ISRestoreIndices(__pyx_v_facet_is->iset,
(&__pyx_v_facets))); if (unlikely(__pyx_t_9 == -1))
__PYX_ERR(0, 1070, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscvec.h:9:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscmat.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:6,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscis.h:53:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode ISRestoreIndices(IS,const
PetscInt *[]);
^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_28get_cell_remote_ranks’:
firedrake/dmplex.c:15485:123: warning: passing argument 4 of
‘PetscSFGetGraph’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_10 =
__pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf,
(&__pyx_v_nroots), (&__pyx_v_nleaves),
(&__pyx_v_ilocal), (&__pyx_v_iremote))); if
(unlikely(__pyx_t_10 == -1)) __PYX_ERR(0, 1101, __pyx_L1_error)
^
In file included from firedrake/dmplex.c:416:0:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt
*nroots,PetscInt *nleaves,const PetscInt **ilocal,const
PetscSFNode **iremote);
^
firedrake/dmplex.c:15485:142: warning: passing argument 5 of
‘PetscSFGetGraph’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_10 =
__pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf,
(&__pyx_v_nroots), (&__pyx_v_nleaves),
(&__pyx_v_ilocal), (&__pyx_v_iremote))); if
(unlikely(__pyx_t_10 == -1)) __PYX_ERR(0, 1101, __pyx_L1_error)
^
In file included from firedrake/dmplex.c:416:0:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29:
note: expected ‘const PetscSFNode ** {aka const struct
<anonymous> **}’ but argument is of type ‘PetscSFNode **
{aka struct <anonymous> **}’
PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt
*nroots,PetscInt *nleaves,const PetscInt **ilocal,const
PetscSFNode **iremote);
^
firedrake/dmplex.c: In function
‘__pyx_f_9firedrake_6dmplex_get_edge_global_vertices’:
firedrake/dmplex.c:15751:96: warning: passing argument 3 of
‘DMPlexGetCone’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_1 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm,
__pyx_v_facet, (&__pyx_v_vs))); if (unlikely(__pyx_t_1 == -1))
__PYX_ERR(0, 1138, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:58:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const
PetscInt *[]);
^
firedrake/dmplex.c: In function
‘__pyx_f_9firedrake_6dmplex_get_communication_lists’:
firedrake/dmplex.c:16430:97: warning: passing argument 3 of
‘DMPlexGetSupport’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_3 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetSupport(__pyx_v_plex->dm,
__pyx_v_f, (&__pyx_v_support))); if (unlikely(__pyx_t_3 ==
-1)) __PYX_ERR(0, 1241, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:66:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode DMPlexGetSupport(DM, PetscInt,
const PetscInt *[]);
^
firedrake/dmplex.c:16906:126: warning: passing argument 4 of
‘qsort’ from incompatible pointer type
[-Wincompatible-pointer-types]
qsort(__pyx_v_cfacets,
((__pyx_v_offsets[0])[(__pyx_v_nranks[0])]), (sizeof(struct
__pyx_t_9firedrake_6dmplex_CommFacet)),
(&__pyx_f_9firedrake_6dmplex_CommFacet_cmp));
^
In file included from /usr/include/python2.7/Python.h:42:0,
from firedrake/dmplex.c:4:
/usr/include/stdlib.h:764:13: note: expected ‘__compar_fn_t
{aka int (*)(const void *, const void *)}’ but argument is of type
‘int (*)(void *, void *)’
extern void qsort (void *__base, size_t __nmemb, size_t
__size,
^
firedrake/dmplex.c: In function
‘__pyx_f_9firedrake_6dmplex_plex_get_restricted_support’:
firedrake/dmplex.c:17060:95: warning: passing argument 3 of
‘DMPlexGetSupport’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_1 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetSupport(__pyx_v_plex->dm,
__pyx_v_f, (&__pyx_v_support))); if (unlikely(__pyx_t_1 ==
-1)) __PYX_ERR(0, 1361, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:66:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode DMPlexGetSupport(DM, PetscInt,
const PetscInt *[]);
^
firedrake/dmplex.c: In function
‘__pyx_f_9firedrake_6dmplex_traverse_cell_string’:
firedrake/dmplex.c:17274:94: warning: passing argument 3 of
‘DMPlexGetCone’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_1 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm,
__pyx_v_c, (&__pyx_v_cone))); if (unlikely(__pyx_t_1 == -1))
__PYX_ERR(0, 1425, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:58:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const
PetscInt *[]);
^
firedrake/dmplex.c:17355:105: warning: passing argument 3 of
‘DMPlexGetConeOrientation’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_1 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetConeOrientation(__pyx_v_plex->dm,
__pyx_v_c, (&__pyx_v_cone_orient))); if (unlikely(__pyx_t_1 ==
-1)) __PYX_ERR(0, 1434, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:62:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode DMPlexGetConeOrientation(DM,
PetscInt, const PetscInt *[]);
^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_32orientations_facet2cell’:
firedrake/dmplex.c:20346:97: warning: passing argument 3 of
‘DMPlexGetCone’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_10 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm,
__pyx_v_c, (&__pyx_v_cone))); if (unlikely(__pyx_t_10 == -1))
__PYX_ERR(0, 1802, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:58:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const
PetscInt *[]);
^
firedrake/dmplex.c:20355:108: warning: passing argument 3 of
‘DMPlexGetConeOrientation’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_10 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetConeOrientation(__pyx_v_plex->dm,
__pyx_v_c, (&__pyx_v_cone_orient))); if (unlikely(__pyx_t_10
== -1)) __PYX_ERR(0, 1803, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:62:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode DMPlexGetConeOrientation(DM,
PetscInt, const PetscInt *[]);
^
firedrake/dmplex.c:20558:101: warning: passing argument 3 of
‘DMPlexGetCone’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_10 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetCone(__pyx_v_plex->dm,
__pyx_v_facet, (&__pyx_v_cone))); if (unlikely(__pyx_t_10 ==
-1)) __PYX_ERR(0, 1859, __pyx_L1_error)
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:15:0,
from firedrake/dmplex.c:408:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmplex.h:58:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const
PetscInt *[]);
^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_34exchange_cell_orientations’:
firedrake/dmplex.c:20885:122: warning: passing argument 4 of
‘PetscSFGetGraph’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_5 =
__pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf,
(&__pyx_v_nroots), (&__pyx_v_nleaves),
(&__pyx_v_ilocal), (&__pyx_v_iremote))); if
(unlikely(__pyx_t_5 == -1)) __PYX_ERR(0, 1897, __pyx_L1_error)
^
In file included from firedrake/dmplex.c:416:0:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt
*nroots,PetscInt *nleaves,const PetscInt **ilocal,const
PetscSFNode **iremote);
^
firedrake/dmplex.c:20885:141: warning: passing argument 5 of
‘PetscSFGetGraph’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_5 =
__pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf,
(&__pyx_v_nroots), (&__pyx_v_nleaves),
(&__pyx_v_ilocal), (&__pyx_v_iremote))); if
(unlikely(__pyx_t_5 == -1)) __PYX_ERR(0, 1897, __pyx_L1_error)
^
In file included from firedrake/dmplex.c:416:0:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29:
note: expected ‘const PetscSFNode ** {aka const struct
<anonymous> **}’ but argument is of type ‘PetscSFNode **
{aka struct <anonymous> **}’
PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt
*nroots,PetscInt *nleaves,const PetscInt **ilocal,const
PetscSFNode **iremote);
^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_38prune_sf’:
firedrake/dmplex.c:21596:120: warning: passing argument 4 of
‘PetscSFGetGraph’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_1 =
__pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf,
(&__pyx_v_nroots), (&__pyx_v_nleaves),
(&__pyx_v_ilocal), (&__pyx_v_iremote))); if
(unlikely(__pyx_t_1 == -1)) __PYX_ERR(0, 1957, __pyx_L1_error)
^
In file included from firedrake/dmplex.c:416:0:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument
is of type ‘PetscInt ** {aka int **}’
PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt
*nroots,PetscInt *nleaves,const PetscInt **ilocal,const
PetscSFNode **iremote);
^
firedrake/dmplex.c:21596:139: warning: passing argument 5 of
‘PetscSFGetGraph’ from incompatible pointer type
[-Wincompatible-pointer-types]
__pyx_t_1 =
__pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_sf->sf,
(&__pyx_v_nroots), (&__pyx_v_nleaves),
(&__pyx_v_ilocal), (&__pyx_v_iremote))); if
(unlikely(__pyx_t_1 == -1)) __PYX_ERR(0, 1957, __pyx_L1_error)
^
In file included from firedrake/dmplex.c:416:0:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscsf.h:75:29:
note: expected ‘const PetscSFNode ** {aka const struct
<anonymous> **}’ but argument is of type ‘PetscSFNode **
{aka struct <anonymous> **}’
PETSC_EXTERN PetscErrorCode PetscSFGetGraph(PetscSF,PetscInt
*nroots,PetscInt *nleaves,const PetscInt **ilocal,const
PetscSFNode **iremote);
^
firedrake/dmplex.c: In function
‘__pyx_f_9firedrake_6dmplex_traverse_cell_string’:
firedrake/dmplex.c:17508:7: warning: ‘__pyx_v_support_size’
may be used uninitialized in this function [-Wmaybe-uninitialized]
for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4;
__pyx_t_5+=1) {
^
firedrake/dmplex.c: In function
‘__pyx_f_9firedrake_6dmplex_locally_orient_quadrilateral_plex’:
firedrake/dmplex.c:17869:12: warning: ‘__pyx_v_size’ may be
used uninitialized in this function [-Wmaybe-uninitialized]
if (unlikely(!(__pyx_t_14 != 0))) {
^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_30quadrilateral_facet_orientations.isra.33’:
firedrake/dmplex.c:19827:7: warning: ‘__pyx_v_size’ may be
used uninitialized in this function [-Wmaybe-uninitialized]
for (__pyx_t_48 = 0; __pyx_t_48 < __pyx_t_6;
__pyx_t_48+=1) {
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1
-Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro
-fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g
-fstack-protector-strong -Wformat -Werror=format-security
-Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time
-D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat
-Werror=format-security
build/temp.linux-x86_64-2.7/firedrake/dmplex.o -lpetsc -o
build/lib.linux-x86_64-2.7/firedrake/dmplex.so
-L/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib
-Wl,-rpath,/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib
-Wl,-rpath,/home/tmb15/src/firedrake/lib
cythoning firedrake/hdf5interface.pyx to
firedrake/hdf5interface.c
building 'firedrake.hdf5interface' extension
mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes
-fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g
-fstack-protector-strong -Wformat -Werror=format-security -fPIC
-I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include
-I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc4py/include
-I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include
-I/usr/include/python2.7 -c firedrake/hdf5interface.c -o
build/temp.linux-x86_64-2.7/firedrake/hdf5interface.o
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdmda.h:4:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:12,
from firedrake/hdf5interface.c:403:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:270:1:
warning: function declaration isn’t a prototype
[-Wstrict-prototypes]
PETSC_EXTERN PetscErrorCode DMAddBoundary(DM,
DMBoundaryConditionType, const char[], const char[], PetscInt,
PetscInt, const PetscInt *, void (*)(), PetscInt, const PetscInt
*, void *);
^
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscdm.h:272:1:
warning: function declaration isn’t a prototype
[-Wstrict-prototypes]
PETSC_EXTERN PetscErrorCode DMGetBoundary(DM, PetscInt,
DMBoundaryConditionType *, const char **, const char **, PetscInt
*, PetscInt *, const PetscInt **, void (**)(), PetscInt *, const
PetscInt **, void **);
^
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petsc.h:21:0,
from firedrake/hdf5interface.c:403:
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscds.h:273:1:
warning: function declaration isn’t a prototype
[-Wstrict-prototypes]
PETSC_EXTERN PetscErrorCode PetscDSAddBoundary(PetscDS,
DMBoundaryConditionType, const char[], const char[], PetscInt,
PetscInt, const PetscInt *, void (*)(), PetscInt, const PetscInt
*, void *);
^
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/include/petscds.h:275:1:
warning: function declaration isn’t a prototype
[-Wstrict-prototypes]
PETSC_EXTERN PetscErrorCode PetscDSGetBoundary(PetscDS,
PetscInt, DMBoundaryConditionType *, const char **, const char **,
PetscInt *, PetscInt *, const PetscInt **, void (**)(), PetscInt
*, const PetscInt **, void **);
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1
-Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro
-fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g
-fstack-protector-strong -Wformat -Werror=format-security
-Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time
-D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat
-Werror=format-security
build/temp.linux-x86_64-2.7/firedrake/hdf5interface.o -lpetsc -o
build/lib.linux-x86_64-2.7/firedrake/hdf5interface.so
-L/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib
-Wl,-rpath,/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/petsc/lib
-Wl,-rpath,/home/tmb15/src/firedrake/lib
cythoning firedrake/spatialindex.pyx to
firedrake/spatialindex.c
building 'firedrake.spatialindex' extension
mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes
-fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g
-fstack-protector-strong -Wformat -Werror=format-security -fPIC
-I/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include
-I/home/tmb15/src/firedrake/include -I/usr/include/python2.7 -c
firedrake/spatialindex.c -o
build/temp.linux-x86_64-2.7/firedrake/spatialindex.o
In file included from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from
/home/tmb15/src/firedrake/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from firedrake/spatialindex.c:406:
/home/tmb15/src/firedrake/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
/usr/include/spatialindex/SpatialIndex.h:30:0,
from
/usr/include/spatialindex/capi/sidx_config.h:56,
from
/usr/include/spatialindex/capi/sidx_api.h:34,
from firedrake/spatialindex.c:409:
/usr/include/spatialindex/tools/Tools.h:59:20: fatal error:
iostream: No such file or directory
compilation terminated.
error: command 'mpicc' failed with exit status 1
----------------------------------------
Command "/home/tmb15/src/firedrake/bin/python -u -c "import
setuptools,
tokenize;__file__='/tmp/pip-3AwIsU-build/setup.py';exec(compile(getattr(tokenize,
'open', open)(__file__).read().replace('\r\n', '\n'), __file__,
'exec'))" install --record
/tmp/pip-XNmbta-record/install-record.txt
--single-version-externally-managed --compile --install-headers
/home/tmb15/src/firedrake/include/site/python2.7/firedrake" failed
with error code 1 in /tmp/pip-3AwIsU-build/
Traceback (most recent call last):
File "firedrake-install", line 702, in <module>
install(p+"/")
File "firedrake-install", line 431, in install
run_pip_install(["--ignore-installed", package])
File "firedrake-install", line 294, in run_pip_install
check_call(pipinstall + args)
File "firedrake-install", line 181, in check_call
subprocess.check_call(arguments)
File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command
'['/home/tmb15/src/firedrake/bin/pip', 'install', '--no-deps',
'--ignore-installed', 'firedrake/']' returned non-zero exit status
1
On 01/11/16 14:52, T. M. Bendall wrote:Hi Lawrence, Thanks very much for your help. I now tried reinstalling and it failed again, coming up against this: Checking for presence of package python-pip...installed. Creating firedrake virtualenv. Traceback (most recent call last): File "firedrake-install", line 668, in <module> virtualenv.create_environment("firedrake", site_packages=False) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 924, in create_environment site_packages=site_packages, clear=clear, symlink=symlink)) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 1129, in install_python copyfile(join(stdlib_dir, fn), join(lib_dir, fn), symlink) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 352, in copyfile copyfileordir(src, dest, symlink) File "/home/tmb15/.local/lib/python2.7/site-packages/virtualenv.py", line 327, in copyfileordir shutil.copytree(src, dest, symlink) File "/usr/lib/python2.7/shutil.py", line 177, in copytree os.makedirs(dst) File "/usr/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 17] File exists: '/home/tmb15/src/firedrake/lib/python2.7/lib-dynload'If you don't care about any existing "firedrake" virtualenv in /home/tmb15/src/firedrake, please remove that entire directory tree. I assume you are running firedrake-install from /home/tmb15/src. If you do care, move it out the way, and then do firedrake-install. Lawrence
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