[firedrake] hello

24 Apr 2018


      I did not succed to install firedrake too bad for me could you help me
please ?

here is what i get when runing make alltests

the errors are at the end of this log


(firedrake) naceur@kahina:~/Documents/firedrake/src/firedrake$ make
alltest    Building extension modules
running build_ext
cythoning firedrake/dmplex.pyx to firedrake/dmplex.c
building 'firedrake.dmplex' extension
creating build
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/firedrake
mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fPIC
-I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include
-I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc4py/include
-I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include
-I/home/naceur/Documents/firedrake/include -I/usr/include/python3.5m -c
firedrake/dmplex.c -o build/temp.linux-x86_64-3.5/firedrake/dmplex.o
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from firedrake/dmplex.c:566:
/home/naceur/Documents/firedrake/lib/python3.5/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/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscbag.h:4:0,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:5,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsys.h:255:0:
warning: "__STDC_FORMAT_MACROS" redefined
 #define __STDC_FORMAT_MACROS /* required for using PRId64 from c++ */
 ^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/numpyconfig.h:4:0,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/npy_common.h:5,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:4,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from firedrake/dmplex.c:566:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/_numpyconfig.h:31:0:
note: this is the location of the previous definition
 #define __STDC_FORMAT_MACROS 1
 ^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_facet_numbering’:
firedrake/dmplex.c:4524:229: warning: passing argument 3 of
‘DMPlexGetSupport’ from incompatible pointer type
[-Wincompatible-pointer-types]
     __pyx_t_11 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetSupport(__pyx_v_plex->dm,
(*__Pyx_BufPtrCContig1d(PetscInt *,
__pyx_pybuffernd_facets.rcbuffer->pybuffer.buf, __pyx_t_17,
__pyx_pybuffernd_facets.diminfo[0].strides)), (&__pyx_v_cells))); if
(unlikely(__pyx_t_11 == ((int)-1))) __PYX_ERR(0, 64, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:71:29:
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:5955:126: 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 == ((int)-1))) __PYX_ERR(0, 190, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:63:29:
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_20mark_entity_classes’:
firedrake/dmplex.c:14346:115: warning: passing argument 4 of
‘PetscSFGetGraph’ from incompatible pointer type
[-Wincompatible-pointer-types]
     __pyx_t_8 =
__pyx_f_9firedrake_6dmplex_CHKERR(PetscSFGetGraph(__pyx_v_point_sf->sf,
NULL, (&__pyx_v_nleaves), (&__pyx_v_ilocal), NULL)); if (unlikely(__pyx_t_8
== ((int)-1))) __PYX_ERR(0, 901, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument is of
type ‘PetscInt ** {aka int **}’
 PETSC_EXTERN PetscErrorCode
PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const
PetscSFNode**);
                             ^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_22get_entity_classes’:
firedrake/dmplex.c:15262:90: warning: passing argument 2 of ‘ISGetIndices’
from incompatible pointer type [-Wincompatible-pointer-types]
       __pyx_t_7 =
__pyx_f_9firedrake_6dmplex_CHKERR(ISGetIndices(__pyx_v_class_is->iset,
(&__pyx_v_indices))); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0,
975, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscvec.h:9:0,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscmat.h:6,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdm.h:6,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmda.h:4,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:13,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/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:15343:94: warning: passing argument 2 of
‘ISRestoreIndices’ from incompatible pointer type
[-Wincompatible-pointer-types]
       __pyx_t_7 =
__pyx_f_9firedrake_6dmplex_CHKERR(ISRestoreIndices(__pyx_v_class_is->iset,
(&__pyx_v_indices))); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0,
981, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscvec.h:9:0,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscmat.h:6,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdm.h:6,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmda.h:4,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:13,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/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_36get_cell_remote_ranks’:
firedrake/dmplex.c:19792:122: warning: passing argument 4 of
‘PetscSFGetGraph’ from incompatible pointer type
[-Wincompatible-pointer-types]
     __pyx_t_9 =
__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_9 == ((int)-1))) __PYX_ERR(0,
1297, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument is of
type ‘PetscInt ** {aka int **}’
 PETSC_EXTERN PetscErrorCode
PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const
PetscSFNode**);
                             ^
firedrake/dmplex.c:19792:141: warning: passing argument 5 of
‘PetscSFGetGraph’ from incompatible pointer type
[-Wincompatible-pointer-types]
     __pyx_t_9 =
__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_9 == ((int)-1))) __PYX_ERR(0,
1297, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29:
note: expected ‘const PetscSFNode ** {aka const struct <anonymous> **}’ but
argument is of type ‘PetscSFNode ** {aka struct <anonymous> **}’
 PETSC_EXTERN PetscErrorCode
PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const
PetscSFNode**);
                             ^
firedrake/dmplex.c: In function
‘__pyx_f_9firedrake_6dmplex_get_edge_global_vertices’:
firedrake/dmplex.c:20058:96: 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 == ((int)-1)))
__PYX_ERR(0, 1334, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:63:29:
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:20732:97: 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 == ((int)-1)))
__PYX_ERR(0, 1437, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:71:29:
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:21213:126: 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/python3.5m/Python.h:34:0,
                 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:21369:95: 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 == ((int)-1)))
__PYX_ERR(0, 1557, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:71:29:
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:21585:94: 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 == ((int)-1)))
__PYX_ERR(0, 1621, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:63:29:
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:21666:105: 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 == ((int)-1)))
__PYX_ERR(0, 1630, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:67:29:
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_40orientations_facet2cell’:
firedrake/dmplex.c:24681:96: 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_c, (&__pyx_v_cone))); if (unlikely(__pyx_t_9 == ((int)-1)))
__PYX_ERR(0, 1998, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:63:29:
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:24690:107: warning: passing argument 3 of
‘DMPlexGetConeOrientation’ from incompatible pointer type
[-Wincompatible-pointer-types]
       __pyx_t_9 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexGetConeOrientation(__pyx_v_plex->dm,
__pyx_v_c, (&__pyx_v_cone_orient))); if (unlikely(__pyx_t_9 == ((int)-1)))
__PYX_ERR(0, 1999, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:67:29:
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:24893:100: 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_facet, (&__pyx_v_cone))); if (unlikely(__pyx_t_9 == ((int)-1)))
__PYX_ERR(0, 2055, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:16:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscdmplex.h:63:29:
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_42exchange_cell_orientations’:
firedrake/dmplex.c:25444:123: 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 == ((int)-1))) __PYX_ERR(0,
2101, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument is of
type ‘PetscInt ** {aka int **}’
 PETSC_EXTERN PetscErrorCode
PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const
PetscSFNode**);
                             ^
firedrake/dmplex.c:25444:142: 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 == ((int)-1))) __PYX_ERR(0,
2101, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29:
note: expected ‘const PetscSFNode ** {aka const struct <anonymous> **}’ but
argument is of type ‘PetscSFNode ** {aka struct <anonymous> **}’
 PETSC_EXTERN PetscErrorCode
PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const
PetscSFNode**);
                             ^
firedrake/dmplex.c: In function ‘__pyx_pf_9firedrake_6dmplex_46prune_sf’:
firedrake/dmplex.c:26190:120: 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 == ((int)-1))) __PYX_ERR(0,
2161, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29:
note: expected ‘const PetscInt ** {aka const int **}’ but argument is of
type ‘PetscInt ** {aka int **}’
 PETSC_EXTERN PetscErrorCode
PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const
PetscSFNode**);
                             ^
firedrake/dmplex.c:26190:139: 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 == ((int)-1))) __PYX_ERR(0,
2161, __pyx_L1_error)

^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:12:0,
                 from firedrake/dmplex.c:568:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsf.h:76:29:
note: expected ‘const PetscSFNode ** {aka const struct <anonymous> **}’ but
argument is of type ‘PetscSFNode ** {aka struct <anonymous> **}’
 PETSC_EXTERN PetscErrorCode
PetscSFGetGraph(PetscSF,PetscInt*,PetscInt*,const PetscInt**,const
PetscSFNode**);
                             ^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_8get_cell_nodes.isra.79’:
firedrake/dmplex.c:2282:82: warning:
‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
 #define __Pyx_BufPtrCContig2d(type, buf, i0, s0, i1, s1)
((type)((char*)buf + i0 * s0) + i1)

^
firedrake/dmplex.c:8816:21: note:
‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ was declared here
   __Pyx_LocalBuf_ND __pyx_pybuffernd_layer_extents;
                     ^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_6create_section.isra.80’:
firedrake/dmplex.c:8602:19: warning: ‘__pyx_v_ndof’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
       __pyx_t_7 =
__pyx_f_9firedrake_6dmplex_CHKERR(PetscSectionSetDof(__pyx_v_section->sec,
__pyx_v_p, __pyx_v_ndof)); if (unlikely(__pyx_t_7 == ((int)-1)))
__PYX_ERR(0, 472, __pyx_L1_error)
                   ^
firedrake/dmplex.c:2282:82: warning:
‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
 #define __Pyx_BufPtrCContig2d(type, buf, i0, s0, i1, s1)
((type)((char*)buf + i0 * s0) + i1)

^
firedrake/dmplex.c:7858:21: note:
‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ was declared here
   __Pyx_LocalBuf_ND __pyx_pybuffernd_layer_extents;
                     ^
firedrake/dmplex.c: In function
‘__pyx_f_9firedrake_6dmplex_DMPlexGetAdjacency_Facet_Support’:
firedrake/dmplex.c:27239:15: warning: ‘__pyx_v_point’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_1 =
__pyx_f_9firedrake_6dmplex_CHKERR(DMPlexRestoreTransitiveClosure(__pyx_v_dm,
__pyx_v_point, PETSC_TRUE, (&__pyx_v_closureSize), (&__pyx_v_closure))); if
(unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 2317, __pyx_L1_error)
               ^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_10get_facet_nodes.isra.78’:
firedrake/dmplex.c:2282:82: warning:
‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
 #define __Pyx_BufPtrCContig2d(type, buf, i0, s0, i1, s1)
((type)((char*)buf + i0 * s0) + i1)

^
firedrake/dmplex.c:9771:21: note:
‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ was declared here
   __Pyx_LocalBuf_ND __pyx_pybuffernd_layer_extents;
                     ^
firedrake/dmplex.c: In function
‘__pyx_pf_9firedrake_6dmplex_12boundary_nodes.isra.77’:
firedrake/dmplex.c:10809:21: warning:
‘__pyx_pybuffernd_layer_extents.diminfo[0].strides’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
   __Pyx_LocalBuf_ND __pyx_pybuffernd_layer_extents;
                     ^
firedrake/dmplex.c:10791:7: warning: ‘__pyx_v_layers’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
   int __pyx_v_layers;
       ^
firedrake/dmplex.c: In function
‘__pyx_f_9firedrake_6dmplex_traverse_cell_string’:
firedrake/dmplex.c:21821:7: warning: ‘__pyx_v_support_size’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
       for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
       ^
firedrake/dmplex.c: In function
‘__pyx_f_9firedrake_6dmplex_locally_orient_quadrilateral_plex’:
firedrake/dmplex.c:22177:12: 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_38quadrilateral_facet_orientations.isra.59’:
firedrake/dmplex.c:24163:7: warning: ‘__pyx_v_size’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
       for (__pyx_t_49 = 0; __pyx_t_49 < __pyx_t_48; __pyx_t_49+=1) {
       ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro
-g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/firedrake/dmplex.o -lpetsc
-o /home/naceur/Documents/firedrake/src/firedrake/firedrake/
dmplex.cpython-35m-x86_64-linux-gnu.so
-L/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/lib
-Wl,-rpath,/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/lib
-Wl,-rpath,/home/naceur/Documents/firedrake/lib
cythoning firedrake/extrusion_numbering.pyx to
firedrake/extrusion_numbering.c
building 'firedrake.extrusion_numbering' extension
mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fPIC
-I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include
-I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc4py/include
-I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include
-I/home/naceur/Documents/firedrake/include -I/usr/include/python3.5m -c
firedrake/extrusion_numbering.c -o
build/temp.linux-x86_64-3.5/firedrake/extrusion_numbering.o
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from firedrake/extrusion_numbering.c:567:
/home/naceur/Documents/firedrake/lib/python3.5/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/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscbag.h:4:0,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petsc.h:5,
                 from firedrake/extrusion_numbering.c:569:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include/petscsys.h:255:0:
warning: "__STDC_FORMAT_MACROS" redefined
 #define __STDC_FORMAT_MACROS /* required for using PRId64 from c++ */
 ^
In file included from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/numpyconfig.h:4:0,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/npy_common.h:5,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:4,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from firedrake/extrusion_numbering.c:567:
/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include/numpy/_numpyconfig.h:31:0:
note: this is the location of the previous definition
 #define __STDC_FORMAT_MACROS 1
 ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro
-g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2
build/temp.linux-x86_64-3.5/firedrake/extrusion_numbering.o -lpetsc -o
/home/naceur/Documents/firedrake/src/firedrake/firedrake/
extrusion_numbering.cpython-35m-x86_64-linux-gnu.so
-L/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/lib
-Wl,-rpath,/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/lib
-Wl,-rpath,/home/naceur/Documents/firedrake/lib
cythoning firedrake/hdf5interface.pyx to firedrake/hdf5interface.c
building 'firedrake.hdf5interface' extension
mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fPIC
-I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/numpy/core/include
-I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc4py/include
-I/home/naceur/Documents/firedrake/lib/python3.5/site-packages/petsc/include
-I/home/naceur/Documents/firedrake/include -I/usr/include/python3.5m -c
firedrake/hdf5interface.c -o
build/temp.linux-x86_64-3.5/firedrake/hdf5interface.o
firedrake/hdf5interface.c:565:18: fatal error: hdf5.h: Aucun fichier ou
dossier de ce type
compilation terminated.
warning: firedrake/dmplexinc.pxi:61:4: 'PetscSFNode' redeclared
warning: firedrake/dmplex.pyx:1393:4: Buffer unpacking not optimized away.
warning: firedrake/dmplex.pyx:1393:4: Buffer unpacking not optimized away.
warning: firedrake/dmplex.pyx:1785:4: Buffer unpacking not optimized away.
warning: firedrake/dmplex.pyx:1785:4: Buffer unpacking not optimized away.
warning: firedrake/dmplex.pyx:1786:4: Buffer unpacking not optimized away.
warning: firedrake/dmplex.pyx:1786:4: Buffer unpacking not optimized away.
warning: firedrake/dmplexinc.pxi:61:4: 'PetscSFNode' redeclared
error: command 'mpicc' failed with exit status 1
    Linting firedrake codebase
    Linting firedrake test suite
    Linting firedrake scripts
    Running all regression tests
============================= test session starts
==============================
platform linux -- Python 3.5.2, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
rootdir: /home/naceur/Documents/firedrake/src/firedrake, inifile: setup.cfg
collected 0 items / 1
errors

==================================== ERRORS
====================================
______________________________ ERROR collecting
_______________________________
../../lib/python3.5/site-packages/_pytest/config.py:334: in
_getconftestmodules
    return self._path2confmods[path]
E   KeyError:
local('/home/naceur/Documents/firedrake/src/firedrake/tests/extrusion')

During handling of the above exception, another exception occurred:
../../lib/python3.5/site-packages/_pytest/config.py:365: in _importconftest
    return self._conftestpath2mod[conftestpath]
E   KeyError:
local('/home/naceur/Documents/firedrake/src/firedrake/tests/extrusion/conftest.py')

During handling of the above exception, another exception occurred:
../../lib/python3.5/site-packages/_pytest/config.py:371: in _importconftest
    mod = conftestpath.pyimport()
../../lib/python3.5/site-packages/py/_path/local.py:668: in pyimport
    __import__(modname)
<frozen importlib._bootstrap>:969: in _find_and_load
    ???
<frozen importlib._bootstrap>:958: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:664: in _load_unlocked
    ???
<frozen importlib._bootstrap>:634: in _load_backward_compatible
    ???
../../lib/python3.5/site-packages/_pytest/assertion/rewrite.py:213: in
load_module
    py.builtin.exec_(co, mod.__dict__)
tests/extrusion/conftest.py:2: in <module>
    from firedrake import ExtrudedMesh, UnitSquareMesh, UnitIntervalMesh
firedrake/__init__.py:27: in <module>
    firedrake_configuration.setup_cache_dirs()
firedrake_configuration/__init__.py:46: in setup_cache_dirs
    os.environ["PYOP2_CACHE_DIR"] =
os.path.join(config["options"]["cache_dir"], "pyop2")
E   TypeError: 'NoneType' object is not subscriptable

During handling of the above exception, another exception occurred:
../../lib/python3.5/site-packages/py/_path/common.py:377: in visit
    for x in Visitor(fil, rec, ignore, bf, sort).gen(self):
../../lib/python3.5/site-packages/py/_path/common.py:418: in gen
    dirs = self.optsort([p for p in entries
../../lib/python3.5/site-packages/py/_path/common.py:419: in <listcomp>
    if p.check(dir=1) and (rec is None or rec(p))])
../../lib/python3.5/site-packages/_pytest/main.py:434: in _recurse
    ihook = self.gethookproxy(path)
../../lib/python3.5/site-packages/_pytest/main.py:338: in gethookproxy
    my_conftestmodules = pm._getconftestmodules(fspath)
../../lib/python3.5/site-packages/_pytest/config.py:348: in
_getconftestmodules
    mod = self._importconftest(conftestpath)
../../lib/python3.5/site-packages/_pytest/config.py:376: in _importconftest
    raise ConftestImportFailure(conftestpath, sys.exc_info())
E   _pytest.config.ConftestImportFailure: TypeError("'NoneType' object is
not subscriptable",)
E     File "<frozen importlib._bootstrap>", line 969, in _find_and_load
E     File "<frozen importlib._bootstrap>", line 958, in
_find_and_load_unlocked
E     File "<frozen importlib._bootstrap>", line 664, in _load_unlocked
E     File "<frozen importlib._bootstrap>", line 634, in
_load_backward_compatible
E     File
"/home/naceur/Documents/firedrake/lib/python3.5/site-packages/_pytest/assertion/rewrite.py",
line 213, in load_module
E       py.builtin.exec_(co, mod.__dict__)
E     File
"/home/naceur/Documents/firedrake/src/firedrake/tests/extrusion/conftest.py",
line 2, in <module>
E       from firedrake import ExtrudedMesh, UnitSquareMesh, UnitIntervalMesh
E     File
"/home/naceur/Documents/firedrake/src/firedrake/firedrake/__init__.py",
line 27, in <module>
E       firedrake_configuration.setup_cache_dirs()
E     File
"/home/naceur/Documents/firedrake/src/firedrake/firedrake_configuration/__init__.py",
line 46, in setup_cache_dirs
E       os.environ["PYOP2_CACHE_DIR"] =
os.path.join(config["options"]["cache_dir"], "pyop2")
!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection
!!!!!!!!!!!!!!!!!!!!
=========================== 1 error in 0.42 seconds
============================
Makefile:60 : la recette pour la cible « test » a échouée
make: *** [test] Erreur 2
(firedrake) naceur@kahina:~/Documents/firedrake/src/firedrake$

[firedrake] hello

Naceur Bouziani