[firedrake] petsc4py installation on ARCHER: directory lib/petsc-conf not found

Tue Jan 27 13:21:12 GMT 2015

Dear firedrakers,

I'm trying to update my firedrake installation on ARCHER, and I came 
across an issue with petsc4py.

I'm using the dmplex-1d-refinement branch of PETSc (latest version from 
mapdes), which I can build without problems. When I then try to install 
petsc4py (branch firedrake, also from mapdes) I get:

eike at eslogin006 $ python setup.py install --prefix=`pwd`/$PETSC_ARCH
running install
running build
running build_src
running build_py
running build_ext
error: 
/work/n02/n02/eike/git_workspace/petsc/cray-gnu-shared/lib/petsc-conf/variables: 
No such file or directory

This directory is not created during the PETSc installation, so it's odd 
that petsc4py is looking for it.

There seem to have been some recent changes to the configuration, see 
e.g. here:

commit 76e91a3c243d089c5102cc8e68a0881b5d48a885
Author: Barry Smith <bsmith at mcs.anl.gov>
Date:   Tue Jan 13 10:11:20 2015 -0600

     location of PETSc configuration files was changed to
     lib/petsc-conf from the previous directory conf

I rolled back to petsc4py commit 
99a07fb395949e1c03fb0af8954d784f5c3b18fe, but if I try to build then I 
get the error message below.

I suspect that the dmplex-1d-refinement PETSc branch is missing the 
relevant changes in the master? Should I use a different PETSc branch?

Thanks a lot,

Eike

eike at eslogin006 $ git log -1
commit 99a07fb395949e1c03fb0af8954d784f5c3b18fe
Merge: bcfcbe4 02ee487
Author: Lisandro Dalcin <dalcinl at gmail.com>
Date:   Tue Jan 13 17:46:49 2015 +0300

     Merge branch 'maint'

eike at eslogin006 $ python setup.py install --prefix=`pwd`/$PETSC_ARCH
running install
running build
running build_src
running build_py
running build_ext
PETSC_DIR:   /work/n02/n02/eike/git_workspace/petsc
PETSC_ARCH:  cray-gnu-shared
version:     3.5.2 development
scalar-type: real
precision:   double
language:    CONLY
compiler:    cc
linker:      cc
building 'PETSc' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/cray-gnu-shared
creating build/temp.linux-x86_64-2.7/cray-gnu-shared/src
cc -pthread -fPIC -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv 
-O3 -Wall -DPETSC_DIR=/work/n02/n02/eike/git_workspace/petsc 
-I/fs2/n02/n02/eike/git_workspace/petsc/cray-gnu-shared/include 
-I/work/n02/n02/eike/git_workspace/petsc/cray-gnu-shared/include 
-I/work/n02/n02/eike/git_workspace/petsc/include -Isrc/include 
-I/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include 
-I/work/y07/y07/cse/anaconda/1.9.2/include/python2.7 -c src/PETSc.c -o 
build/temp.linux-x86_64-2.7/cray-gnu-shared/src/PETSc.o
In file included from 
/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760:0,
                  from 
/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                  from 
/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                  from src/include/petsc4py/numpy.h:11,
                  from src/petsc4py.PETSc.c:240,
                  from src/PETSc.c:3:
/work/y07/y07/cse/anaconda/1.9.2/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_4SNES_56hasNPC':
src/petsc4py.PETSc.c:150802:3: warning: implicit declaration of function 
'SNESHasNPC' [-Wimplicit-function-declaration]
    __pyx_t_1 = 
__pyx_f_8petsc4py_5PETSc_CHKERR(SNESHasNPC(__pyx_v_self->snes, 
(&__pyx_v_has_npc))); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = 
__pyx_f[35]; __pyx_lineno = 238; __pyx_clineno = __LINE__; goto 
__pyx_L1_error;}
    ^
src/petsc4py.PETSc.c: In function 
'__pyx_pf_8petsc4py_5PETSc_4SNES_188getCompositeNumber':
src/petsc4py.PETSc.c:159512:3: warning: implicit declaration of function 
'SNESCompositeGetNumber' [-Wimplicit-function-declaration]
    __pyx_t_1 = 
__pyx_f_8petsc4py_5PETSc_CHKERR(SNESCompositeGetNumber(__pyx_v_self->snes, 
(&__pyx_v_cn))); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = 
__pyx_f[35]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto 
__pyx_L1_error;}
    ^
src/petsc4py.PETSc.c: In function 
'__pyx_pf_8petsc4py_5PETSc_6DMPlex_120distributeOverlap':
src/petsc4py.PETSc.c:211458:47: warning: passing argument 3 of 
'DMPlexDistributeOverlap' from incompatible pointer type
    __pyx_t_3 = 
__pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistributeOverlap(__pyx_v_self->__pyx_base.dm, 
__pyx_v_coverlap, (&__pyx_v_sf->sf), (&__pyx_v_dmOverlap))); if 
(unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[41]; __pyx_lineno 
= 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                ^
In file included from 
/work/n02/n02/eike/git_workspace/petsc/include/petsc.h:16:0,
                  from src/petsc4py.PETSc.c:236,
                  from src/PETSc.c:3:
/work/n02/n02/eike/git_workspace/petsc/include/petscdmplex.h:186:29: 
note: expected 'ISLocalToGlobalMapping' but argument is of type 'struct 
_p_PetscSF **'
  PETSC_EXTERN PetscErrorCode DMPlexDistributeOverlap(DM, PetscInt, 
ISLocalToGlobalMapping, PetscSF *, DM *);
                              ^
In file included from src/PETSc.c:3:0:
src/petsc4py.PETSc.c:211458:47: warning: passing argument 4 of 
'DMPlexDistributeOverlap' from incompatible pointer type
    __pyx_t_3 = 
__pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistributeOverlap(__pyx_v_self->__pyx_base.dm, 
__pyx_v_coverlap, (&__pyx_v_sf->sf), (&__pyx_v_dmOverlap))); if 
(unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[41]; __pyx_lineno 
= 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                ^
In file included from 
/work/n02/n02/eike/git_workspace/petsc/include/petsc.h:16:0,
                  from src/petsc4py.PETSc.c:236,
                  from src/PETSc.c:3:
/work/n02/n02/eike/git_workspace/petsc/include/petscdmplex.h:186:29: 
note: expected 'struct _p_PetscSF **' but argument is of type 'struct 
_p_DM **'
  PETSC_EXTERN PetscErrorCode DMPlexDistributeOverlap(DM, PetscInt, 
ISLocalToGlobalMapping, PetscSF *, DM *);
                              ^
In file included from src/PETSc.c:3:0:
src/petsc4py.PETSc.c:211458:47: error: too few arguments to function 
'DMPlexDistributeOverlap'
    __pyx_t_3 = 
__pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistributeOverlap(__pyx_v_self->__pyx_base.dm, 
__pyx_v_coverlap, (&__pyx_v_sf->sf), (&__pyx_v_dmOverlap))); if 
(unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[41]; __pyx_lineno 
= 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                ^
In file included from 
/work/n02/n02/eike/git_workspace/petsc/include/petsc.h:16:0,
                  from src/petsc4py.PETSc.c:236,
                  from src/PETSc.c:3:
/work/n02/n02/eike/git_workspace/petsc/include/petscdmplex.h:186:29: 
note: declared here
  PETSC_EXTERN PetscErrorCode DMPlexDistributeOverlap(DM, PetscInt, 
ISLocalToGlobalMapping, PetscSF *, DM *);
                              ^
error: command 'cc' failed with exit status 1