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