[firedrake] problem with scripts/firedrake-clean

[Florian Rathgeber]

On 13/11/14 15:47, Eike Mueller wrote:
> Dear firedrakers,
> 
> I get a strange error message when I run ./scripts/firedrake-clean
> (branch multigrid-parallel, just pulled from remote):
> 
> eikemueller at 138-38-169-12 $ ./scripts/firedrake-clean 
> Traceback (most recent call last):
>   File "./scripts/firedrake-clean", line 3, in <module>
>     from firedrake.ffc_interface import clear_cache, FFCKernel
>   File
> "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/__init__.py",
> line 2, in <module>
>     import petsc
>   File
> "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/petsc.py",
> line 4, in <module>
>     petsc4py.init(sys.argv)
>   File
> "/Users/eikemueller/PostDocBath/EllipticSolvers/petsc4py/arch-darwin-c-opt/lib/python2.7/site-packages/petsc4py/__init__.py",
> line 42, in init
>     PETSc = petsc4py.lib.ImportPETSc(arch)
>   File
> "/Users/eikemueller/PostDocBath/EllipticSolvers/petsc4py/arch-darwin-c-opt/lib/python2.7/site-packages/petsc4py/lib/__init__.py",
> line 29, in ImportPETSc
>     return Import('petsc4py', 'PETSc', path, arch)
>   File
> "/Users/eikemueller/PostDocBath/EllipticSolvers/petsc4py/arch-darwin-c-opt/lib/python2.7/site-packages/petsc4py/lib/__init__.py",
> line 64, in Import
>     module = imp.load_module(fullname, fo, fn, stuff)
>   File "PETSc.pyx", line 100, in init petsc4py.PETSc
> (src/petsc4py.PETSc.c:221273)
> RuntimeError: module compiled against API version 9 but this version of
> numpy is 7

This means that at some point you have built NumPy 1.9 as a dependency
for either PyOP2, Firedrake or petsc4py and the built petsc4py against
NumPy 1.9. However now you seem to be using the system NumPy 1.7.

Remove NumPy 1.9 and rebuild petsc4py.

> This is odd, because I just recompiled petsc4py (git pull; make clean;
> python setup.py install --prefix=`pwd`/$PETSC_ARCH). I did, however, get
> the following during petsc4py building:
> 
> In file included from
> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760:0,
>                  from
> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
>                  from
> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
>                  from src/include/petsc4py/numpy.h:11,
>                  from src/petsc4py.PETSc.c:347,
>                  from src/PETSc.c:3:
> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/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 " \
> 
> Also, I can build and use firedrake without any problems.

You can safely ignore that warning, it's only a deprecation warning.

Florian

> Thanks,
> 
> Eike

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