[SciPy-user] umfpack and building scipy from source

Thu Nov 30 14:07:13 EST 2006

I may have had the misfortune of checking out of svn last night while
numpy and scipy were out of sync.  I re-did my svn checkout just now
and numpy didn't change, but scipy went from version 2339 to 2342.  I
now get fewer errors.  I also did a python setup.py clean for each
before rebuilding and deleted site-packages/numpy and /scipy before
rebuilding.  I am still getting an error from scipy.test that it is
built against a different version of the API (see below).  Is this
detrimental?

Thanks,

Ryan

>>> scipy.test()
RuntimeError: module compiled against version 1000002 of C-API but this version
of numpy is 1000009
RuntimeError: module compiled against version 1000002 of C-API but this version
of numpy is 1000009
RuntimeError: module compiled against version 1000002 of C-API but this version
of numpy is 1000009
RuntimeError: module compiled against version 1000002 of C-API but this version
of numpy is 1000009
RuntimeError: module compiled against version 1000002 of C-API but this version
of numpy is 1000009
RuntimeError: module compiled against version 1000002 of C-API but this version
of numpy is 1000009
RuntimeError: module compiled against version 1000002 of C-API but this version
of numpy is 1000009
RuntimeError: module compiled against version 1000002 of C-API but this version
of numpy is 1000009
Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack.umfpack' fr
om '...y\\linsolve\\umfpack\\umfpack.pyc'>
C:\Python24\Lib\site-packages\scipy\linsolve\_superlu.py:3: ImportError: numpy.c
ore.multiarray failed to import (in ?)
  Found 128 tests for scipy.linalg.fblas
  Found 397 tests for scipy.ndimage
  Found 53 tests for scipy.linalg.decomp
RuntimeError: module compiled against version 1000002 of C-API but this version
of numpy is 1000009
Warning: FAILURE importing tests for <module 'scipy.sparse.sparse' from '...ckag
es\\scipy\\sparse\\sparse.pyc'>
C:\Python24\Lib\site-packages\scipy\linsolve\_superlu.py:4: ImportError: numpy.c
ore.multiarray failed to import (in ?)
  Found 20 tests for scipy.fftpack.pseudo_diffs
Warning: FAILURE importing tests for <module 'scipy.optimize.optimize' from '...
es\\scipy\\optimize\\optimize.pyc'>
C:\Python24\Lib\site-packages\scipy\optimize\minpack.py:6: AttributeError: 'modu
le' object has no attribute 'error' (in ?)
  Found 4 tests for scipy.linalg.lapack
  Found 18 tests for scipy.fftpack.basic
Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack' from '...\
\linsolve\\umfpack\\__init__.pyc'>
C:\Python24\Lib\site-packages\scipy\linsolve\umfpack\tests\test_umfpack.py:17: A
ttributeError: 'module' object has no attribute 'umfpack' (in ?)
  Found 42 tests for scipy.lib.lapack
  Found 128 tests for scipy.lib.blas.fblas
  Found 7 tests for scipy.linalg.matfuncs
  Found 41 tests for scipy.linalg.basic
  Found 16 tests for scipy.lib.blas
  Found 14 tests for scipy.linalg.blas
  Found 95 tests for scipy.sparse
  Found 4 tests for scipy.fftpack.helper
  Found 0 tests for __main__
...caxpy:n=4
..caxpy:n=3
....ccopy:n=4
..ccopy:n=3
.............cscal:n=4
....cswap:n=4
..cswap:n=3
.....daxpy:n=4
..daxpy:n=3
....dcopy:n=4
..dcopy:n=3
.............dscal:n=4
....dswap:n=4
..dswap:n=3
.....saxpy:n=4
..saxpy:n=3
....scopy:n=4
..scopy:n=3
.............sscal:n=4
....sswap:n=4
..sswap:n=3
.....zaxpy:n=4
..zaxpy:n=3
....zcopy:n=4
..zcopy:n=3
.............zscal:n=4
....zswap:n=4
..zswap:n=3
................................................................................
................................................................................
................................................................................
................................................................................
................................................................................
................................................................................
...........................................................caxpy:n=4
..caxpy:n=3
....ccopy:n=4
..ccopy:n=3
.............cscal:n=4
....cswap:n=4
..cswap:n=3
.....daxpy:n=4
..daxpy:n=3
....dcopy:n=4
..dcopy:n=3
.............dscal:n=4
....dswap:n=4
..dswap:n=3
.....saxpy:n=4
..saxpy:n=3
....scopy:n=4
..scopy:n=3
.............sscal:n=4
....sswap:n=4
..sswap:n=3
.....zaxpy:n=4
..zaxpy:n=3
....zcopy:n=4
..zcopy:n=3
.............zscal:n=4
....zswap:n=4
..zswap:n=3
...Result may be inaccurate, approximate err = 5.69043366261e-009
...Result may be inaccurate, approximate err = 1.39218513881e-010
................................................................................
..Resizing... 16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
.....Use minimum degree ordering on A'+A.
........................Use minimum degree ordering on A'+A.
...................Resizing... 16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
.....Use minimum degree ordering on A'+A.
.................Resizing... 16 17 24
Resizing... 20 7 35
Resizing... 23 7 47
Resizing... 24 25 58
Resizing... 28 7 68
Resizing... 28 27 73
.....Use minimum degree ordering on A'+A.
................
----------------------------------------------------------------------
Ran 967 tests in 2.422s

OK
<unittest.TextTestRunner object at 0x00FFBFD0>
>>>

On 11/30/06, Robert Cimrman <cimrman3 at ntc.zcu.cz> wrote:
> Ryan Krauss wrote:
> > I am trying to build scipy/numpy from source on Windows XP.  I do not
> > have umfpack installed.  When I build scipy I get this warning:
> >
> > C:\Python24\lib\site-packages\numpy\distutils\system_info.py:401: UserWarning:
> >     UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/)
> >     not found. Directories to search for the libraries can be specified in the
> >     numpy/distutils/site.cfg file (section [umfpack]) or by setting
> >     the UMFPACK environment variable.
> >   warnings.warn(self.notfounderror.__doc__)
> >
> > numpy.test() runs without problems.  The output of scipy.test() is
> > slightly scary:
> >
> > scipy.test()
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> >   Found 397 tests for scipy.ndimage
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > Warning: FAILURE importing tests for <module 'scipy.sparse.sparse'
> > from '...ckages\\scipy\\sparse\\sparse.pyc'>
> > C:\Python24\Lib\site-packages\scipy\linsolve\_superlu.py:2:
> > ImportError: numpy.core.multiarray failed to import (in ?)
> > Warning: FAILURE importing tests for <module 'scipy.optimize.optimize'
> > from '...es\\scipy\\optimize\\optimize.pyc'>
> > C:\Python24\Lib\site-packages\scipy\optimize\minpack.py:6:
> > AttributeError: 'module' object has no attribute 'error' (in ?)
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > Warning: FAILURE importing tests for <module
> > 'scipy.linsolve.umfpack.umfpack' from
> > '...y\\linsolve\\umfpack\\umfpack.pyc'>
> > C:\Python24\Lib\site-packages\scipy\linsolve\_superlu.py:3:
> > ImportError: numpy.core.multiarray failed to import (in ?)
> > RuntimeError: module compiled against version 1000002 of C-API but
> > this version of numpy is 1000009
> > Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack'
> > from '...\\linsolve\\umfpack\\__init__.pyc'>
> > C:\Python24\Lib\site-packages\scipy\linsolve\_superlu.py:4:
> > ImportError: numpy.core.multiarray failed to import (in ?)
> >   Found 95 tests for scipy.sparse
> >   Found 0 tests for __main__
> > .............................................................................................................................................................................................................................................................................................................................................................................................................EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE...E.EE.......EEE..EE.EE.E.EEEEEEEE.EEE.E.E.E
> > ======================================================================
> > ERROR: check_eye (scipy.tests.test_sparse.test_construct_utils)
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "C:\Python24\Lib\site-packages\scipy\sparse\tests\test_sparse.py",
> > line 626, in check_eye
> >     a = speye(2, 3 )
> >   File "C:\Python24\Lib\site-packages\scipy\sparse\sparse.py", line
> > 2833, in speye
> >     return spdiags(diags, k, n, m)
> >   File "C:\Python24\Lib\site-packages\scipy\sparse\sparse.py", line
> > 2811, in spdiags
> >     diagfunc = eval('sparsetools.'+_transtabl[mtype]+'diatocsc')
> >   File "<string>", line 0, in ?
> > AttributeError: 'module' object has no attribute 'ddiatocsc'
> >
>  > ....
> >
> > What have I done wrong?  I did not try to build Atlas/Blas/Lapack from
> > source but just down loaded the precomipled versions into
> > C:\BlasLapackLibs.  My scipy and numpy svn folders are not on my PATH
> > or my PYTHONPATH.  I had some trouble getting numpy's setup.py to find
> > the atlas, lapack, blas libs until I set an ATLAS environment
> > variable.
>
> Ryan,
>
> it seems you try to run scipy with different version of numpy than it
> was compiled with. did you try removing existing installation and
> rebuilding all sources?
>
> Anyway missing umfpack would not cause all those errors.
>
> > Oh, and the example site.cfg mentions libamd.a as well as umfpack.  Do
> > I need the amd lib?  I am running an amd processor under windows
> > (Athlon X2).
>
> libamd.a has nothing to do with the amd processors - it it a library (a
> part of umfpack-related package) for ordering a sparse matrix prior to
> Cholesky factorization (http://www.cise.ufl.edu/research/sparse/amd/)
> and you do not need it if you do not use umfpack.
>
> r.
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