[SciPy-user] Partial success (was: numpy-1.0rc2 still does not build on MacOS X)

Tom Bridgman cygnusx1 at mac.com
Wed Oct 18 19:58:29 CDT 2006


Okay, I tried using gfortran instead of g77 for the Tiger PPC build  
(make sure /usr/bin/g77 is gone because scipy will try to use it if  
there).

A number of scipy tests fail, some apparently in some more important  
modules:

'cblas module is empty'
FAIL: check_rvs (scipy.stats.tests.test_distributions.test_randint)
FAIL: check loadmat case vec
FAIL: check_dot (scipy.lib.tests.test_blas.test_fblas1_simple)
FAIL: check_dot (scipy.linalg.tests.test_blas.test_fblas1_simple)

I'm concerned about some of these failures.

Suggestions?

Thanks,
Tom

Here's my general build instructions and scipy test output:


> gFortran
> % gunzip gfortran-bin.tar.gz
> % sudo tar -xvf gfortran-bin.tar -C /
>
> FFTW Libraries
> % sudo gcc_select 4.0
> % gnutar xzf fftw-3.1.2.tar.gz
> % cd fftw-3.1.2
> % ./configure
> % make
> % sudo make install
> % sudo ln -s /usr/local/lib/libfftw3.a /usr/local/lib/libfftw.a
> % sudo ln -s /usr/local/lib/libfftw3.la /usr/local/lib/libfftw.la
> % sudo ln -s /usr/local/include/fftw3.h /usr/local/include/fftw.h
>
> numpy
> % gnutar xzf numpy-1.0rc2.tar.gz
> % cd numpy-1.0rc2
> % sudo python setup.py install
> % python
> >>> import numpy
> >>> numpy.test(1,1)
> (ALL PASSED)
>
> % gnutar xzf scipy-0.5.1.tar.gz
> % cd scipy-0.5.1
> % sudo ln -s /usr/lib/gcc/powerpc-apple-darwin8/4.0.1/libgcc.a /usr/ 
> local/lib/libcc_dynamic.a
> % python setup.py build
> % sudo python setup.py install
> % python
> >>> import scipy
> >>> scipy.test(level=2)

Here the result of the test run

 >>> scipy.test(level=2)
   Found 4 tests for scipy.io.array_import
   Found 128 tests for scipy.linalg.fblas
   Found 397 tests for scipy.ndimage
   Found 10 tests for scipy.integrate.quadpack
   Found 97 tests for scipy.stats.stats
   Found 47 tests for scipy.linalg.decomp
   Found 2 tests for scipy.integrate.quadrature
   Found 95 tests for scipy.sparse.sparse
   Found 20 tests for scipy.fftpack.pseudo_diffs
   Found 6 tests for scipy.optimize.optimize
   Found 5 tests for scipy.interpolate.fitpack
   Found 1 tests for scipy.interpolate
   Found 70 tests for scipy.stats.distributions
   Found 12 tests for scipy.io.mmio
   Found 10 tests for scipy.stats.morestats
   Found 4 tests for scipy.linalg.lapack
   Found 18 tests for scipy.fftpack.basic
   Found 4 tests for scipy.linsolve.umfpack
   Found 4 tests for scipy.optimize.zeros
   Found 17 tests for scipy.io.mio
   Found 41 tests for scipy.linalg.basic
   Found 2 tests for scipy.maxentropy.maxentropy
   Found 358 tests for scipy.special.basic
   Found 128 tests for scipy.lib.blas.fblas
   Found 7 tests for scipy.linalg.matfuncs

****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
   then scipy uses flapack instead of clapack.
****************************************************************

   Found 42 tests for scipy.lib.lapack
   Found 1 tests for scipy.optimize.cobyla
   Found 16 tests for scipy.lib.blas
   Found 1 tests for scipy.integrate
   Found 14 tests for scipy.linalg.blas
   Found 4 tests for scipy.fftpack.helper
   Found 4 tests for scipy.signal.signaltools
   Found 0 tests for __main__

Don't worry about a warning regarding the number of bytes read.
Warning: 1000000 bytes requested, 20 bytes read.
.......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
........................................................................ 
........................................................................ 
........................................................................ 
........................................................................ 
........................................................................ 
........................................................................ 
........................................................................ 
.................................................Took 13 points.
..........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.
....................................../Library/Frameworks/ 
Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/ 
interpolate/fitpack2.py:410: UserWarning:
The coefficients of the spline returned have been computed as the
minimal norm least-squares solution of a (numerically) rank deficient
system (deficiency=7). If deficiency is large, the results may be
inaccurate. Deficiency may strongly depend on the value of eps.
   warnings.warn(message)
..................................................................F..... 
..................Ties preclude use of exact statistic.
..Ties preclude use of exact statistic.
........
****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
   then scipy uses flapack instead of clapack.
****************************************************************

....................data-ftype: z compared to data D
Calling _superlu.zgssv
Use minimum degree ordering on A'+A.
.data-ftype: c compared to data F
Calling _superlu.cgssv
Use minimum degree ordering on A'+A.
.data-ftype: d compared to data d
Calling _superlu.dgssv
Use minimum degree ordering on A'+A.
.data-ftype: s compared to data f
Calling _superlu.sgssv
Use minimum degree ordering on A'+A.
.......E.............Warning: 184549376 bytes requested, 73 bytes read.
F....................................................................... 
........................................................................ 
........................................................................ 
........................................................................ 
........................................................................ 
.............................................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 = 1.6582899877e-08
...Result may be inaccurate, approximate err = 4.54747350886e-13
......................................................F.......Residual:  
1.05006926991e-07
.
****************************************************************
WARNING: cblas module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
   then scipy uses fblas instead of cblas.
****************************************************************

.......F..............
======================================================================
ERROR: check loadmat case cellnest
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/io/tests/test_mio.py", line 80, in cc
     self._check_case(name, expected)
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/io/tests/test_mio.py", line 75, in  
_check_case
     self._check_level(k_label, expected, matdict[k])
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/io/tests/test_mio.py", line 33, in  
_check_level
     self._check_level(level_label, ev, actual[i])
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/io/tests/test_mio.py", line 33, in  
_check_level
     self._check_level(level_label, ev, actual[i])
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/io/tests/test_mio.py", line 33, in  
_check_level
     self._check_level(level_label, ev, actual[i])
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/io/tests/test_mio.py", line 30, in  
_check_level
     assert len(expected) == len(actual), "Different list lengths at % 
s" % label
TypeError: len() of unsized object

======================================================================
FAIL: check_rvs (scipy.stats.tests.test_distributions.test_randint)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/stats/tests/test_distributions.py",  
line 84, in check_rvs
     assert isinstance(val, numpy.ScalarType),`type(val)`
AssertionError: <type 'numpy.ndarray'>

======================================================================
FAIL: check loadmat case vec
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/io/tests/test_mio.py", line 80, in cc
     self._check_case(name, expected)
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/io/tests/test_mio.py", line 74, in  
_check_case
     assert k in matdict, "Missing key at %s" % k_label
AssertionError: Missing key at Test 'vec', file:/Library/Frameworks/ 
Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/io/ 
tests/./data/testvec_4_GLNX86.mat, variable fit_params

======================================================================
FAIL: check_dot (scipy.lib.tests.test_blas.test_fblas1_simple)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/lib/blas/tests/test_blas.py", line 76,  
in check_dot
     assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/numpy/testing/utils.py", line 156, in  
assert_almost_equal
     assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
ACTUAL: (-1.9988694190979004+6.3421880632634224e-37j)
DESIRED: (-9+2j)

======================================================================
FAIL: check_dot (scipy.linalg.tests.test_blas.test_fblas1_simple)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/scipy/linalg/tests/test_blas.py", line 75, in  
check_dot
     assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j)
   File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages/numpy/testing/utils.py", line 156, in  
assert_almost_equal
     assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
ACTUAL: (-1.9988694190979004+6.3421880632634224e-37j)
DESIRED: (-9+2j)

----------------------------------------------------------------------
Ran 1569 tests in 10.511s

FAILED (failures=4, errors=1)
<unittest.TextTestRunner object at 0x2db4f70>
 >>>



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