[SciPy-dev] All but two tests passing for me

Arnd Baecker arnd.baecker at web.de
Fri Oct 28 03:29:45 CDT 2005


umpf - pressed send to early ....

Hi Travis

On Thu, 27 Oct 2005, Travis Oliphant wrote:

> Travis Oliphant wrote:
>
> >After a fix to PyArray_Correlate all but two tests are passing for me on
> >a 32-bit platform.
> >
> >
> >
> Now all tests are passing.
>
> I'm sure issues will still be resolved.  But, I'm so pleased, I just had
> to show everybody :-)
>
> ----------------------------------------------------------------------
> Ran 1127 tests in 85.453s
>
> OK
> <unittest.TextTestRunner object at 0x43807fec>
>
> Thanks for all who are helping in the bug-fixing and conversion process.

That is good news!!

I don't want to spoil your party, but I think I have to ;-)

In [3]: scipy.__core_version__
Out[3]: '0.4.3.1371'
In [4]: scipy.__scipy_version__
Out[4]: '0.4.2_1393'

scipy.test(10,verbosity=10)

gives on the opteron


======================================================================
ERROR: check_integer
(scipy.io.array_import.test_array_import.test_read_array)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/io/tests/test_array_import.py",
line 62, in check_integer
    b = io.read_array(fname,atype=N.Int)
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/io/array_import.py",
line 359, in read_array
    raise ValueError, "One of the array types is invalid, k=%d" % k
ValueError: One of the array types is invalid, k=0


This is might be caused by:

compile options:
'-I/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/base/include
-I/scr/python/include/python2.4 -c'
gcc: Lib/io/numpyiomodule.c
Lib/io/numpyiomodule.c: In function `numpyio_tofile':
Lib/io/numpyiomodule.c:282: warning: passing arg 1 of pointer to function
from incompatible pointer type
Lib/io/numpyiomodule.c: In function `numpyio_convert_objects':
Lib/io/numpyiomodule.c:743: warning: passing arg 2 of pointer to function
from incompatible pointer type
gcc -pthread -shared build/temp.linux-x86_64-2.4/Lib/io/numpyiomodule.o
-Lbuild/temp.linux-x86_64-2.4 -o
build/lib.linux-x86_64-2.4/scipy/io/numpyio.so
building 'scipy.fftpack._fftpack' extension
compiling C sources



======================================================================
ERROR: check_simple_sym (scipy.linalg.basic.test_basic.test_solve)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/linalg/tests/test_basic.py",
line 80, in check_simple_sym
    x = solve(a,b,sym_pos=1,lower=lower)
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/linalg/basic.py",
line 127, in solve
    raise LinAlgError, "singular matrix"
LinAlgError: singular matrix

======================================================================
FAIL: check_simple (scipy.linalg.decomp.test_decomp.test_cholesky)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/linalg/tests/test_decomp.py",
line 261, in check_simple
    assert_array_almost_equal(dot(transpose(c),c),a)
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [[-1885965976648932823  7796773222197633577
-761725725645001531]
 [ 7796773222197633577 -6619736815450336083  789149371...
        Array 2: [[8 2 3]
 [2 9 3]
 [3 3 6]]


======================================================================
FAIL: check_matvec (scipy.sparse.sparse.test_sparse.test_csc)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/sparse/tests/test_sparse.py",
line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]

======================================================================
FAIL: check_matvec (scipy.sparse.sparse.test_sparse.test_csr)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/sparse/tests/test_sparse.py",
line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]


======================================================================
FAIL: check_matvec (scipy.sparse.sparse.test_sparse.test_dok)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/sparse/tests/test_sparse.py",
line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]


======================================================================
FAIL: check_simple (scipy.linalg.basic.test_basic.test_det)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/linalg/tests/test_basic.py",
line 273, in check_simple
    assert_almost_equal(a_det,-2.0)
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 649, in assert_almost_equal
    assert round(abs(desired - actual),decimal) == 0, msg
AssertionError:
Items are not equal:
DESIRED: -2.0
ACTUAL: -0.0

======================================================================
FAIL: check_simple (scipy.linalg.basic.test_basic.test_inv)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/linalg/tests/test_basic.py",
line 202, in check_simple
    [[1,0],[0,1]])
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [[9216616637413720064   -4503599627370496]
 [9207609438158979072   -9007199254740992]]
        Array 2: [[1 0]
 [0 1]]


======================================================================
FAIL: check_simple_exact (scipy.linalg.basic.test_basic.test_lstsq)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/linalg/tests/test_basic.py",
line 356, in check_simple_exact
    assert_array_almost_equal(Numeric.matrixmultiply(a,x),b)
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 50.0%):
        Array 1: [0 0]
        Array 2: [1 0]


======================================================================
FAIL: check_simple_overdet (scipy.linalg.basic.test_basic.test_lstsq)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/linalg/tests/test_basic.py",
line 363, in check_simple_overdet
    assert_array_almost_equal(x,direct_lstsq(a,b))
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [-9223372036854775808                    1]
        Array 2: [-0.4285714  0.8571429]


======================================================================
FAIL: check_simple (scipy.linalg.basic.test_basic.test_solve)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/linalg/tests/test_basic.py",
line 74, in check_simple
    assert_array_almost_equal(Numeric.matrixmultiply(a,x),b)
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [[       nan        nan]
 [       nan        nan]]
        Array 2: [[1 0]
 [0 1]]

======================================================================
FAIL: check_matvec (scipy.sparse.test_sparse.test_csc)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/sparse/tests/test_sparse.py",
line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]


======================================================================
FAIL: check_matvec (scipy.sparse.test_sparse.test_csr)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/sparse/tests/test_sparse.py",
line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]


======================================================================
FAIL: check_matvec (scipy.sparse.test_sparse.test_dok)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/sparse/tests/test_sparse.py",
line 66, in check_matvec
    assert_array_almost_equal([1,2,3,4]*b,dot([1,2,3,4],b.todense()))
  File
"/home/abaecker/BUILDS2/Build_52//inst_scipy_newcore/lib/python2.4/site-packages/scipy/test/testing.py",
line 727, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [  8.3991160e-323   6.9169190e-323   4.4465908e-323]
        Array 2: [ 17.  14.   9.]


----------------------------------------------------------------------
Ran 1124 tests in 45.943s

FAILED (failures=12, errors=2)

==========================================================
==========================================================

Further pointer problems:
  cat build_log |  grep -A 5 -B 5 "incompatible pointer"

                 from Lib/signal/sigtoolsmodule.c:9:
/scr/python/include/python2.4/pyconfig.h:835:1: warning: "_POSIX_C_SOURCE"
redefined
In file included from /usr/include/setjmp.h:26,
                 from Lib/signal/sigtoolsmodule.c:8:
/usr/include/features.h:190:1: warning: this is the location of the
previous definition
Lib/signal/sigtoolsmodule.c:1610: warning: initialization from
incompatible pointer type
Lib/signal/sigtoolsmodule.c:1610: warning: initialization from
incompatible pointer type
Lib/signal/sigtoolsmodule.c:1610: warning: initialization from
incompatible pointer type
Lib/signal/sigtoolsmodule.c:1610: warning: initialization from
incompatible pointer type
Lib/signal/sigtoolsmodule.c: In function `sigtools_convolve2d':
Lib/signal/sigtoolsmodule.c:1763: warning: passing arg 2 of pointer to
function from incompatible pointer type
Lib/signal/sigtoolsmodule.c:1773: warning: passing arg 2 of pointer to
function from incompatible pointer type
Lib/signal/sigtoolsmodule.c: In function `sigtools_median2d':
Lib/signal/sigtoolsmodule.c:2140: warning: passing arg 3 of `b_medfilt2'
from incompatible pointer type
Lib/signal/sigtoolsmodule.c:2143: warning: passing arg 3 of `f_medfilt2'
from incompatible pointer type
Lib/signal/sigtoolsmodule.c:2146: warning: passing arg 3 of `d_medfilt2'
from incompatible pointer type
gcc: Lib/signal/medianfilter.c
gcc: Lib/signal/firfilter.c
gcc -pthread -shared
build/temp.linux-x86_64-2.4/Lib/signal/sigtoolsmodule.o
build/temp.linux-x86_64-2.4/Lib/signal/firfilter.o
build/temp.linux-x86_64-2.4/Lib/signal/medianfilter.o
-Lbuild/temp.linux-x86_64-2.4 -o
build/lib.linux-x86_64-2.4/scipy/signal/sigtools.so
building 'scipy.signal.spline' extension
compiling C sources
gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
-Wstrict-prototypes -fPIC'
compile options:
'-I/home/abaecker/BUILDS2/Build_52/inst_scipy_newcore/lib/python2.4/site-packages/scipy/base/include
-I/scr/python/include/python2.4 -c'
gcc: Lib/signal/Z_bspline_util.c
gcc: Lib/signal/splinemodule.c
Lib/signal/splinemodule.c: In function `cspline2d':
Lib/signal/splinemodule.c:84: warning: passing arg 2 of pointer to
function from incompatible pointer type
Lib/signal/splinemodule.c:89: warning: passing arg 1 of `convert_strides'
from incompatible pointer type
Lib/signal/splinemodule.c: In function `qspline2d':
Lib/signal/splinemodule.c:143: warning: passing arg 2 of pointer to
function from incompatible pointer type
Lib/signal/splinemodule.c:148: warning: passing arg 1 of `convert_strides'
from incompatible pointer type
Lib/signal/splinemodule.c: In function `FIRsepsym2d':
Lib/signal/splinemodule.c:200: warning: passing arg 2 of pointer to
function from incompatible pointer type
Lib/signal/splinemodule.c:205: warning: passing arg 1 of `convert_strides'
from incompatible pointer type
Lib/signal/splinemodule.c: In function `IIRsymorder1':
Lib/signal/splinemodule.c:308: warning: passing arg 2 of pointer to
function from incompatible pointer type
Lib/signal/splinemodule.c:312: warning: passing arg 1 of `convert_strides'
from incompatible pointer type
Lib/signal/splinemodule.c: In function `IIRsymorder2':
Lib/signal/splinemodule.c:428: warning: passing arg 2 of pointer to
function from incompatible pointer type
Lib/signal/splinemodule.c:432: warning: passing arg 1 of `convert_strides'
from incompatible pointer type
gcc: Lib/signal/S_bspline_util.c
gcc: Lib/signal/D_bspline_util.c
gcc: Lib/signal/bspline_util.c
gcc: Lib/signal/C_bspline_util.c
gcc -pthread -shared build/temp.linux-x86_64-2.4/Lib/signal/splinemodule.o
build/temp.linux-x86_64-2.4/Lib/signal/S_bspline_util.o
build/temp.linux-x86_64-2.4/Lib/signal/D_bspline_util.o
build/temp.linux-x86_64-2.4/Lib/signal/C_bspline_util.o
build/temp.linux-x86_64-2.4/Lib/signal/Z_bspline_util.o
build/temp.linux-x86_64-2.4/Lib/signal/bspline_util.o
-Lbuild/temp.linux-x86_64-2.4 -o
build/lib.linux-x86_64-2.4/scipy/signal/spline.so

I am completely swamped at the moment, so I won't have time
today to track any of these - maybe much later today.

Best, Arnd

P.S.:

gcc -v
Reading specs from
/scr/python/bin/../lib/gcc/x86_64-unknown-linux-gnu/3.4.4/specs
Configured with: ../gcc-3.4.4/configure --prefix=/scr/python/
--enable-shared --enable-threads=posix --enable-__cxa_atexit
--enable-clocale=gnu --enable-languages=c,c++,f77,objc
Thread model: posix
gcc version 3.4.4

python -V
Python 2.4.2


In [2]: scipy.__core_config__.show()
atlas_threads_info:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/scr/python/lib64']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')]
    include_dirs = ['/scr/python/include']

blas_opt_info:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/scr/python/lib64']
    define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')]
    language = c
    include_dirs = ['/scr/python/include']

atlas_blas_threads_info:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/scr/python/lib64']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')]
    include_dirs = ['/scr/python/include']

lapack_opt_info:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/scr/python/lib64']
    define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')]
    language = f77
    include_dirs = ['/scr/python/include']

In [3]: scipy.__scipy_config__.show()
lapack_opt_info:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/scr/python/lib64']
    define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')]
    language = f77
    include_dirs = ['/scr/python/include']

blas_opt_info:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/scr/python/lib64']
    define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')]
    language = c
    include_dirs = ['/scr/python/include']

atlas_blas_threads_info:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/scr/python/lib64']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')]
    include_dirs = ['/scr/python/include']

djbfft_info:
  NOT AVAILABLE

fftw_info:
    libraries = ['rfftw', 'fftw']
    library_dirs = ['/scr/python/lib']
    define_macros = [('SCIPY_FFTW_H', None)]
    include_dirs = ['/scr/python/include']

atlas_threads_info:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/scr/python/lib64']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.7.11\\""')]
    include_dirs = ['/scr/python/include']





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