[SciPy-dev] All but two tests passing for me
Arnd Baecker
arnd.baecker at web.de
Fri Oct 28 04:29:45 EDT 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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