[SciPy-User] ANN: SciPy 0.10.1 release candidate 1
Scott Lasley
slasley at space.umd.edu
Mon Feb 13 10:26:38 EST 2012
Thanks for the help. /usr/bin/gcc -> llvm-gcc-4.2 so it appears to be the llvm-gcc issue from ticket 1496. I installed http://r.research.att.com/tools/gcc-42-5666.3-darwin11.pkg to be sure I had the correct gcc-4.2 and gfortran for XCode 4.2.1. I was not able to make a universal version of scipy with gcc-4.2, but I could build scipy-0.10.1rc1 after specifying the -arch CFLAG. scipy failed 7 tests from test_arpack.test_symmetric_modes
export MACOSX_DEPLOYMENT_TARGET=10.7
export CC=/usr/bin/gcc-4.2
export CXX=/usr/bin/g++-4.2
export CFLAGS="-arch x86_64"
export FFLAGS=-ff2c
python setupegg.py build --fcompiler=gfortran
python setupegg.py bdist_egg
$ export CFLAGS="-arch x86_64"
$ python
>>> import scipy
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.6.1
NumPy is installed in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy
SciPy version 0.10.1rc1
SciPy is installed in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy
Python version 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
nose version 1.1.2
............................................................................................................................................................................................................................K............................................................................................................/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/interpolate/fitpack2.py:674: 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)
....../Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/interpolate/fitpack2.py:605: UserWarning:
The required storage space exceeds the available storage space: nxest
or nyest too small, or s too small.
The weighted least-squares spline corresponds to the current set of
knots.
warnings.warn(message)
........................K..K....../Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/core/numeric.py:1920: RuntimeWarning: invalid value encountered in absolute
return all(less_equal(absolute(x-y), atol + rtol * absolute(y)))
............................................................................................................................................................................................................................................................................................................................................................................................................................................./Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/io/wavfile.py:31: WavFileWarning: Unfamiliar format bytes
warnings.warn("Unfamiliar format bytes", WavFileWarning)
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/io/wavfile.py:121: WavFileWarning: chunk not understood
warnings.warn("chunk not understood", WavFileWarning)
...............................................................................................................................................................................................................................SSSSSS......SSSSSS......SSSS...............................................................................S............................................................................................................................................................................................................................................................K......................................................................................................................................................................................................SSSSS............S..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSSS.........../Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/sparse/linalg/eigen/arpack/arpack.py:63: UserWarning: Single-precision types in `eigs` and `eighs` are not supported currently. Double precision routines are used instead.
warnings.warn("Single-precision types in `eigs` and `eighs` "
....F.F.....................F...........F.F..............................................................................................F........................F.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K...............................................................K...........................................................................................................................................................KK.............................................................................................................................................................................................................................................................................................................................................................................................................................................K.K.............................................................................................................................................................................................................................................................................................................................................................................................K........K..............SSSSSSS..........................................................................................................................................................S..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <function aslinearoperator at 0x103ba5758>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
x: array([[ 0.23815642, 0.1763755 ],
[-0.10785346, -0.32103487],
[ 0.12468303, -0.11230416],...
y: array([[ 0.23815642, 0.24814051],
[-0.10785347, -0.15634772],
[ 0.12468302, 0.05671416],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <function aslinearoperator at 0x103ba5758>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[ 0.23815693, -0.33630507],
[-0.10785286, 0.02168 ],
[ 0.12468344, -0.11036437],...
y: array([[ 0.23815643, -0.2405392 ],
[-0.10785349, 0.14390968],
[ 0.12468311, -0.04574991],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LA', None, 0.5, <function aslinearoperator at 0x103ba5758>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
x: array([[ 28.80129188, -0.6379945 ],
[ 34.79312355, 0.27066791],
[-270.23255444, 0.4851834 ],...
y: array([[ 3.93467650e+03, -6.37994494e-01],
[ 3.90913859e+03, 2.70667916e-01],
[ -3.62176382e+04, 4.85183382e-01],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SA', None, 0.5, <function aslinearoperator at 0x103ba5758>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
x: array([[ 0.26260981, 0.23815559],
[-0.09760907, -0.10785484],
[ 0.06149647, 0.12468203],...
y: array([[ 0.23744165, 0.2381564 ],
[-0.13633069, -0.10785359],
[ 0.03132561, 0.12468301],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SA', None, 0.5, <function aslinearoperator at 0x103ba5758>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[ 0.29524244, -0.2381569 ],
[-0.08169955, 0.10785299],
[ 0.06645597, -0.12468332],...
y: array([[ 0.24180251, -0.23815646],
[-0.14191195, 0.10785349],
[ 0.03568392, -0.12468307],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'f', 2, 'SM', None, 0.5, <function aslinearoperator at 0x103ba5758>, None, 'buckling')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:general, typ=f, which=SM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=buckling
(mismatch 100.0%)
x: array([[-0.10940548, 0.01676016],
[-0.07154097, 0.4628113 ],
[ 0.06895222, 0.49206394],...
y: array([[-0.10940547, 0.05459438],
[-0.07154103, 0.31407543],
[ 0.06895217, 0.37578294],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'f', 2, 'SA', None, 0.5, <function aslinearoperator at 0x103ba5758>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy-1.6.1-py2.7-macosx-10.6-intel.egg/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:general, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[-0.4404992 , -0.01935683],
[-0.25650678, -0.11053132],
[-0.36893024, -0.13223556],...
y: array([[-0.44017013, -0.0193569 ],
[-0.25525379, -0.11053158],
[-0.36818443, -0.13223571],...
----------------------------------------------------------------------
Ran 5101 tests in 84.089s
FAILED (KNOWNFAIL=12, SKIP=42, failures=7)
<nose.result.TextTestResult run=5101 errors=0 failures=7>
On Feb 13, 2012, at 1:02 AM, Ralf Gommers wrote:
>
>
> On Sun, Feb 12, 2012 at 10:02 PM, Scott Lasley <slasley at space.umd.edu> wrote:
> I downloaded scipy-0.10.1rc1.tar.gz from sourceforge and installed it on a MacPro running OS X 10.7.3, XCode 4.2.1, gfortran from the R Project, numpy 1.6.1 from sourceforge, and python 2.7.2 from python.org with these commands
>
> export MACOSX_DEPLOYMENT_TARGET=10.7
> export CC=/usr/bin/gcc
> python setupegg.py build --fcompiler=gfortran
> python setupegg.py bdist_egg
> unset MACOSX_DEPLOYMENT_TARGET
> unset CC
> easy_install -U dist/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg
>
> scipy crashes python and python-32 in TestDoubleIFFT. I get similar crashes with scipy 2.0.0.dev-8d1b91e and numpy 0.11.0.dev-912768f from github.
>
> This looks like http://projects.scipy.org/scipy/ticket/1496, using 0.10.0 with the above build recipe should crash in the same way. Can you comment on that ticket, double check that you're using non-LLVM gcc (looks unrelated, but you forgot to export CXX) and the correct fortran compiler (there are two from R-project, the one linked on the front page is the wrong one last time I checked), and try the recipe linked to there?
>
> OS X Lion build is still very painful, if someone wants to have a go at making numpy/scipy work with llvm-gcc that would be very helpful.
>
> Thanks,
> Ralf
>
>
> $ python
> Python 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34)
> [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scipy
> >>> scipy.test(verbose=10)
> Running unit tests for scipy
> NumPy version 1.6.1
> NumPy is installed in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy
> SciPy version 0.10.1rc1
> SciPy is installed in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy
> Python version 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
> nose version 1.1.2
> nose.config: INFO: Ignoring files matching ['^\\.', '^_', '^setup\\.py$']
> nose.config: INFO: Excluding tests matching ['f2py_ext', 'f2py_f90_ext', 'gen_ext', 'pyrex_ext', 'swig_ext']
> Tests cophenet(Z) on tdist data set. ... ok
> ...
> Check that updating stored values with exact ones worked. ... ok
> test_constants.test_fahrenheit_to_celcius ... ok
> test_constants.test_celcius_to_kelvin ... ok
> test_constants.test_kelvin_to_celcius ... ok
> test_constants.test_fahrenheit_to_kelvin ... ok
> test_constants.test_kelvin_to_fahrenheit ... ok
> test_constants.test_celcius_to_fahrenheit ... ok
> test_constants.test_lambda_to_nu ... ok
> test_constants.test_nu_to_lambda ... ok
> test_definition (test_basic.TestDoubleFFT) ... ok
> test_djbfft (test_basic.TestDoubleFFT) ... ok
> test_n_argument_real (test_basic.TestDoubleFFT) ... ok
> test_definition (test_basic.TestDoubleIFFT) ... FAIL
> test_definition_real (test_basic.TestDoubleIFFT) ... ok
> test_djbfft (test_basic.TestDoubleIFFT) ... FAIL
> test_random_complex (test_basic.TestDoubleIFFT) ... FAIL
> Python(68720) malloc: *** error for object 0x105312530: pointer being freed was not allocated
> *** set a breakpoint in malloc_error_break to debug
> Abort trap: 6
> $
>
> $ python-32
> Python 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34)
> [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import scipy
> >>> scipy.test(verbose=10)
> Running unit tests for scipy
> NumPy version 1.6.1
> NumPy is installed in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy
> SciPy version 0.10.1rc1
> SciPy is installed in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy-0.10.1rc1-py2.7-macosx-10.6-intel.egg/scipy
> Python version 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
> nose version 1.1.2
> nose.config: INFO: Ignoring files matching ['^\\.', '^_', '^setup\\.py$']
> nose.config: INFO: Excluding tests matching ['f2py_ext', 'f2py_f90_ext', 'gen_ext', 'pyrex_ext', 'swig_ext']
> ...
> test_definition (test_basic.TestDoubleFFT) ... ok
> test_djbfft (test_basic.TestDoubleFFT) ... ok
> test_n_argument_real (test_basic.TestDoubleFFT) ... ok
> test_definition (test_basic.TestDoubleIFFT) ... Python(68743) malloc: *** error for object 0x3a33604: incorrect checksum for freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> FAIL
> test_definition_real (test_basic.TestDoubleIFFT) ... ok
> test_djbfft (test_basic.TestDoubleIFFT) ... Python(68743) malloc: *** error for object 0x3a2e2c4: incorrect checksum for freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> FAIL
> test_random_complex (test_basic.TestDoubleIFFT) ... FAIL
> test_random_real (test_basic.TestDoubleIFFT) ... Python(68743) malloc: *** error for object 0x354c604: incorrect checksum for freed object - object was probably modified after being freed.
> *** set a breakpoint in malloc_error_break to debug
> FAIL
> test_size_accuracy (test_basic.TestDoubleIFFT) ... Bus error: 10
> $
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