FWIW: "regressions" of dependees of nukmpy 1.7.0b1
Recently Sandro uploaded 1.7.0b1 into Debian experimental so I decided to see if this bleeding edge version doesn't break some of its dependees... Below is a copy of http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... first FAILED/ok column is when building against sid numpy version 1.6.2-1 and the second one is against 1.7.0~b1. I think some 'ok -> FAILED' might be indicative of regressions (myself looking into two new funny failures in pymvpa2's master). Some FAILED->FAILED could be ignored (e.g. I forgotten to provide /dev/shm so multiprocessing was failing)... Enjoy Testing builds against python-numpy_1.7.0~b1-1.dsc aster_10.6.0-1-4.dsc FAILED FAILED aster_10.6.0-1-4_amd64.build avogadro_1.0.3-5.dsc FAILED ok babel_1.4.0.dfsg-8.dsc ok ok basemap_1.0.3+dfsg-2.dsc ok ok biosig4c++_1.3.0-2.dsc ok ok brian_1.3.1-1.dsc ok ok cfflib_2.0.5-1.dsc ok ok cmor_2.8.0-2.dsc ok ok connectomeviewer_2.1.0-1.dsc ok ok cython_0.15.1-2.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... dballe_5.18-1.dsc ok ok dipy_0.5.0-3.dsc ok ok dolfin_1.0.0-7.dsc FAILED ok flann_1.7.1-4.dsc ok ok fonttools_2.3-1.dsc ok ok gamera_3.3.3-2.dsc ok ok gdal_1.9.0-3.dsc ok ok getfem++_4.1.1-10.dsc FAILED ok gnudatalanguage_0.9.2-4.dsc ok ok gnuradio_3.6.1-1.dsc FAILED ok guiqwt_2.1.6-4.dsc FAILED ok h5py_2.0.1-2.dsc ok ok joblib_0.6.4-3.dsc ok ok lazyarray_0.1.0-1.dsc ok ok libfreenect_0.1.2+dfsg-6.dsc ok ok libgetdata_0.7.3-6.dsc ok ok libmpikmeans_1.5-1.dsc ok ok libvigraimpex_1.7.1+dfsg1-3.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... lintian_2.5.10.1.dsc FAILED ok magics++_2.14.11-4.dsc ok ok mathgl_1.11.2-14.dsc FAILED ok matplotlib_1.1.1~rc2-1.dsc FAILED ok mayavi2_4.1.0-1.dsc FAILED ok mdp_3.2+git78-g7db3c50-3.dsc ok ok mgltools-bhtree_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-dejavu_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-geomutils_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-gle_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-molkit_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-opengltk_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-pyglf_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-sff_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-utpackages_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-vision_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-visionlibraries_1.5.6~rc3~cvs.20120601-1.dsc ok ok mlpy_2.2.0~dfsg1-2.dsc ok ok mmass_5.2.0-2.dsc ok ok model-builder_0.4.1-6.dsc ok ok mpi4py_1.3+hg20120611-1.dsc ok ok mypaint_1.0.0-1.dsc ok ok necpp_1.5.0+cvs20101003-2.1.dsc ok ok neo_0.2.0-1.dsc ok ok nexus_4.2.1-svn1614-1.dsc FAILED ok nibabel_1.2.2-1.dsc ok ok nipy_0.2.0-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... nitime_0.4-2.dsc ok ok nlopt_2.2.4+dfsg-2.dsc ok ok numexpr_2.0.1-3.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... numm_0.4-1.dsc FAILED ok opencv_2.3.1-11.dsc ok ok openmeeg_2.0.0.dfsg-5.dsc FAILED ok openopt_0.38+svn1589-1.dsc ok ok pandas_0.8.1-1.dsc ok ok pdb2pqr_1.8-1.dsc ok ok pebl_1.0.2-2.dsc ok ok plplot_5.9.9-5.dsc FAILED ok psignifit3_3.0~beta.20120611.1-1.dsc ok ok pycuda_2012.1-1.dsc ok ok pydicom_0.9.6-1.dsc ok ok pyentropy_0.4.1-1.dsc ok ok pyepr_0.6.1-2.dsc ok ok pyevolve_0.6~rc1+svn398+dfsg-2.dsc ok ok pyfai_0.3.5-1.dsc ok ok pyfits_3.0.8-2.dsc ok ok pyformex_0.8.6-4.dsc ok ok pygame_1.9.1release+dfsg-6.dsc FAILED ok pygrib_1.9.3-1.dsc ok ok pygtk_2.24.0-3.dsc ok ok pylibtiff_0.3.0~svn78-3.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pymca_4.6.0-2.dsc ok ok pymol_1.5.0.1-2.dsc ok ok pymvpa_0.4.8-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pymvpa2_2.1.0-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pynifti_0.20100607.1-4.dsc ok ok pynn_0.7.4-1.dsc ok ok pyopencl_2012.1-1.dsc ok ok pyqwt3d_0.1.7~cvs20090625-9.dsc FAILED ok pyqwt5_5.2.1~cvs20091107+dfsg-6.dsc FAILED ok pysparse_1.1-1.dsc ok ok pysurfer_0.3+git15-gae6cbb1-1.1.dsc ok ok pytables_2.3.1-3.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pytango_7.2.3-2.dsc ok ok python-ase_3.6.0.2515-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... python-biggles_1.6.6-1.dsc ok ok python-biom-format_1.0.0-1.dsc ok ok python-biopython_1.59-1.dsc ok ok python-chaco_4.1.0-1.dsc ok ok python-cogent_1.5.1-2.dsc ok ok python-cpl_0.3.6-1.dsc ok ok python-csa_0.1.0-1.1.dsc ok ok python-enable_4.1.0-1.dsc ok ok python-fabio_0.0.8-1.dsc ok ok python-fftw_0.2.2-1.dsc ok ok python-gnuplot_1.8-1.1.dsc ok ok python-networkx_1.7~rc1-3.dsc ok ok python-neuroshare_0.8.5-1.dsc ok ok python-pywcs_1.11-1.dsc ok ok python-scientific_2.8-3.dsc ok ok python-scipy_0.10.1+dfsg1-4.dsc ok ok python-shapely_1.2.14-1.dsc ok ok python-visual_5.12-1.4.dsc ok ok pytools_2011.5-2.dsc ok ok pywavelets_0.2.0-5.dsc ok ok pyzmq_2.2.0-1.dsc ok ok qiime_1.5.0-2.dsc ok ok rdkit_201203-3.dsc ok ok rpy_1.0.3-22.dsc ok ok rpy2_2.2.6-1.dsc ok ok scikit-learn_0.11.0-2.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... shogun_1.1.0-6.dsc FAILED ok skimage_0.6.1-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... spherepack_3.2-4.dsc ok ok statsmodels_0.4.2-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... stimfit_0.10.18-1.1.dsc ok ok syfi_1.0.0.dfsg-1.dsc ok ok taurus_3.0.0-1.dsc FAILED ok tifffile_20120421-1.dsc ok ok uncertainties_1.8-1.dsc ok ok veusz_1.15-1.dsc FAILED ok vistrails_2.0.alpha~1-3.dsc ok ok wrapitk-python_3.20.1.5.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... wsjt_5.9.7.r383-1.6.dsc ok ok yade_0.80.1-2.dsc FAILED ok yp-svipc_0.14-2.dsc ok ok -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
quick question -- either this is a desired effect that ndarray.base is no longer chains to point to all parent arrays? following code produces different outputs with 1.6.3 and 1.7.0b1: $> python -c 'import numpy as np; print np.__version__; a=np.arange(10); print a[:4].base is a, a[:4][:3].base is a, a[:4][:3].base.base is a' 1.6.2 True False True 1.7.0rc1.dev-ea23de8 True True False On Wed, 05 Sep 2012, Yaroslav Halchenko wrote:
pymvpa2_2.1.0-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
On Wed, Sep 5, 2012 at 10:02 PM, Yaroslav Halchenko <lists@onerussian.com> wrote:
quick question -- either this is a desired effect that ndarray.base is no longer chains to point to all parent arrays? following code produces different outputs with 1.6.3 and 1.7.0b1:
$> python -c 'import numpy as np; print np.__version__; a=np.arange(10); print a[:4].base is a, a[:4][:3].base is a, a[:4][:3].base.base is a'
1.6.2 True False True
1.7.0rc1.dev-ea23de8 True True False
It is an intentional change: https://github.com/numpy/numpy/commit/b7cc20ad#L5R77 but the benefits aren't necessarily *that* compelling, so it could certainly be revisited if there are unforeseen downsides. (Mostly it means that intermediate view objects can be deallocated when not otherwise referenced.) Is it somehow causing a problem for you? AFAICT introspection on .base is just a bad idea to start with, but... -n
On Wed, 05 Sep 2012, Nathaniel Smith wrote:
It is an intentional change: https://github.com/numpy/numpy/commit/b7cc20ad#L5R77 but the benefits aren't necessarily *that* compelling, so it could certainly be revisited if there are unforeseen downsides. (Mostly it means that intermediate view objects can be deallocated when not otherwise referenced.) Is it somehow causing a problem for you?
introspection on .base is just a bad idea to start with, but...
not really -- just fails our unittests which relied upon public interface and previous assumptions ;) since this chaining is actually not of importance for that test (we just cared to not deal with a copy of the actual load), I will tune it up so it would work under any numpy's handling here (chain or not to chain). -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
and another, quite weird one -- initially it was crashing with the same error on np.dot(Vh.T, U.T) but while adding print statements to troubleshoot it, started to fail on print: File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/mappers/procrustean.py", line 164, in _train print "Vh:", Vh File "/home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/numeric.py", line 1471, in array_str return array2string(a, max_line_width, precision, suppress_small, ' ', "", str) File "/home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/arrayprint.py", line 440, in array2string elif reduce(product, a.shape) == 0: TypeError: object of type 'float' has no len() here is part of pdb session: Vh: > /home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/arrayprint.py(440)array2string() -> elif reduce(product, a.shape) == 0: (Pdb) up
/home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/numeric.py(1471)array_str() -> return array2string(a, max_line_width, precision, suppress_small, ' ', "", str) (Pdb) print a [[-0.99818262 0.06026149] [ 0.06026149 0.99818262]] *(Pdb) print a.__class__ <type 'numpy.ndarray'> (Pdb) down /home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/arrayprint.py(440)array2string() -> elif reduce(product, a.shape) == 0: (Pdb) print reduce(product, a.shape) 4 (Pdb) c ERROR
it might be that this valgrind msg would be relevant ;) : ==10281== Invalid read of size 4 ==10281== at 0x88C6973: _descriptor_from_pep3118_format (buffer.c:791) ==10281== by 0x88C6B0E: _array_from_buffer_3118 (ctors.c:1193) ==10281== by 0x88E7ABB: PyArray_GetArrayParamsFromObject (ctors.c:1378) ==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580) ==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758) ==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644) ==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EB221: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== Address 0x75c3a04 is 4 bytes inside a block of size 6 alloc'd ==10281== at 0x4C28BED: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==10281== by 0x88C6911: _descriptor_from_pep3118_format (buffer.c:776) ==10281== by 0x88C6B0E: _array_from_buffer_3118 (ctors.c:1193) ==10281== by 0x88E7ABB: PyArray_GetArrayParamsFromObject (ctors.c:1378) ==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580) ==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758) ==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644) ==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== ==10281== Invalid read of size 4 ==10281== at 0x88C6973: _descriptor_from_pep3118_format (buffer.c:791) ==10281== by 0x88E0BAB: PyArray_DTypeFromObjectHelper (common.c:287) ==10281== by 0x88E1012: PyArray_DTypeFromObject.constprop.277 (common.c:111) ==10281== by 0x88E7C74: PyArray_GetArrayParamsFromObject (ctors.c:1453) ==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580) ==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758) ==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644) ==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== Address 0x7852e94 is 4 bytes inside a block of size 6 alloc'd ==10281== at 0x4C28BED: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==10281== by 0x88C6911: _descriptor_from_pep3118_format (buffer.c:776) ==10281== by 0x88E0BAB: PyArray_DTypeFromObjectHelper (common.c:287) ==10281== by 0x88E1012: PyArray_DTypeFromObject.constprop.277 (common.c:111) ==10281== by 0x88E7C74: PyArray_GetArrayParamsFromObject (ctors.c:1453) ==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580) ==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758) ==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644) ==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) On Wed, 05 Sep 2012, Yaroslav Halchenko wrote:
Recently Sandro uploaded 1.7.0b1 into Debian experimental so I decided to see if this bleeding edge version doesn't break some of its dependees... Below is a copy of http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... first FAILED/ok column is when building against sid numpy version 1.6.2-1 and the second one is against 1.7.0~b1. I think some 'ok -> FAILED' might be indicative of regressions (myself looking into two new funny failures in pymvpa2's master). Some FAILED->FAILED could be ignored (e.g. I forgotten to provide /dev/shm so multiprocessing was failing)... Enjoy
Testing builds against python-numpy_1.7.0~b1-1.dsc aster_10.6.0-1-4.dsc FAILED FAILED aster_10.6.0-1-4_amd64.build avogadro_1.0.3-5.dsc FAILED ok babel_1.4.0.dfsg-8.dsc ok ok basemap_1.0.3+dfsg-2.dsc ok ok biosig4c++_1.3.0-2.dsc ok ok brian_1.3.1-1.dsc ok ok cfflib_2.0.5-1.dsc ok ok cmor_2.8.0-2.dsc ok ok connectomeviewer_2.1.0-1.dsc ok ok cython_0.15.1-2.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... dballe_5.18-1.dsc ok ok dipy_0.5.0-3.dsc ok ok dolfin_1.0.0-7.dsc FAILED ok flann_1.7.1-4.dsc ok ok fonttools_2.3-1.dsc ok ok gamera_3.3.3-2.dsc ok ok gdal_1.9.0-3.dsc ok ok getfem++_4.1.1-10.dsc FAILED ok gnudatalanguage_0.9.2-4.dsc ok ok gnuradio_3.6.1-1.dsc FAILED ok guiqwt_2.1.6-4.dsc FAILED ok h5py_2.0.1-2.dsc ok ok joblib_0.6.4-3.dsc ok ok lazyarray_0.1.0-1.dsc ok ok libfreenect_0.1.2+dfsg-6.dsc ok ok libgetdata_0.7.3-6.dsc ok ok libmpikmeans_1.5-1.dsc ok ok libvigraimpex_1.7.1+dfsg1-3.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... lintian_2.5.10.1.dsc FAILED ok magics++_2.14.11-4.dsc ok ok mathgl_1.11.2-14.dsc FAILED ok matplotlib_1.1.1~rc2-1.dsc FAILED ok mayavi2_4.1.0-1.dsc FAILED ok mdp_3.2+git78-g7db3c50-3.dsc ok ok mgltools-bhtree_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-dejavu_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-geomutils_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-gle_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-molkit_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-opengltk_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-pyglf_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-sff_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-utpackages_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-vision_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-visionlibraries_1.5.6~rc3~cvs.20120601-1.dsc ok ok mlpy_2.2.0~dfsg1-2.dsc ok ok mmass_5.2.0-2.dsc ok ok model-builder_0.4.1-6.dsc ok ok mpi4py_1.3+hg20120611-1.dsc ok ok mypaint_1.0.0-1.dsc ok ok necpp_1.5.0+cvs20101003-2.1.dsc ok ok neo_0.2.0-1.dsc ok ok nexus_4.2.1-svn1614-1.dsc FAILED ok nibabel_1.2.2-1.dsc ok ok nipy_0.2.0-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... nitime_0.4-2.dsc ok ok nlopt_2.2.4+dfsg-2.dsc ok ok numexpr_2.0.1-3.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... numm_0.4-1.dsc FAILED ok opencv_2.3.1-11.dsc ok ok openmeeg_2.0.0.dfsg-5.dsc FAILED ok openopt_0.38+svn1589-1.dsc ok ok pandas_0.8.1-1.dsc ok ok pdb2pqr_1.8-1.dsc ok ok pebl_1.0.2-2.dsc ok ok plplot_5.9.9-5.dsc FAILED ok psignifit3_3.0~beta.20120611.1-1.dsc ok ok pycuda_2012.1-1.dsc ok ok pydicom_0.9.6-1.dsc ok ok pyentropy_0.4.1-1.dsc ok ok pyepr_0.6.1-2.dsc ok ok pyevolve_0.6~rc1+svn398+dfsg-2.dsc ok ok pyfai_0.3.5-1.dsc ok ok pyfits_3.0.8-2.dsc ok ok pyformex_0.8.6-4.dsc ok ok pygame_1.9.1release+dfsg-6.dsc FAILED ok pygrib_1.9.3-1.dsc ok ok pygtk_2.24.0-3.dsc ok ok pylibtiff_0.3.0~svn78-3.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pymca_4.6.0-2.dsc ok ok pymol_1.5.0.1-2.dsc ok ok pymvpa_0.4.8-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pymvpa2_2.1.0-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pynifti_0.20100607.1-4.dsc ok ok pynn_0.7.4-1.dsc ok ok pyopencl_2012.1-1.dsc ok ok pyqwt3d_0.1.7~cvs20090625-9.dsc FAILED ok pyqwt5_5.2.1~cvs20091107+dfsg-6.dsc FAILED ok pysparse_1.1-1.dsc ok ok pysurfer_0.3+git15-gae6cbb1-1.1.dsc ok ok pytables_2.3.1-3.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pytango_7.2.3-2.dsc ok ok python-ase_3.6.0.2515-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... python-biggles_1.6.6-1.dsc ok ok python-biom-format_1.0.0-1.dsc ok ok python-biopython_1.59-1.dsc ok ok python-chaco_4.1.0-1.dsc ok ok python-cogent_1.5.1-2.dsc ok ok python-cpl_0.3.6-1.dsc ok ok python-csa_0.1.0-1.1.dsc ok ok python-enable_4.1.0-1.dsc ok ok python-fabio_0.0.8-1.dsc ok ok python-fftw_0.2.2-1.dsc ok ok python-gnuplot_1.8-1.1.dsc ok ok python-networkx_1.7~rc1-3.dsc ok ok python-neuroshare_0.8.5-1.dsc ok ok python-pywcs_1.11-1.dsc ok ok python-scientific_2.8-3.dsc ok ok python-scipy_0.10.1+dfsg1-4.dsc ok ok python-shapely_1.2.14-1.dsc ok ok python-visual_5.12-1.4.dsc ok ok pytools_2011.5-2.dsc ok ok pywavelets_0.2.0-5.dsc ok ok pyzmq_2.2.0-1.dsc ok ok qiime_1.5.0-2.dsc ok ok rdkit_201203-3.dsc ok ok rpy_1.0.3-22.dsc ok ok rpy2_2.2.6-1.dsc ok ok scikit-learn_0.11.0-2.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... shogun_1.1.0-6.dsc FAILED ok skimage_0.6.1-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... spherepack_3.2-4.dsc ok ok statsmodels_0.4.2-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... stimfit_0.10.18-1.1.dsc ok ok syfi_1.0.0.dfsg-1.dsc ok ok taurus_3.0.0-1.dsc FAILED ok tifffile_20120421-1.dsc ok ok uncertainties_1.8-1.dsc ok ok veusz_1.15-1.dsc FAILED ok vistrails_2.0.alpha~1-3.dsc ok ok wrapitk-python_3.20.1.5.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... wsjt_5.9.7.r383-1.6.dsc ok ok yade_0.80.1-2.dsc FAILED ok yp-svipc_0.14-2.dsc ok ok -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
Are you running the valgrind test with the Python suppression file: http://svn.python.org/projects/python/trunk/Misc/valgrind-python.supp ? Cheers, A On Wed, Sep 5, 2012 at 10:14 PM, Yaroslav Halchenko <lists@onerussian.com>wrote:
and another, quite weird one -- initially it was crashing with the same error on
np.dot(Vh.T, U.T)
but while adding print statements to troubleshoot it, started to fail on print:
File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/mappers/procrustean.py", line 164, in _train print "Vh:", Vh File "/home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/numeric.py", line 1471, in array_str return array2string(a, max_line_width, precision, suppress_small, ' ', "", str) File "/home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/arrayprint.py", line 440, in array2string elif reduce(product, a.shape) == 0: TypeError: object of type 'float' has no len()
here is part of pdb session:
Vh: > /home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/arrayprint.py(440)array2string() -> elif reduce(product, a.shape) == 0: (Pdb) up
/home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/numeric.py(1471)array_str() -> return array2string(a, max_line_width, precision, suppress_small, ' ', "", str) (Pdb) print a [[-0.99818262 0.06026149] [ 0.06026149 0.99818262]] *(Pdb) print a.__class__ <type 'numpy.ndarray'> (Pdb) down
/home/yoh/python-env/numpy/local/lib/python2.7/site-packages/numpy/core/arrayprint.py(440)array2string() -> elif reduce(product, a.shape) == 0: (Pdb) print reduce(product, a.shape) 4 (Pdb) c ERROR
it might be that this valgrind msg would be relevant ;) :
==10281== Invalid read of size 4 ==10281== at 0x88C6973: _descriptor_from_pep3118_format (buffer.c:791) ==10281== by 0x88C6B0E: _array_from_buffer_3118 (ctors.c:1193) ==10281== by 0x88E7ABB: PyArray_GetArrayParamsFromObject (ctors.c:1378) ==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580) ==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758) ==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644) ==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EB221: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== Address 0x75c3a04 is 4 bytes inside a block of size 6 alloc'd ==10281== at 0x4C28BED: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==10281== by 0x88C6911: _descriptor_from_pep3118_format (buffer.c:776) ==10281== by 0x88C6B0E: _array_from_buffer_3118 (ctors.c:1193) ==10281== by 0x88E7ABB: PyArray_GetArrayParamsFromObject (ctors.c:1378) ==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580) ==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758) ==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644) ==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== ==10281== Invalid read of size 4 ==10281== at 0x88C6973: _descriptor_from_pep3118_format (buffer.c:791) ==10281== by 0x88E0BAB: PyArray_DTypeFromObjectHelper (common.c:287) ==10281== by 0x88E1012: PyArray_DTypeFromObject.constprop.277 (common.c:111) ==10281== by 0x88E7C74: PyArray_GetArrayParamsFromObject (ctors.c:1453) ==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580) ==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758) ==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644) ==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== Address 0x7852e94 is 4 bytes inside a block of size 6 alloc'd ==10281== at 0x4C28BED: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==10281== by 0x88C6911: _descriptor_from_pep3118_format (buffer.c:776) ==10281== by 0x88E0BAB: PyArray_DTypeFromObjectHelper (common.c:287) ==10281== by 0x88E1012: PyArray_DTypeFromObject.constprop.277 (common.c:111) ==10281== by 0x88E7C74: PyArray_GetArrayParamsFromObject (ctors.c:1453) ==10281== by 0x88E7F98: PyArray_FromAny (ctors.c:1580) ==10281== by 0x88EE895: PyArray_CheckFromAny (ctors.c:1758) ==10281== by 0x88EF7E2: _array_fromobject (multiarraymodule.c:1644) ==10281== by 0x4F148D: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4EAFD7: PyEval_EvalFrameEx (in /home/yoh/python-env/numpy/bin/python) ==10281== by 0x4F1DAF: PyEval_EvalCodeEx (in /home/yoh/python-env/numpy/bin/python)
On Wed, 05 Sep 2012, Yaroslav Halchenko wrote:
Recently Sandro uploaded 1.7.0b1 into Debian experimental so I decided to see if this bleeding edge version doesn't break some of its dependees... Below is a copy of
http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr...
first FAILED/ok column is when building against sid numpy version 1.6.2-1 and the second one is against 1.7.0~b1. I think some 'ok -> FAILED' might be indicative of regressions (myself looking into two new funny failures in pymvpa2's master). Some FAILED->FAILED could be ignored (e.g. I forgotten to provide /dev/shm so multiprocessing was failing)... Enjoy
Testing builds against python-numpy_1.7.0~b1-1.dsc aster_10.6.0-1-4.dsc FAILED FAILED aster_10.6.0-1-4_amd64.build avogadro_1.0.3-5.dsc FAILED ok babel_1.4.0.dfsg-8.dsc ok ok basemap_1.0.3+dfsg-2.dsc ok ok biosig4c++_1.3.0-2.dsc ok ok brian_1.3.1-1.dsc ok ok cfflib_2.0.5-1.dsc ok ok cmor_2.8.0-2.dsc ok ok connectomeviewer_2.1.0-1.dsc ok ok cython_0.15.1-2.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... dballe_5.18-1.dsc ok ok dipy_0.5.0-3.dsc ok ok dolfin_1.0.0-7.dsc FAILED ok flann_1.7.1-4.dsc ok ok fonttools_2.3-1.dsc ok ok gamera_3.3.3-2.dsc ok ok gdal_1.9.0-3.dsc ok ok getfem++_4.1.1-10.dsc FAILED ok gnudatalanguage_0.9.2-4.dsc ok ok gnuradio_3.6.1-1.dsc FAILED ok guiqwt_2.1.6-4.dsc FAILED ok h5py_2.0.1-2.dsc ok ok joblib_0.6.4-3.dsc ok ok lazyarray_0.1.0-1.dsc ok ok libfreenect_0.1.2+dfsg-6.dsc ok ok libgetdata_0.7.3-6.dsc ok ok libmpikmeans_1.5-1.dsc ok ok libvigraimpex_1.7.1+dfsg1-3.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... lintian_2.5.10.1.dsc FAILED ok magics++_2.14.11-4.dsc ok ok mathgl_1.11.2-14.dsc FAILED ok matplotlib_1.1.1~rc2-1.dsc FAILED ok mayavi2_4.1.0-1.dsc FAILED ok mdp_3.2+git78-g7db3c50-3.dsc ok ok mgltools-bhtree_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-dejavu_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-geomutils_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-gle_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-molkit_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-opengltk_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-pyglf_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-sff_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-utpackages_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-vision_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-visionlibraries_1.5.6~rc3~cvs.20120601-1.dsc ok ok mlpy_2.2.0~dfsg1-2.dsc ok ok mmass_5.2.0-2.dsc ok ok model-builder_0.4.1-6.dsc ok ok mpi4py_1.3+hg20120611-1.dsc ok ok mypaint_1.0.0-1.dsc ok ok necpp_1.5.0+cvs20101003-2.1.dsc ok ok neo_0.2.0-1.dsc ok ok nexus_4.2.1-svn1614-1.dsc FAILED ok nibabel_1.2.2-1.dsc ok ok nipy_0.2.0-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... nitime_0.4-2.dsc ok ok nlopt_2.2.4+dfsg-2.dsc ok ok numexpr_2.0.1-3.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... numm_0.4-1.dsc FAILED ok opencv_2.3.1-11.dsc ok ok openmeeg_2.0.0.dfsg-5.dsc FAILED ok openopt_0.38+svn1589-1.dsc ok ok pandas_0.8.1-1.dsc ok ok pdb2pqr_1.8-1.dsc ok ok pebl_1.0.2-2.dsc ok ok plplot_5.9.9-5.dsc FAILED ok psignifit3_3.0~beta.20120611.1-1.dsc ok ok pycuda_2012.1-1.dsc ok ok pydicom_0.9.6-1.dsc ok ok pyentropy_0.4.1-1.dsc ok ok pyepr_0.6.1-2.dsc ok ok pyevolve_0.6~rc1+svn398+dfsg-2.dsc ok ok pyfai_0.3.5-1.dsc ok ok pyfits_3.0.8-2.dsc ok ok pyformex_0.8.6-4.dsc ok ok pygame_1.9.1release+dfsg-6.dsc FAILED ok pygrib_1.9.3-1.dsc ok ok pygtk_2.24.0-3.dsc ok ok pylibtiff_0.3.0~svn78-3.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pymca_4.6.0-2.dsc ok ok pymol_1.5.0.1-2.dsc ok ok pymvpa_0.4.8-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pymvpa2_2.1.0-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pynifti_0.20100607.1-4.dsc ok ok pynn_0.7.4-1.dsc ok ok pyopencl_2012.1-1.dsc ok ok pyqwt3d_0.1.7~cvs20090625-9.dsc FAILED ok pyqwt5_5.2.1~cvs20091107+dfsg-6.dsc FAILED ok pysparse_1.1-1.dsc ok ok pysurfer_0.3+git15-gae6cbb1-1.1.dsc ok ok pytables_2.3.1-3.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... pytango_7.2.3-2.dsc ok ok python-ase_3.6.0.2515-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... python-biggles_1.6.6-1.dsc ok ok python-biom-format_1.0.0-1.dsc ok ok python-biopython_1.59-1.dsc ok ok python-chaco_4.1.0-1.dsc ok ok python-cogent_1.5.1-2.dsc ok ok python-cpl_0.3.6-1.dsc ok ok python-csa_0.1.0-1.1.dsc ok ok python-enable_4.1.0-1.dsc ok ok python-fabio_0.0.8-1.dsc ok ok python-fftw_0.2.2-1.dsc ok ok python-gnuplot_1.8-1.1.dsc ok ok python-networkx_1.7~rc1-3.dsc ok ok python-neuroshare_0.8.5-1.dsc ok ok python-pywcs_1.11-1.dsc ok ok python-scientific_2.8-3.dsc ok ok python-scipy_0.10.1+dfsg1-4.dsc ok ok python-shapely_1.2.14-1.dsc ok ok python-visual_5.12-1.4.dsc ok ok pytools_2011.5-2.dsc ok ok pywavelets_0.2.0-5.dsc ok ok pyzmq_2.2.0-1.dsc ok ok qiime_1.5.0-2.dsc ok ok rdkit_201203-3.dsc ok ok rpy_1.0.3-22.dsc ok ok rpy2_2.2.6-1.dsc ok ok scikit-learn_0.11.0-2.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... shogun_1.1.0-6.dsc FAILED ok skimage_0.6.1-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... spherepack_3.2-4.dsc ok ok statsmodels_0.4.2-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... stimfit_0.10.18-1.1.dsc ok ok syfi_1.0.0.dfsg-1.dsc ok ok taurus_3.0.0-1.dsc FAILED ok tifffile_20120421-1.dsc ok ok uncertainties_1.8-1.dsc ok ok veusz_1.15-1.dsc FAILED ok vistrails_2.0.alpha~1-3.dsc ok ok wrapitk-python_3.20.1.5.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testr... wsjt_5.9.7.r383-1.6.dsc ok ok yade_0.80.1-2.dsc FAILED ok yp-svipc_0.14-2.dsc ok ok -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
On Thu, 06 Sep 2012, Aron Ahmadia wrote:
Are you running the valgrind test with the Python suppression file:�[1]http://svn.python.org/projects/python/trunk/Misc/valgrind-python.supp
yes -- on Debian there is /usr/lib/valgrind/python.supp which comes with python package and I believe enabled by default, and it is identical to above (just dynamic library versions different) but it still produces lots of false positives -- IIRC it needs additional tune ups per architecture etc... I just ignored those messages "manually" and listed the relevant one which comes from numpy functionality. -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
preamble: the bug here seems to be due to incorrect np.asarray(ctypes.cdouble array) ok -- I tried with a debug build of python and -O0 build of numpy, and the same old valgrind... this time valgrind is silent BUT then python itself says test_simple (mvpa2.tests.test_procrust.ProcrusteanMapperTests) ... XXX undetected error ERROR and nose failure (now I see it) has nothing actually to do with the operation on the object but just get reported to the first line after the function call where I guess a problematic object was created... ====================================================================== ERROR: test_simple (mvpa2.tests.test_procrust.ProcrusteanMapperTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/testing/sweepargs.py", line 67, in do_sweep method(*args_, **kwargs_) File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/testing/sweepargs.py", line 67, in do_sweep method(*args_, **kwargs_) File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/testing/tools.py", line 179, in newfunc return func(*arg, **kwargs) File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/tests/test_procrust.py", line 67, in test_simple pm.train(ds) File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/base/learner.py", line 119, in train result = self._train(ds) File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/mappers/procrustean.py", line 161, in _train print "------------" TypeError: object of type 'float' has no len() that function is fancy only in that it uses ctypes to call a function from the cdll.LoadLibrary('liblapack.so'): https://github.com/PyMVPA/PyMVPA/blob/HEAD/mvpa2/support/lapack_svd.py but even if I comment out that call to lapacklib. it still screws up the same way -- so it has to do with those variable definitions before then I guess... ok -- it boils down to numpy.asarray(s) in return statement... I improved it with a printout now where I assigned constructed array to a variable first NB if I swap print lines, it would lead me to crash above, but with this order -- it manages to continue without crashing BUT showing incorrect values. s_arr = numpy.asarray(s) print "s_arr", s_arr print "s:", s return vt, s_arr, u so it gives me $> MVPA_SEED=1928295852 `which nosetests` -s -v mvpa2/tests/test_procrust.py T: MVPA_SEED=1928295852 test_simple (mvpa2.tests.test_procrust.ProcrusteanMapperTests) ... VERSION 1.7.0rc1.dev-ea23de8 s_arr [[ 6.90689888e-310 1.83759219e-316] [ -3.16388621e+134 -3.16388621e+134]] s: <mvpa2.support.lapack_svd.c_double_Array_2 object at 0x28c4ae0> FAIL ====================================================================== FAIL: test_simple (mvpa2.tests.test_procrust.ProcrusteanMapperTests) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/testing/tools.py", line 179, in newfunc return func(*arg, **kwargs) File "/home/yoh/proj/pymvpa/pymvpa/mvpa2/tests/test_procrust.py", line 93, in test_simple "perfectly. Now got d scale*R=%g" % dsR) AssertionError: Single scenario lead to failures of unittest test_simple: on oblique=False : Single scenario lead to failures of unittest test_simple: on svd=dgesvd : We should have got reconstructed rotation+scaling perfectly. Now got d scale*R=1.34232e+134 ---------------------------------------------------------------------- Ran 1 test in 0.222s FAILED (failures=1) [161643 refs] when with 1.6.2 (using the same seed, so if numpy's RNG didn't change -- data should be the same): $> MVPA_SEED=1928295852 nosetests -s -v mvpa2/tests/test_procrust.py T: MVPA_SEED=1928295852 test_simple (mvpa2.tests.test_procrust.ProcrusteanMapperTests) ... VERSION 1.6.2 s_arr [0.775771814652 0.224228185348] s: <mvpa2.support.lapack_svd.c_double_Array_2 object at 0xad65d40> s_arr [0.775771814652 0.224228185348] s: <mvpa2.support.lapack_svd.c_double_Array_2 object at 0xad65c20> s_arr [0.365993114976 0.101324191354 0.0959100894799 0.0861936270658 0.0712098129231 0.0694159685405 0.0636016740376 0.056058975141 0.0481853714064 0.042107175076] s: <mvpa2.support.lapack_svd.c_double_Array_10 object at 0xad65d40> s_arr [0.365993114976 0.101324191354 0.0959100894799 0.0861936270658 0.0712098129231 0.0694159685405 0.0636016740376 0.056058975141 0.0481853714064 0.042107175076] s: <mvpa2.support.lapack_svd.c_double_Array_10 object at 0xad65c20> s_arr [0.775771814652 0.224228185348 0.0] s: <mvpa2.support.lapack_svd.c_double_Array_3 object at 0xad65d40> s_arr [0.775771814652 0.224228185348 0.0] s: <mvpa2.support.lapack_svd.c_double_Array_3 object at 0xad65c20> s_arr [0.703907195999 0.200251541932 0.0] s: <mvpa2.support.lapack_svd.c_double_Array_3 object at 0xad65d40> s_arr [0.703907195999 0.200251541932 0.0] s: <mvpa2.support.lapack_svd.c_double_Array_3 object at 0xad65c20> ok ---------------------------------------------------------------------- Ran 1 test in 7.031s OK MVPA_SEED=1928295852 nosetests -s -v mvpa2/tests/test_procrust.py 7,14s user 0,79s system 96% cpu 8,219 total which immediately shows that np.asarray created a 2d array whenever it should have been a 1d (original definition of s is s=(c_double*min(x,y))()) ok -- added printing of dtype of that array -- with 1.6.2 it is reported as object while with 1.7.0b1 -- float64... from here I pass it onto experts! ;) On Thu, 06 Sep 2012, Yaroslav Halchenko wrote:
On Thu, 06 Sep 2012, Aron Ahmadia wrote:
Are you running the valgrind test with the Python suppression file:�[1]http://svn.python.org/projects/python/trunk/Misc/valgrind-python.supp
yes -- on Debian there is /usr/lib/valgrind/python.supp which comes with python package and I believe enabled by default, and it is identical to above (just dynamic library versions different) but it still produces lots of false positives -- IIRC it needs additional tune ups per architecture etc... I just ignored those messages "manually" and listed the relevant one which comes from numpy functionality. -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
On Wed, Sep 5, 2012 at 1:38 PM, Yaroslav Halchenko <lists@onerussian.com> wrote:
skimage_0.6.1-1.dsc ok FAILED
This breakage is due to https://github.com/numpy/numpy/issues/392 Thanks for checking! Stéfan
participants (4)
-
Aron Ahmadia -
Nathaniel Smith -
Stéfan van der Walt -
Yaroslav Halchenko