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 <[email protected]>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.testrdepends.debian-sid/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid.summary > > 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.testrdepends.debian-sid/cython_0.15.1-2_amd64.build > > 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.testrdepends.debian-sid/libvigraimpex_1.7.1+dfsg1-3_amd64.build > > 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.testrdepends.debian-sid/nipy_0.2.0-1_amd64.build > > 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.testrdepends.debian-sid/numexpr_2.0.1-3_amd64.build > > 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.testrdepends.debian-sid/pylibtiff_0.3.0~svn78-3_amd64.build > > 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.testrdepends.debian-sid/pymvpa_0.4.8-1_amd64.build > > pymvpa2_2.1.0-1.dsc ok FAILED > http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.testrdepends.debian-sid/pymvpa2_2.1.0-1_amd64.build > > 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.testrdepends.debian-sid/pytables_2.3.1-3_amd64.build > > 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.testrdepends.debian-sid/python-ase_3.6.0.2515-1_amd64.build > > 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.testrdepends.debian-sid/scikit-learn_0.11.0-2_amd64.build > > 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.testrdepends.debian-sid/skimage_0.6.1-1_amd64.build > > 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.testrdepends.debian-sid/statsmodels_0.4.2-1_amd64.build > > 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.testrdepends.debian-sid/wrapitk-python_3.20.1.5_amd64.build > > 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 > [email protected] > http://mail.scipy.org/mailman/listinfo/numpy-discussion >
_______________________________________________ NumPy-Discussion mailing list [email protected] http://mail.scipy.org/mailman/listinfo/numpy-discussion
