SciPy 0.9.0.dev6651 test failures (segfault)
import scipy scipy.test('full') Running unit tests for scipy NumPy version 2.0.0.dev8671 NumPy is installed in /usr/lib/python2.6/site-packages/numpy SciPy version 0.9.0.dev6651 SciPy is installed in /usr/lib/python2.6/site-packages/scipy Python version 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] nose version 0.11.3 ................................................................................................................................................................................................................................................................................/usr/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:670: 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) ....../usr/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:601: 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............................................................Warning:
Hello, Again on Fedora 13 Virtualbox setup: Linux a 2.6.33.6-147.2.4.fc13.i686 #1 SMP Fri Jul 23 17:27:40 UTC 2010 i686 i686 i386 GNU/Linux Python 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] on linux2 Type "help", "copyright", "credits" or "license" for more information. divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply .Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply .Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply .........Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply ...................................................................................................................................................................................................................................................................................................................................................../usr/lib/python2.6/site-packages/scipy/io/recaster.py:328: ComplexWarning: Casting complex values to real discards the imaginary part test_arr = arr.astype(T) ../usr/lib/python2.6/site-packages/scipy/io/recaster.py:375: ComplexWarning: Casting complex values to real discards the imaginary part return arr.astype(idt) ../usr/lib/python2.6/site-packages/scipy/io/wavfile.py:30: WavFileWarning: Unfamiliar format bytes warnings.warn("Unfamiliar format bytes", WavFileWarning) /usr/lib/python2.6/site-packages/scipy/io/wavfile.py:120: WavFileWarning: chunk not understood warnings.warn("chunk not understood", WavFileWarning) .......................................................................................F............................................/usr/lib/python2.6/site-packages/scipy/lib/blas/tests/test_fblas.py:86: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) ....../usr/lib/python2.6/site-packages/scipy/lib/blas/tests/test_fblas.py:196: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) .................../usr/lib/python2.6/site-packages/scipy/lib/blas/tests/test_fblas.py:279: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) ..................................................................SSSSSS......SSSSSS......SSSS.....................................................FF........F..Warning: invalid value encountered in divide .....Warning: invalid value encountered in divide Warning: invalid value encountered in divide .......................................................................................................................................................................................................K............................................./usr/lib/python2.6/site-packages/scipy/linalg/tests/test_fblas.py:89: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) ....../usr/lib/python2.6/site-packages/scipy/linalg/tests/test_fblas.py:199: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) .................../usr/lib/python2.6/site-packages/scipy/linalg/tests/test_fblas.py:282: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) ....................................................................../usr/lib/python2.6/site-packages/scipy/linalg/matfuncs.py:94: ComplexWarning: Casting complex values to real discards the imaginary part return dot(dot(vr,diag(exp(s))),vri).astype(t) .................................................................................................................................................................................................................................................../usr/lib/python2.6/site-packages/scipy/ndimage/tests/test_ndimage.py:56: ComplexWarning: Casting complex values to real discards the imaginary part a = a.astype(numpy.float64) /usr/lib/python2.6/site-packages/scipy/ndimage/tests/test_ndimage.py:58: ComplexWarning: Casting complex values to real discards the imaginary part b = b.astype(numpy.float64) ......................................................................................................Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide .....................................................................Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide ........................Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide ..............................................9 7 ....F...............Warning: invalid value encountered in divide ................./usr/lib/python2.6/site-packages/scipy/signal/filter_design.py:247: BadCoefficients: Badly conditioned filter coefficients (numerator): the results may be meaningless "results may be meaningless", BadCoefficients) ..............................................................................................................................................................................................................................................................................................SSSSSSSSSSS..........Segmentation fault (core dumped) -- Gökhan
On 08/27/2010 10:58 AM, Gökhan Sever wrote:
Hello,
Again on Fedora 13 Virtualbox setup: Linux a 2.6.33.6-147.2.4.fc13.i686 #1 SMP Fri Jul 23 17:27:40 UTC 2010 i686 i686 i386 GNU/Linux
import scipy scipy.test('full') Running unit tests for scipy NumPy version 2.0.0.dev8671 NumPy is installed in /usr/lib/python2.6/site-packages/numpy SciPy version 0.9.0.dev6651 SciPy is installed in /usr/lib/python2.6/site-packages/scipy Python version 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] nose version 0.11.3 ................................................................................................................................................................................................................................................................................/usr/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:670: 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) ....../usr/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:601: 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............................................................Warning:
Python 2.6.4 (r264:75706, Jun 4 2010, 18:20:16) [GCC 4.4.4 20100503 (Red Hat 4.4.4-2)] on linux2 Type "help", "copyright", "credits" or "license" for more information. divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply .Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply .Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply .........Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply ...................................................................................................................................................................................................................................................................................................................................................../usr/lib/python2.6/site-packages/scipy/io/recaster.py:328: ComplexWarning: Casting complex values to real discards the imaginary part test_arr = arr.astype(T) ../usr/lib/python2.6/site-packages/scipy/io/recaster.py:375: ComplexWarning: Casting complex values to real discards the imaginary part return arr.astype(idt) ../usr/lib/python2.6/site-packages/scipy/io/wavfile.py:30: WavFileWarning: Unfamiliar format bytes warnings.warn("Unfamiliar format bytes", WavFileWarning) /usr/lib/python2.6/site-packages/scipy/io/wavfile.py:120: WavFileWarning: chunk not understood warnings.warn("chunk not understood", WavFileWarning) .......................................................................................F............................................/usr/lib/python2.6/site-packages/scipy/lib/blas/tests/test_fblas.py:86: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) ....../usr/lib/python2.6/site-packages/scipy/lib/blas/tests/test_fblas.py:196: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) .................../usr/lib/python2.6/site-packages/scipy/lib/blas/tests/test_fblas.py:279: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) ..................................................................SSSSSS......SSSSSS......SSSS.....................................................FF........F..Warning: invalid value encountered in divide .....Warning: invalid value encountered in divide Warning: invalid value encountered in divide .......................................................................................................................................................................................................K............................................./usr/lib/python2.6/site-packages/scipy/linalg/tests/test_fblas.py:89: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) ....../usr/lib/python2.6/site-packages/scipy/linalg/tests/test_fblas.py:199: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) .................../usr/lib/python2.6/site-packages/scipy/linalg/tests/test_fblas.py:282: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) ....................................................................../usr/lib/python2.6/site-packages/scipy/linalg/matfuncs.py:94: ComplexWarning: Casting complex values to real discards the imaginary part return dot(dot(vr,diag(exp(s))),vri).astype(t) .................................................................................................................................................................................................................................................../usr/lib/python2.6/site-packages/scipy/ndimage/tests/test_ndimage.py:56: ComplexWarning: Casting complex values to real discards the imaginary part a = a.astype(numpy.float64) /usr/lib/python2.6/site-packages/scipy/ndimage/tests/test_ndimage.py:58: ComplexWarning: Casting complex values to real discards the imaginary part b = b.astype(numpy.float64) ......................................................................................................Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide .....................................................................Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide ........................Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide Warning: invalid value encountered in divide ..............................................9 7 ....F...............Warning: invalid value encountered in divide ................./usr/lib/python2.6/site-packages/scipy/signal/filter_design.py:247: BadCoefficients: Badly conditioned filter coefficients (numerator): the results may be meaningless "results may be meaningless", BadCoefficients) ..............................................................................................................................................................................................................................................................................................SSSSSSSSSSS..........Segmentation fault (core dumped)
-- Gökhan
_______________________________________________ SciPy-Dev mailing list SciPy-Dev@scipy.org http://mail.scipy.org/mailman/listinfo/scipy-dev Hi, It would be useful to know which test is involved regardless of the issue. Can you please run the tests with the verbose option such as: 'scipy.test(verbose=10)'?
This may have something to do with your numpy problem so please fix that up once you have identified the test (failure in linalg would confirm that). As a reference, my Fedora 13 x64 bit system uses gfortran - 'gcc version 4.4.4 20100630 (Red Hat 4.4.4-10) (GCC)'. Did you completely wipe the previous numpy installation especially the installed numpy files in $PATH2PYTHON/site-packages/ and remove any prior build directories? If so, then you need to create suitable site.cfg file to ensure the correct compiler is being used because something has changed in either your distro or numpy install. Bruce
On Fri, Aug 27, 2010 at 1:14 PM, Bruce Southey <bsouthey@gmail.com> wrote:
Hi, It would be useful to know which test is involved regardless of the issue. Can you please run the tests with the verbose option such as: 'scipy.test(verbose=10)'?
This may have something to do with your numpy problem so please fix that up once you have identified the test (failure in linalg would confirm that).
As a reference, my Fedora 13 x64 bit system uses gfortran - 'gcc version 4.4.4 20100630 (Red Hat 4.4.4-10) (GCC)'.
Did you completely wipe the previous numpy installation especially the installed numpy files in $PATH2PYTHON/site-packages/ and remove any prior build directories? If so, then you need to create suitable site.cfg file to ensure the correct compiler is being used because something has changed in either your distro or numpy install.
Bruce
Hello, Following David and your suggestions I resolved NumPy and SciPy install problems from the source repo. SciPy tests don't give any segfaults anymore.
From the verbose=10 run I get a long list of test execution giving:
Ran 4668 tests in 105.707s FAILED (KNOWNFAIL=12, SKIP=34, failures=2) I couldn't get it write into a file with piping -> python -c 'import scipy; scipy.test(verbose=10)' >> scipy_test How can I get it logging? I might upload the file somewhere for further investigation. -- Gökhan
On Fri, Aug 27, 2010 at 8:00 PM, Gökhan Sever <gokhansever@gmail.com> wrote:
On Fri, Aug 27, 2010 at 1:14 PM, Bruce Southey <bsouthey@gmail.com> wrote:
Hi, It would be useful to know which test is involved regardless of the issue. Can you please run the tests with the verbose option such as: 'scipy.test(verbose=10)'?
This may have something to do with your numpy problem so please fix that up once you have identified the test (failure in linalg would confirm that).
As a reference, my Fedora 13 x64 bit system uses gfortran - 'gcc version 4.4.4 20100630 (Red Hat 4.4.4-10) (GCC)'.
Did you completely wipe the previous numpy installation especially the installed numpy files in $PATH2PYTHON/site-packages/ and remove any prior build directories? If so, then you need to create suitable site.cfg file to ensure the correct compiler is being used because something has changed in either your distro or numpy install.
Bruce
Hello,
Following David and your suggestions I resolved NumPy and SciPy install problems from the source repo. SciPy tests don't give any segfaults anymore. From the verbose=10 run I get a long list of test execution giving:
Ran 4668 tests in 105.707s
FAILED (KNOWNFAIL=12, SKIP=34, failures=2)
I couldn't get it write into a file with piping -> python -c 'import scipy; scipy.test(verbose=10)' >> scipy_test
In bash: python -c 'import scipy; scipy.test(verbose=10)' &> scipy_test Chuck
On Fri, Aug 27, 2010 at 9:10 PM, Charles R Harris <charlesr.harris@gmail.com
wrote:
In bash: python -c 'import scipy; scipy.test(verbose=10)' &> scipy_test
Chuck
Thanks Chuck, & does the trick. See the test results at http://pastebin.com/qg2x2vdV
participants (3)
-
Bruce Southey -
Charles R Harris -
Gökhan Sever