[SciPy-Dev] Fwd: Package: scipy-0.11.0-0.1.rc2.fc18 Tag: f18-updates-candidate Status: failed Built by: orion

Orion Poplawski orion@cora.nwra....
Mon Sep 24 12:02:48 CDT 2012


On 09/20/2012 05:33 PM, Orion Poplawski wrote:
> This is a plea for some help.  We've been having trouble getting scipy to pass
> all of the tests in the Fedora 18 build with python 3.3 (although it seems to
> build okay in Fedora 19).  Below are the logs of the build.  There appears to
> be some kind of memory corruption that manifests itself a little differently
> on 32-bit vs. 64-bit.  I really have no idea myself how to pursue debugging
> this, though I'm happy to provide any more needed information.
>

Well, I've at least been able to determine that is happens in 
scipy/linalg/test_decomp.py test_dsbevx(), though it doesn't fail the same way 
each time:

Compare dsbevx eigenvalues and eigenvectors ... Segmentation fault

$ python3 
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python3.3/site-packages/scipy/linalg/tests/test_decomp.py
..............E.....E.........................................................................................................................................................................................................................................................................E
======================================================================
ERROR: Compare dsbevx eigenvalues and eigenvectors
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python3.3/site-packages/scipy/linalg/tests/test_decomp.py", 
line 373, in test_dsbevx
     evec_ = evec[:,argsort(w)]
IndexError: index (1) out of range (0<=index<0) in dimension 1

======================================================================
ERROR: Compare zhbevx eigenvalues and eigenvectors
----------------------------------------------------------------------
Traceback (most recent call last):
   File 
"/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python3.3/site-packages/scipy/linalg/tests/test_decomp.py", 
line 395, in test_zhbevx
     evec_ = evec[:,argsort(w)]
IndexError: index (1) out of range (0<=index<0) in dimension 1

======================================================================
ERROR: test_decomp.test_lapack_misaligned
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/usr/lib/python3.3/site-packages/nose/case.py", line 198, in runTest
     self.test(*self.arg)
   File "/usr/lib/python3.3/site-packages/numpy/testing/decorators.py", line 
214, in knownfailer
     raise KnownFailureTest(msg)
numpy.testing.noseclasses.KnownFailureTest: Ticket #1152, triggers a segfault 
in rare cases.

----------------------------------------------------------------------
Ran 287 tests in 1.915s

FAILED (errors=3)

$ python3 
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python3.3/site-packages/scipy/linalg/tests/test_decomp.py
..............Segmentation fault
$ python3 
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python3.3/site-packages/scipy/linalg/tests/test_decomp.py
..............E.....E....................................................................................................................Segmentation 
fault

Valgrind reports lots of messages like:

==7641== Invalid write of size 8
==7641==    at 0x73AF360: ATL_dswap_xp0yp0aXbX (in /usr/lib/atlas/libatlas.so.3.0)
==7641==    by 0x73AF1A2: ATL_dswap (in /usr/lib/atlas/libatlas.so.3.0)
==7641==    by 0x722FEC7: atl_f77wrap_dswap_ (in 
/usr/lib/atlas/libptf77blas.so.3.0)
==7641==    by 0x7238C27: dswap_ (in /usr/lib/atlas/libptf77blas.so.3.0)
==7641==    by 0x79C405A: dsteqr_ (in /usr/lib/atlas/liblapack.so.3.0)
==7641==    by 0x79A8DB4: dsbevx_ (in /usr/lib/atlas/liblapack.so.3.0)
==7641==    by 0x7F56A85: f2py_rout_flapack_dsbevx (flapackmodule.c:25876)
==7641==    by 0x7F5ECB9: fortran_call (fortranobject.c:346)
==7641==    by 0x406CBB0: PyObject_Call (in /usr/lib/libpython3.3m.so.1.0)
==7641==    by 0x412096C: PyEval_EvalFrameEx (in /usr/lib/libpython3.3m.so.1.0)
==7641==    by 0x41236E4: PyEval_EvalFrameEx (in /usr/lib/libpython3.3m.so.1.0)
==7641==    by 0x4125713: PyEval_EvalCodeEx (in /usr/lib/libpython3.3m.so.1.0)
==7641==  Address 0x4c5e228 is 0 bytes after a block of size 16 alloc'd
==7641==    at 0x4029E3F: malloc (vg_replace_malloc.c:270)
==7641==    by 0x40B43D8: PyMem_Malloc (in /usr/lib/libpython3.3m.so.1.0)
==7641==    by 0x6D124C1: ??? (in 
/usr/lib/python3.3/site-packages/numpy/core/multiarray.cpython-33m.so)
==7641==    by 0x7F5F238: array_from_pyobj (fortranobject.c:630)
==7641==    by 0x7F5693F: f2py_rout_flapack_dsbevx (flapackmodule.c:25864)
==7641==    by 0x7F5ECB9: fortran_call (fortranobject.c:346)
==7641==    by 0x406CBB0: PyObject_Call (in /usr/lib/libpython3.3m.so.1.0)
==7641==    by 0x412096C: PyEval_EvalFrameEx (in /usr/lib/libpython3.3m.so.1.0)
==7641==    by 0x41236E4: PyEval_EvalFrameEx (in /usr/lib/libpython3.3m.so.1.0)
==7641==    by 0x4125713: PyEval_EvalCodeEx (in /usr/lib/libpython3.3m.so.1.0)
==7641==    by 0x41233A1: PyEval_EvalFrameEx (in /usr/lib/libpython3.3m.so.1.0)
==7641==    by 0x4125713: PyEval_EvalCodeEx (in /usr/lib/libpython3.3m.so.1.0)


Also, looking at the spec, it was running the python3 checks first.  I 
switched that to see what I would see with python2 and it doesn't fail, 
although I get plenty of warnings/notices:

+ python -c 'import scipy; scipy.test('\''full'\'')'
..............................................................................................................................................................................................................................K........................................................................................................K..................................................................K..K...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................!
 ..........
...........................................................SSSSSS......SSSSSS......SSSS..............................................................................................................................................................................................................................................................................................................................................................................K................................................................................................................................................................................................................SSSSS.K..........S.....................................................................................................................................................................................................................................................................................................................!
 ..........
.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................!
 ..........
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K..................................................................K................................................................................................................................................................KK.....................................................................................................................................................................!
 ..........
..................................................................................................................................................................................................F.................../builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/special/tests/test_basic.py:1645: 
RuntimeWarning: divide by zero encountered in iv
   c1 = special.iv(v, x)
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/special/tests/test_basic.py:1645: 
RuntimeWarning: overflow encountered in iv
   c1 = special.iv(v, x)
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/special/tests/test_basic.py:1646: 
RuntimeWarning: invalid value encountered in iv
   c2 = special.iv(v, x+0j)
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/special/tests/test_basic.py:1652: 
RuntimeWarning: divide by zero encountered in divide
   dc = abs(c1/c2 - 1)
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/special/tests/test_basic.py:1652: 
RuntimeWarning: invalid value encountered in divide
   dc = abs(c1/c2 - 1)
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/special/tests/test_basic.py:1659: 
RuntimeWarning: overflow encountered in iv
   assert_(dc[k] < 2e-7, (v[k], x[k], special.iv(v[k], x[k]), special.iv(v[k], 
x[k]+0j)))
F...................................................K.K........................................................./builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/special/tests/test_basic.py:153: 
RuntimeWarning: invalid value encountered in fdtri
   cephes.fdtri(1,1,0.5)
....................................................................................................................................................................................................................................................................................................................................K........K..............SSSSSSSS........................................................................................................................................................................................................................................................................................................................................./builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:4163: 
RuntimeWarning: overflow encountered in exp
   return exp(c*x-exp(x)-gamln(c))
............/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:4645: 
RuntimeWarning: invalid value encountered in sqrt
   vals = 2*(bt+1.0)*sqrt(b-2.0)/((b-3.0)*sqrt(b))
............................................................................................................................................................................................................................../builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:6787: 
RuntimeWarning: divide by zero encountered in log
   lvals = where(vals==0.0,0.0,log(vals))
............................S................/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/optimize/optimize.py:1605: 
RuntimeWarning: invalid value encountered in double_scalars
   tmp2 = (x - v)*(fx - fw)
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/optimize/optimize.py:1606: 
RuntimeWarning: invalid value encountered in double_scalars
   p = (x - v)*tmp2 - (x - w)*tmp1;
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/optimize/optimize.py:447: 
RuntimeWarning: invalid value encountered in subtract
   and max(abs(fsim[0] - fsim[1:])) <= ftol):
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/optimize/optimize.py:2105: 
RuntimeWarning: invalid value encountered in subtract
   if (fx2 - fval) > delta:
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/optimize/optimize.py:2113: 
RuntimeWarning: invalid value encountered in subtract
   if (2.0*(fx - fval) <= ftol*(abs(fx) + abs(fval)) + 1e-20): break
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:2421: 
RuntimeWarning: overflow encountered in double_scalars
   k = gd*g2c*g2cd - g1c**2 * g1cd**2
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:2421: 
RuntimeWarning: invalid value encountered in double_scalars
   k = gd*g2c*g2cd - g1c**2 * g1cd**2
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:1924: 
RuntimeWarning: invalid value encountered in double_scalars
   Lhat = muhat - Shat*mu
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:1222: 
RuntimeWarning: divide by zero encountered in log
   return log(self._pdf(x, *args))
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:2332: 
RuntimeWarning: divide by zero encountered in divide
   return where(b > 1, a/(b-1.0), inf)
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:2334: 
RuntimeWarning: divide by zero encountered in divide
   return where(b > 2, a*(a+1.0)/((b-2.0)*(b-1.0)), inf)
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:1676: 
RuntimeWarning: invalid value encountered in subtract
   mu2 = mu2p - mu*mu
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/optimize/optimize.py:1604: 
RuntimeWarning: invalid value encountered in double_scalars
   tmp1 = (x - w)*(fx - fv)
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/optimize/optimize.py:1873: 
RuntimeWarning: invalid value encountered in double_scalars
   w = xb - ((xb - xc)*tmp2 - (xb - xa)*tmp1) / denom
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:2980: 
RuntimeWarning: divide by zero encountered in double_scalars
   g1 = 2*(v2+2*v1-2)/(v2-6)*sqrt((2*v2-4)/(v1*(v2+v1-2)))
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:2980: 
RuntimeWarning: invalid value encountered in sqrt
   g1 = 2*(v2+2*v1-2)/(v2-6)*sqrt((2*v2-4)/(v1*(v2+v1-2)))
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:3192: 
RuntimeWarning: divide by zero encountered in divide
   val = (-1.0/c)**n * sum(comb(n,k)*(-1)**k / (1.0-c*k),axis=0)
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:4583: 
RuntimeWarning: overflow encountered in double_scalars
   var -= nc*nc*df* val1**2 / 2.0 / val2**2
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/optimize/optimize.py:2105: 
RuntimeWarning: invalid value encountered in double_scalars
   if (fx2 - fval) > delta:
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/optimize/optimize.py:2113: 
RuntimeWarning: invalid value encountered in double_scalars
   if (2.0*(fx - fval) <= ftol*(abs(fx) + abs(fval)) + 1e-20): break
./builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:1222: 
RuntimeWarning: invalid value encountered in log
   return log(self._pdf(x, *args))
/builddir/build/BUILDROOT/scipy-0.11.0-0.1.rc2.fc18.i386/usr/lib/python2.7/site-packages/scipy/stats/distributions.py:5025: 
RuntimeWarning: divide by zero encountered in divide
   return where(x < c, 2*x/c, 2*(1-x)/(1-c))
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

I don't know if any of these are normal.



-- 
Orion Poplawski
Technical Manager                     303-415-9701 x222
NWRA, Boulder Office                  FAX: 303-415-9702
3380 Mitchell Lane                       orion@nwra.com
Boulder, CO 80301                   http://www.nwra.com


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