Re: numpy errors in test-suite -- May 31, 2011 - 13:43

Hi Ed,

No problem. I just wanted you to know...

Thanks for trying to hunt down the problem !

Cheers,


Séb  :)


On 11-05-16 10:32 AM, Edward d'Auvergne wrote:
> Hi,
>
> This looks like a Numpy specific problem.  I have seen this as well
> using the 2.0.0 development version.  I would suggest waiting until a
> stable release of numpy 2 is made, or simply ignore the warnings for
> now.  I tried chasing down the exact location of these warnings but
> gave up in the end.  I think it is somewhere in minfx, but I could be
> wrong as I could not find the exact location.
>
> Regards,
>
> Edward
>
>
>
> On 25 April 2011 15:21, Sébastien Morin<sebastien.morin.1@xxxxxxxxx>  wrote:
> > Hi,
> >
> > As just discussed in a different post on the topic of the relax gui
> > (https://mail.gna.org/public/relax-devel/2011-04/msg00052.html ; #
> > Message-id:<4DB53313.7060505@xxxxxxxxx>), I manually switched to using
> > 32-bit python (2.6.6), numpy (1.5.1) and scipy (0.9.0) from fink (instead of
> > 64-bit python 2.6.1, numpy 2.0.0, and scipy 0.10.0 directly under Mac OS X).
> > As relax uses the "/usr/bin/env python" in order to get the python path
> > (header of executable file "relax"), I had to manually change it to
> > "/sw/bin/python2.6" (the fink path for python-2.6 binary) to do so.
> >
> > The unit tests all passed without the warnings discussed before (post at
> > https://mail.gna.org/public/relax-devel/2011-04/msg00050.html ; Message-id:
> > <4DB419A4.1030201@xxxxxxxxx>). The warnings were also absent from the system
> > tests, although 9 errors arose because of the unavailability of the C
> > modules (discussed at
> > https://mail.gna.org/public/relax-devel/2011-04/msg00052.html ; #
> > Message-id:<4DB53313.7060505@xxxxxxxxx>).
> >
> > Hence, it seems that these warnings arose because of either the numpy/scipy
> > version, or the 32-bit/64-bit issue...
> >
> > Is this worth fixing within relax's test-suite (as the tests passed, but
> > with warnings) ???
> >
> > All the best,
> >
> >
> > Séb  :)
> >
> >
> > On 11-04-24 2:37 PM, Sébastien Morin wrote:
> > > Hi,
> > >
> > > I just ran the numpy test in python with "numpy.test()" and it passed with
> > > the following message:
> > >
> > >     OK (KNOWNFAIL=3, SKIP=1)
> > > <nose.result.TextTestResult run=3399 errors=0 failures=0>
> > >
> > > However, scipy (ran with "scipy.test()") got4 errors and 1 failure:
> > >
> > >     FAILED (KNOWNFAIL=12, SKIP=42, errors=4, failures=1)
> > > <nose.result.TextTestResult run=4766 errors=4 failures=1>
> > >
> > > The 4 errors were:
> > >
> > >     ERROR: test_complex_nonsymmetric_modes
> > > (test_arpack.TestEigenComplexNonSymmetric)
> > >     ERROR: test_complex_symmetric_modes
> > > (test_arpack.TestEigenComplexSymmetric)
> > >     ERROR: test_nonsymmetric_modes (test_arpack.TestEigenNonSymmetric)
> > >     ERROR: test_starting_vector (test_arpack.TestEigenNonSymmetric)
> > >
> > > and originated from the same problem:
> > >
> > >     ArpackError: ARPACK error -8: Error return from trid. eigenvalue
> > > calculation; Informational error from LAPACK routine dsteqr.
> > >
> > > The failure was:
> > >
> > >     FAIL: test_expon (test_morestats.TestAnderson)
> > >
> > >
> > > Any idea if these problems cause the warning in relax's test-suite ?
> > >
> > > Thanks !
> > >
> > >
> > > Séb  :)
> > >
> > >
> > >
> > > On 11-04-24 2:00 PM, Sébastien Morin wrote:
> > > > Hi,
> > > >
> > > > When running relax's test-suite on Mac OS X, I get many times this
> > > > warning (although both the unit tests and system tests pass):
> > > >
> > > >       "Warning: invalid value encountered in double_scalars"
> > > >
> > > > This originated after my installation of numpy (version
> > > > 2.0.0.dev-ac2c160, running with scipy-0.10.0.dev) with relax-1.3 from
> > > > the repository (r12825).
> > > >
> > > > Any idea was causes these warnings and if they are important ?
> > > >
> > > > Thanks !
> > > >
> > > >
> > > > Séb
> > --
> > Sébastien Morin, Ph.D.
> > Postdoctoral fellow
> > S. Grzesiek NMR Laboratory
> > Biozentrum, Universität Basel
> > Basel, Switzerland
> >
> >
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> >
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--
Sébastien Morin, Ph.D.
Postdoctoral Fellow, S. Grzesiek NMR Laboratory
Department of Structural Biology
Biozentrum, Universität Basel
Klingelbergstrasse 70
4056 Basel
Switzerland