NetBSD Problem Report #47683

From www@NetBSD.org  Fri Mar 22 14:13:58 2013
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Date: Fri, 22 Mar 2013 14:13:56 +0000 (UTC)
From: joern.clausen@uni-bielefeld.de
Reply-To: joern.clausen@uni-bielefeld.de
To: gnats-bugs@NetBSD.org
Subject: math/py-scipy fails unit test, segfaults in liblapack.so
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>Number:         47683
>Category:       pkg
>Synopsis:       math/py-scipy fails unit test, segfaults in liblapack.so
>Confidential:   no
>Severity:       serious
>Priority:       low
>Responsible:    markd
>State:          open
>Class:          sw-bug
>Submitter-Id:   net
>Arrival-Date:   Fri Mar 22 14:15:00 +0000 2013
>Last-Modified:  Wed Apr 17 07:00:07 +0000 2013
>Originator:     Jörn Clausen
>Release:        
>Organization:
University of Bielefeld
>Environment:
NetBSD 6.0/amd64
>Description:
After installing math/py-scipy and devel/py-nose, the unit test bails out with a segmentation fault. gdb reveals this:

#0  0x00007f7ff1cd7598 in cladiv_ () from /usr/pkg/lib/liblapack.so.3
#1  0x00007f7fde8432e9 in wcladiv_ () from /usr/pkg/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
#2  0x00007f7fde83e6eb in clahqr_ () from /usr/pkg/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
#3  0x00007f7fde844aa3 in cneigh_ () from /usr/pkg/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
#4  0x00007f7fde84396a in cnaup2_ () from /usr/pkg/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
#5  0x00007f7fde81f1ce in cnaupd_ () from /usr/pkg/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
#6  0x00007f7fde81990e in f2py_rout__arpack_cnaupd ()
   from /usr/pkg/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
#7  0x00007f7ff784632f in PyObject_Call () from /usr/pkg/lib/libpython2.7.so.1.0
#8  0x00007f7ff78cd5c7 in PyEval_EvalFrameEx () from /usr/pkg/lib/libpython2.7.so.1.0
#9  0x00007f7ff78d05ca in PyEval_EvalCodeEx () from /usr/pkg/lib/libpython2.7.so.1.0
...

and about 160 more function calls.
>How-To-Repeat:
See INSTALL.txt from py-scipy: Install math/py-scipy and devel/py-nose, run python:

   >>> import scipy
   >>> scipy.test()

>Fix:

>Release-Note:

>Audit-Trail:

Responsible-Changed-From-To: pkg-manager->markd
Responsible-Changed-By: obache@NetBSD.org
Responsible-Changed-When: Thu, 11 Apr 2013 13:01:49 +0000
Responsible-Changed-Why:
Over to maintainer of math/py-scipy


From: Mark Davies <mark@ecs.vuw.ac.nz>
To: gnats-bugs@netbsd.org
Cc: 
Subject: Re: pkg/47683 (math/py-scipy fails unit test, segfaults in liblapack.so)
Date: Sun, 14 Apr 2013 12:36:25 +1200

 Does the newly committed 0.12.0 still segfault for you?  I couldn't 
 reproduce on NetBSD-6.0_STABLE/i386 or 64bit ArchLinux.

 mark

From: =?ISO-8859-1?Q?J=F6rn_Clausen?= <joern.clausen@uni-bielefeld.de>
To: gnats-bugs@NetBSD.org
Cc: Mark Davies <mark@ecs.vuw.ac.nz>, markd@NetBSD.org, gnats-admin@NetBSD.org,
 pkgsrc-bugs@NetBSD.org
Subject: Re: pkg/47683 (math/py-scipy fails unit test,
 segfaults in liblapack.so)
Date: Mon, 15 Apr 2013 13:25:19 +0200

 On 14.04.13 02:40, Mark Davies wrote:
 >   Does the newly committed 0.12.0 still segfault for you?  I couldn't
 >   reproduce on NetBSD-6.0_STABLE/i386 or 64bit ArchLinux.

 It fails differently. Again, scipy.test() in GDB:

 #0  0x00007f7ff1606f10 in d_cnjg () from /usr/pkg/lib/libf2c.so.0
 #1  0x00007f7ff1a3cd1e in zdotc_ () from /usr/pkg/lib/libblas.so.1
 #2  0x00007f7fe38212ac in wzdotc_ () from 
 /usr/pkg/lib/python2.7/site-packages/scipy/linalg/_fblas.so
 #3  0x00007f7fe381b567 in f2py_rout__fblas_zdotc () from 
 /usr/pkg/lib/python2.7/site-packages/scipy/linalg/_fblas.so
 #4  0x00007f7ff78467ff in PyObject_Call () from 
 /usr/pkg/lib/libpython2.7.so.1.0
 #5  0x00007f7ff78cef17 in PyEval_EvalFrameEx () from 
 /usr/pkg/lib/libpython2.7.so.1.0
 #6  0x00007f7ff78d1f1a in PyEval_EvalCodeEx () from 
 /usr/pkg/lib/libpython2.7.so.1.0

 math/blas and lang/f2c are up to date.

 Joern

 -- 
   Jörn Clausen                             joern.clausen@uni-bielefeld.de
   Hochschulrechenzentrum                 http://www.uni-bielefeld.de/hrz/
   Universität Bielefeld

From: =?ISO-8859-1?Q?J=F6rn_Clausen?= <joern.clausen@uni-bielefeld.de>
To: gnats-bugs@NetBSD.org
Cc: markd@NetBSD.org, gnats-admin@NetBSD.org, pkgsrc-bugs@NetBSD.org
Subject: Re: pkg/47683 (math/py-scipy fails unit test,
 segfaults in liblapack.so)
Date: Wed, 17 Apr 2013 08:56:43 +0200

 The good news is, that now the self-test completes on Solaris/i86. It 
 throws a bunch of warnings, but it doesn't stop with an exception.

 -- 
   Jörn Clausen                             joern.clausen@uni-bielefeld.de
   Hochschulrechenzentrum                 http://www.uni-bielefeld.de/hrz/
   Universität Bielefeld

>Unformatted:

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