Your message dated Wed, 14 Jul 2010 07:24:32 +0200
with message-id <[email protected]>
and subject line Re: [Python-modules-team] Bug#544274: python-numpy: "*** glibc
detected *** ... " error when running numpy.test()
has caused the Debian Bug report #544274,
regarding python-numpy: "*** glibc detected *** ... " error when running
numpy.test()
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
544274: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=544274
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: python-numpy
Version: 1:1.3.0-2
Severity: normal
Hi,
While running numpy.test(), it got hanged and shows
"*** glibc detected *** /usr/bin/python: free(): invalid next size (fast):
0x0000000001ac4d30 ***"
Here's the backtrace when run under gdb and forcing a break using ^C:
"Starting program: /usr/bin/python
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
[Thread debugging using libthread_db enabled]
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
Python 2.5.4 (r254:67916, Feb 18 2009, 03:00:47)
[GCC 4.3.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
(no debugging symbols found)
....
>>> import numpy
(no debugging symbols found)
....
>>> numpy.test()
Running unit tests for numpy
(no debugging symbols found)
....
NumPy version 1.3.0
NumPy is installed in /usr/lib/python2.5/site-packages/numpy
Python version 2.5.4 (r254:67916, Feb 18 2009, 03:00:47) [GCC 4.3.3]
nose version 0.11.1
(no debugging symbols found)
....
...................................................(no debugging symbols found)
................................SSSSSSSS..........................................................................................................................................................................................................................................................SSS.................................................................................................................................................................................(no
debugging symbols found)
................(no debugging symbols found)
...................K...............................................................................................................(no
debugging symbols found)
...........(no debugging symbols found)
(no debugging symbols found)
...........................(no debugging symbols found)
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
..............................*** glibc detected *** /usr/bin/python: free():
invalid next size (fast): 0x0000000001ac4d30 ***
^C
Program received signal SIGINT, Interrupt.
0x00007ffff72c2efe in ?? () from /lib/libc.so.6
(gdb) bt
#0 0x00007ffff72c2efe in ?? () from /lib/libc.so.6
#1 0x00007ffff7261b1e in ?? () from /lib/libc.so.6
#2 0x00007ffff725e1cb in free () from /lib/libc.so.6
#3 0x00007ffff7df2512 in ?? () from /lib64/ld-linux-x86-64.so.2
#4 0x00007ffff7decebf in ?? () from /lib64/ld-linux-x86-64.so.2
#5 0x00007ffff7df2761 in ?? () from /lib64/ld-linux-x86-64.so.2
#6 0x00007ffff7dee2d6 in ?? () from /lib64/ld-linux-x86-64.so.2
#7 0x00007ffff7df20fb in ?? () from /lib64/ld-linux-x86-64.so.2
#8 0x00007ffff72ec250 in ?? () from /lib/libc.so.6
#9 0x00007ffff7dee2d6 in ?? () from /lib64/ld-linux-x86-64.so.2
#10 0x00007ffff72ec305 in ?? () from /lib/libc.so.6
#11 0x00007ffff72ec3f7 in __libc_dlopen_mode () from /lib/libc.so.6
#12 0x00007ffff72caa55 in ?? () from /lib/libc.so.6
#13 0x00007ffff7bd1d03 in pthread_once () from /lib/libpthread.so.0
#14 0x00007ffff72cab7c in backtrace () from /lib/libc.so.6
#15 0x00007ffff7252d0c in ?? () from /lib/libc.so.6
#16 0x00007ffff725c6c8 in ?? () from /lib/libc.so.6
#17 0x00007ffff725e1d6 in free () from /lib/libc.so.6
#18 0x00007ffff5dae78c in ?? ()
from /usr/lib/python2.5/site-packages/numpy/core/multiarray.so
#19 0x000000000048cc5f in PyEval_EvalFrameEx ()
#20 0x0000000000491ce2 in PyEval_EvalFrameEx ()
#21 0x00000000004924cd in PyEval_EvalCodeEx ()
---Type <return> to continue, or q <return> to quit---
#22 0x0000000000490f18 in PyEval_EvalFrameEx ()
#23 0x00000000004924cd in PyEval_EvalCodeEx ()
#24 0x00000000004dca89 in ?? ()
#25 0x0000000000418843 in PyObject_Call ()
#26 0x000000000048fac7 in PyEval_EvalFrameEx ()
#27 0x00000000004924cd in PyEval_EvalCodeEx ()
#28 0x00000000004dc992 in ?? ()
#29 0x0000000000418843 in PyObject_Call ()
#30 0x000000000041f6e8 in ?? ()
#31 0x0000000000418843 in PyObject_Call ()
#32 0x000000000046648c in ?? ()
#33 0x0000000000418843 in PyObject_Call ()
#34 0x000000000048e061 in PyEval_EvalFrameEx ()
#35 0x0000000000491ce2 in PyEval_EvalFrameEx ()
#36 0x00000000004924cd in PyEval_EvalCodeEx ()
#37 0x00000000004dca89 in ?? ()
#38 0x0000000000418843 in PyObject_Call ()
#39 0x000000000048fac7 in PyEval_EvalFrameEx ()
#40 0x00000000004924cd in PyEval_EvalCodeEx ()
#41 0x00000000004dc992 in ?? ()
#42 0x0000000000418843 in PyObject_Call ()
#43 0x000000000041f6e8 in ?? ()
#44 0x0000000000418843 in PyObject_Call ()
---Type <return> to continue, or q <return> to quit---
#45 0x000000000046648c in ?? ()
#46 0x0000000000418843 in PyObject_Call ()
#47 0x000000000048e061 in PyEval_EvalFrameEx ()
#48 0x00000000004924cd in PyEval_EvalCodeEx ()
#49 0x00000000004dca89 in ?? ()
#50 0x0000000000418843 in PyObject_Call ()
#51 0x000000000048fac7 in PyEval_EvalFrameEx ()
#52 0x00000000004924cd in PyEval_EvalCodeEx ()
#53 0x00000000004dc992 in ?? ()
#54 0x0000000000418843 in PyObject_Call ()
#55 0x000000000041f6e8 in ?? ()
#56 0x0000000000418843 in PyObject_Call ()
#57 0x000000000046648c in ?? ()
#58 0x0000000000418843 in PyObject_Call ()
#59 0x000000000048e061 in PyEval_EvalFrameEx ()
#60 0x00000000004924cd in PyEval_EvalCodeEx ()
#61 0x00000000004dca89 in ?? ()
#62 0x0000000000418843 in PyObject_Call ()
#63 0x000000000048fac7 in PyEval_EvalFrameEx ()
#64 0x00000000004924cd in PyEval_EvalCodeEx ()
#65 0x00000000004dc992 in ?? ()
#66 0x0000000000418843 in PyObject_Call ()
#67 0x000000000041f6e8 in ?? ()
---Type <return> to continue, or q <return> to quit---
#68 0x0000000000418843 in PyObject_Call ()
#69 0x000000000046648c in ?? ()
#70 0x0000000000418843 in PyObject_Call ()
#71 0x000000000048e061 in PyEval_EvalFrameEx ()
#72 0x00000000004924cd in PyEval_EvalCodeEx ()
#73 0x00000000004dca89 in ?? ()
#74 0x0000000000418843 in PyObject_Call ()
#75 0x000000000048fac7 in PyEval_EvalFrameEx ()
#76 0x00000000004924cd in PyEval_EvalCodeEx ()
#77 0x00000000004dc992 in ?? ()
#78 0x0000000000418843 in PyObject_Call ()
#79 0x000000000041f6e8 in ?? ()
#80 0x0000000000418843 in PyObject_Call ()
#81 0x000000000046648c in ?? ()
#82 0x0000000000418843 in PyObject_Call ()
#83 0x000000000048e061 in PyEval_EvalFrameEx ()
#84 0x00000000004924cd in PyEval_EvalCodeEx ()
#85 0x00000000004dca89 in ?? ()
#86 0x0000000000418843 in PyObject_Call ()
#87 0x000000000048fac7 in PyEval_EvalFrameEx ()
#88 0x00000000004924cd in PyEval_EvalCodeEx ()
#89 0x00000000004dc992 in ?? ()
#90 0x0000000000418843 in PyObject_Call ()
---Type <return> to continue, or q <return> to quit---
#91 0x000000000041f6e8 in ?? ()
#92 0x0000000000418843 in PyObject_Call ()
#93 0x000000000046648c in ?? ()
#94 0x0000000000418843 in PyObject_Call ()
#95 0x000000000048e061 in PyEval_EvalFrameEx ()
#96 0x00000000004924cd in PyEval_EvalCodeEx ()
#97 0x00000000004dca89 in ?? ()
#98 0x0000000000418843 in PyObject_Call ()
#99 0x000000000048fac7 in PyEval_EvalFrameEx ()
#100 0x00000000004924cd in PyEval_EvalCodeEx ()
#101 0x00000000004dc992 in ?? ()
#102 0x0000000000418843 in PyObject_Call ()
#103 0x000000000041f6e8 in ?? ()
#104 0x0000000000418843 in PyObject_Call ()
#105 0x000000000046648c in ?? ()
#106 0x0000000000418843 in PyObject_Call ()
#107 0x000000000048e061 in PyEval_EvalFrameEx ()
#108 0x00000000004924cd in PyEval_EvalCodeEx ()
#109 0x00000000004dca89 in ?? ()
#110 0x0000000000418843 in PyObject_Call ()
#111 0x000000000048fac7 in PyEval_EvalFrameEx ()
#112 0x00000000004924cd in PyEval_EvalCodeEx ()
#113 0x00000000004dc992 in ?? ()
---Type <return> to continue, or q <return> to quit---
#114 0x0000000000418843 in PyObject_Call ()
#115 0x000000000041f6e8 in ?? ()
#116 0x0000000000418843 in PyObject_Call ()
#117 0x000000000046648c in ?? ()
#118 0x0000000000418843 in PyObject_Call ()
#119 0x000000000048e061 in PyEval_EvalFrameEx ()
#120 0x0000000000491ce2 in PyEval_EvalFrameEx ()
#121 0x0000000000491ce2 in PyEval_EvalFrameEx ()
#122 0x00000000004924cd in PyEval_EvalCodeEx ()
#123 0x00000000004dca89 in ?? ()
#124 0x0000000000418843 in PyObject_Call ()
#125 0x000000000041f6e8 in ?? ()
#126 0x0000000000418843 in PyObject_Call ()
#127 0x000000000048e061 in PyEval_EvalFrameEx ()
#128 0x00000000004924cd in PyEval_EvalCodeEx ()
#129 0x00000000004dca89 in ?? ()
#130 0x0000000000418843 in PyObject_Call ()
#131 0x000000000041f6e8 in ?? ()
#132 0x0000000000418843 in PyObject_Call ()
#133 0x0000000000465f66 in ?? ()
#134 0x000000000046e04b in ?? ()
#135 0x0000000000418843 in PyObject_Call ()
#136 0x000000000048e061 in PyEval_EvalFrameEx ()
---Type <return> to continue, or q <return> to quit---
#137 0x00000000004924cd in PyEval_EvalCodeEx ()
#138 0x0000000000490f18 in PyEval_EvalFrameEx ()
#139 0x00000000004924cd in PyEval_EvalCodeEx ()
#140 0x00000000004926c2 in PyEval_EvalCode ()
#141 0x00000000004b1c08 in PyRun_InteractiveOneFlags ()
#142 0x00000000004b1e3e in PyRun_InteractiveLoopFlags ()
#143 0x00000000004b251e in PyRun_AnyFileExFlags ()
#144 0x0000000000414572 in Py_Main ()
#145 0x00007ffff72095c6 in __libc_start_main () from /lib/libc.so.6
#146 0x00000000004139b9 in _start ()"
Don't know if it's a numpy or python problem, though.
Regards,
ST
-- System Information:
Debian Release: squeeze/sid
APT prefers unstable
APT policy: (900, 'unstable'), (500, 'transitional'), (500, 'gutsy'), (500,
'experimental'), (500, 'testing')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.30-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_HK.UTF-8, LC_CTYPE=en_US.UTF8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Versions of packages python-numpy depends on:
ii libatlas3gf-base [liblapack.s 3.6.0-24 Automatically Tuned Linear Algebra
ii libblas3gf [libblas.so.3gf] 1.2-2 Basic Linear Algebra Subroutines 3
ii libc6 2.9-25 GNU C Library: Shared libraries
ii libgcc1 1:4.4.1-3 GCC support library
ii libgfortran3 4.4.1-3 Runtime library for GNU Fortran ap
ii liblapack3gf [liblapack.so.3g 3.2.1-1 library of linear algebra routines
ii python 2.5.4-2 An interactive high-level object-o
ii python-central 0.6.11 register and build utility for Pyt
python-numpy recommends no packages.
Versions of packages python-numpy suggests:
ii python-nose 0.11.1-1 test discovery and running for Pyt
pn python-numpy-dbg <none> (no description available)
pn python-numpy-doc <none> (no description available)
-- no debconf information
--- End Message ---
--- Begin Message ---
Hi all,
On Tue, Jun 29, 2010 at 21:03, Sandro Tosi <[email protected]> wrote:
> tags 544274 + unreproducible moreinfo
> thanks
>
> Hi all,
>
> On Sun, Aug 30, 2009 at 11:25, LUK ShunTim <[email protected]> wrote:
>> Package: python-numpy
>> Version: 1:1.3.0-2
>> Severity: normal
>>
>> Hi,
>>
>> While running numpy.test(), it got hanged and shows
>>
>> "*** glibc detected *** /usr/bin/python: free(): invalid next size (fast):
>> 0x0000000001ac4d30 ***"
>
> Are you still able to replicate this? I am not with 1:1.3.0-3+b2. I'm
> on amd64 and I have libatlas3gf-base installed. Could you please let
> me know if the several update on the atlas side, and the -3 revision
> of numpy fixed this bug?
I followed the steps described by reporters in a clean chroot, and I
can't replicate the bug (sorry for the poor formatting that probably
will result):
# apt-get install python-numpy
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
libblas3gf libgfortran3 liblapack3gf libssl0.9.8 mime-support python
python-central python-minimal python2.6
python2.6-minimal
Suggested packages:
python-doc python-tk python-profiler python-numpy-doc
python-numpy-dbg python-nose python2.6-doc
python2.6-profiler binfmt-support
Recommended packages:
file
The following NEW packages will be installed:
libblas3gf libgfortran3 liblapack3gf libssl0.9.8 mime-support python
python-central python-minimal
python-numpy python2.6 python2.6-minimal
...
update-alternatives: using /usr/lib/libblas/libblas.so.3gf to provide
/usr/lib/libblas.so.3gf (libblas.so.3gf) in auto mode.
Setting up liblapack3gf (3.2.2-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3gf to provide
/usr/lib/liblapack.so.3gf (liblapack.so.3gf) in auto mode.
Setting up python-numpy (1:1.3.0-3+b2) ...
Processing triggers for python-central ...
# apt-get install python-nose
...
# python -c "import numpy ; numpy.test()"
Running unit tests for numpy
NumPy version 1.3.0
NumPy is installed in /usr/lib/python2.6/dist-packages/numpy
Python version 2.6.5+ (release26-maint, Jul 6 2010, 12:58:20) [GCC 4.4.4]
nose version 0.11.1
.................................................................................SSSSSSSS..........................................................................................................................................................................................................................................................SSS..................................................................................................................................................................................................................K.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 2016 tests in 4.711s
OK (KNOWNFAIL=1, SKIP=11)
r...@zion:/# apt-get install libatlas3gf-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following NEW packages will be installed:
libatlas3gf-base
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 0B/6745kB of archives.
After this operation, 21.4MB of additional disk space will be used.
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously deselected package libatlas3gf-base.
(Reading database ... 12568 files and directories currently installed.)
Unpacking libatlas3gf-base (from .../libatlas3gf-base_3.8.3-24_amd64.deb) ...
Setting up libatlas3gf-base (3.8.3-24) ...
update-alternatives: using /usr/lib/atlas-base/atlas/libblas.so.3gf to
provide /usr/lib/libblas.so.3gf (libblas.so.3gf) in auto mode.
update-alternatives: using /usr/lib/atlas-base/atlas/liblapack.so.3gf
to provide /usr/lib/liblapack.so.3gf (liblapack.so.3gf) in auto mode.
r...@zion:/# python -c "import numpy ; numpy.test()"
Running unit tests for numpy
NumPy version 1.3.0
NumPy is installed in /usr/lib/python2.6/dist-packages/numpy
Python version 2.6.5+ (release26-maint, Jul 6 2010, 12:58:20) [GCC 4.4.4]
nose version 0.11.1
.................................................................................SSSSSSSS..........................................................................................................................................................................................................................................................SSS..................................................................................................................................................................................................................K.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 2016 tests in 4.665s
OK (KNOWNFAIL=1, SKIP=11)
except for the different number of tests executed, probably due to
some capabilities detection in the test suite, the test() method
executes fine, hence I'm closing this bug.
Regards,
--
Sandro Tosi (aka morph, morpheus, matrixhasu)
My website: http://matrixhasu.altervista.org/
Me at Debian: http://wiki.debian.org/SandroTosi
--- End Message ---
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