[gentoo-science] notebook backtrace

[gentoo-science] notebook backtrace

[Steven Trogdon]

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Hello,

Has anyone experienced the following after closing a worksheet and then  
the notebook? I believe I've seen something similar on another  
(sage-4.4) occasion unrelated to the notebook.

Steve

----------------------------------------------------------------------
| Sage Version 4.4, Release Date: 2010-04-24                         |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------
sage: notebook()
The notebook files are stored in: sage_notebook.sagenb
**************************************************
*                                                *
* Open your web browser to http://localhost:8000 *
*                                                *
**************************************************
2010-04-29 10:11:49-0500 [-] Log opened.
2010-04-29 10:11:49-0500 [-] twistd 9.0.0 (/usr/bin/python2.6 2.6.4)  
starting up.
2010-04-29 10:11:49-0500 [-] reactor class:  
twisted.internet.selectreactor.SelectReactor.
2010-04-29 10:11:50-0500 [-] twisted.web2.channel.http.HTTPFactory  
starting on 8000
2010-04-29 10:11:50-0500 [-] Starting factory  
<twisted.web2.channel.http.HTTPFactory instance at 0x4001bd8>
^C2010-04-29 10:14:11-0500 [-] Quitting all running worksheets...
2010-04-29 10:14:11-0500 [-] Saving notebook...
2010-04-29 10:14:12-0500 [-] Notebook cleanly saved.
2010-04-29 10:14:12-0500 [-] (Port 8000 Closed)
2010-04-29 10:14:12-0500 [-] Stopping factory  
<twisted.web2.channel.http.HTTPFactory instance at 0x4001bd8>
2010-04-29 10:14:12-0500 [-] Main loop terminated.
2010-04-29 10:14:12-0500 [-] Server Shut Down.
*** glibc detected *** /usr/bin/python2.6: corrupted double-linked  
list: 0x0000000002932b60 ***
======= Backtrace: =========
/lib/libc.so.6[0x7f4d195f0808]
/lib/libc.so.6[0x7f4d195f0b00]
/lib/libc.so.6[0x7f4d195f2078]
/lib/libc.so.6(cfree+0x6c)[0x7f4d195f524c]
/lib/libc.so.6[0x7f4d195b1ea5]
/lib/libc.so.6[0x7f4d195b1ef5]
/lib/libc.so.6(__libc_start_main+0xed)[0x7f4d1959ba2d]
/usr/bin/python2.6[0x400789]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:03  
6523994                            /usr/bin/python2.6
00600000-00601000 r--p 00000000 08:03  
6523994                            /usr/bin/python2.6
00601000-00602000 rw-p 00001000 08:03  
6523994                            /usr/bin/python2.6
00602000-04521000 rw-p 00000000 00:00  
0                                  [heap]
7f4ceb4fa000-7f4ceb4fb000 r-xp 00000000 08:03  
6439827                     
/usr/lib64/python2.6/site-packages/gnutls/library/_init.so
7f4ceb4fb000-7f4ceb6fa000 ---p 00001000 08:03  
6439827                     
/usr/lib64/python2.6/site-packages/gnutls/library/_init.so
7f4ceb6fa000-7f4ceb6fb000 r--p 00000000 08:03  
6439827                     
/usr/lib64/python2.6/site-packages/gnutls/library/_init.so
7f4ceb6fb000-7f4ceb6fc000 rw-p 00001000 08:03  
6439827                     
/usr/lib64/python2.6/site-packages/gnutls/library/_init.so
7f4ceb6fc000-7f4ceb703000 r-xp 00000000 08:03  
7096149                    /usr/lib64/libgnutls-extra.so.26.14.12
7f4ceb703000-7f4ceb902000 ---p 00007000 08:03  
7096149                    /usr/lib64/libgnutls-extra.so.26.14.12
7f4ceb902000-7f4ceb903000 r--p 00006000 08:03  
7096149                    /usr/lib64/libgnutls-extra.so.26.14.12
7f4ceb903000-7f4ceb904000 rw-p 00007000 08:03  
7096149                    /usr/lib64/libgnutls-extra.so.26.14.12
7f4ceb904000-7f4ceb907000 r-xp 00000000 08:03  
7982983                    /usr/lib64/libgpg-error.so.0.5.0
7f4ceb907000-7f4cebb06000 ---p 00003000 08:03  
7982983                    /usr/lib64/libgpg-error.so.0.5.0
7f4cebb06000-7f4cebb07000 r--p 00002000 08:03  
7982983                    /usr/lib64/libgpg-error.so.0.5.0
7f4cebb07000-7f4cebb08000 rw-p 00003000 08:03  
7982983                    /usr/lib64/libgpg-error.so.0.5.0
7f4cebb08000-7f4cebb7b000 r-xp 00000000 08:03  
6424259                    /usr/lib64/libgcrypt.so.11.5.3
7f4cebb7b000-7f4cebd7a000 ---p 00073000 08:03  
6424259                    /usr/lib64/libgcrypt.so.11.5.3
7f4cebd7a000-7f4cebd7b000 r--p 00072000 08:03  
6424259                    /usr/lib64/libgcrypt.so.11.5.3
7f4cebd7b000-7f4cebd7e000 rw-p 00073000 08:03  
6424259                    /usr/lib64/libgcrypt.so.11.5.3
7f4cebd7e000-7f4cebd8e000 r-xp 00000000 08:03  
6423324                    /usr/lib64/libtasn1.so.3.1.7
7f4cebd8e000-7f4cebf8d000 ---p 00010000 08:03  
6423324                    /usr/lib64/libtasn1.so.3.1.7
7f4cebf8d000-7f4cebf8e000 r--p 0000f000 08:03  
6423324                    /usr/lib64/libtasn1.so.3.1.7
7f4cebf8e000-7f4cebf8f000 rw-p 00010000 08:03  
6423324                    /usr/lib64/libtasn1.so.3.1.7
7f4cebf8f000-7f4cec02c000 r-xp 00000000 08:03  
7096159                    /usr/lib64/libgnutls.so.26.14.12
7f4cec02c000-7f4cec22c000 ---p 0009d000 08:03  
7096159                    /usr/lib64/libgnutls.so.26.14.12
7f4cec22c000-7f4cec232000 r--p 0009d000 08:03  
7096159                    /usr/lib64/libgnutls.so.26.14.12
7f4cec232000-7f4cec233000 rw-p 000a3000 08:03  
7096159                    /usr/lib64/libgnutls.so.26.14.12
7f4cec233000-7f4cec234000 rw-p 00000000 00:00 0
7f4cec234000-7f4cec23c000 r-xp 00000000 08:03  
6524039                    /usr/lib64/python2.6/lib-dynload/array.so
7f4cec23c000-7f4cec43b000 ---p 00008000 08:03  
6524039                    /usr/lib64/python2.6/lib-dynload/array.so
7f4cec43b000-7f4cec43c000 r--p 00007000 08:03  
6524039                    /usr/lib64/python2.6/lib-dynload/array.so
7f4cec43c000-7f4cec43e000 rw-p 00008000 08:03  
6524039                    /usr/lib64/python2.6/lib-dynload/array.so
7f4cec43e000-7f4cec43f000 r-xp 00000000 08:03  
6916193                     
/usr/lib64/python2.6/site-packages/twisted/protocols/_c_urlarg.so
7f4cec43f000-7f4cec63f000 ---p 00001000 08:03  
6916193                     
/usr/lib64/python2.6/site-packages/twisted/protocols/_c_urlarg.so
7f4cec63f000-7f4cec640000 r--p 00001000 08:03  
6916193                     
/usr/lib64/python2.6/site-packages/twisted/protocols/_c_urlarg.so
7f4cec640000-7f4cec641000 rw-p 00002000 08:03  
6916193                     
/usr/lib64/python2.6/site-packages/twisted/protocols/_c_urlarg.so
7f4cec641000-7f4cec649000 r-xp 00000000 08:03  
6605568                     
/usr/lib64/python2.6/site-packages/Crypto/Cipher/AES.so
7f4cec649000-7f4cec848000 ---p 00008000 08:03  
6605568                     
/usr/lib64/python2.6/site-packages/Crypto/Cipher/AES.so
7f4cec848000-7f4cec849000 r--p 00007000 08:03  
6605568                     
/usr/lib64/python2.6/site-packages/Crypto/Cipher/AES.so
7f4cec849000-7f4cec84a000 rw-p 00008000 08:03  
6605568                     
/usr/lib64/python2.6/site-packages/Crypto/Cipher/AES.so
7f4cec84a000-7f4cec84d000 r-xp 00000000 08:03  
6605769                     
/usr/lib64/python2.6/site-packages/Crypto/Util/_counter.so
7f4cec84d000-7f4ceca4c000 ---p 00003000 08:03  
6605769                     
/usr/lib64/python2.6/site-packages/Crypto/Util/_counter.so
7f4ceca4c000-7f4ceca4d000 r--p 00002000 08:03  
6605769                     
/usr/lib64/python2.6/site-packages/Crypto/Util/_counter.so
7f4ceca4d000-7f4ceca4e000 rw-p 00003000 08:03  
6605769                     
/usr/lib64/python2.6/site-packages/Crypto/Util/_counter.so
7f4ceca4e000-7f4ceca52000 r-xp 00000000 08:03  
6605569                     
/usr/lib64/python2.6/site-packages/Crypto/PublicKey/_fastmath.soTrue


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Re: [gentoo-science] notebook backtrace

[François Bissey]

> Hello,
> 
> Has anyone experienced the following after closing a worksheet and then
> the notebook? I believe I've seen something similar on another
> (sage-4.4) occasion unrelated to the notebook.
> 
If you only saw that in sage, that could point to twisted-web2 which is a real
piece of garbage abandoned upstream but that sage-notebook doesn't want
to let go. If it is not related to the notebook at all, then that's a problem 
that could creep into other non-sage apps in my opinion.
Did you use anything special in that worksheet? maxima, etc...?

Francois

Re: [gentoo-science] notebook backtrace

[Steven Trogdon]

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On   04/29/10 - 19:18:03, François Bissey wrote:
> > Hello,
> >
> > Has anyone experienced the following after closing a worksheet and  
> then
> > the notebook? I believe I've seen something similar on another
> > (sage-4.4) occasion unrelated to the notebook.
> >
> If you only saw that in sage, that could point to twisted-web2 which  
> is a real
> piece of garbage abandoned upstream but that sage-notebook doesn't  
> want
> to let go. If it is not related to the notebook at all, then that's a  
> problem
> that could creep into other non-sage apps in my opinion.
> Did you use anything special in that worksheet? maxima, etc...?
> 
> Francois
> 
Hi François,

There was only plotting in the worksheet. I'm thinking it's something  
other than the notebook. I ran the test suite on sage-4.4 and there are  
lots of these backtrace dumps with

	/usr/bin/python2.6: corrupted double-linked list

issues. I reverted back to 4.3.5 in an attempt to get "sane" test  
results. I'm unable to get the same test results; although there are no  
backtrace dumps! There has been several upgrades (flint, fplll,  
sqlalchemy, maxima, ..., etc) since previous tests and, as much as  
possible, I've reverted back to previous versions but still the tests  
don't match. The first failing test (sage-4.3.5) that passed previously  
is

sage -t -force_lib "devel/sage/doc/en/tutorial/tour_advanced.rst"
**********************************************************************
File "/opt/sage/devel/sage/doc/en/tutorial/tour_advanced.rst", line 358:
     sage: G.gens()
Expected:
     (Dirichlet character modulo 20 of conductor 4 mapping 11 |--> -1,  
17 |--> 1,
     Dirichlet character modulo 20 of conductor 5 mapping 11 |--> 1, 17  
|--> i)
Got:
     ([-1, 1], [1, i])
**********************************************************************

I'd be interested in your 4.4 test results. Maybe there's something  
I've missed.

Steve

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Re: [gentoo-science] notebook backtrace

[François Bissey]

> On   04/29/10 - 19:18:03, François Bissey wrote:
> > > Hello,
> > > 
> > > Has anyone experienced the following after closing a worksheet and
> > 
> > then
> > 
> > > the notebook? I believe I've seen something similar on another
> > > (sage-4.4) occasion unrelated to the notebook.
> > 
> > If you only saw that in sage, that could point to twisted-web2 which
> > is a real
> > piece of garbage abandoned upstream but that sage-notebook doesn't
> > want
> > to let go. If it is not related to the notebook at all, then that's a
> > problem
> > that could creep into other non-sage apps in my opinion.
> > Did you use anything special in that worksheet? maxima, etc...?
> > 
> > Francois
> 
> Hi François,
> 
> There was only plotting in the worksheet. I'm thinking it's something
> other than the notebook. I ran the test suite on sage-4.4 and there are
> lots of these backtrace dumps with
> 
> 	/usr/bin/python2.6: corrupted double-linked list
Are you using python-2.6.4-r99 (recommended) or python-2.6.5-r99
(not recommended)?

Francois

Re: [gentoo-science] notebook backtrace

[Steven Trogdon]

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On   04/29/10 - 20:09:10, François Bissey wrote:
> > On   04/29/10 - 19:18:03, François Bissey wrote:
> 
> Are you using python-2.6.4-r99 (recommended) or python-2.6.5-r99
> (not recommended)?
> 
> Francois
> 

python-2.6.4-r99

Steve

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Re: [gentoo-science] notebook backtrace

[François Bissey]

> sage -t -force_lib "devel/sage/doc/en/tutorial/tour_advanced.rst"
That particular one works for me. I am running the full test suite at 
the moment. I will probably run the tests on ppc over the week end
as well, that may be interesting.

The only thing that jump at my mind for that test would be 
scipy. You should have 0.7.1 not 0.7.2 as there has been a change
of interface, that would do that kind of things I think.
But that's a shot in the dark and that wouldn't solve the first
problem you reported.

Francois

Re: [gentoo-science] notebook backtrace

[Steven Trogdon]

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On   04/29/10 - 20:54:32, François Bissey wrote:
> > sage -t -force_lib "devel/sage/doc/en/tutorial/tour_advanced.rst"
> That particular one works for me. I am running the full test suite at
> the moment. I will probably run the tests on ppc over the week end
> as well, that may be interesting.
> 
> The only thing that jump at my mind for that test would be
> scipy. You should have 0.7.1 not 0.7.2 as there has been a change
> of interface, that would do that kind of things I think.
> But that's a shot in the dark and that wouldn't solve the first
> problem you reported.
> 
> Francois
> 
François,

Apparently in masking sage-4.4 to revert to 4.3.5 I had neglected to  
mask sage-doc-4.4. I had the wrong sage-doc installed for the test! In  
reverting to 4.3.5 other test failures were due to scipy as you  
indicate and others were due to matplotlib. I now have been able to  
reproduce test results I had previously for 4.3.5. Upon then upgrading  
to 4.4 I have _many_ failures of the "type" indicated in the first post  
of this thread; i.e. of the "type"

*** glibc detected *** /usr/bin/python2.6: corrupted double-linked list:

with an associated backtrace and memory dump. I suppose Christopher  
will observe the same on his amd64.

Steve


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Re: [gentoo-science] notebook backtrace

[François Bissey]

> Apparently in masking sage-4.4 to revert to 4.3.5 I had neglected to  
> mask sage-doc-4.4. I had the wrong sage-doc installed for the test! In  
> reverting to 4.3.5 other test failures were due to scipy as you  
> indicate and others were due to matplotlib. I now have been able to  
> reproduce test results I had previously for 4.3.5. Upon then upgrading  
> to 4.4 I have many failures of the "type" indicated in the first post  
> of this thread; i.e. of the "type"
> 
> *** glibc detected *** /usr/bin/python2.6: corrupted double-linked list:
> 
> with an associated backtrace and memory dump. I suppose Christopher  
> will observe the same on his amd64.
For the record on x86 I have a number of tests failing due to 
maxima-5.21.1/ecls-10.4. Hopefully those will go away in sage-4.4.1.
Most of the other failures are old.
I do not have anything like you do. What is worrying is I am guessing you
don't see any patterns in the failures. If it is all over the place I would 
have a serious look at sage-lib and sage-core.

Francois

Re: [gentoo-science] notebook backtrace

[Steven Trogdon]

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On   04/30/10 - 17:15:49, François Bissey wrote:
> For the record on x86 I have a number of tests failing due to
> maxima-5.21.1/ecls-10.4. Hopefully those will go away in sage-4.4.1.
> Most of the other failures are old.
> I do not have anything like you do. What is worrying is I am guessing  
> you
> don't see any patterns in the failures. If it is all over the place I  
> would
> have a serious look at sage-lib and sage-core.
> 
> Francois
> 

I have ~130 failures of the indicated type. It would be tough to check  
all of them, but a good number have

/usr/lib64/python2.6/site-packages/sage/libs/flint/flint.so

appearing first in the memory dump. Do you know of anything significant  
that was changed in going from 4.3.5 -> 4.4?

Steve

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Re: [gentoo-science] notebook backtrace

[François Bissey]

> I have ~130 failures of the indicated type. It would be tough to check  
> all of them, but a good number have
> 
> /usr/lib64/python2.6/site-packages/sage/libs/flint/flint.so
> 
> appearing first in the memory dump. Do you know of anything significant  
> that was changed in going from 4.3.5 -> 4.4?
Going from flint-1.5.1 to flint-1.5.2 is a good start, further it appears that 
sage ship only flint-1.5.0 so that could be a possible culprit.

Francois