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Dec 14, 2011, 1:12:50 AM12/14/11

to sage-release, Martin Albrecht

Hi,

I tried building sage-4.8.alpha5 on Ubuntu 11.10 64-bit, and was

disappointed when I try to start it and get a Segmentation fault

immediately on startup. Here is the traceback [5] below, which I

guess suggests an issue with Martin Albrecht's new matrix_modn code

that uses Linbox directly [1], which was evidently merged into

4.8.alpha3. To test this, I made a clone back to right before this

4260 was included (using [2]), and did "sage -br" and then "sage -ba".

Then I hit [3]. Then I rebuilt singular again, and hit [4], which

made me see that "sage -ba" doesn't work right -- it leaves old code

in devel/sage/build. ARGH. Anyways. So I manually deleted

devel/sage/build completely and do "sage -ba" again, and Sage actually

starts. So evidently "sage -ba" is broken.

To summarize: we will not release sage-4.8 until it builds out of the

box on at least Ubuntu 11.10.

[1] http://trac.sagemath.org/sage_trac/ticket/4260

[2] sage-4.8.alpha5$ ./sage -clone -r 16293 pre4260

sage-4.8.alpha5$ ./sage -ba

[3] "ImportError:

/home/wstein/sage/sage-4.8.alpha5/local/lib/libsingular.so: undefined

symbol: UP"

[4] "ImportError:

/home/wstein/sage/sage-4.8.alpha5/local/lib/python2.6/site-packages/sage/matrix/matrix_modn_dense_double.so:

undefined symbol: _ZNK7IntegercvlEv"

[5] Program received signal SIGSEGV, Segmentation fault.

0x0000000000012336 in ?? ()

(gdb) bt

#0 0x0000000000012336 in ?? ()

#1 0x00007fffdf226612 in __Pyx_check_binary_version () at

sage/matrix/matrix_modn_dense_float.cpp:17227

#2 initmatrix_modn_dense_float () at

sage/matrix/matrix_modn_dense_float.cpp:15808

#3 0x00007ffff7b1c625 in _PyImport_LoadDynamicModule (

name=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float",

pathname=0x7ffffffc70f0

"/home/wstein/sage/sage-4.8.alpha5/local/lib/python2.6/site-packages/sage/matrix/matrix_modn_dense_float.so",

fp=<optimized out>) at ./Python/importdl.c:53

#4 0x00007ffff7b1a6bc in import_submodule (mod=0x17df750,

subname=0x7ffffffc81cc "matrix_modn_dense_float",

fullname=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float") at

Python/import.c:2589

#5 0x00007ffff7b1a93f in load_next (mod=0x17df750, altmod=0x17df750,

p_name=<optimized out>,

buf=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float",

p_buflen=0x7ffffffc81b0)

at Python/import.c:2409

--

William Stein

Professor of Mathematics

University of Washington

http://wstein.org

Dec 14, 2011, 3:35:37 AM12/14/11

to sage-r...@googlegroups.com

On 2011-12-14 07:12, William Stein wrote:

> To summarize: we will not release sage-4.8 until it builds out of the

> box on at least Ubuntu 11.10.

Have you tried a different gcc version? That's an obvious thing to try> To summarize: we will not release sage-4.8 until it builds out of the

> box on at least Ubuntu 11.10.

if you get segmentation faults.

Dec 14, 2011, 6:30:55 AM12/14/11

to sage-r...@googlegroups.com

On Wednesday 14 December 2011, William Stein wrote:

> Hi,

> Hi,

Hi,

> [5] Program received signal SIGSEGV, Segmentation fault.

> 0x0000000000012336 in ?? ()

> (gdb) bt

> #0 0x0000000000012336 in ?? ()

> #1 0x00007fffdf226612 in __Pyx_check_binary_version () at

> sage/matrix/matrix_modn_dense_float.cpp:17227

> #2 initmatrix_modn_dense_float () at

> sage/matrix/matrix_modn_dense_float.cpp:15808

If I understand this backtrace correctly it crashes in the initialisation of

the module ("__Pyx_check_binary_version ()"). Is there any 11.10 box where I

can ssh into?

> #3 0x00007ffff7b1c625 in _PyImport_LoadDynamicModule (

> name=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float",

> pathname=0x7ffffffc70f0

> "/home/wstein/sage/sage-4.8.alpha5/local/lib/python2.6/site-packages/sage/m

> atrix/matrix_modn_dense_float.so", fp=<optimized out>) at

> ./Python/importdl.c:53

> #4 0x00007ffff7b1a6bc in import_submodule (mod=0x17df750,

> subname=0x7ffffffc81cc "matrix_modn_dense_float",

> fullname=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float") at

> Python/import.c:2589

> #5 0x00007ffff7b1a93f in load_next (mod=0x17df750, altmod=0x17df750,

> p_name=<optimized out>,

> buf=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float",

> p_buflen=0x7ffffffc81b0)

> at Python/import.c:2409

Cheers,

Martin

--

name: Martin Albrecht

_pgp: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99

_otr: 47F43D1A 5D68C36F 468BAEBA 640E8856 D7951CCF

_www: http://martinralbrecht.wordpress.com/

_jab: martinr...@jabber.ccc.de

Dec 14, 2011, 6:55:32 AM12/14/11

to sage-r...@googlegroups.com

On Wed, 14 Dec 2011 11:30:55 Martin Albrecht wrote:

> On Wednesday 14 December 2011, William Stein wrote:

> > Hi,

>

> Hi,

>

> > [5] Program received signal SIGSEGV, Segmentation fault.

> > 0x0000000000012336 in ?? ()

> > (gdb) bt

> > #0 0x0000000000012336 in ?? ()

> > #1 0x00007fffdf226612 in __Pyx_check_binary_version () at

> > sage/matrix/matrix_modn_dense_float.cpp:17227

> > #2 initmatrix_modn_dense_float () at

> > sage/matrix/matrix_modn_dense_float.cpp:15808

>

> If I understand this backtrace correctly it crashes in the initialisation of

> the module ("__Pyx_check_binary_version ()"). Is there any 11.10 box where

> I can ssh into?

>

> > #3 0x00007ffff7b1c625 in _PyImport_LoadDynamicModule (

> >

> > name=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float",

> > pathname=0x7ffffffc70f0

> >

> > "/home/wstein/sage/sage-4.8.alpha5/local/lib/python2.6/site-packages/sag

> > e/m atrix/matrix_modn_dense_float.so", fp=<optimized out>) at> On Wednesday 14 December 2011, William Stein wrote:

> > Hi,

>

> Hi,

>

> > [5] Program received signal SIGSEGV, Segmentation fault.

> > 0x0000000000012336 in ?? ()

> > (gdb) bt

> > #0 0x0000000000012336 in ?? ()

> > #1 0x00007fffdf226612 in __Pyx_check_binary_version () at

> > sage/matrix/matrix_modn_dense_float.cpp:17227

> > #2 initmatrix_modn_dense_float () at

> > sage/matrix/matrix_modn_dense_float.cpp:15808

>

> If I understand this backtrace correctly it crashes in the initialisation of

> the module ("__Pyx_check_binary_version ()"). Is there any 11.10 box where

> I can ssh into?

>

> > #3 0x00007ffff7b1c625 in _PyImport_LoadDynamicModule (

> >

> > name=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float",

> > pathname=0x7ffffffc70f0

> >

> > "/home/wstein/sage/sage-4.8.alpha5/local/lib/python2.6/site-packages/sag

> > ./Python/importdl.c:53

> > #4 0x00007ffff7b1a6bc in import_submodule (mod=0x17df750,

> >

> > subname=0x7ffffffc81cc "matrix_modn_dense_float",

> > fullname=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float")

> > at

> >

> > Python/import.c:2589

> > #5 0x00007ffff7b1a93f in load_next (mod=0x17df750, altmod=0x17df750,

> > p_name=<optimized out>,

> >

> > buf=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float",

> >

> > p_buflen=0x7ffffffc81b0)

> >

> > at Python/import.c:2409

>

gentoo. matrix_modn_dense_float and matrix_modn_dense_double should

both depend on givaro as well as linbox. That solved the issue for us and

I told Burcin about it but I haven't had time to open a ticket for it.

See

https://github.com/cschwan/sage-on-gentoo/issues/108

for how thing unfolded in sage-on-gentoo

Francois

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Dec 14, 2011, 7:10:11 AM12/14/11

to sage-r...@googlegroups.com

On Thu, 15 Dec 2011 00:55:32 Francois Bissey wrote:

> On Wed, 14 Dec 2011 11:30:55 Martin Albrecht wrote:

> > On Wednesday 14 December 2011, William Stein wrote:

> > > Hi,

> >

> > Hi,

> >

> > > [5] Program received signal SIGSEGV, Segmentation fault.

> > > 0x0000000000012336 in ?? ()

> > > (gdb) bt

> > > #0 0x0000000000012336 in ?? ()

> > > #1 0x00007fffdf226612 in __Pyx_check_binary_version () at

> > > sage/matrix/matrix_modn_dense_float.cpp:17227

> > > #2 initmatrix_modn_dense_float () at

> > > sage/matrix/matrix_modn_dense_float.cpp:15808

> >

> > If I understand this backtrace correctly it crashes in the

> > initialisation of the module ("__Pyx_check_binary_version ()"). Is

> > there any 11.10 box where I can ssh into?

> >

> > > #3 0x00007ffff7b1c625 in _PyImport_LoadDynamicModule (

> > >

> > > name=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float",

> > > pathname=0x7ffffffc70f0

> > >

> > > "/home/wstein/sage/sage-4.8.alpha5/local/lib/python2.6/site-packages

> > > /sag e/m atrix/matrix_modn_dense_float.so", fp=<optimized out>) at

> > > ./Python/importdl.c:53

> > > #4 0x00007ffff7b1a6bc in import_submodule (mod=0x17df750,

> > >

> > > subname=0x7ffffffc81cc "matrix_modn_dense_float",

> > > fullname=0x7ffffffc81c0

> > > "sage.matrix.matrix_modn_dense_float")

> > > at

> > >

> > > Python/import.c:2589

> > > #5 0x00007ffff7b1a93f in load_next (mod=0x17df750,

> > > altmod=0x17df750,

> > > p_name=<optimized out>,

> > >

> > > buf=0x7ffffffc81c0 "sage.matrix.matrix_modn_dense_float",

> > >

> > > p_buflen=0x7ffffffc81b0)

> > >

> > > at Python/import.c:2409

>

> I got that exact same problem the first time I built 4.8.alpha3 in sage-on-

> gentoo. matrix_modn_dense_float and matrix_modn_dense_double should

> both depend on givaro as well as linbox. That solved the issue for us and

> I told Burcin about it but I haven't had time to open a ticket for it.

> See

> https://github.com/cschwan/sage-on-gentoo/issues/108

> for how thing unfolded in sage-on-gentoo

>

I got a proper sage patch for it too since I was planning to open a ticket.

See attachment.

Dec 14, 2011, 10:03:37 PM12/14/11

to sage-r...@googlegroups.com

On Thu, 15 Dec 2011 at 01:10AM +1300, Francois Bissey wrote:

> I got a proper sage patch for it too since I was planning to open a ticket.

> See attachment.

> I got a proper sage patch for it too since I was planning to open a ticket.

> See attachment.

Your patch allows 4.8.alpha4 to start and pass doctests in sage/matrix

on my Ubuntu 11.10 machine. Other doctests are running, but I think

everything is okay.

Dan

--

--- Dan Drake

----- http://mathsci.kaist.ac.kr/~drake

-------

Dec 15, 2011, 5:48:14 AM12/15/11

to sage-r...@googlegroups.com, Martin Albrecht

This bug is now http://trac.sagemath.org/sage_trac/ticket/12157

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