Re: [sage-devel] Debugging some cython code / Pynac

2011-04-02 Thread Dr. David Kirkby 

On 04/ 1/11 11:46 PM, Burcin Erocal wrote:

On Fri, 01 Apr 2011 17:20:57 +0100
Dr. David Kirkbydavid.kir...@onetel.net  wrote:


On 04/ 1/11 12:54 PM, Burcin Erocal wrote:

On Fri, 01 Apr 2011 00:37:46 +0100
Dr. David Kirkbydavid.kir...@onetel.net   wrote:


I've built Sage 64-bit on OpenSolaris but it crashes at startup. I've
run gdb and find the bit of code that's causing the crash is this.



It seems that cones.py looks for posets.py, which needs the graphs
module, which initializes the graph_editor. The graph editor tries to
see if it's in the notebook or the command line, but sagenb imports SR
and Expression from sage.symbolic.all (line 563 of
sagenb/misc/support.py). This tries to initialize the functions
(integrate in this case) before pynac is initialized...

We need a better solution for making sure modules are initialized
properly before anything is imported from them. I thought putting an
__init__.py file in sage/symbolic/ with import pynac would solve the
problem. However, it seems that python just ignores that file.

Any suggestions on how to solve the general problem properly?



BTW, telling people to import from .all if they are outside the current
module is just asking for trouble. We can't put initialization code in
all.py, since it would just get imported to the main namespace.


Cheers,
Burcin



This issue is now

http://trac.sagemath.org/sage_trac/ticket/6


--
A: Because it messes up the order in which people normally read text.
Q: Why is top-posting such a bad thing?
A: Top-posting.
Q: What is the most annoying thing in e-mail?

Dave

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Re: [sage-devel] Debugging some cython code / Pynac

2011-04-01 Thread Burcin Erocal 
On Fri, 01 Apr 2011 00:37:46 +0100
Dr. David Kirkby david.kir...@onetel.net wrote:

 I've built Sage 64-bit on OpenSolaris but it crashes at startup. I've
 run gdb and find the bit of code that's causing the crash is this.
 
 ./devel/sage-main/sage/symbolic/function.cpp
 
 
   /* sage/symbolic/function.pyx:109
   * raise ValueError,  real_fname +  parameter must
 be callable *
   * if not self._is_registered(): # 
   * self._register_function()
   *
   */
snip
 allows Sage to run. It's not 100% stable, but much better than before.
 
snip
 Can anyone see if there might be something wrong with this code,
 which is causing Sage to segfault?

It might be due to the linker initializing the library in a different
order. Can you post a backtrace so we can see which function it is
trying to construct?

Moving the lines

# This must come before Calculus -- it initializes the Pynac library.
import sage.symbolic.pynac

in sage/all.py higher in the file might work around this problem. The
correct solution would be to import the offending function lazily or
locally.


Cheers,
Burcin

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Re: [sage-devel] Debugging some cython code / Pynac

2011-04-01 Thread David Kirkby 
On 1 April 2011 12:54, Burcin Erocal bur...@erocal.org wrote:
 On Fri, 01 Apr 2011 00:37:46 +0100
 Dr. David Kirkby david.kir...@onetel.net wrote:

 I've built Sage 64-bit on OpenSolaris but it crashes at startup. I've
 run gdb and find the bit of code that's causing the crash is this.

 ./devel/sage-main/sage/symbolic/function.cpp


   /* sage/symbolic/function.pyx:109
   *                 raise ValueError,  real_fname +  parameter must
 be callable *
   *         if not self._is_registered():             # 
   *             self._register_function()
   *
   */
 snip
 allows Sage to run. It's not 100% stable, but much better than before.

 snip
 Can anyone see if there might be something wrong with this code,
 which is causing Sage to segfault?

 It might be due to the linker initializing the library in a different
 order. Can you post a backtrace so we can see which function it is
 trying to construct?

 Moving the lines

 # This must come before Calculus -- it initializes the Pynac library.
 import sage.symbolic.pynac

 in sage/all.py higher in the file might work around this problem. The
 correct solution would be to import the offending function lazily or
 locally.


 Cheers,
 Burcin

I just started to download 4.7.alpha3. Once I have that downloaded and
built it, I'll post a backtrace. If it helps, I'm willing to give you
an account on the machine hawk which is used by the buildbot. Unlike
t2.math, it is pretty quick (quad core 3.33 GHz Xeon).

Dave

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Re: [sage-devel] Debugging some cython code / Pynac

2011-04-01 Thread Dr. David Kirkby 

On 04/ 1/11 12:54 PM, Burcin Erocal wrote:

On Fri, 01 Apr 2011 00:37:46 +0100
Dr. David Kirkbydavid.kir...@onetel.net  wrote:


I've built Sage 64-bit on OpenSolaris but it crashes at startup. I've
run gdb and find the bit of code that's causing the crash is this.

./devel/sage-main/sage/symbolic/function.cpp


   /* sage/symbolic/function.pyx:109
   * raise ValueError,  real_fname +  parameter must
be callable *
   * if not self._is_registered(): #
   * self._register_function()
   *
   */

snip

allows Sage to run. It's not 100% stable, but much better than before.


snip

Can anyone see if there might be something wrong with this code,
which is causing Sage to segfault?


It might be due to the linker initializing the library in a different
order. Can you post a backtrace so we can see which function it is
trying to construct?


Here's a backtrace

drkirkby@hawk:~/64/sage-4.7.alpha3$ ./sage -gdb
Building Sage on Solaris in 64-bit mode
Creating SAGE_LOCAL/lib/sage-64.txt since it does not exist
Detected SAGE64 flag
Building Sage on Solaris in 64-bit mode
--
| Sage Version 4.7.alpha3, Release Date: 2011-03-31  |
| Type notebook() for the GUI, and license() for information.|
--
**
**
* Warning: this is a prerelease version, and it may be unstable. *
**
**
/export/home/drkirkby/64/sage-4.7.alpha3/local/bin/sage-ipython
GNU gdb 6.8
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type show copying
and show warranty for details.
This GDB was configured as i386-pc-solaris2.11...
warning: Lowest section in /lib/amd64/libdl.so.1 is .dynamic at 00b0
Python 2.6.4 (r264:75706, Apr  1 2011, 15:07:52)
[GCC 4.5.0] on sunos5
Type help, copyright, credits or license for more information.
warning: Lowest section in /lib/amd64/libintl.so.1 is .dynamic at 
00b0
warning: Lowest section in /lib/amd64/libpthread.so.1 is .dynamic at 
00b0


Program received signal SIGSEGV, Segmentation fault.
0x003eb0a5 in ?? ()
(gdb) bt
#0  0x003eb0a5 in ?? ()
#1  0xfd7fff2ac5d1 in _Unwind_RaiseException_Body () from /lib/64/libc.so.1
#2  0xfd7fff2ac855 in _Unwind_RaiseException () from /lib/64/libc.so.1
#3  0xfd7ff91d6729 in __cxa_throw (obj=value optimized out, tinfo=value 
optimized out, dest=value optimized out)

at ../../../../../gcc-4.5.0/libstdc++-v3/libsupc++/eh_throw.cc:78
#4  0xfd7fcec6d5ff in GiNaC::function::find_function (name=@0x4a359b0, 
nparams=2) at function.cpp:1446
#5  0xfd7fce9454ad in 
__pyx_f_4sage_8symbolic_8function_15BuiltinFunction__is_registered 
(__pyx_v_self=0x4a142f0) at sage/symbolic/function.cpp:7301
#6  0xfd7fce950755 in __pyx_pf_4sage_8symbolic_8function_8Function___init__ 
(__pyx_v_self=0x4a142f0, __pyx_args=value optimized out,

__pyx_kwds=value optimized out) at sage/symbolic/function.cpp:2374
#7  0xfd7fffde7a70 in ?? ()
#8  0x0016745f5f63 in ?? ()
#9  0x04a0e5a8 in ?? ()
#10 0x04a142f0 in ?? ()
#11 0x000b in ?? ()
#12 0x04a0e5a8 in ?? ()
#13 0x02c913e8 in ?? ()
#14 0xfd7fd76c2b30 in module_members () from 
/export/home/drkirkby/64/sage-4.7.alpha3/local/lib//libpython2.6.so.1.0

#15 0x002752657572 in ?? ()
#16 0xfd7fd76d5c60 in ?? () from 
/export/home/drkirkby/64/sage-4.7.alpha3/local/lib//libpython2.6.so.1.0

#17 0x28004052 in ?? ()
#18 0xfd7fd76d5920 in ?? () from 
/export/home/drkirkby/64/sage-4.7.alpha3/local/lib//libpython2.6.so.1.0

#19 0x0005 in ?? ()
#20 0x049e4db8 in ?? ()
---Type return to continue, or q return to quit---
#21 0x in ?? ()

The line starting:

  __pyx_t_2 = ((struct __pyx_vtabstruct_4sage_8symbolic_8function_Function *)

below is sage/symbolic/function.cpp line 2374


  /* sage/symbolic/function.pyx:109
 * raise ValueError,  real_fname +  parameter must be callable
 *
 * if not self._is_registered(): # 
 * self._register_function()
 *
 */
  __pyx_t_2 = ((struct __pyx_vtabstruct_4sage_8symbolic_8function_Function 
*)((struct __pyx_obj_4sage_8symbolic_8function_Function 
*)__pyx_v_self)-__pyx_vtab)-_is_registered(((struct 
__pyx_obj_4sage_8symbolic_8function_Function *)__pyx_v_self)); if 
(unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 109;

Re: [sage-devel] Debugging some cython code / Pynac

2011-04-01 Thread Burcin Erocal 
On Fri, 01 Apr 2011 17:20:57 +0100
Dr. David Kirkby david.kir...@onetel.net wrote:

 On 04/ 1/11 12:54 PM, Burcin Erocal wrote:
  On Fri, 01 Apr 2011 00:37:46 +0100
  Dr. David Kirkbydavid.kir...@onetel.net  wrote:
 
  I've built Sage 64-bit on OpenSolaris but it crashes at startup. I've
  run gdb and find the bit of code that's causing the crash is this.
 
  ./devel/sage-main/sage/symbolic/function.cpp
 
 
 /* sage/symbolic/function.pyx:109
 * raise ValueError,  real_fname +  parameter must
  be callable *
 * if not self._is_registered(): #
 * self._register_function()
 *
 */
  snip
  allows Sage to run. It's not 100% stable, but much better than before.
 
  snip
  Can anyone see if there might be something wrong with this code,
  which is causing Sage to segfault?
 
  It might be due to the linker initializing the library in a different
  order. Can you post a backtrace so we can see which function it is
  trying to construct?
 
 Here's a backtrace
snip
 
 Program received signal SIGSEGV, Segmentation fault.
 0x003eb0a5 in ?? ()
 (gdb) bt
 #0  0x003eb0a5 in ?? ()
 #1  0xfd7fff2ac5d1 in _Unwind_RaiseException_Body () from 
 /lib/64/libc.so.1
 #2  0xfd7fff2ac855 in _Unwind_RaiseException () from /lib/64/libc.so.1
 #3  0xfd7ff91d6729 in __cxa_throw (obj=value optimized out, 
 tinfo=value 
 optimized out, dest=value optimized out)
  at ../../../../../gcc-4.5.0/libstdc++-v3/libsupc++/eh_throw.cc:78
 #4  0xfd7fcec6d5ff in GiNaC::function::find_function (name=@0x4a359b0, 
 nparams=2) at function.cpp:1446
 #5  0xfd7fce9454ad in 
 __pyx_f_4sage_8symbolic_8function_15BuiltinFunction__is_registered 
 (__pyx_v_self=0x4a142f0) at sage/symbolic/function.cpp:7301
 #6  0xfd7fce950755 in 
 __pyx_pf_4sage_8symbolic_8function_8Function___init__ 
 (__pyx_v_self=0x4a142f0, __pyx_args=value optimized out,
  __pyx_kwds=value optimized out) at sage/symbolic/function.cpp:2374
 #7  0xfd7fffde7a70 in ?? ()
the stack is corrupted so the rest is useless

David gave me an account on the machine. Here is the Python call stack:

  File /export/home/burcin/sage-4.7.alpha3/local/bin/sage-ipython, line 21, 
in module
ipy_sage = IPython.Shell.start()
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/Shell.py,
 line 1233, in start
return shell(user_ns = user_ns)
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/Shell.py,
 line 78, in __init__
debug=debug,shell_class=shell_class)
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/ipmaker.py,
 line 644, in make_IPython
force_import(profmodname)
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/ipmaker.py,
 line 66, in force_import
__import__(modname)
  File ipy_profile_sage.py, line 7, in module
import sage.all_cmdline
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/all_cmdline.py,
 line 14, in module
from sage.all import *
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/all.py,
 line 75, in module
from sage.schemes.allimport *
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/all.py,
 line 25, in module
from hyperelliptic_curves.all import *
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/all.py,
 line 1, in module
from constructor import HyperellipticCurve
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/constructor.py,
 line 11, in module
from sage.schemes.generic.all import ProjectiveSpace
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/all.py,
 line 4, in module
from affine_space import AffineSpace, is_AffineSpace
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/affine_space.py,
 line 24, in module
import algebraic_scheme
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/algebraic_scheme.py,
 line 143, in module
import toric_variety
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/toric_variety.py,
 line 236, in module
from sage.geometry.cone import Cone, is_Cone
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/geometry/cone.py,
 line 174, in module
from sage.combinat.posets.posets import FinitePoset
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/combinat/posets/posets.py,
 line 24, in module
from sage.graphs.all import DiGraph
  File 
/export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/graphs/all.py,
 line 16, in module
from

Re: [sage-devel] Debugging some cython code / Pynac

2011-04-01 Thread Robert Bradshaw 
On Fri, Apr 1, 2011 at 3:46 PM, Burcin Erocal bur...@erocal.org wrote:
 On Fri, 01 Apr 2011 17:20:57 +0100
 Dr. David Kirkby david.kir...@onetel.net wrote:

 On 04/ 1/11 12:54 PM, Burcin Erocal wrote:
  On Fri, 01 Apr 2011 00:37:46 +0100
  Dr. David Kirkbydavid.kir...@onetel.net  wrote:
 
  I've built Sage 64-bit on OpenSolaris but it crashes at startup. I've
  run gdb and find the bit of code that's causing the crash is this.
 
  ./devel/sage-main/sage/symbolic/function.cpp
 
 
     /* sage/symbolic/function.pyx:109
     *                 raise ValueError,  real_fname +  parameter must
  be callable *
     *         if not self._is_registered():             #
     *             self._register_function()
     *
     */
  snip
  allows Sage to run. It's not 100% stable, but much better than before.
 
  snip
  Can anyone see if there might be something wrong with this code,
  which is causing Sage to segfault?
 
  It might be due to the linker initializing the library in a different
  order. Can you post a backtrace so we can see which function it is
  trying to construct?

 Here's a backtrace
 snip

 Program received signal SIGSEGV, Segmentation fault.
 0x003eb0a5 in ?? ()
 (gdb) bt
 #0  0x003eb0a5 in ?? ()
 #1  0xfd7fff2ac5d1 in _Unwind_RaiseException_Body () from 
 /lib/64/libc.so.1
 #2  0xfd7fff2ac855 in _Unwind_RaiseException () from /lib/64/libc.so.1
 #3  0xfd7ff91d6729 in __cxa_throw (obj=value optimized out, 
 tinfo=value
 optimized out, dest=value optimized out)
      at ../../../../../gcc-4.5.0/libstdc++-v3/libsupc++/eh_throw.cc:78
 #4  0xfd7fcec6d5ff in GiNaC::function::find_function (name=@0x4a359b0,
 nparams=2) at function.cpp:1446
 #5  0xfd7fce9454ad in
 __pyx_f_4sage_8symbolic_8function_15BuiltinFunction__is_registered
 (__pyx_v_self=0x4a142f0) at sage/symbolic/function.cpp:7301
 #6  0xfd7fce950755 in 
 __pyx_pf_4sage_8symbolic_8function_8Function___init__
 (__pyx_v_self=0x4a142f0, __pyx_args=value optimized out,
      __pyx_kwds=value optimized out) at sage/symbolic/function.cpp:2374
 #7  0xfd7fffde7a70 in ?? ()
 the stack is corrupted so the rest is useless

 David gave me an account on the machine. Here is the Python call stack:

  File /export/home/burcin/sage-4.7.alpha3/local/bin/sage-ipython, line 21, 
 in module
    ipy_sage = IPython.Shell.start()
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/Shell.py,
  line 1233, in start
    return shell(user_ns = user_ns)
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/Shell.py,
  line 78, in __init__
    debug=debug,shell_class=shell_class)
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/ipmaker.py,
  line 644, in make_IPython
    force_import(profmodname)
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/ipmaker.py,
  line 66, in force_import
    __import__(modname)
  File ipy_profile_sage.py, line 7, in module
    import sage.all_cmdline
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/all_cmdline.py,
  line 14, in module
    from sage.all import *
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/all.py,
  line 75, in module
    from sage.schemes.all    import *
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/all.py,
  line 25, in module
    from hyperelliptic_curves.all import *
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/all.py,
  line 1, in module
    from constructor import HyperellipticCurve
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/constructor.py,
  line 11, in module
    from sage.schemes.generic.all import ProjectiveSpace
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/all.py,
  line 4, in module
    from affine_space     import AffineSpace, is_AffineSpace
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/affine_space.py,
  line 24, in module
    import algebraic_scheme
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/algebraic_scheme.py,
  line 143, in module
    import toric_variety
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/toric_variety.py,
  line 236, in module
    from sage.geometry.cone import Cone, is_Cone
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/geometry/cone.py,
  line 174, in module
    from sage.combinat.posets.posets import FinitePoset
  File 
 /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/combinat/posets/posets.py,
  line 24, in module
    from sage.graphs.all import DiGraph
  File