[sage-devel] Re: Fwd: bug in isprime()

2007-09-08 Thread John Cremona

Thanks for the extra explanations, Bill.

I wrote an extra item in pari's online FAQ, and an additional note in
the manual, while Karim has put into the pari cvs already.  But (at
least as far as mwrank is concerned) we still need a proof=true
version of factorint().

John

On 9/8/07, Bill Hart [EMAIL PROTECTED] wrote:

 factor is a general factoring function for integers, polynomials and
 various other types. It also takes an optional parameter to tell it
 how many primes to use in the factorisation. So for example if you
 want to know all prime factors of an integer up to 1000 you'd use
 factor(n, 1000).

 factorint only factors integers and takes an optional parameter to
 tell it which factorisation algorithms to use. For example you may
 know that your integer is an RSA modulus and only divisible by two
 large primes. As such running a trial factoring routine, an elliptic
 curve factorisation or a SQUFOF test is not going to find a factor.
 Similarly you may have a very large integer which has no hope of being
 factored by the quadratic sieve and your only hope of finding a factor
 is if it is relatively small, in which case you'd want to use the
 elliptic curve method without giving up. factorint allows you to do
 that.

 Bill.


 



-- 
John Cremona

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[sage-devel] Re: compiling on AIX/PowerPPC

2007-09-08 Thread Hamptonio

It turns out that I also have access to a linux-based supercomputer,
(an IBM BladeCenter with about 300 quad-processor nodes), which should
be faster than the Power4 system anyway.  So I will give up, for the
moment, trying to install sage on AIX.  I have installed sage-2.8.3.6
on the BladeCenter successfully, with the following make test
failures:

sage -t  devel/sage-main/sage/modular/modform/ambient_g1.py
sage -t  devel/sage-main/sage/modular/modform/
eisenstein_submodule.py
sage -t  devel/sage-main/sage/modular/modform/submodule.py
sage -t  devel/sage-main/sage/rings/real_rqdf.pyx
Total time for all tests: 2137.4 seconds

Probably some of those have been fixed in 2.8.4.

Now I'll have to learn more about DSage; I am not sure how to exploit
all those processors the way I usually code.

Cheers,
Marshall

On Sep 7, 1:50 pm, William Stein [EMAIL PROTECTED] wrote:
 On 9/7/07, Hamptonio [EMAIL PROTECTED] wrote:



  Thanks guys.  I can't use the notebook anyway from that machine, I
  would be running pre-written scripts to do heavy calculations.  It got
  far enough that I am hopeful I can get it to where it does what I
  need.

 Please post anything you figure out.  We would be very happy
 to have AIX officially supported one day!!

 William


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[sage-devel] cannot build 2.8.4 on sage.math

2007-09-08 Thread David Harvey

I am tearing my hair out.

I do a clean build of sage 2.8.4 on sage.math, and when I run it I  
get this:

==


--
| SAGE Version 2.8.4, Release Date: 2007-09-07   |
| Type notebook() for the GUI, and license() for information.|
--
 
---
type 'exceptions.ImportError'   Traceback (most recent call  
last)

/home/dmharvey/sage-2.8.4/local/bin/string in module()

/home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/ 
preparser_ipython.py in module()
   6  
 
###
   7
 8 import sage.misc.interpreter
   9
  10 import preparser

/home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/ 
interpreter.py in module()
 102
 103 import os
-- 104 import log
 105
 106 import remote_file

/home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/ 
log.py in module()
  51
  52 import interpreter
--- 53 import latex
  54 import misc
  55

/home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/ 
latex.py in module()
  41 import random
  42
--- 43 import sage.plot.all
  44
  45 from misc import tmp_dir

/home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/ 
all.py in module()
   2   text, circle, disk, hue, graphics_array,
   3   list_plot, networkx_plot, parametric_plot,
   4   polar_plot, contour_plot, arrow,
   5   plot_vector_field, matrix_plot, bar_chart,
   6   is_Graphics,

/home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/ 
plot.py in module()
 126  
 

 127
-- 128 from sage.structure.sage_object import SageObject
 129
 130 ## IMPORTANT: Do *not* import matplotlib at module scope.   
It takes a

type 'exceptions.ImportError': /home/dmharvey/sage-2.8.4/local/lib/ 
libcsage.so: undefined symbol: __stack_chk_fail
WARNING: Failure executing code: 'import  
sage.misc.preparser_ipython;   
sage.misc.preparser_ipython.magma_colon_equals=True'

 
---
type 'exceptions.ImportError'   Traceback (most recent call  
last)

/home/dmharvey/sage-2.8.4/local/bin/ipython console in module()

/home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/ 
interpreter.py in module()
 102
 103 import os
-- 104 import log
 105
 106 import remote_file

/home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/ 
log.py in module()
  51
  52 import interpreter
--- 53 import latex
  54 import misc
  55

/home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/ 
latex.py in module()
  41 import random
  42
--- 43 import sage.plot.all
  44
  45 from misc import tmp_dir

/home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/ 
all.py in module()
   2   text, circle, disk, hue, graphics_array,
   3   list_plot, networkx_plot, parametric_plot,
   4   polar_plot, contour_plot, arrow,
   5   plot_vector_field, matrix_plot, bar_chart,
   6   is_Graphics,

/home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/ 
plot.py in module()
 126  
 

 127
-- 128 from sage.structure.sage_object import SageObject
 129
 130 ## IMPORTANT: Do *not* import matplotlib at module scope.   
It takes a

type 'exceptions.ImportError': /home/dmharvey/sage-2.8.4/local/lib/ 
libcsage.so: undefined symbol: __stack_chk_fail
ERROR: name 'sage_prompt' is not defined

==

This was happening to me towards the second half of the bug squash too.

I took special precautions before building this time. I removed  
everything in my home directory (packed away everything into  
tarballs), except for the following files:

.bash_profile
.bashrc
el
.emacs
.emacs.d
flint-home
flint_trac
.gnupg
.hgrc
.ssh
.svn
.viminfo

and a few text files and pdf files.

My environment is the following:

TERM=xterm-color
SHELL=/bin/bash
SSH_CLIENT=140.247.248.30 52541 22
SSH_TTY=/dev/pts/4
SVN_EDITOR=emacs
USER=dmharvey
LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40 
; 
33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37; 
44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31: 

[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread Joel B. Mohler

Hi David, 

I think this may be something in your ambient environment which scons handles 
differently than autoconf and friends.  You could try replacing 
***
env = Environment()
*** with
env = Environment(ENV = os.environ)
***
near the top of the c_lib/SConstruct file.  SCons does not copy environment 
variables into it's environment.  I think it is a strange design, but the 
SCons developers are quite dogmatic about it.

This fixed a build problem for Kiran with thread title 2.8.3.x build 
problem.   I'm not sure what that SConstruct looks like in 2.8.4, but I 
don't think this change made it in.  I wasn't quite certain that I 
recommended the change, but if it fixes your problem as well, I'd say we 
should put it in.

--
Joel

On Saturday 08 September 2007 10:44, David Harvey wrote:
 I am tearing my hair out.

 I do a clean build of sage 2.8.4 on sage.math, and when I run it I
 get this:

 ==


 --

 | SAGE Version 2.8.4, Release Date: 2007-09-07   |
 | Type notebook() for the GUI, and license() for information.|

 --
 
 ---
 type 'exceptions.ImportError'   Traceback (most recent call
 last)

 /home/dmharvey/sage-2.8.4/local/bin/string in module()

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 preparser_ipython.py in module()
6
 
 ###
7
  8 import sage.misc.interpreter
9
   10 import preparser

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 interpreter.py in module()
  102
  103 import os
 -- 104 import log
  105
  106 import remote_file

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 log.py in module()
   51
   52 import interpreter
 --- 53 import latex
   54 import misc
   55

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 latex.py in module()
   41 import random
   42
 --- 43 import sage.plot.all
   44
   45 from misc import tmp_dir

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/
 all.py in module()
2   text, circle, disk, hue, graphics_array,
3   list_plot, networkx_plot, parametric_plot,
4   polar_plot, contour_plot, arrow,
5   plot_vector_field, matrix_plot, bar_chart,
6   is_Graphics,

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/
 plot.py in module()
  126
 
 
  127
 -- 128 from sage.structure.sage_object import SageObject
  129
  130 ## IMPORTANT: Do *not* import matplotlib at module scope.
 It takes a

 type 'exceptions.ImportError': /home/dmharvey/sage-2.8.4/local/lib/
 libcsage.so: undefined symbol: __stack_chk_fail
 WARNING: Failure executing code: 'import
 sage.misc.preparser_ipython;
 sage.misc.preparser_ipython.magma_colon_equals=True'

 
 ---
 type 'exceptions.ImportError'   Traceback (most recent call
 last)

 /home/dmharvey/sage-2.8.4/local/bin/ipython console in module()

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 interpreter.py in module()
  102
  103 import os
 -- 104 import log
  105
  106 import remote_file

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 log.py in module()
   51
   52 import interpreter
 --- 53 import latex
   54 import misc
   55

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 latex.py in module()
   41 import random
   42
 --- 43 import sage.plot.all
   44
   45 from misc import tmp_dir

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/
 all.py in module()
2   text, circle, disk, hue, graphics_array,
3   list_plot, networkx_plot, parametric_plot,
4   polar_plot, contour_plot, arrow,
5   plot_vector_field, matrix_plot, bar_chart,
6   is_Graphics,

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/
 plot.py in module()
  126
 
 
  127
 -- 128 from sage.structure.sage_object import SageObject
  129
  130 ## IMPORTANT: Do *not* import matplotlib at module scope.
 It takes a

 type 'exceptions.ImportError': /home/dmharvey/sage-2.8.4/local/lib/
 libcsage.so: undefined symbol: __stack_chk_fail
 

[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread David Harvey


On Sep 8, 2007, at 11:00 AM, Joel B. Mohler wrote:


 Hi David,

 I think this may be something in your ambient environment which  
 scons handles
 differently than autoconf and friends.

Is ambient environment a technical unix term? Is that the same as  
my environment?


   You could try replacing
 ***
 env = Environment()
 *** with
 env = Environment(ENV = os.environ)
 ***
 near the top of the c_lib/SConstruct file.  SCons does not copy  
 environment
 variables into it's environment.  I think it is a strange design,  
 but the
 SCons developers are quite dogmatic about it.

 This fixed a build problem for Kiran with thread title 2.8.3.x build
 problem.   I'm not sure what that SConstruct looks like in 2.8.4,  
 but I
 don't think this change made it in.  I wasn't quite certain that I
 recommended the change, but if it fixes your problem as well, I'd  
 say we
 should put it in.

It's already got that line in 2.8.4.

Has anyone else actually built sage-2.8.4 from scratch on sage.math?

david


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[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread mabshoff



On Sep 8, 5:09 pm, David Harvey [EMAIL PROTECTED] wrote:
 On Sep 8, 2007, at 11:00 AM, Joel B. Mohler wrote:



Hello,


  Hi David,

  I think this may be something in your ambient environment which
  scons handles
  differently than autoconf and friends.

 Is ambient environment a technical unix term? Is that the same as
 my environment?

;), but I don't see anything suspicious.




You could try replacing
  ***
  env = Environment()
  *** with
  env = Environment(ENV = os.environ)
  ***
  near the top of the c_lib/SConstruct file.  SCons does not copy
  environment
  variables into it's environment.  I think it is a strange design,
  but the
  SCons developers are quite dogmatic about it.

  This fixed a build problem for Kiran with thread title 2.8.3.x build
  problem.   I'm not sure what that SConstruct looks like in 2.8.4,
  but I
  don't think this change made it in.  I wasn't quite certain that I
  recommended the change, but if it fixes your problem as well, I'd
  say we
  should put it in.

 It's already got that line in 2.8.4.


I would suggest commenting it out then. It was merged because of a
build problem on RHEL 5.

 Has anyone else actually built sage-2.8.4 from scratch on sage.math?


I believe William did do, I didn't try in person.

 david

Cheers,

Michael


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[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread David Harvey


On Sep 8, 2007, at 11:21 AM, mabshoff wrote:

 It's already got that line in 2.8.4.


 I would suggest commenting it out then. It was merged because of a
 build problem on RHEL 5.

Okay, I'll try again with that line restored to how it was before.


 Has anyone else actually built sage-2.8.4 from scratch on sage.math?


 I believe William did do, I didn't try in person.

Sorry I should rephrase that question: has anyone else actually built  
2.8.4 and succesfully *run* it on sage.math? (The build itself  
appears to go smoothly.)

david


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[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread mabshoff



On Sep 8, 5:23 pm, David Harvey [EMAIL PROTECTED] wrote:
 On Sep 8, 2007, at 11:21 AM, mabshoff wrote:

  It's already got that line in 2.8.4.

  I would suggest commenting it out then. It was merged because of a
  build problem on RHEL 5.

 Okay, I'll try again with that line restored to how it was before.



  Has anyone else actually built sage-2.8.4 from scratch on sage.math?

  I believe William did do, I didn't try in person.

 Sorry I should rephrase that question: has anyone else actually built
 2.8.4 and succesfully *run* it on sage.math? (The build itself
 appears to go smoothly.)


I am sure William ran testall, but I just started a build to see if I
can replicate your problem. I shall report back in about 2 hours
(unless something big is running on sage.math).

 david

Cheers,

Michael


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[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread Joel B. Mohler

On Saturday 08 September 2007 11:09, David Harvey wrote:
  I think this may be something in your ambient environment which  
  scons handles
  differently than autoconf and friends.

 Is ambient environment a technical unix term? Is that the same as  
 my environment?

No, sorry.  I was intending it as a bit more generic than the technical term 
environment.  The bit that I understood on the similar IRC conversation 
seemed like you were linking to a gmp outside your sage tree.  Now, how that 
would have occurred is probably a matter of the technical-term environment.

--
Joel

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[sage-devel] Re: sage-2.8.4

2007-09-08 Thread Jaap Spies

William Stein wrote:
 Hi,
 
 SAGE-2.8.4 -- a mega bugfix release (70 tickets closed since 2.8.3.6)
 has been released:
http://sagemath.org
 or
sage -upgrade
 

Only this test failed on fedora 7:
Linux paix 2.6.22.4-65.fc7 #1 SMP Tue Aug 21 22:36:56 EDT 2007 i686 i686 i386 
GNU/Linux

sage -t  devel/sage-main/sage/rings/tests.py
**
File tests.py, line 8:
 sage: (1/2)^(2^100)
Expected:
 Traceback (most recent call last):
 ...
 RuntimeError: exponent must be at most 4294967294
Got:
 Traceback (most recent call last):
   File /home/jaap/downloads/sage-2.8.4/local/lib/python2.5/doctest.py, 
line 1212, in __run
 compileflags, 1) in test.globs
   File doctest __main__.example_0[3], line 1, in module
 (Integer(1)/Integer(2))**(Integer(2)**Integer(100))###line 8:
 sage: (1/2)^(2^100)
   File rational.pyx, line 1008, in rational.Rational.__pow__
 raise RuntimeError, exponent must be at most %s % sys.maxint
 RuntimeError: exponent must be at most 2147483647
**
1 items had failures:
1 of   4 in __main__.example_0
***Test Failed*** 1 failures.
For whitespace errors, see the file .doctest_tests.py
  [5.9 s]
exit code: 256


Jaap


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[sage-devel] Re: sage-2.8.4

2007-09-08 Thread mabshoff



On Sep 8, 6:15 pm, Jaap Spies [EMAIL PROTECTED] wrote:
 William Stein wrote:
  Hi,

  SAGE-2.8.4 -- a mega bugfix release (70 tickets closed since 2.8.3.6)
  has been released:
 http://sagemath.org
  or
 sage -upgrade

 Only this test failed on fedora 7:
 Linux paix 2.6.22.4-65.fc7 #1 SMP Tue Aug 21 22:36:56 EDT 2007 i686 i686 i386 
 GNU/Linux

 sage -t  devel/sage-main/sage/rings/tests.py
 **
 File tests.py, line 8:
  sage: (1/2)^(2^100)
 Expected:
  Traceback (most recent call last):
  ...
  RuntimeError: exponent must be at most 4294967294
 Got:
  Traceback (most recent call last):
File /home/jaap/downloads/sage-2.8.4/local/lib/python2.5/doctest.py, 
 line 1212, in __run
  compileflags, 1) in test.globs
File doctest __main__.example_0[3], line 1, in module
  (Integer(1)/Integer(2))**(Integer(2)**Integer(100))###line 8:
  sage: (1/2)^(2^100)
File rational.pyx, line 1008, in rational.Rational.__pow__
  raise RuntimeError, exponent must be at most %s % sys.maxint
  RuntimeError: exponent must be at most 2147483647
 **
 1 items had failures:
 1 of   4 in __main__.example_0
 ***Test Failed*** 1 failures.
 For whitespace errors, see the file .doctest_tests.py
   [5.9 s]
 exit code: 256

 Jaap

Hello Jaap,

the changeset at http://www.sagemath.org/hg/sage-main/rev/f12659f0ebd0
should fix that problem. It happens only on 32 bit systems. William
respun the tarballs after he announced 2.8.4 (which did not contain
the changeset), but I don't believe he mirrored them out. Please let
us know if that fixes your issue.

Cheers,

Michael


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[sage-devel] Re: sage-2.8.4

2007-09-08 Thread Jaap Spies

mabshoff wrote:
 

 
 the changeset at http://www.sagemath.org/hg/sage-main/rev/f12659f0ebd0
 should fix that problem. It happens only on 32 bit systems. William
 respun the tarballs after he announced 2.8.4 (which did not contain
 the changeset), but I don't believe he mirrored them out. Please let
 us know if that fixes your issue.
 

sage -t  devel/sage-main/sage/rings/tests.py
  [1.3 s]

--
All tests passed!
Total time for all tests: 1.3 seconds

Jaap


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[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread Craig Citro

Yeah, that doesn't sound like fun. Try the following from your sage- 
main directory: cd c_lib ; rm -f libcsage.* ; scons install. You  
should see scons rebuild the libcsage.so and then copy it to your  
$SAGE_ROOT/local/lib ... let me know if that works.

If it does, we might just need to be more adamant about how the c_lib  
build happens on install, because it sounds like your c_lib isn't  
getting rebuilt (i.e. your $SAGE_ROOT/local/lib/libcsage.so is bunk).  
In fact, I can see this being pretty likely -- it could be the same  
problem I was having when I switched branches, and I just need to  
make sure the same thing is happening when you do an install. This  
shouldn't be too bad, and it'll save you from having to pull out any  
more hair. ;)

If *not*, it means there's actually a problem with the libcsage.so  
that's getting built, which is bad. This will require more thought.

I'll be gone most of the day, but I'll read your reply when I get  
back and make a fix if it's the first one.

-cc

On Sep 8, 2007, at 7:44 AM, David Harvey wrote:


 I am tearing my hair out.

 I do a clean build of sage 2.8.4 on sage.math, and when I run it I
 get this:

 ==


 --
 | SAGE Version 2.8.4, Release Date: 2007-09-07   |
 | Type notebook() for the GUI, and license() for information.|
 --
 -- 
 --
 ---
 type 'exceptions.ImportError'   Traceback (most recent call
 last)

 /home/dmharvey/sage-2.8.4/local/bin/string in module()

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 preparser_ipython.py in module()
6
 ## 
 ##
 ###
7
  8 import sage.misc.interpreter
9
   10 import preparser

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 interpreter.py in module()
  102
  103 import os
 -- 104 import log
  105
  106 import remote_file

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 log.py in module()
   51
   52 import interpreter
 --- 53 import latex
   54 import misc
   55

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 latex.py in module()
   41 import random
   42
 --- 43 import sage.plot.all
   44
   45 from misc import tmp_dir

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/
 all.py in module()
2   text, circle, disk, hue, graphics_array,
3   list_plot, networkx_plot, parametric_plot,
4   polar_plot, contour_plot, arrow,
5   plot_vector_field, matrix_plot, bar_chart,
6   is_Graphics,

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/
 plot.py in module()
  126
 ## 
 ##
 
  127
 -- 128 from sage.structure.sage_object import SageObject
  129
  130 ## IMPORTANT: Do *not* import matplotlib at module scope.
 It takes a

 type 'exceptions.ImportError': /home/dmharvey/sage-2.8.4/local/lib/
 libcsage.so: undefined symbol: __stack_chk_fail
 WARNING: Failure executing code: 'import
 sage.misc.preparser_ipython;
 sage.misc.preparser_ipython.magma_colon_equals=True'

 -- 
 --
 ---
 type 'exceptions.ImportError'   Traceback (most recent call
 last)

 /home/dmharvey/sage-2.8.4/local/bin/ipython console in module()

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 interpreter.py in module()
  102
  103 import os
 -- 104 import log
  105
  106 import remote_file

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 log.py in module()
   51
   52 import interpreter
 --- 53 import latex
   54 import misc
   55

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/misc/
 latex.py in module()
   41 import random
   42
 --- 43 import sage.plot.all
   44
   45 from misc import tmp_dir

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/
 all.py in module()
2   text, circle, disk, hue, graphics_array,
3   list_plot, networkx_plot, parametric_plot,
4   polar_plot, contour_plot, arrow,
5   plot_vector_field, matrix_plot, bar_chart,
6   is_Graphics,

 /home/dmharvey/sage-2.8.4/local/lib/python2.5/site-packages/sage/plot/
 plot.py in module()
  126
 ## 
 ##
 

[sage-devel] Some observations on #619

2007-09-08 Thread mabshoff

Executive summary for ticket #619:
Matrix_integer_dense__zero_out_matrix does not leak.

But there must be operations on dense matricies that do not properly
deallocate elements that were allocated in
Matrix_integer_dense__zero_out_matrix, so vagrind claims rightfully
that those entries are leaked.

Another interesting tidbit:

A=matrix(ZZ,1000,1000,0)
B=A.copy()

leads to:

==31604== 8,000,000 bytes in 1,000,000 blocks are still reachable in
loss record 1,975 of 1,979
==31604==at 0x4A05A66: malloc (vg_replace_malloc.c:207)
==31604==by 0x95A4C17: __gmpz_init (in /tmp/Work2/sage-2.8.3.6-
clean/local/lib/libgmp.so.3.4.1)
==31604==by 0x205E840F:
__pyx_f_20matrix_integer_dense_20Matrix_integer_dense__zero_out_matrix
(matrix_integer_dense.c:4
649)
==31604==by 0x206161E4:
__pyx_f_20matrix_integer_dense_20Matrix_integer_dense___init__
(matrix_integer_dense.c:3769)
==31604==by 0x45A321: type_call (typeobject.c:436)
==31604==by 0x4156A2: PyObject_Call (abstract.c:1860)
==31604==by 0x480783: PyEval_EvalFrameEx (ceval.c:3775)
==31604==by 0x4865EF: PyEval_EvalCodeEx (ceval.c:2831)
==31604==by 0x4845B3: PyEval_EvalFrameEx (ceval.c:3660)
==31604==by 0x4865EF: PyEval_EvalCodeEx (ceval.c:2831)
==31604==by 0x4CFF37: function_call (funcobject.c:517)
==31604==by 0x4156A2: PyObject_Call (abstract.c:1860)
==31604==
==31604==
==31604== 8,000,000 bytes in 1,000,000 blocks are still reachable in
loss record 1,976 of 1,979
==31604==at 0x4A05A66: malloc (vg_replace_malloc.c:207)
==31604==by 0x95A5BE0: __gmpz_init_set (in /tmp/Work2/sage-2.8.3.6-
clean/local/lib/libgmp.so.3.4.1)
==31604==by 0x20605951:
__pyx_f_20matrix_integer_dense_20Matrix_integer_dense___copy__
(matrix_integer_dense.c:3223)
==31604==by 0x4156A2: PyObject_Call (abstract.c:1860)
==31604==by 0x47DB71: PyEval_CallObjectWithKeywords (ceval.c:3433)
==31604==by 0x1E12C45C: __pyx_f_7matrix0_6Matrix_copy (matrix0.c:
845)
==31604==by 0x485B9B: PyEval_EvalFrameEx (ceval.c:3548)
==31604==by 0x4865EF: PyEval_EvalCodeEx (ceval.c:2831)
==31604==by 0x485BDF: PyEval_EvalFrameEx (ceval.c:494)
==31604==by 0x4865EF: PyEval_EvalCodeEx (ceval.c:2831)
==31604==by 0x4845B3: PyEval_EvalFrameEx (ceval.c:3660)
==31604==by 0x4865EF: PyEval_EvalCodeEx (ceval.c:2831)
==31604==
==31604== 16,000,000 bytes in 1 blocks are still reachable in loss
record 1,977 of 1,979
==31604==at 0x4A05A66: malloc (vg_replace_malloc.c:207)
==31604==by 0x205E9766:
__pyx_f_20matrix_integer_dense_20Matrix_integer_dense___new__
(matrix_integer_dense.c:2966)
==31604==by 0x205E9BE0:
__pyx_tp_new_20matrix_integer_dense_Matrix_integer_dense
(matrix_integer_dense.c:17692)
==31604==by 0x45A90A: tp_new_wrapper (typeobject.c:4022)
==31604==by 0x4156A2: PyObject_Call (abstract.c:1860)
==31604==by 0x47DB71: PyEval_CallObjectWithKeywords (ceval.c:3433)
==31604==by 0x20605868:
__pyx_f_20matrix_integer_dense_20Matrix_integer_dense___copy__
(matrix_integer_dense.c:3189)
==31604==by 0x4156A2: PyObject_Call (abstract.c:1860)
==31604==by 0x47DB71: PyEval_CallObjectWithKeywords (ceval.c:3433)
==31604==by 0x1E12C45C: __pyx_f_7matrix0_6Matrix_copy (matrix0.c:
845)
==31604==by 0x485B9B: PyEval_EvalFrameEx (ceval.c:3548)
==31604==by 0x4865EF: PyEval_EvalCodeEx (ceval.c:2831)
==31604==
==31604==
==31604== 16,000,000 bytes in 1 blocks are still reachable in loss
record 1,978 of 1,979
==31604==at 0x4A05A66: malloc (vg_replace_malloc.c:207)
==31604==by 0x205E9766:
__pyx_f_20matrix_integer_dense_20Matrix_integer_dense___new__
(matrix_integer_dense.c:2966)
==31604==by 0x205E9BE0:
__pyx_tp_new_20matrix_integer_dense_Matrix_integer_dense
(matrix_integer_dense.c:17692)
==31604==by 0x45A272: type_call (typeobject.c:422)
==31604==by 0x4156A2: PyObject_Call (abstract.c:1860)
==31604==by 0x480783: PyEval_EvalFrameEx (ceval.c:3775)
==31604==by 0x4865EF: PyEval_EvalCodeEx (ceval.c:2831)
==31604==by 0x4845B3: PyEval_EvalFrameEx (ceval.c:3660)
==31604==by 0x4865EF: PyEval_EvalCodeEx (ceval.c:2831)
==31604==by 0x4CFF37: function_call (funcobject.c:517)
==31604==by 0x4156A2: PyObject_Call (abstract.c:1860)
==31604==by 0x41BE0C: instancemethod_call (classobject.c:2497)

But with

A=matrix(ZZ,1000,1000,0)
B=A.copy()
del A
del B

the above problem is gone, no more still reachable that are caused
to A or B.

A.echelonize() doesn't leak for that A over ZZ either.

burcin found out that A = random_matrix(ZZ, 100, 120); leaks, as
does A._pari_()

I am currently looking into getting useful information out of the
Python garbage collector. So stay tuned.

Cheers,

Michael


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[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread mabshoff



On Sep 8, 6:38 pm, Craig Citro [EMAIL PROTECTED] wrote:
 Yeah, that doesn't sound like fun. Try the following from your sage-
 main directory: cd c_lib ; rm -f libcsage.* ; scons install. You
 should see scons rebuild the libcsage.so and then copy it to your
 $SAGE_ROOT/local/lib ... let me know if that works.

 If it does, we might just need to be more adamant about how the c_lib
 build happens on install, because it sounds like your c_lib isn't
 getting rebuilt (i.e. your $SAGE_ROOT/local/lib/libcsage.so is bunk).
 In fact, I can see this being pretty likely -- it could be the same
 problem I was having when I switched branches, and I just need to
 make sure the same thing is happening when you do an install. This
 shouldn't be too bad, and it'll save you from having to pull out any
 more hair. ;)

 If *not*, it means there's actually a problem with the libcsage.so
 that's getting built, which is bad. This will require more thought.

 I'll be gone most of the day, but I'll read your reply when I get
 back and make a fix if it's the first one.

 -cc

 On Sep 8, 2007, at 7:44 AM, David Harvey wrote:



SNIP

Ok, I get loads of test failures on sage.math complaining about
__stack_chk_fail. That is gmp related. I am looking trying to use
the old p9 gmp package and see what will happen then.

Cheers,

Michael


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[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread David Harvey


On Sep 8, 2007, at 1:03 PM, mabshoff wrote:

 Ok, I get loads of test failures on sage.math complaining about
 __stack_chk_fail. That is gmp related. I am looking trying to use
 the old p9 gmp package and see what will happen then.

Great, so it's not just me then. I was really starting to go nuts.

david


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[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread mabshoff



On Sep 8, 7:05 pm, David Harvey [EMAIL PROTECTED] wrote:
 On Sep 8, 2007, at 1:03 PM, mabshoff wrote:


Hey David,

  Ok, I get loads of test failures on sage.math complaining about
  __stack_chk_fail. That is gmp related. I am looking trying to use
  the old p9 gmp package and see what will happen then.

 Great, so it's not just me then. I was really starting to go nuts.


:) - I did install gmp-4.2.1p9, did a sage -ba a now I no longer see
the problem about  __stack_chk_fail. Some doctest fail, but that is
to be expected because the we get different but correct output for
various gmp related functions like crt.

Now the interesting question: Why does the new spkg fail on sage.math?
We did test it on many, many systems. Oh well. I will run make check
on both spkgs and see if anything pops up.

 david

Cheers,

Michael


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[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread mabshoff

Why does Sage 2.8.4 crash on sage.math?

Executive Summary: SCons somehow gets its LD_LIBRARY_PATH or env in
general wrong and ends up linking against the gmp 4.2.1 provided by
Debian. Somehow the compiler gets it all wrong and *boom*

How to fix: Fix SCons *ducks* - a short term solution seems to be to
source local/sage/env before building sage-2.8.4.spkg.

The detailed story:

untar sage 2.8.4, make, wait a while. Then:

[EMAIL PROTECTED]:/tmp/Work-mabshoff/sage-2.8.4-2$ ldd local/lib/
libcsage.so
libntl.so = not found
libgmp.so.3 = /usr/lib/libgmp.so.3 (0x2abf99d8d000)
libstdc++.so.6 = /usr/lib/libstdc++.so.6 (0x2abf99ecb000)
libm.so.6 = /lib/libm.so.6 (0x2abf9a0c9000)
libgcc_s.so.1 = /lib/libgcc_s.so.1 (0x2abf9a24c000)
libc.so.6 = /lib/libc.so.6 (0x2abf9a359000)
/lib64/ld-linux-x86-64.so.2 (0x4000)

That doesn't look good. start Sage: *boom*

[EMAIL PROTECTED]:/tmp/Work-mabshoff/sage-2.8.4-2$ ./sage
--
| SAGE Version 2.8.4, Release Date: 2007-09-07   |
| Type notebook() for the GUI, and license() for information.|
--
---
type 'exceptions.ImportError'   Traceback (most recent call
last)

/tmp/Work-mabshoff/sage-2.8.4-2/local/bin/string in module()

/tmp/Work-mabshoff/sage-2.8.4-2/local/lib/python2.5/site-packages/sage/
misc/preparser_ipython.py in module()
  6
###
  7
 8 import sage.misc.interpreter
  9
 10 import preparser
SNIP
/tmp/Work-mabshoff/sage-2.8.4-2/local/lib/python2.5/site-packages/sage/
plot/all.py in module()
  2   text, circle, disk, hue, graphics_array,
  3   list_plot, networkx_plot, parametric_plot,
  4   polar_plot, contour_plot, arrow,
  5   plot_vector_field, matrix_plot, bar_chart,
  6   is_Graphics,

/tmp/Work-mabshoff/sage-2.8.4-2/local/lib/python2.5/site-packages/sage/
plot/plot.py in module()
126

127
-- 128 from sage.structure.sage_object import SageObject
129
130 ## IMPORTANT: Do *not* import matplotlib at module scope.  It
takes a

type 'exceptions.ImportError': /tmp/Work-mabshoff/sage-2.8.4-2/local/
lib/libcsage.so: undefined symbol: __stack_chk_fail
ERROR: name 'sage_prompt' is not defined

source local/bin/sage-env - Now it looks a little better:

[EMAIL PROTECTED]:/tmp/Work-mabshoff/sage-2.8.4-2$ source local/bin/sage-
env
[EMAIL PROTECTED]:/tmp/Work-mabshoff/sage-2.8.4-2$ ldd local/lib/
libcsage.so
libntl.so = /tmp/Work-mabshoff/sage-2.8.4-2/local/lib/
libntl.so (0x2b67db845000)
libgmp.so.3 = /tmp/Work-mabshoff/sage-2.8.4-2/local/lib/
libgmp.so.3 (0x2b67dbb0c000)
libstdc++.so.6 = /usr/lib/libstdc++.so.6 (0x2b67dbc5f000)
libm.so.6 = /lib/libm.so.6 (0x2b67dbe5d000)
libgcc_s.so.1 = /lib/libgcc_s.so.1 (0x2b67dbfe)
libc.so.6 = /lib/libc.so.6 (0x2b67dc0ed000)
/lib64/ld-linux-x86-64.so.2 (0x4000)


But still:
SNIP
type 'exceptions.ImportError': /tmp/Work-mabshoff/sage-2.8.4-2/local/
lib/libcsage.so: undefined symbol: __stack_chk_fail

Now [having sourced local/bin/sage-env]:

./sage -ba [drink a couple of gin tonics/cups of coffee/tea ...
whatever]
SNIP
running install_scripts
changing mode of /tmp/Work-mabshoff/sage-2.8.4-2/local/bin/
dsage_server.py to 755
changing mode of /tmp/Work-mabshoff/sage-2.8.4-2/local/bin/
dsage_worker.py to 755
changing mode of /tmp/Work-mabshoff/sage-2.8.4-2/local/bin/
dsage_setup.py to 755
running install_egg_info
Removing /tmp/Work-mabshoff/sage-2.8.4-2/local/lib/python2.5/site-
packages/sage-0.0.0-py2.5.egg-info
Writing /tmp/Work-mabshoff/sage-2.8.4-2/local/lib/python2.5/site-
packages/sage-0.0.0-py2.5.egg-info
--
| SAGE Version 2.8.4, Release Date: 2007-09-07   |
| Type notebook() for the GUI, and license() for information.|
--

sage:
Exiting SAGE (CPU time 0m0.00s, Wall time 0m4.86s).

If anybody wants to make a proper patch, open a ticket and send a
patch to William please do so. I gotta get back to fixing Conditional
jump or move depends on uninitialised value(s) in LinBox :)

Thank you, come again.

Cheers,

Michael


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[sage-devel] Python bindings for Ginac

2007-09-08 Thread Pablo De Napoli

The idea of incorporating Ginac into Sage was discussed some time ago
in this list.
Now I see that in its page there is a link to some python bindings for Ginac

http://pyginac.sourceforge.net/

This could be useful for us, however they use boost rather than cython/pyrex

Pablo

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[sage-devel] Re: Python bindings for Ginac

2007-09-08 Thread Ondrej Certik

 The idea of incorporating Ginac into Sage was discussed some time ago
 in this list.
 Now I see that in its page there is a link to some python bindings for Ginac

 http://pyginac.sourceforge.net/

 This could be useful for us, however they use boost rather than cython/pyrex

You can also use swiginac, that I wrote together with Ola Skavhaug:

http://swiginac.berlios.de/

It's using SWIG, instead of boost-python, that I find very cumbersome
to use. But I am not working on it anymore, since it's difficult to
extend ginac with new features and I started SymPy instead. But I
think Ola is still using it.

Ondrej

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[sage-devel] Re: Python bindings for Ginac

2007-09-08 Thread Pablo De Napoli

One more comment:
I see that this project is not actively maintained, in fact in its
e-mail list the last e-mail is from 2005...

On 9/8/07, Pablo De Napoli [EMAIL PROTECTED] wrote:
 The idea of incorporating Ginac into Sage was discussed some time ago
 in this list.
 Now I see that in its page there is a link to some python bindings for Ginac

 http://pyginac.sourceforge.net/

 This could be useful for us, however they use boost rather than cython/pyrex

 Pablo


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[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread Joel B. Mohler

On Saturday 08 September 2007 17:49, mabshoff wrote:
 Executive Summary: SCons somehow gets its LD_LIBRARY_PATH or env in
 general wrong and ends up linking against the gmp 4.2.1 provided by
 Debian. Somehow the compiler gets it all wrong and *boom*

 How to fix: Fix SCons *ducks* - a short term solution seems to be to
 source local/sage/env before building sage-2.8.4.spkg.

This confuses me.  How is source'ing local/sage/env any different from what 
normally happens?  Isn't that always source'd once you get into the internals 
of sage batch files?

So, I thought I could answer that question myself:  In local/bin/sage-build we 
call local/bin/sage-env with-out source, but inside of local/bin/sage-env, we 
say you must:  
#  You must source this; see below!

Thus, I'm thinking that line 45 of sage-build needs 'source ' at the front, 
but I'm too close to my bed-time to actually go test that myself.

I believe that autoconf might have not cared so much about things like this 
because the --prefix option got set which essentially rewrote the environment 
on it's own.

--
Joel

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[sage-devel] Re: cannot build 2.8.4 on sage.math

2007-09-08 Thread mabshoff



On Sep 9, 3:10 am, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On Sep 9, 2:40 am, Joel B. Mohler [EMAIL PROTECTED] wrote:

  On Saturday 08 September 2007 17:49, mabshoff wrote:

   Executive Summary: SCons somehow gets its LD_LIBRARY_PATH or env in
   general wrong and ends up linking against the gmp 4.2.1 provided by
   Debian. Somehow the compiler gets it all wrong and *boom*

   How to fix: Fix SCons *ducks* - a short term solution seems to be to
   source local/sage/env before building sage-2.8.4.spkg.

 Hello Joel,

  This confuses me.

 Oh, me too.

   How is source'ing local/sage/env any different from what
  normally happens?

 Are you saying that in a source blah vs ./blah way or more meta/
 abstract?

   Isn't that always source'd once you get into the internals
  of sage batch files?

 I don't know.

  So, I thought I could answer that question myself:  In local/bin/sage-build 
  we
  call local/bin/sage-env with-out source, but inside of local/bin/sage-env, 
  we
  say you must:  
  #  You must source this; see below!
  
  Thus, I'm thinking that line 45 of sage-build needs 'source ' at the front,
  but I'm too close to my bed-time to actually go test that myself.

 I did that, started a build and will see in the morning - or in about
 90 minutes depending if I stay motivated that long and will let you
 know.


Sorry, but that didn't work. I am out of ideas for the night. Let's
hope somebody else can pick it up from here.

Cheers,

Michael

  I believe that autoconf might have not cared so much about things like this
  because the --prefix option got set which essentially rewrote the 
  environment
  on it's own.

 Well, SCons is without a doubt better than autohell, we just have to
 get through the teething phase until we are good to go.

  --
  Joel

 Cheers,

 Michael


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[sage-devel] Sage 2.8.4 port to PPC Linux 32 bit 99.9% done

2007-09-08 Thread mabshoff

Hello,

2.8.4 + the integer doc + 1 line fix to pari's build system leads to:

[EMAIL PROTECTED] sage-2.8.4]$ uname -a
Linux localhost.localdomain 2.6.21-1.3194.fc7 #1 Wed May 23 22:12:25
EDT 2007 ppc ppc ppc GNU/Linux
[EMAIL PROTECTED] sage-2.8.4]$ ./sage
--
| SAGE Version 2.8.4, Release Date: 2007-09-07   |
| Type notebook() for the GUI, and license() for information.|
--

sage:
Exiting SAGE (CPU time 0m0.01s, Wall time 0m3.58s).

I will post the patch for pari tomorrow. All the doctests pass, expect
some trivial DSage issues:

sage.dsage.twisted.tests.test_remote
  ClientRemoteCallsTest
 
testremoteSubmitBadJob ...
[OK]
 
testremoteSubmitJob ...
[OK]
  MonitorRemoteCallsTest
 
testget_killed_jobs_list ...
[ERROR]
   [ERROR]
 
testremote_get_job ...
[ERROR]
 [ERROR]
 
testremote_job_done ...
[ERROR]
[ERROR]
 
testremote_job_failed ...
[ERROR]
  [ERROR]

===
[ERROR]:
sage.dsage.twisted.tests.test_remote.MonitorRemoteCallsTest.testget_killed_jobs_list

Traceback from remote host -- Traceback unavailable
===
[ERROR]:
sage.dsage.twisted.tests.test_remote.MonitorRemoteCallsTest.testget_killed_jobs_list

Traceback (most recent call last):
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/twisted/pb.py, line 412, in requestAvatar
avatar.attached(avatar, mind)
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/twisted/pb.py, line 258, in attached
self.DSageServer.monitordb.add_monitor(self.host_info)
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/database/monitordb.py, line 120, in add_monitor
cpu_speed = host_info['cpu_speed']
exceptions.KeyError: 'cpu_speed'
===
[ERROR]:
sage.dsage.twisted.tests.test_remote.MonitorRemoteCallsTest.testremote_get_job

Traceback from remote host -- Traceback unavailable
===
[ERROR]:
sage.dsage.twisted.tests.test_remote.MonitorRemoteCallsTest.testremote_get_job

Traceback (most recent call last):
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/twisted/pb.py, line 412, in requestAvatar
avatar.attached(avatar, mind)
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/twisted/pb.py, line 258, in attached
self.DSageServer.monitordb.add_monitor(self.host_info)
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/database/monitordb.py, line 120, in add_monitor
cpu_speed = host_info['cpu_speed']
exceptions.KeyError: 'cpu_speed'
===
[ERROR]:
sage.dsage.twisted.tests.test_remote.MonitorRemoteCallsTest.testremote_job_done

Traceback from remote host -- Traceback unavailable
===
[ERROR]:
sage.dsage.twisted.tests.test_remote.MonitorRemoteCallsTest.testremote_job_done

Traceback (most recent call last):
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/twisted/pb.py, line 412, in requestAvatar
avatar.attached(avatar, mind)
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/twisted/pb.py, line 258, in attached
self.DSageServer.monitordb.add_monitor(self.host_info)
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/database/monitordb.py, line 120, in add_monitor
cpu_speed = host_info['cpu_speed']
exceptions.KeyError: 'cpu_speed'
===
[ERROR]:
sage.dsage.twisted.tests.test_remote.MonitorRemoteCallsTest.testremote_job_failed

Traceback from remote host -- Traceback unavailable
===
[ERROR]:
sage.dsage.twisted.tests.test_remote.MonitorRemoteCallsTest.testremote_job_failed

Traceback (most recent call last):
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/twisted/pb.py, line 412, in requestAvatar
avatar.attached(avatar, mind)
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/twisted/pb.py, line 258, in attached
self.DSageServer.monitordb.add_monitor(self.host_info)
  File /tmp/Work/sage-2.8.4/local/lib/python2.5/site-packages/sage/
dsage/database/monitordb.py, line 120, in add_monitor
cpu_speed = host_info['cpu_speed']
exceptions.KeyError: 'cpu_speed'