[sage-devel] Solaris problem when building readline - due to Darwin test in SAGE

[Dr. David Kirkby]

I tried building sage 3.0 on an x86 laptop running Solaris Express
Developer Edition snv_79b. At the time of writing this is the latest
developer edition, but there are later community editions of Solaris.
I was using gcc 4.0.2, but Sun's make program in /usr/bin/make.

bash-3.2$ cat /etc/release
   Solaris Express Developer Edition 1/08 snv_79b X86
  Copyright 2008 Sun Microsystems, Inc.  All Rights Reserved.
   Use is subject to license terms.
   Assembled 24 January 2008

bash-3.2$ uname -a
SunOS kingfisher 5.11 snv_79a i86pc i386 i86pc


I hit a problem while when sage is trying to build readline, which I
believe was probably introduced when someone added a test for Darwin.
*
*
gcc -c -DHAVE_CONFIG_H   -I. -I.. -I.. -DRL_LIBRARY_VERSION='"5.2"' -g
-O -fpic -DREADLINE_LIBRARY -c -o tilde.o ../tilde.c
mv tilde.o tilde.so
rm -f compat.so
gcc -c -DHAVE_CONFIG_H   -I. -I.. -I.. -DRL_LIBRARY_VERSION='"5.2"' -g
-O -fpic -o compat.o ../compat.c
mv compat.o compat.so
rm -f libreadline.so.5
gcc -shared -Wl,-i -Wl,-h,libreadline.so.5  -o libreadline.so.5
readline.so vi_mode.so funmap.so keymaps.so parens.so search.so
rltty.so complete.so bind.so isearch.so display.so signals.so  util.so
kill.so undo.so macro.so input.so callback.so terminal.so  text.so
nls.so misc.so xmalloc.so history.so histexpand.so histfile.so
histsearch.so shell.so  mbutil.so tilde.so  compat.so
rm -f libhistory.so.5
gcc -shared -Wl,-i -Wl,-h,libhistory.so.5  -o libhistory.so.5
history.so histexpand.so histfile.so histsearch.so shell.so  mbutil.so
xmalloc.so
( cd shlib ; make  DESTDIR= install )
/bin/sh ../support/mkdirs /export/home/drkirkby/sage-3.0/local/lib
/bin/sh ../support/shlib-install -O solaris2.11 -d /export/home/
drkirkby/sage-3.0/local/lib -b /export/home/drkirkby/sage-3.0/local/
bin -i "/usr/bin/ginstall -c -m 644" libhistory.so.5
/bin/sh ../support/shlib-install -O solaris2.11 -d /export/home/
drkirkby/sage-3.0/local/lib -b /export/home/drkirkby/sage-3.0/local/
bin -i "/usr/bin/ginstall -c -m 644" libreadline.so.5
install: you may need to run ldconfig
Error building readline

real0m21.815s
user0m12.931s
sys 0m8.218s
sage: An error occurred while installing readline-5.2.p1
Please email sage-devel http://groups.google.com/group/sage-devel
***
***

On investigation, I found that the test for Darwin in the script

sage-3.0/spkg/build/readline-5.2.p1/spkg-install

is the source of the problem. It uses '==" for a comparison, but
should I believe use '='.

bash-3.2$ diff readline-5.2.p1/spkg-install sage-3.0/spkg/build/
readline-5.2.p1/spkg-install
11,12c11,12
< if [ `uname` = 'Darwin' ]; then
<   if [ `uname -r | awk -F. '{ print $1; }'` = '9' ]; then
---
> if [ `uname` == 'Darwin' ]; then
>   if [ `uname -r | awk -F. '{ print $1; }'` == '9' ]; then
23c23
< if [ `uname` = 'Darwin' ]; then
---
> if [ `uname` == 'Darwin' ]; then



Once I changed that, readline works fine. (Later I get a problem with
pari, but that is another issue).

David Kirkby

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[sage-devel] Re: Test errors for Sage 3.0 on OS X

[mabshoff]

On Apr 24, 1:54 am, Bjake Hammersholt Roune <[EMAIL PROTECTED]>
wrote:

Hi Bjake,

> It just now occured to me that this might be due to counting wall-time
> instead of CPU-time, since I put the machine to sleep during a lecture
> while it was running the tests.

Ok, that explains it. On OSX time prints the time elapsed [at least
per default] while on Linux it actually prints the CPU time used. I
guess this boils down to BSD vs. GNU default behavior. Should we
actually fix this? If somebody thinks so please open a ticket and
mention the fact here.

> /Bjarke

Cheers,

Michael
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[sage-devel] Re: Initial support for posets

[William Stein]

On Wed, Apr 23, 2008 at 1:42 PM, Franco Saliola <[EMAIL PROTECTED]> wrote:
>
>  On Wed, Apr 23, 2008 at 4:05 PM, Robert Miller <[EMAIL PROTECTED]> wrote:
>
>  >  We might want to think about the naming conventions for Lattice. As
>  >  with all words in mathematics, this one has multiple meanings. A
>  >  lattice can be a poset with a meet and a join, or it can be a free
>  >  abelian group with an inner product.

I call dibs on Lattice being "free abelian group with an inner product".

:-)

>
>  This is a good point. The only thing I can think of is to append
>  something: for example, LatticeGroup. I'm not sure how natural that
>  is. LatticePoset is definitely not. Other suggestions?
>
>
>
>  --
>
>  >
>



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: Sage, Maxima, Lisp

[Carl Witty]

On Apr 23, 12:08 pm, "Bill Page" <[EMAIL PROTECTED]> wrote:
...
> Both you and Gaby have discussed the possibility of defining an
> abstract machine (aka. run-time system) to replace the role that Lisp
> plays for Axiom. We also know that Aldor has already defined such a
> machine called FOAM. FOAM can be implemented either in Lisp (for
> interface with Axiom) or by a run-time system written entirely in C
> for stand alone use. In fact this strategy is quite common and we here
> a lot for example about the Java Virtual Machine.
>
> Now it turns out that Python also has this notion of an abstract
> virtual machine that is the target for the Python interpreter. There
> are already some languages other than Python that can produce low
> level code for the Python virtual machine. I believe that the current
> Python virtual machine would very likely be adequate to support the
> run time requirements of Axiom/Aldor. So my question is: Is there be
> any possibility and interest in producing either an Axiom/Spad or
> Aldor compiler that targets this same virtual machine?

I found a little information about FOAM on the web, and it looks like
it's probably much faster than the Python VM for any sort of low-level
code.  For instance, FOAM has an instruction for doing floating-point
addition which is presumably very fast; the Python VM has a single
addition instruction that checks that the operands are numbers of the
same type, then calls the addition method on the left object with the
right object as an argument; then the method creates a new object with
the result.  A Python floating-point addition on my laptop takes
around 40ns.

Carl
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[sage-devel] Re: notebook features discussion

[William Stein]

On Wed, Apr 23, 2008 at 8:29 PM, John Voight <[EMAIL PROTECTED]> wrote:
>
>  Hello!
>
>  I've run some Sage labs using the notebook here at UVM and two things
>  have come up.
>
>  (1) At the end of class, I asked my students to print out their work
>  and turn it in.  I stopped this almost immediately, since the
>  printouts are hugely wasteful: blank pages, things overrun the
>  margins, etc.  This is in Firefox, which is certainly not working very
>  hard in this regard.  Perhaps there could be a "printer-friendly"
>  version of a notebook like so many other webpages?

I put some effort into improving the printing friendliness in sage-3.0.
Especially the text in input cells should never overrun margins, etc.
The output could.  Click on the print button for the printer friendly version
of a page.

>  (2) One student did this, as did I: accidentally clicked on a bookmark
>  while working, then clicked back to the page to see work was lost.

It wasn't lost.  They should have pressed refresh.  This would have
updated the page to the current state.  The server always has
the current state even without autosave.  Saving only makes a snapshot
that's in the browsable revision log.

There are two ideas about how to fix the browse away and press back button
issue:
  (1) make it so any time any browser window is looking at a worksheet, if it
gets out of sync with the server's view of that worksheet a refresh is forced.
This is useful also if multiple browsers are viewing the same page.
  (2) somehow make it hard to navigate away from a worksheet (e.g., via
an alert).

I've tried (2) but didn't like it.  Implementing (1) is nontrivial and
opens a can
of worms, but I would still like it to happen.

>  How do you change the autosave interval to be something shorter?  (I
>  found an _user_autosave_interval function for the class Worksheet...)

There is no way to do that beyond hacking on source code.

william


>
> >
>



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Re: small documentation problem: "\ " at the end of a line

[Daniel Bump]

> On Wed, 23 Apr 2008 at 01:25PM -0700, John H Palmieri wrote:
> This is exactly why die-hard Python people say "don't use backslashes to
> continue statements":
> 
> http://docs.python.org/dev/howto/doanddont.html#using-backslash-to-continue-statements
> 
> Perhaps we should link to the above guide in the Sage Programming Guide?

Perhaps backslashes followed by whitespace and a newline
could be handled by the preparser. Strip the whitespace
so the newline is properly escaped.

This wouldn't help with .py files where the preparser
is not invoked but it would help with the problem at hand,
unless I'm missing something.

Dan




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[sage-devel] Re: sage OSX 10.4.4 dmg

[William Stein]

On Wed, Apr 23, 2008 at 9:28 PM, root <[EMAIL PROTECTED]> wrote:
>
>  Have you copied the image?
>  Can I remove it?
>

Yep it's here:

http://sagemath.org/SAGEbin/apple_osx/powerpc/

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[sage-devel] Re: notebook features discussion

[John Voight]

Hello!

I've run some Sage labs using the notebook here at UVM and two things
have come up.

(1) At the end of class, I asked my students to print out their work
and turn it in.  I stopped this almost immediately, since the
printouts are hugely wasteful: blank pages, things overrun the
margins, etc.  This is in Firefox, which is certainly not working very
hard in this regard.  Perhaps there could be a "printer-friendly"
version of a notebook like so many other webpages?
(2) One student did this, as did I: accidentally clicked on a bookmark
while working, then clicked back to the page to see work was lost.
How do you change the autosave interval to be something shorter?  (I
found an _user_autosave_interval function for the class Worksheet...)

JV
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[sage-devel] Re: sage OSX 10.4.4 dmg

[root]

My Mac box is generally idle except when I'm doing the every-other-month
Axiom release. If you need images I can build them for OSX 10.4

Tim

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[sage-devel] Re: small documentation problem: "\ " at the end of a line

[Dan Drake]

On Wed, 23 Apr 2008 at 09:45PM -0400, Alex Ghitza wrote:
> Dan Drake wrote:
> > On Wed, 23 Apr 2008 at 01:25PM -0700, John H Palmieri wrote:
> > This is exactly why die-hard Python people say "don't use backslashes to
> > continue statements":
> > 
> > http://docs.python.org/dev/howto/doanddont.html#using-backslash-to-continue-statements
> > 
> > Perhaps we should link to the above guide in the Sage Programming Guide?
> > 
> 
> I'm responsible for most (all?) of those backslashes, and at the time 
> this seemed to be the easiest solution to the problem of having very 
> long example lines that don't get wrapped in verbatim environments (and 
> so get cut off in the pdf version of the tutorial, constructions, etc.).
> 
> I agree that it wasn't the most elegant solution.  On the other hand, 
> not doing it at all rendered chunks of the pdf documentation useless, 
> since an example that you cannot read is basically useless.
> 
> But the spirit of Sage (and of these lists) is: "tell me how I can do 
> this properly, or better yet, do it yourself and post a patch".  The one 
> sticky point is that whatever solution we come up with must behave well 
> with respect to making both pdf and html documentation.

The easiest and best way is to slap parentheses around your long
statement. Python automatically continues such lines:

  if ( very_long_statement and another_long_statement and
   this_is_getting_ridiculous ):
 blah
 blah
  else:
 blah
 blah

I can get a patch for this up in the next day or so if no one else does.

Dan

-- 
---  Dan Drake <[EMAIL PROTECTED]>
-  KAIST Department of Mathematical Sciences
---  http://math.kaist.ac.kr/~drake


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[sage-devel] Re: sage OSX 10.4.4 dmg

[root]

Have you copied the image?
Can I remove it?

Tim

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[sage-devel] Re: sage OSX 10.4.4 dmg

[William Stein]

On Wed, Apr 23, 2008 at 7:49 PM,  <[EMAIL PROTECTED]> wrote:
>
>  Here is a disk image of the vanilla Sage release for OSX 10.4.4
>
>  
> http://daly.axiom-developer.org/sage-3.0-osx10.4-ppc-PowerMacintosh-Darwin.dmg
>

Thanks!!  I've posted it.

William

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[sage-devel] sage OSX 10.4.4 dmg

[daly]

Here is a disk image of the vanilla Sage release for OSX 10.4.4

http://daly.axiom-developer.org/sage-3.0-osx10.4-ppc-PowerMacintosh-Darwin.dmg

Tim Daly

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[sage-devel] Re: Readline and Solaris: Testing strings with == is not portable.

[mabshoff]

Hi,

One more thing about Solaris: The game plan of the Solaris port has
slightly changed. The initial port will be Solaris 10 and no longer
Solaris 9. The compiler I will use is Sun Fort 12 [or whatever cc 5.9
corresponds to]. The main reason is that the header situation with
Sun's compiler is much better and building even Python with Sun's
compiler in 64 bit mode is fairly trivial while doing so with gcc is a
huge pain when you actually want to use stuff like the md5 module.
Additionally in most cases many installs have crap in /usr/local and
that really, really produces a lot of problems with gcc, while it
seems that with Sun's cc and CC I have much tighter control over that
issue.

On top of that dealing with the 32 vs. 64 bit issue on Solaris
[multilib is a really, really dumb idea, especially if you default to
32 bit on as 64 bit platform - but I could bitch about that for hours,
so I will spare you the details] is something that seems to be less of
a problem with Sun's tool chain. Apple's decision to do the exact same
kind of move doesn't bode to well, but at least they have universal
binaries/library support to lessen that blow.

Oh well, porting sucks ;)

Michael
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[sage-devel] Re: small documentation problem: "\ " at the end of a line

[Alex Ghitza]

Dan Drake wrote:
> On Wed, 23 Apr 2008 at 01:25PM -0700, John H Palmieri wrote:
> This is exactly why die-hard Python people say "don't use backslashes to
> continue statements":
> 
> http://docs.python.org/dev/howto/doanddont.html#using-backslash-to-continue-statements
> 
> Perhaps we should link to the above guide in the Sage Programming Guide?
> 

I'm responsible for most (all?) of those backslashes, and at the time 
this seemed to be the easiest solution to the problem of having very 
long example lines that don't get wrapped in verbatim environments (and 
so get cut off in the pdf version of the tutorial, constructions, etc.).

I agree that it wasn't the most elegant solution.  On the other hand, 
not doing it at all rendered chunks of the pdf documentation useless, 
since an example that you cannot read is basically useless.

But the spirit of Sage (and of these lists) is: "tell me how I can do 
this properly, or better yet, do it yourself and post a patch".  The one 
sticky point is that whatever solution we come up with must behave well 
with respect to making both pdf and html documentation.

Best,
Alex


-- 
Alexandru Ghitza
Assistant Professor
Department of Mathematics
Colby College
Waterville, ME 04901
http://bayes.colby.edu/~ghitza/

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[sage-devel] Re: Readline and Solaris: Testing strings with == is not portable.

[mabshoff]

On Apr 24, 2:42 am, "Dr. David Kirkby" <[EMAIL PROTECTED]>
wrote:

Hi David,

> I tried building sage 3.0 on an x86 laptop running Solaris Express
> Developer Edition snv_79b. At the time of writing this is the latest
> developer edition, but there are later community editions of Solaris.
> I was using gcc 4.0.2, but Sun's make program in /usr/bin/make.
>
> bash-3.2$ /usr/sbin/psrinfo -v
> Status of virtual processor 0 as of: 04/23/2008 13:52:18
>   on-line since 04/23/2008 13:42:46.
>   The i386 processor operates at 2000 MHz,
>         and has an i387 compatible floating point processor.
> Status of virtual processor 1 as of: 04/23/2008 13:52:18
>   on-line since 04/23/2008 13:42:49.
>   The i386 processor operates at 2000 MHz,
>         and has an i387 compatible floating point processor.
>
> bash-3.2$ cat /etc/release
>                Solaris Express Developer Edition 1/08 snv_79b X86
>           Copyright 2008 Sun Microsystems, Inc.  All Rights Reserved.
>                        Use is subject to license terms.
>                            Assembled 24 January 2008
>
> bash-3.2$ uname -a
> SunOS kingfisher 5.11 snv_79a i86pc i386 i86pc
>
>  'spkg-install' uses '==' to check equality. That might be ok in bash,
> but it is not ok in /bin/sh which is the shell that the script uses.

Yeah, the curse of nearly ever Linux distro linking sh to bash. The
problem is known and on my list of things to clean up. The general
plan is to change all shebangs to

#!/usr/bin/env bash

since Sage requires bash anyway and a some of the configure scripts in
Sage's components do not play nicely with the Solaris 9 sh for
example.

> The following works ok - I replaced == by = whenever == was seen

I put fixing readline on the list of things to do.



The plan on my end right now is to fix the OSX 10.5 64 bit and FreeBSD
ports in 3.0.1 and 3.0.2 and then tackle the Solaris port in earnest
again once coercion is merged. Sorry for never getting back to you on
your last email about the use of your Solaris boxen, post 3.0.2 you
will definitely hear from me again.

Cheers,

Michael
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[sage-devel] Re: small documentation problem: "\ " at the end of a line

[David Joyner]

A point of clarification: AFAIK, no newlines were used originally in the
tutorial or construction docs. They were introduced only to increase
the readability
of the pdf versions. Even as it is, in the 2008.01.18 version of the tutorial
sold on lulu, there are 10 pages or so which have lines cut off because they
ran off the edge of the page.

On Wed, Apr 23, 2008 at 7:48 PM, Dan Drake <[EMAIL PROTECTED]> wrote:
> On Wed, 23 Apr 2008 at 01:25PM -0700, John H Palmieri wrote:
>  >
>  > In the section of the tutorial on 3d plotting,
>  >
>  >   
>  >
>  > the continuation characters "\" all have spaces after them, which
>  > messes up cutting and pasting.  Also in the section on Maxima,
>  >
>  >   
>  >
>  > two of the backslashes have spaces after them (in the Mobius strip and
>  > the Klein bottle examples).
>  >
>  > The same thing happens half a dozen times in "SAGE Constructions".
>
>  This is exactly why die-hard Python people say "don't use backslashes to
>  continue statements":
>
>  
> http://docs.python.org/dev/howto/doanddont.html#using-backslash-to-continue-statements
>
>  Perhaps we should link to the above guide in the Sage Programming Guide?
>
>  Dan
>
>  --
>  ---  Dan Drake <[EMAIL PROTECTED]>
>  -  KAIST Department of Mathematical Sciences
>  ---  http://math.kaist.ac.kr/~drake
>
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>

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[sage-devel] Re: Sage 3.0 released

[mabshoff]

On Apr 24, 2:22 am, mark mcclure <[EMAIL PROTECTED]> wrote:
> On Apr 23, 6:24 pm, mark mcclure <[EMAIL PROTECTED]> wrote:


Hi Mark,

> make; followed by "sage -ba" seems to have done the trick.  Everything
> seems to be working great and "./sage -testall" passed all tests.
>
> I've got a working G5 binary built on OS X 10.4.11 now.  I'm happy to
> distribute, if necessary, but I really have no clue how.

Good. I think somebody else got binaries by now, but since William is
missing in action and I haven't paid attention to the binary problem
none is up on the website.

> > Incidentally, I unpacked the original .tar file containing the
> > source.  The full file 'singular-3-0-4-2-20080405.p1.spkg' is
> > most certainly there.  How the kg got cut off, I have no clue.
>
> Examining the filenames in spkg/standard, I find that
> 'singular-3-0-4-2-20080405.p1.spkg' is the longest by two
> characters.  Conspicuous. :)

Yes, but quite interesting. "singular-3-0-4-2-20080405.p1.sp" is 32
characters long. What file system are you on? How did you unpack the
tar file? I would rather expect the utility used to uncompress the tar
archive to be buggy. My Pre-OSX Mac-Fu is a little rusty, but IIRC
even then the filesystem didn't have a 32 bit char file name limit.

> Thanks a lot for the help,
> Mark

Cheers,

Michael
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[sage-devel] enumerating colorings of graphs

[Jason Grout]

Robert, this question might be mainly to you:

I have a need to enumerate all possible black and white colorings of a 
graph, up to (colored) isomorphism.  Is there a way to use some of the 
NICE code to make this fast?  It seems like I read somewhere that Robert 
was going to generalize NICE to let you compute enumeration/canonical 
things for more general combinatorial objects.

Thanks,

Jason


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[sage-devel] Re: small documentation problem: "\ " at the end of a line

[Dan Drake]

On Wed, 23 Apr 2008 at 01:25PM -0700, John H Palmieri wrote:
> 
> In the section of the tutorial on 3d plotting,
> 
>   
> 
> the continuation characters "\" all have spaces after them, which
> messes up cutting and pasting.  Also in the section on Maxima,
> 
>   
> 
> two of the backslashes have spaces after them (in the Mobius strip and
> the Klein bottle examples).
> 
> The same thing happens half a dozen times in "SAGE Constructions".

This is exactly why die-hard Python people say "don't use backslashes to
continue statements":

http://docs.python.org/dev/howto/doanddont.html#using-backslash-to-continue-statements

Perhaps we should link to the above guide in the Sage Programming Guide?

Dan

-- 
---  Dan Drake <[EMAIL PROTECTED]>
-  KAIST Department of Mathematical Sciences
---  http://math.kaist.ac.kr/~drake


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Description: Digital signature

[sage-devel] Re: Sage 3.0 released

[mark mcclure]

On Apr 23, 6:24 pm, mark mcclure <[EMAIL PROTECTED]> wrote:
> On Apr 23, 6:17 pm, mabshoff <[EMAIL PROTECTED]
>
> dortmund.de> wrote:
> > On Apr 24, 12:14 am, mark mcclure <[EMAIL PROTECTED]> wrote:
> > > The trailing kg is missing.  Should I simply change the
> > > name and try again?
>
> > Yes. Run make, then a "sage -b". If Sage starts up all ought be be
> > fixed. If not run a "sage -ba"
>
> Will do.

make; followed by "sage -ba" seems to have done the trick.  Everything
seems to be working great and "./sage -testall" passed all tests.

I've got a working G5 binary built on OS X 10.4.11 now.  I'm happy to
distribute, if necessary, but I really have no clue how.

> Incidentally, I unpacked the original .tar file containing the
> source.  The full file 'singular-3-0-4-2-20080405.p1.spkg' is
> most certainly there.  How the kg got cut off, I have no clue.

Examining the filenames in spkg/standard, I find that
'singular-3-0-4-2-20080405.p1.spkg' is the longest by two
characters.  Conspicuous. :)

Thanks a lot for the help,
Mark

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[sage-devel] Readline and Solaris: Testing strings with == is not portable.

[Dr. David Kirkby]

I tried building sage 3.0 on an x86 laptop running Solaris Express
Developer Edition snv_79b. At the time of writing this is the latest
developer edition, but there are later community editions of Solaris.
I was using gcc 4.0.2, but Sun's make program in /usr/bin/make.

bash-3.2$ /usr/sbin/psrinfo -v
Status of virtual processor 0 as of: 04/23/2008 13:52:18
  on-line since 04/23/2008 13:42:46.
  The i386 processor operates at 2000 MHz,
and has an i387 compatible floating point processor.
Status of virtual processor 1 as of: 04/23/2008 13:52:18
  on-line since 04/23/2008 13:42:49.
  The i386 processor operates at 2000 MHz,
and has an i387 compatible floating point processor.


bash-3.2$ cat /etc/release
   Solaris Express Developer Edition 1/08 snv_79b X86
  Copyright 2008 Sun Microsystems, Inc.  All Rights Reserved.
   Use is subject to license terms.
   Assembled 24 January 2008

bash-3.2$ uname -a
SunOS kingfisher 5.11 snv_79a i86pc i386 i86pc

 'spkg-install' uses '==' to check equality. That might be ok in bash,
but it is not ok in /bin/sh which is the shell that the script uses.

The following works ok - I replaced == by = whenever == was seen


#!/bin/sh
###
## Readline 5.2
###

cd src/

build()
{
./configure --prefix=$SAGE_LOCAL
if [ `uname` = 'Darwin' ]; then
  if [ `uname -r | awk -F. '{ print $1; }'` = '9' ]; then
echo "Fixing Makefile for OSX 10.5 compatibility"
sed -e 's/-dynamic/-dynamiclib/' shlib/Makefile > shlib/
Makefile.ok
mv shlib/Makefile.ok shlib/Makefile
  fi
fi
make install
}

build

if [ `uname` = 'Darwin' ]; then
  DYLIB_NAME=$SAGE_LOCAL/lib/libreadline.dylib
else
  DYLIB_NAME=$SAGE_LOCAL/lib/libreadline.so
fi

if [ -f $DYLIB_NAME -a -f $SAGE_LOCAL/lib/libreadline.a ]; then
  chmod 755 $SAGE_LOCAL/lib/libreadline.*
  chmod 755 $SAGE_LOCAL/lib/libhistory.*
  exit 0
else
  echo "Error building readline"
  exit 1
fi


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[sage-devel] Re: Test errors for Sage 3.0 on OS X

[Bjake Hammersholt Roune]

> > sage -t  devel/sage/sage/modular/abvar/morphism.py  *** ***
> > Error: TIMED
> >  OUT! *** ***
> > *** *** Error: TIMED OUT! *** ***
> > [1358.6 s]
> > [...]
>
> Odd, it shouldn't time out on that machine. I am hoping William or
> Craig can take a close look since they are much more familiar with the
> code. That it isn't reproducible is slightly worrying. I did valgrind
> all doctests of 3.0, so maybe something will pop up there.
>
It just now occured to me that this might be due to counting wall-time
instead of CPU-time, since I put the machine to sleep during a lecture
while it was running the tests.

/Bjarke

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[sage-devel] Re: Trouble finding the normalizer of a subgroup

[David Joyner]

AFAIK, the normalizer of a group is not yet implemented.
If you type
sage: s6.normalizer?
you'll see the synax for that command. My guess is that normalizer_of_group
would be an easy function to implement (and I can do that if no one
else wants to).

On Wed, Apr 23, 2008 at 4:06 PM, Hy Ginsberg <[EMAIL PROTECTED]> wrote:
>
>  Hi All,
>
>  Perhaps someone can help me figure this out.  I am trying to create an
>  elementary abelian subgroup of a symmetric group and then look at its
>  normalizer.  Here's what doesn't work:
>
> s6 = SymmetricGroup(6)
>
> c1 = s6([(1,2)])
> c2 = s6([(3,4)])
> c3 = s6([(5,6)])
>
> e8 = s6.subgroup([c1,c2,c3])
> print e8.order()
>
> n = s6.normalizer(e8)
>
>  It's good through printing the order of "e8".  Then the horrible
>  traceback which
>  follows.
>
>  Many thanks,
>  - Hy
>
>
>
>
>  Traceback (most recent call last):
>   File "", line 1, in 
>   File "/home/hy/.sage/sage_notebook/worksheets/admin/13/code/42.py",
>  line 4, in
>  
> n = s6.normalizer(e8)
>   File
>  "/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
>  packages/sympy/plotting/",
>  line 1, in 
>
>   File
>  "/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
>  packages/sage/groups/perm_gps/permgroup.py",
>  line 1253, in normalizer
> N = self._gap_().Normalizer(str(g))
>   File
>  "/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
>  packages/sage/interfaces/expect.py",
>  line 954, in __call__
> return self._obj.parent().function_call(self._name, [self._obj] +
>  list(args))
>   File
>  "/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
>  packages/sage/interfaces/expect.py",
>  line 900, in function_call
> args[i] = self.new(args[i])
>   File
>  "/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
>  packages/sage/interfaces/expect.py",
>  line 803, in new
> return self(code)
>   File
>  "/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
>  packages/sage/interfaces/expect.py",
>  line 738, in __call__
> return cls(self, x)
>   File
>  "/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
>  packages/sage/interfaces/expect.py",
>  line 989, in __init__
> raise TypeError, x
>  TypeError: Gap produced error output
>  Syntax error: ; expected
>  $sage20:=Subgroup of SymmetricGroup(6) generated by [(1,2), (3,4),
>  (5,6)];;
>^
>  Variable: 'by' must have a value
>
>
>executing $sage20:=Subgroup of SymmetricGroup(6) generated by
>  [(1,2), (3,4),
>  (5,6)];;
>  >
>

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[sage-devel] Re: Sage 3.0 released

[mark mcclure]

On Apr 23, 6:17 pm, mabshoff <[EMAIL PROTECTED]
dortmund.de> wrote:
> On Apr 24, 12:14 am, mark mcclure <[EMAIL PROTECTED]> wrote:
> > The trailing kg is missing.  Should I simply change the
> > name and try again?
>
> Yes. Run make, then a "sage -b". If Sage starts up all ought be be
> fixed. If not run a "sage -ba"

Will do.

Incidentally, I unpacked the original .tar file containing the
source.  The full file 'singular-3-0-4-2-20080405.p1.spkg' is
most certainly there.  How the kg got cut off, I have no clue.

Mark

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[sage-devel] Re: Sage 3.0 released

[mabshoff]

On Apr 24, 12:14 am, mark mcclure <[EMAIL PROTECTED]> wrote:
> On Apr 23, 6:10 pm, mabshoff <[EMAIL PROTECTED]
>
> dortmund.de> wrote:
> > for whatever reason there is no Singular in your build log. Right at
> > the top it says:
> > ...
> > Could you check if spkg/standard contains any file called
> > singular-3-0-4-2-20080405.p1.spkg, i.e:
>
> No, there's not.  Strangely, there's a file called:
> singular-3-0-4-2-20080405.p1.sp
> The trailing kg is missing.  Should I simply change the
> name and try again?

Yes. Run make, then a "sage -b". If Sage starts up all ought be be
fixed. If not run a "sage -ba"

I am thinking on how to fix the issue that "make" doesn't crap out on
us like that. You have certainly hit an odd bug to say the least.

> Mark

Cheers,

Michael
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[sage-devel] Re: Sage 3.0 released

[mark mcclure]

On Apr 23, 6:10 pm, mabshoff <[EMAIL PROTECTED]
dortmund.de> wrote:
> for whatever reason there is no Singular in your build log. Right at
> the top it says:
> ...
> Could you check if spkg/standard contains any file called
> singular-3-0-4-2-20080405.p1.spkg, i.e:

No, there's not.  Strangely, there's a file called:
singular-3-0-4-2-20080405.p1.sp
The trailing kg is missing.  Should I simply change the
name and try again?

Mark

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[sage-devel] Re: [fricas-devel] Re: [sage-devel] Re: FriCAS/Open-Axiom and SAGE

[root]

Yes, both books are part of the documentation that ships with Axiom.

The Jenks book (ISBN 0-387-97855-0) is in src/doc/book.pamphlet
(the latex sources). It is also available as a pdf file at 


The Daly book (ISBN 1-411-66597-X) is in src/doc/bookvol1.pamphlet
(the latex sources). It is also available as a pdf file at 




Tim

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[sage-devel] Re: Sage 3.0 released

[mabshoff]

On Apr 23, 11:51 pm, mark mcclure <[EMAIL PROTECTED]> wrote:
> On Apr 23, 4:43 pm, mabshoff <[EMAIL PROTECTED]
>
> dortmund.de> wrote:
> >  We will be much more aggressive from now on in blacklisting know
> > broken compilers since at least on OSX it should work out of the box
> > because there is so little variety of the OS itself and Apple usually
> > is the tool chain provider. In general: if anything breaks keep the
> > log - usually there is a clue in there what went wrong. Upgrading to
> > 10.4.11 is unlikely to fix the  issues, but then I have seen pigs fly
> > before ;)
>
> Sorry, I'll remember this.
>
> Surprisingly, my new build on the G5 with Mac OS X 10.4.11,
> sage has successfully compiled.  On startup, however, I get
> the following:
>
> ### Sage messages ###
>            Traceback (most recent call
> last)
>
> /Applications/sage-3.0/local/bin/ in ()
>
> : No module named
> sage.misc.preparser_ipython
> WARNING: Failure executing code: 'import sage.misc.preparser_ipython;
> sage.misc.preparser_ipython.magma_colon_equals=True'
> ---
>            Traceback (most recent call
> last)
>
> /Applications/sage-3.0/local/bin/ in ()
>
> : No module named sage.misc.misc
> 
> ### end Sage messages 
>
> I've uploaded the full 9.2 MB install.log 
> here:http://facstaff.unca.edu/mcmcclur/install.log.txt
>
> Mark

Hi Mark,

for whatever reason there is no Singular in your build log. Right at
the top it says:

ls: singular-*.spkg: No such file or directory
standard/deps:205: warning: overriding commands for target `installed'
standard/deps:158: warning: ignoring old commands for target
`installed'
base/dir-0.1-install

Could you check if spkg/standard contains any file called
singular-3-0-4-2-20080405.p1.spkg, i.e:

 sage-3.0$ ls -la spkg/standard/singular-3-0-4-2-20080405.p1.spkg
-rw-r--r-- 1 mabshoff 1090 8742413 2008-04-19 21:19 spkg/standard/
singular-3-0-4-2-20080405.p1.spkg

Cheers,

Michael
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[sage-devel] Re: Sage 3.0 released

[mark mcclure]

On Apr 23, 5:54 pm, "William Stein" <[EMAIL PROTECTED]> wrote:

> Could you type
>./sage -br
> form the SAGE_ROOT directory and send the output?


Sure:

--
sage: Building and installing modified SAGE library files.


Installing c_lib
g++ -o libcsage.dylib -single_module -flat_namespace -undefined
dynamic_lookup -dynamiclib src/convert.os src/interrupt.os src/
mpn_pylong.os src/mpz_pylong.os src/stdsage.os src/gmp_globals.os src/
ZZ_pylong.os src/ntl_wrap.os -L/Applications/sage-3.0/local/lib -lntl -
lgmp -lpari
Updating Cython code
sage/modules/free_module_element.pyx --> /Applications/sage-3.0/local//
lib/python/site-packages//sage/modules/free_module_element.pyx
sage/modules/complex_double_vector.pyx --> /Applications/sage-3.0/
local//lib/python/site-packages//sage/modules/
complex_double_vector.pyx
sage/modules/real_double_vector.pyx --> /Applications/sage-3.0/local//
lib/python/site-packages//sage/modules/real_double_vector.pyx
sage/modules/vector_integer_dense.pyx --> /Applications/sage-3.0/
local//lib/python/site-packages//sage/modules/vector_integer_dense.pyx
sage/modules/vector_modn_dense.pyx --> /Applications/sage-3.0/local//
lib/python/site-packages//sage/modules/vector_modn_dense.pyx
sage/modules/vector_rational_dense.pyx --> /Applications/sage-3.0/
local//lib/python/site-packages//sage/modules/
vector_rational_dense.pyx
sage/libs/pari/gen.pyx --> /Applications/sage-3.0/local//lib/python/
site-packages//sage/libs/pari/gen.pyx
sage/libs/mwrank/mwrank.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/mwrank/mwrank.pyx
sage/libs/flint/fmpz_poly.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/flint/fmpz_poly.pyx
sage/libs/ntl/ntl_ZZ.pyx --> /Applications/sage-3.0/local//lib/python/
site-packages//sage/libs/ntl/ntl_ZZ.pyx
sage/libs/ntl/ntl_ZZX.pyx --> /Applications/sage-3.0/local//lib/python/
site-packages//sage/libs/ntl/ntl_ZZX.pyx
sage/libs/ntl/ntl_ZZ_pContext.pyx --> /Applications/sage-3.0/local//
lib/python/site-packages//sage/libs/ntl/ntl_ZZ_pContext.pyx
sage/libs/ntl/ntl_ZZ_p.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/ntl/ntl_ZZ_p.pyx
sage/libs/ntl/ntl_ZZ_pX.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/ntl/ntl_ZZ_pX.pyx
sage/libs/ntl/ntl_ZZ_pEContext.pyx --> /Applications/sage-3.0/local//
lib/python/site-packages//sage/libs/ntl/ntl_ZZ_pEContext.pyx
sage/libs/ntl/ntl_ZZ_pE.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/ntl/ntl_ZZ_pE.pyx
sage/libs/ntl/ntl_ZZ_pEX.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/ntl/ntl_ZZ_pEX.pyx
sage/libs/ntl/ntl_lzz_pContext.pyx --> /Applications/sage-3.0/local//
lib/python/site-packages//sage/libs/ntl/ntl_lzz_pContext.pyx
sage/libs/ntl/ntl_lzz_p.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/ntl/ntl_lzz_p.pyx
sage/libs/ntl/ntl_lzz_pX.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/ntl/ntl_lzz_pX.pyx
sage/libs/ntl/ntl_GF2.pyx --> /Applications/sage-3.0/local//lib/python/
site-packages//sage/libs/ntl/ntl_GF2.pyx
sage/libs/ntl/ntl_GF2X.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/ntl/ntl_GF2X.pyx
sage/libs/ntl/ntl_GF2EContext.pyx --> /Applications/sage-3.0/local//
lib/python/site-packages//sage/libs/ntl/ntl_GF2EContext.pyx
sage/libs/ntl/ntl_GF2E.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/ntl/ntl_GF2E.pyx
sage/libs/ntl/ntl_GF2EX.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/ntl/ntl_GF2EX.pyx
sage/libs/ntl/ntl_mat_ZZ.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/ntl/ntl_mat_ZZ.pyx
sage/libs/ntl/ntl_mat_GF2E.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/libs/ntl/ntl_mat_GF2E.pyx
sage/matrix/matrix.pyx --> /Applications/sage-3.0/local//lib/python/
site-packages//sage/matrix/matrix.pyx
sage/matrix/action.pyx --> /Applications/sage-3.0/local//lib/python/
site-packages//sage/matrix/action.pyx
sage/matrix/misc.pyx --> /Applications/sage-3.0/local//lib/python/site-
packages//sage/matrix/misc.pyx
sage/matrix/matrix_dense.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/matrix/matrix_dense.pyx
sage/matrix/matrix_generic_dense.pyx --> /Applications/sage-3.0/local//
lib/python/site-packages//sage/matrix/matrix_generic_dense.pyx
sage/matrix/matrix_sparse.pyx --> /Applications/sage-3.0/local//lib/
python/site-packages//sage/matrix/matrix_sparse.pyx
sage/matrix/matrix_generic_sparse.pyx --> /Applications/sage-3.0/
local//lib/python/site-packages//sage/matrix/matrix_generic_sparse.pyx
sage/matrix/matrix_integer_dense.pyx --> /Applications/sage-3.0/local//
lib/python/site-packages//sage/matrix/matrix_integer_dense.pyx
sage/matrix/matrix_rational_dense.pyx --> /Applications/sage-3.0/
local//lib/python/site-packages//sage/matrix/matrix_ra

[sage-devel] Re: Test errors for Sage 3.0 on OS X

[mabshoff]

On Apr 23, 11:46 pm, Bjake Hammersholt Roune <[EMAIL PROTECTED]>
wrote:
> Sage builds without problems on this system

Hi Bjarke,

> SAGE Version 3.0, Release Date: 2008-04-22
> Mac OS X 10.5.2
> 1.8 GHz Intel Core 2 Duo
> 2 GB RAM
> gcc version 4.0.1 (Apple Inc. build 5465)
>
> while make test produces the following errors (that I noticed)
>
> [listing begin]
> [...]
> sage -t  devel/sage/sage/plot/animate.py                    sh:
> convert: command
>  not found

This is just an annoying error message from the system. It can
certainly be fixed. This is now #3012.

> [...]
> sage -t  devel/sage/sage/libs/pari/gen.pyx
> python(18109) malloc
> : *** mmap(size=409600) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> [...]

This is a case where "failure is a success" is the case. It is
slightly scary, but the expected behavior since we test that pari
fails to allocate a huge amount (128+ GB) of RAM. We intent to fix the
issue and we are tracking it at

http://trac.sagemath.org/sage_trac/ticket/1595

> sage -t  devel/sage/sage/modular/abvar/morphism.py          *** ***
> Error: TIMED
>  OUT! *** ***
> *** *** Error: TIMED OUT! *** ***
>         [1358.6 s]
> [...]

Odd, it shouldn't time out on that machine. I am hoping William or
Craig can take a close look since they are much more familiar with the
code. That it isn't reproducible is slightly worrying. I did valgrind
all doctests of 3.0, so maybe something will pop up there.

> --
> The following tests failed:
>
>        sage -t  devel/sage/sage/modular/abvar/morphism.py
> Total time for all tests: 10219.5 seconds
> [listing done]
>
> It seems to me that the final report should mention three errors
> instead of just the one in morphism.py. Rerunning the individual tests
> that failed produces the following output.

Well, only the morphism.py is actually a failure.

> /Bjarke

Thanks for reporting the problems.

Cheers,

Michael
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[sage-devel] Re: Sage 3.0 released

[William Stein]

On Wed, Apr 23, 2008 at 2:51 PM, mark mcclure <[EMAIL PROTECTED]> wrote:
>
>  On Apr 23, 4:43 pm, mabshoff <[EMAIL PROTECTED]
>
> dortmund.de> wrote:
>
>  >  We will be much more aggressive from now on in blacklisting know
>  > broken compilers since at least on OSX it should work out of the box
>  > because there is so little variety of the OS itself and Apple usually
>  > is the tool chain provider. In general: if anything breaks keep the
>  > log - usually there is a clue in there what went wrong. Upgrading to
>  > 10.4.11 is unlikely to fix the  issues, but then I have seen pigs fly
>  > before ;)
>
>  Sorry, I'll remember this.
>
>  Surprisingly, my new build on the G5 with Mac OS X 10.4.11,
>  sage has successfully compiled.  On startup, however, I get
>  the following:
>
>  ### Sage messages ###
> Traceback (most recent call
>  last)
>
>  /Applications/sage-3.0/local/bin/ in ()
>
>  : No module named
>  sage.misc.preparser_ipython
>  WARNING: Failure executing code: 'import sage.misc.preparser_ipython;
>  sage.misc.preparser_ipython.magma_colon_equals=True'
>  ---
> Traceback (most recent call
>  last)
>
>  /Applications/sage-3.0/local/bin/ in ()
>
>  : No module named sage.misc.misc
>  
>  ### end Sage messages 
>
>
>  I've uploaded the full 9.2 MB install.log here:
>  http://facstaff.unca.edu/mcmcclur/install.log.txt
>

Could you type

   ./sage -br

form the SAGE_ROOT directory and send the output?

 -- William

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[sage-devel] Re: Sage 3.0 released

[mark mcclure]

On Apr 23, 4:43 pm, mabshoff <[EMAIL PROTECTED]
dortmund.de> wrote:

>  We will be much more aggressive from now on in blacklisting know
> broken compilers since at least on OSX it should work out of the box
> because there is so little variety of the OS itself and Apple usually
> is the tool chain provider. In general: if anything breaks keep the
> log - usually there is a clue in there what went wrong. Upgrading to
> 10.4.11 is unlikely to fix the  issues, but then I have seen pigs fly
> before ;)

Sorry, I'll remember this.

Surprisingly, my new build on the G5 with Mac OS X 10.4.11,
sage has successfully compiled.  On startup, however, I get
the following:

### Sage messages ###
   Traceback (most recent call
last)

/Applications/sage-3.0/local/bin/ in ()

: No module named
sage.misc.preparser_ipython
WARNING: Failure executing code: 'import sage.misc.preparser_ipython;
sage.misc.preparser_ipython.magma_colon_equals=True'
---
   Traceback (most recent call
last)

/Applications/sage-3.0/local/bin/ in ()

: No module named sage.misc.misc

### end Sage messages 


I've uploaded the full 9.2 MB install.log here:
http://facstaff.unca.edu/mcmcclur/install.log.txt

Mark

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[sage-devel] Re: construction of finite fields GF(2^n)

[John Cremona]

2008/4/23 David Harvey <[EMAIL PROTECTED]>:
>
>
>  On Apr 23, 2008, at 5:38 PM, Martin Albrecht wrote:
>
>  > 3) search for a tri- or pentanomial with some code similar to the
>  > one in blog
>  > post
>
>  You might want to check the NTL code for whether NTL "auto-detects"
>  that you have supplied a sparse polynomial (and hence uses faster
>  code for arithmetic), or whether you have to tell it explicitly. I
>  vaguely remember that the preconditioned division struct has a flag
>  for this, but I can't remember whether it gets set automatically.

Good point -- I'll check that.

John

>
>  david
>
>
>
>
>  >
>

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[sage-devel] Re: rpy build script fails for sage-3.0

[strogdon]

Michael,

On Apr 23, 4:23 pm, mabshoff <[EMAIL PROTECTED]
dortmund.de> wrote:
> Hi Steve,
>
> we are now tracking the issue at #3011.
>
> On Apr 23, 10:08 pm, strogdon <[EMAIL PROTECTED]> wrote:
>
>

--- CUT ---

>
>
> > I've built sage previously, but without R installed. I suspect the
> > installed (Portage) R is conflicting with what sage does. Let me know
> > if you wish to see the install.log. I'm presently re-building sage in
> > a shell where I've disabled the R_HOME variable.
>
> Good. Let me know what that works. R itself is rather brittle and uses
> hard coded locations in a bunch of shell files. I mean to patch that
> out of the files and upgrading to R 2.6.2 or 2.7 [once it is out] will
> be a good occasion to clean that up.
>

Everything built in a shell where R_HOME was disabled and the test

 ./sage -t  devel/sage/sage/stats/test.py

passed in that shell. The test failed in a shell where the R_HOME
variable was set with the same failure as noted above.

>
> Cheers,
>
> Michael

Steve
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[sage-devel] Re: construction of finite fields GF(2^n)

[John Cremona]

Thanks for the debugging.  I am trying it out (sage -br takes many
minutes with this for some reason).  If that works then I'll follow
your suggestion to move this polynomial selection somewhere else.
Should have a patch ready tomorrow...

John

2008/4/23 Martin Albrecht <[EMAIL PROTECTED]>:
>
>  On Wednesday 23 April 2008, John Cremona wrote:
>
> > Thanks, Martin.  I agree with your comments.  All I am really talking
>  > about here is the time taken to construct the field -- I know that a
>  > lot more work will be needed to get a really good finite field setup
>  > in Sage (including arbitrary coercions into extension fields, as
>  > previously discussed).
>  >
>  > I did already implement my (1)+(2) but it doesn't work, probably
>  > because I don't know cython.  It's also a bit ugly since the .pyx file
>  > now has a 340-line assignment which starts
>  > GF2X_irred_tab = ((0), (0),
>  > (1), (1), (1), (2), (1), (1),
>  > (4,3,1), (1), (3), (2), (3), (4,3,1),
>  > (5), (1), (5,3,1), (3), (3), (5,2,1),
>
>  Try (0,) instead of (0) to create a tuple with only the zero in it.
>
>  So to summarise the strategy is:
>
>  1) If a Conway polynomial exists use that (for now)
>  2) If an element int he GF2X_irred_tab (which should probably be in another
>  file) exists, use that
>  3) search for a tri- or pentanomial with some code similar to the one in blog
>  post
>
>  Thoughts?
>
>
> Martin
>
>  --
>  name: Martin Albrecht
>  _pgp: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99
>  _www: http://www.informatik.uni-bremen.de/~malb
>  _jab: [EMAIL PROTECTED]
>
>
>  >
>

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[sage-devel] Re: construction of finite fields GF(2^n)

[David Harvey]

On Apr 23, 2008, at 5:38 PM, Martin Albrecht wrote:

> 3) search for a tri- or pentanomial with some code similar to the  
> one in blog
> post

You might want to check the NTL code for whether NTL "auto-detects"  
that you have supplied a sparse polynomial (and hence uses faster  
code for arithmetic), or whether you have to tell it explicitly. I  
vaguely remember that the preconditioned division struct has a flag  
for this, but I can't remember whether it gets set automatically.

david


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[sage-devel] Test errors for Sage 3.0 on OS X

[Bjake Hammersholt Roune]

Sage builds without problems on this system

SAGE Version 3.0, Release Date: 2008-04-22
Mac OS X 10.5.2
1.8 GHz Intel Core 2 Duo
2 GB RAM
gcc version 4.0.1 (Apple Inc. build 5465)

while make test produces the following errors (that I noticed)

[listing begin]
[...]
sage -t  devel/sage/sage/plot/animate.pysh:
convert: command
 not found
[...]
sage -t  devel/sage/sage/libs/pari/gen.pyx
python(18109) malloc
: *** mmap(size=409600) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
[...]
sage -t  devel/sage/sage/modular/abvar/morphism.py  *** ***
Error: TIMED
 OUT! *** ***
*** *** Error: TIMED OUT! *** ***
[1358.6 s]
[...]
--
The following tests failed:


   sage -t  devel/sage/sage/modular/abvar/morphism.py
Total time for all tests: 10219.5 seconds
[listing done]

It seems to me that the final report should mention three errors
instead of just the one in morphism.py. Rerunning the individual tests
that failed produces the following output.

> ./sage -t  devel/sage/sage/plot/animate.py
sage -t  devel/sage/sage/plot/animate.pysh:
convert: command not found

[7.8 s]


> ./sage -t  devel/sage/sage/modular/abvar/morphism.py
sage -t  devel/sage/sage/modular/abvar/morphism.py
[34.8 s]

> ./sage -t  devel/sage/sage/libs/pari/gen.pyx
sage -t  devel/sage/sage/libs/pari/gen.pyx
python(42217) malloc: *** mmap(size=409600) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

[12.2 s]

/Bjarke
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[sage-devel] Re: Initial support for posets

[John Cremona]

As someone who is much more likely to use the non-poset lattices, I
could certainly live with ZLattice (that's Z as in ZZ).  Would either
side get to keep plain Lattice?

John

2008/4/23 Franco Saliola <[EMAIL PROTECTED]>:
>
>  On Wed, Apr 23, 2008 at 4:05 PM, Robert Miller <[EMAIL PROTECTED]> wrote:
>
>  >  We might want to think about the naming conventions for Lattice. As
>  >  with all words in mathematics, this one has multiple meanings. A
>  >  lattice can be a poset with a meet and a join, or it can be a free
>  >  abelian group with an inner product.
>
>  This is a good point. The only thing I can think of is to append
>  something: for example, LatticeGroup. I'm not sure how natural that
>  is. LatticePoset is definitely not. Other suggestions?
>
>
>
>  --
>
>  >
>

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[sage-devel] Re: construction of finite fields GF(2^n)

[Martin Albrecht]

On Wednesday 23 April 2008, John Cremona wrote:
> Thanks, Martin.  I agree with your comments.  All I am really talking
> about here is the time taken to construct the field -- I know that a
> lot more work will be needed to get a really good finite field setup
> in Sage (including arbitrary coercions into extension fields, as
> previously discussed).
>
> I did already implement my (1)+(2) but it doesn't work, probably
> because I don't know cython.  It's also a bit ugly since the .pyx file
> now has a 340-line assignment which starts
> GF2X_irred_tab = ((0), (0),
> (1), (1), (1), (2), (1), (1),
> (4,3,1), (1), (3), (2), (3), (4,3,1),
> (5), (1), (5,3,1), (3), (3), (5,2,1),

Try (0,) instead of (0) to create a tuple with only the zero in it.

So to summarise the strategy is:

1) If a Conway polynomial exists use that (for now)
2) If an element int he GF2X_irred_tab (which should probably be in another 
file) exists, use that
3) search for a tri- or pentanomial with some code similar to the one in blog 
post

Thoughts?
Martin

-- 
name: Martin Albrecht
_pgp: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99
_www: http://www.informatik.uni-bremen.de/~malb
_jab: [EMAIL PROTECTED]


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[sage-devel] Re: [fricas-devel] Re: [sage-devel] Re: FriCAS/Open-Axiom and SAGE

[Michael.Abshoff]

root wrote:
> Gary,

Hi Tim,

> If you're interested in exploring Axiom's type system 
> the best source of material available is the Jenk's book.
> It would be useful if Sage's type hierarchy was close to
> the one Axiom uses, making it possible to share algorithms.
> If you'll mail me a postal address (offline), 
> I'll send you a copy of the book.

according to 
http://www.axiom-developer.org/axiom-website/currentstate.html the 
"Axiom book" by Jenks is part of Axiom's documentation. Is that correct?

> Tim

Cheers,

Michael

> 
> > 
> 


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[sage-devel] Re: construction of finite fields GF(2^n)

[John Cremona]

Thanks, Martin.  I agree with your comments.  All I am really talking
about here is the time taken to construct the field -- I know that a
lot more work will be needed to get a really good finite field setup
in Sage (including arbitrary coercions into extension fields, as
previously discussed).

I did already implement my (1)+(2) but it doesn't work, probably
because I don't know cython.  It's also a bit ugly since the .pyx file
now has a 340-line assignment which starts
GF2X_irred_tab = ((0), (0),
(1), (1), (1), (2), (1), (1),
(4,3,1), (1), (3), (2), (3), (4,3,1),
(5), (1), (5,3,1), (3), (3), (5,2,1),

I am trying to extract that data with lines like
mc = GF2X_irred_tab[k]
followed by references to mc[0] (and sometimes mc[1], mc[2] also).
But I get the error
: 'int' object is unsubscriptable

Any ideas?

John


2008/4/23 Martin Albrecht <[EMAIL PROTECTED]>:
>
>
>  On Wednesday 23 April 2008, John Cremona wrote:
>  > There's a serious inefficiency in the construction of finite fields
>  > GF(2^n) in Sage at the moment.
>  > For n<=15 these are constructed of type
>  > sage.rings.finite_field_givaro.FiniteField_givaro, about which I have
>  > nothing to say now;  for n>=16 they have type
>  > sage.rings.finite_field_ntl_gf2e.FiniteField_ntl_gf2e and are
>  > constructed by wrapping the appropriate NTL class.
>  >
>  > The problem lies with how the defining polynomial for te field is
>  > chosen: any irreducible poly of degree n over GF(2) will do in
>  > principle.
>  >
>  > The code in sage/rings/finite_field_ntl_gf2e.pyx chooses random
>  > polynomials of degree n until it finds an irreducible one, the n
>  > passes it (actually its coefficients) to a wrapped NTL constructor.
>  > Two problems:
>  > (1) The random polynomials have expected number of terms n/2, so even
>  > when one is found whcih is irreducuble it is inefficient to work with
>  > (reduction mod f is faster if f is sparse);
>  > (2) Many many trials may be needed before a polynomial is found, so
>  > the constructor can take for ages (eg 15s for n=500, and 314 s for
>  > n=600)
>  >
>  > Some solutions:
>  > (1) Use sparse polynomials only.  These are better to use as defining
>  > polynomials.  Shoup says there are no known n for which there is no
>  > known irreducible trinomial (x^n+x^k+1) or 5-term
>  > (x^n+x^k1+x^k2+x^k3+1).
>  > (2) In NTL suitable sparse polys are precomputed for n<2048;  we could
>  > copy that list.   (It is called GF2X_irred_tab in GF2XFactring.c in
>  > NTL)
>  > (3) We could let NTL get the poly for us, using its
>  > BuildSparseIrred() function.
>  >
>  > I propose that (3) is best;  I can try to do that but it will be
>  > harder than (1)+(2).  Shall I open a trac for this?  I should be able
>  > to put in a patch based on (1)+(2) very easily.
>
>  I implemented that (in fact, I copied it from the generic GF(q) constructor)
>  and favour (3) too but only if no conway polynomial is known (which is the
>  case when the random search is triggered only anyway). Later, we could use a
>  sparse polynomial internally but represent everything using Conway
>  polynomials to the user/rest of the library.
>
>  Btw. a while ago I timed the influence of the moduli for GF(2^n) here:
>
>  
> http://www.informatik.uni-bremen.de/cgi-bin/cgiwrap/malb/blosxom.pl/2007/11/07
>
>  Martin
>
>  --
>  name: Martin Albrecht
>  _pgp: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99
>  _www: http://www.informatik.uni-bremen.de/~malb
>  _jab: [EMAIL PROTECTED]
>
>
>  >
>

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[sage-devel] Re: notebook features discussion

[gerhard]

> Does it go away if you pass the "fragile" option to the frame
> environment?  It seems that that is how people overcame this in the
> past.  Can you look in the source to the slides that was posted previously?
>
> \begin{frame}[fragile]

Yes indeed, that works.
I remember the problem, now that you have pointed it out to me!
Thank you, Jason.

-gerhard
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[sage-devel] Re: rpy build script fails for sage-3.0

[mabshoff]

Hi Steve,

we are now tracking the issue at #3011.

On Apr 23, 10:08 pm, strogdon <[EMAIL PROTECTED]> wrote:
> Michael,
>
> Yes I do have R installed on my system. No, RHOMES is not set;
> however, R_HOMES is set to /usr/lib64/R. Apparently, the R
> installation does this.

ok. We can certainly overwrite that variable in sage-env for example
so the R install from Sage is used.



> I've built sage previously, but without R installed. I suspect the
> installed (Portage) R is conflicting with what sage does. Let me know
> if you wish to see the install.log. I'm presently re-building sage in
> a shell where I've disabled the R_HOME variable.

Good. Let me know what that works. R itself is rather brittle and uses
hard coded locations in a bunch of shell files. I mean to patch that
out of the files and upgrading to R 2.6.2 or 2.7 [once it is out] will
be a good occasion to clean that up.

> Steve

Cheers,

Michael
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[sage-devel] Re: Trouble finding the normalizer of a subgroup

[Daniel Bump]

> Perhaps someone can help me figure this out.  I am trying to create an
> elementary abelian subgroup of a symmetric group and then look at its
> normalizer.  Here's what doesn't work:
> 
> s6 = SymmetricGroup(6)
> 
> c1 = s6([(1,2)])
> c2 = s6([(3,4)])
> c3 = s6([(5,6)])
> 
> e8 = s6.subgroup([c1,c2,c3])
> print e8.order()
> 
> n = s6.normalizer(e8)
> 
> It's good through printing the order of "e8".  Then the horrible
> traceback which follows.

I think this is a bug. But the following works:

sage: s6._gap_().Normalizer(gap(e8).name())
Group( [ (5,6), (3,4), (1,2), (3,5,4,6), (1,3,5,2,4,6) ] )

Daniel Bump

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[sage-devel] Re: notebook features discussion

[Jason Grout]

gerhard wrote:
>> What problems are you having? Beamer and SageTeX are largely orthogonal,
>> but there are some tricky bits with verbatim environments
> 
> When I add a sageblock in a frame, e.g.,
> \begin{sageblock}
>   var('x')
>   f = log(sin(x)/x)
> \end{sageblock}
> 
> I get  the error message
> 
> Runaway argument?
> ! Paragraph ended before \next was complete.
> 
> \par
> 


Does it go away if you pass the "fragile" option to the frame 
environment?  It seems that that is how people overcame this in the 
past.  Can you look in the source to the slides that was posted previously?

\begin{frame}[fragile]

(I think...)

Jason


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[sage-devel] Re: Sage 3.0.rc1 released!

[Michael.Abshoff]

Andrzej Giniewicz wrote:
> One test failed on standard rc1+clisp...p15, running 32 bit Arch linux
> with GCC 4.3, /proc/cpuinfo below and doctest below it.
> 
> cheers,
> Andrzej.
> 

> and only test that failed:
> 
> sage -t  devel/sage-main/sage/rings/complex_double.pyx
> **
> File "/opt/sage-3.0.rc1/tmp/complex_double.py", line 1659:
> sage: z^2 - z + 1
> Expected:
> 2.22044604925e-16 + ...e-16*I
> Got:
> 2.22044604925e-16
> **
> 1 items had failures:
>1 of   7 in __main__.example_93
> ***Test Failed*** 1 failures.
> For whitespace errors, see the file /opt/sage-3.0.rc1/
> tmp/.doctest_complex_double.py
>  [4.1 s]
> exit code: 1024
> 
> --
> The following tests failed:
> 

Hi Andrzej,

this is now #3010.

Cheers,

Michael

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[sage-devel] Re: Sage 3.0 released

[mabshoff]

On Apr 23, 10:04 pm, mark mcclure <[EMAIL PROTECTED]> wrote:
> On Apr 23, 3:53 pm, mabshoff <[EMAIL PROTECTED]
>
> dortmund.de> wrote:
> > This looks like Singular did not build properly.
> > 
> > Please post a link to the  whole install.log here so I can take a
> > look.

Hi Mark,

> Unfortunately, I no longer have the whole install.log.  In hopes of
> fixing the problem, I upgraded to OS X 10.4.11.  A rebuild is in
> progress and the install.log has already been overwritten.  Sorry
> about that; perhaps I'll learn for the future. :)

 We will be much more aggressive from now on in blacklisting know
broken compilers since at least on OSX it should work out of the box
because there is so little variety of the OS itself and Apple usually
is the tool chain provider. In general: if anything breaks keep the
log - usually there is a clue in there what went wrong. Upgrading to
10.4.11 is unlikely to fix the  issues, but then I have seen pigs fly
before ;)

> Presumably, by 5:30 or so I'll either have a working copy or
> I'll be able to post the install.log.

Thanks.

> Mark

Cheers,

Michael
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[sage-devel] Re: Initial support for posets

[Franco Saliola]

On Wed, Apr 23, 2008 at 4:05 PM, Robert Miller <[EMAIL PROTECTED]> wrote:

>  We might want to think about the naming conventions for Lattice. As
>  with all words in mathematics, this one has multiple meanings. A
>  lattice can be a poset with a meet and a join, or it can be a free
>  abelian group with an inner product.

This is a good point. The only thing I can think of is to append
something: for example, LatticeGroup. I'm not sure how natural that
is. LatticePoset is definitely not. Other suggestions?

--

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[sage-devel] Re: small documentation problem: "\ " at the end of a line

[mabshoff]

On Apr 23, 10:25 pm, John H Palmieri <[EMAIL PROTECTED]> wrote:
> In the section of the tutorial on 3d plotting,
>
>   
>
> the continuation characters "\" all have spaces after them, which
> messes up cutting and pasting.  Also in the section on Maxima,
>
>   
>
> two of the backslashes have spaces after them (in the Mobius strip and
> the Klein bottle examples).
>
> The same thing happens half a dozen times in "SAGE Constructions".
>
> I've only searched the tutorial and the constructions documentation
> for this issue (by searching the files "tut.tex" and "const.tex"); I
> haven't looked at the rest of the documentation.

Hi John,

thanks for reporting this. It is now #3009.

Cheers,

Michael
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[sage-devel] Re: Sage 3.0 released

[mark mcclure]

On Apr 23, 3:53 pm, mabshoff <[EMAIL PROTECTED]
dortmund.de> wrote:
> This looks like Singular did not build properly.
> 
> Please post a link to the  whole install.log here so I can take a
> look.

Unfortunately, I no longer have the whole install.log.  In hopes of
fixing the problem, I upgraded to OS X 10.4.11.  A rebuild is in
progress and the install.log has already been overwritten.  Sorry
about that; perhaps I'll learn for the future. :)

Presumably, by 5:30 or so I'll either have a working copy or
I'll be able to post the install.log.

Mark

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[sage-devel] Re: Sage 3.0 released

[mark mcclure]

On Apr 23, 3:54 pm, mhampton <[EMAIL PROTECTED]> wrote:

> I'm not sure what the problem is, probably William Stein or Michael
> Abshoff will be able to answer that, but maybe its simplest to just
> upgrade your gcc with the latest stuff from apple.  My gcc is build
> 5465; I'm not sure how they pick those version numbers.

Thanks, I might give that a try depending on how things go.


> I know you are (or were?) a fairly hardcore Mathematica user so I
> wanted to write and encourage you to keep exploring sage.  It took me
> a while to get over the learning curve but I think its worth it.

Yes, I remember when you visited Asheville.  I had great fun creating
some pictures of your amoebas with Mathematica.  I guess I am a
hardcore Mathematica user, if anyone is, and will certainly remain
so,
but I'm a growing fan of open source software as well.

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[sage-devel] small documentation problem: "\ " at the end of a line

[John H Palmieri]

In the section of the tutorial on 3d plotting,

  

the continuation characters "\" all have spaces after them, which
messes up cutting and pasting.  Also in the section on Maxima,

  

two of the backslashes have spaces after them (in the Mobius strip and
the Klein bottle examples).

The same thing happens half a dozen times in "SAGE Constructions".

I've only searched the tutorial and the constructions documentation
for this issue (by searching the files "tut.tex" and "const.tex"); I
haven't looked at the rest of the documentation.

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[sage-devel] Re: Initial support for posets

[Franco Saliola]

On Wed, Apr 23, 2008 at 3:48 PM, mhampton <[EMAIL PROTECTED]> wrote:

>  I'm not really qualified to comment in detail, but I thought I would
>  mention that I am interested in computing face lattices of polytopes
>  as part of my polytope module.  Perhaps you could comment on whether
>  there is (or could be) anything in your code that might help me out
>  with that.

At the very least you can inherit from the Lattice and LatticeElement
classes. And use the plotting functionality.

Tell me what kind of things you want to be able to do, and if it is
missing, then I can add it. (For example, what kind of data you want
to hand me.)

I posted my code so that I find out how people intend to use it, so it
can be improved.

Take care,
Franco

--

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[sage-devel] Re: construction of finite fields GF(2^n)

[Martin Albrecht]

On Wednesday 23 April 2008, John Cremona wrote:
> There's a serious inefficiency in the construction of finite fields
> GF(2^n) in Sage at the moment.
> For n<=15 these are constructed of type
> sage.rings.finite_field_givaro.FiniteField_givaro, about which I have
> nothing to say now;  for n>=16 they have type
> sage.rings.finite_field_ntl_gf2e.FiniteField_ntl_gf2e and are
> constructed by wrapping the appropriate NTL class.
>
> The problem lies with how the defining polynomial for te field is
> chosen: any irreducible poly of degree n over GF(2) will do in
> principle.
>
> The code in sage/rings/finite_field_ntl_gf2e.pyx chooses random
> polynomials of degree n until it finds an irreducible one, the n
> passes it (actually its coefficients) to a wrapped NTL constructor.
> Two problems:
> (1) The random polynomials have expected number of terms n/2, so even
> when one is found whcih is irreducuble it is inefficient to work with
> (reduction mod f is faster if f is sparse);
> (2) Many many trials may be needed before a polynomial is found, so
> the constructor can take for ages (eg 15s for n=500, and 314 s for
> n=600)
>
> Some solutions:
> (1) Use sparse polynomials only.  These are better to use as defining
> polynomials.  Shoup says there are no known n for which there is no
> known irreducible trinomial (x^n+x^k+1) or 5-term
> (x^n+x^k1+x^k2+x^k3+1).
> (2) In NTL suitable sparse polys are precomputed for n<2048;  we could
> copy that list.   (It is called GF2X_irred_tab in GF2XFactring.c in
> NTL)
> (3) We could let NTL get the poly for us, using its
> BuildSparseIrred() function.
>
> I propose that (3) is best;  I can try to do that but it will be
> harder than (1)+(2).  Shall I open a trac for this?  I should be able
> to put in a patch based on (1)+(2) very easily.

I implemented that (in fact, I copied it from the generic GF(q) constructor) 
and favour (3) too but only if no conway polynomial is known (which is the 
case when the random search is triggered only anyway). Later, we could use a 
sparse polynomial internally but represent everything using Conway 
polynomials to the user/rest of the library.

Btw. a while ago I timed the influence of the moduli for GF(2^n) here:

http://www.informatik.uni-bremen.de/cgi-bin/cgiwrap/malb/blosxom.pl/2007/11/07

Martin

-- 
name: Martin Albrecht
_pgp: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99
_www: http://www.informatik.uni-bremen.de/~malb
_jab: [EMAIL PROTECTED]


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[sage-devel] Re: [fricas-devel] Re: [sage-devel] Re: FriCAS/Open-Axiom and SAGE

[root]

Gary,

Also of interest, the algebra hierarchy diagram and data hierarchy
diagrams within Axiom (the endpapers from the Axiom book) are online at:



Tim

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[sage-devel] Re: rpy build script fails for sage-3.0

[strogdon]

Michael,

Yes I do have R installed on my system. No, RHOMES is not set;
however, R_HOMES is set to /usr/lib64/R. Apparently, the R
installation does this. And yes I do have the install.log. The
specific test fails as:

sage -t  devel/sage/sage/stats/test.py
**
File "/local/sage-3.0/tmp/test.py", line 5:
sage: import rpy
Exception raised:
Traceback (most recent call last):
  File "/local/sage-3.0/local/lib/python2.5/doctest.py", line
1228, in __run
compileflags, 1) in test.globs
  File "", line 1, in 
import rpy###line 5:
sage: import rpy
  File "/local/sage-3.0/local/lib/python2.5/site-packages/rpy.py",
line 58, in 
RVERSION = rpy_tools.get_R_VERSION(RHOME)
  File "/local/sage-3.0/local/lib/python2.5/site-packages/
rpy_tools.py", line 99,
 in get_R_VERSION
" `%s'.\n" % rexec )
RuntimeError: Couldn't execute the R interpreter `/usr/lib64/R/bin/
R'.

**
1 items had failures:
   1 of   2 in __main__.example_0
***Test Failed*** 1 failures.
For whitespace errors, see the file /local/sage-3.0/
tmp/.doctest_test.py
 [1.5 s]
exit code: 1024

--
The following tests failed:


sage -t  devel/sage/sage/stats/test.py
Total time for all tests: 1.5 seconds

I've built sage previously, but without R installed. I suspect the
installed (Portage) R is conflicting with what sage does. Let me know
if you wish to see the install.log. I'm presently re-building sage in
a shell where I've disabled the R_HOME variable.

Steve

On Apr 23, 2:51 pm, mabshoff <[EMAIL PROTECTED]
dortmund.de> wrote:
> On Apr 23, 4:52 pm, strogdon <[EMAIL PROTECTED]> wrote:
>
> Hi,
>
>
>
> > On my Gentoo box I unpacked the subject tarball, changed to the sage
> > directory and did a make with the results:
>
> > gcc version 4.1.2 (Gentoo 4.1.2 p1.0.2)
> > 
> > 
> > RHOMES= []
> > DEBUG= True
> > Setting RHOMES to  ['/usr/lib64/R']
> > RHOMES= []
> > DEBUG= True
> > Setting RHOMES to  ['/usr/lib64/R']
> > Traceback (most recent call last):
> > Traceback (most recent call last):
> >   File "setup.py", line 106, in 
> >   File "setup.py", line 106, in 
> > RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
> > RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
> >   File "/local/sage-3.0/spkg/build/rpy-1.0.1.p1/src/rpy_tools.py",
> > line 99, in get_R_VERSION
> >   File "/local/sage-3.0/spkg/build/rpy-1.0.1.p1/src/rpy_tools.py",
> > line 99, in get_R_VERSION
> > " `%s'.\n" % rexec )
> > " `%s'.\n" % rexec )
> > RuntimeErrorRuntimeError: : Couldn't execute the R interpreter `/usr/
> > lib64/R/bin/R'.
> > Couldn't execute the R interpreter `/usr/lib64/R/bin/R'.
>
> > Error building RPY -- Python interface to R.
> > Error building RPY -- Python interface to R.
>
> Do you have R installed in the system? Is RHOMES set? Do you have the
> build log?
>
> > I tried several corrective measures and the only one that allowed sage
> > to build was to issue:
>
> > RHOMES="`pwd`/local/lib/R" make
>
> > However, the following test failed:
>
> > sage -t  devel/sage/sage/stats/test.py
>
> What did fail? Can you post the log of only that test?
>
> Cheers,
>
> Michael
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[sage-devel] Re: rpy build script fails for sage-3.0

[strogdon]

Michael,

Yes I do have R installed on my system. No, RHOMES is not set;
however, R_HOMES is set to /usr/lib64/R. Apparently, the R
installation does this. And yes I do have the install.log. The
specific test fails as:

sage -t  devel/sage/sage/stats/test.py
**
File "/local/sage-3.0/tmp/test.py", line 5:
sage: import rpy
Exception raised:
Traceback (most recent call last):
  File "/local/sage-3.0/local/lib/python2.5/doctest.py", line
1228, in __run
compileflags, 1) in test.globs
  File "", line 1, in 
import rpy###line 5:
sage: import rpy
  File "/local/sage-3.0/local/lib/python2.5/site-packages/rpy.py",
line 58, in 
RVERSION = rpy_tools.get_R_VERSION(RHOME)
  File "/local/sage-3.0/local/lib/python2.5/site-packages/
rpy_tools.py", line 99,
 in get_R_VERSION
" `%s'.\n" % rexec )
RuntimeError: Couldn't execute the R interpreter `/usr/lib64/R/bin/
R'.

**
1 items had failures:
   1 of   2 in __main__.example_0
***Test Failed*** 1 failures.
For whitespace errors, see the file /local/sage-3.0/
tmp/.doctest_test.py
 [1.5 s]
exit code: 1024

--
The following tests failed:


sage -t  devel/sage/sage/stats/test.py
Total time for all tests: 1.5 seconds

I've built sage previously, but without R installed. I suspect the
installed (Portage) R is conflicting with what sage does. Let me know
if you wish to see the install.log. I'm presently re-building sage in
a shell where I've disabled the R_HOME variable.

Steve

On Apr 23, 2:51 pm, mabshoff <[EMAIL PROTECTED]
dortmund.de> wrote:
> On Apr 23, 4:52 pm, strogdon <[EMAIL PROTECTED]> wrote:
>
> Hi,
>
>
>
> > On my Gentoo box I unpacked the subject tarball, changed to the sage
> > directory and did a make with the results:
>
> > gcc version 4.1.2 (Gentoo 4.1.2 p1.0.2)
> > 
> > 
> > RHOMES= []
> > DEBUG= True
> > Setting RHOMES to  ['/usr/lib64/R']
> > RHOMES= []
> > DEBUG= True
> > Setting RHOMES to  ['/usr/lib64/R']
> > Traceback (most recent call last):
> > Traceback (most recent call last):
> >   File "setup.py", line 106, in 
> >   File "setup.py", line 106, in 
> > RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
> > RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
> >   File "/local/sage-3.0/spkg/build/rpy-1.0.1.p1/src/rpy_tools.py",
> > line 99, in get_R_VERSION
> >   File "/local/sage-3.0/spkg/build/rpy-1.0.1.p1/src/rpy_tools.py",
> > line 99, in get_R_VERSION
> > " `%s'.\n" % rexec )
> > " `%s'.\n" % rexec )
> > RuntimeErrorRuntimeError: : Couldn't execute the R interpreter `/usr/
> > lib64/R/bin/R'.
> > Couldn't execute the R interpreter `/usr/lib64/R/bin/R'.
>
> > Error building RPY -- Python interface to R.
> > Error building RPY -- Python interface to R.
>
> Do you have R installed in the system? Is RHOMES set? Do you have the
> build log?
>
> > I tried several corrective measures and the only one that allowed sage
> > to build was to issue:
>
> > RHOMES="`pwd`/local/lib/R" make
>
> > However, the following test failed:
>
> > sage -t  devel/sage/sage/stats/test.py
>
> What did fail? Can you post the log of only that test?
>
> Cheers,
>
> Michael
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[sage-devel] Trouble finding the normalizer of a subgroup

[Hy Ginsberg]

Hi All,

Perhaps someone can help me figure this out.  I am trying to create an
elementary abelian subgroup of a symmetric group and then look at its
normalizer.  Here's what doesn't work:

s6 = SymmetricGroup(6)

c1 = s6([(1,2)])
c2 = s6([(3,4)])
c3 = s6([(5,6)])

e8 = s6.subgroup([c1,c2,c3])
print e8.order()

n = s6.normalizer(e8)

It's good through printing the order of "e8".  Then the horrible
traceback which
follows.

Many thanks,
- Hy




Traceback (most recent call last):
  File "", line 1, in 
  File "/home/hy/.sage/sage_notebook/worksheets/admin/13/code/42.py",
line 4, in

n = s6.normalizer(e8)
  File
"/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
packages/sympy/plotting/",
line 1, in 

  File
"/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
packages/sage/groups/perm_gps/permgroup.py",
line 1253, in normalizer
N = self._gap_().Normalizer(str(g))
  File
"/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
packages/sage/interfaces/expect.py",
line 954, in __call__
return self._obj.parent().function_call(self._name, [self._obj] +
list(args))
  File
"/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
packages/sage/interfaces/expect.py",
line 900, in function_call
args[i] = self.new(args[i])
  File
"/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
packages/sage/interfaces/expect.py",
line 803, in new
return self(code)
  File
"/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
packages/sage/interfaces/expect.py",
line 738, in __call__
return cls(self, x)
  File
"/home/hy/sage-2.10-ubuntu32-i686-Linux/local/lib/python2.5/site-
packages/sage/interfaces/expect.py",
line 989, in __init__
raise TypeError, x
TypeError: Gap produced error output
Syntax error: ; expected
$sage20:=Subgroup of SymmetricGroup(6) generated by [(1,2), (3,4),
(5,6)];;
   ^
Variable: 'by' must have a value


   executing $sage20:=Subgroup of SymmetricGroup(6) generated by
[(1,2), (3,4),
(5,6)];;
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[sage-devel] Re: [fricas-devel] Re: [sage-devel] Re: FriCAS/Open-Axiom and SAGE

[root]

Gary,

If you're interested in exploring Axiom's type system 
the best source of material available is the Jenk's book.
It would be useful if Sage's type hierarchy was close to
the one Axiom uses, making it possible to share algorithms.
If you'll mail me a postal address (offline), 
I'll send you a copy of the book.

Tim

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[sage-devel] Re: Initial support for posets

[Robert Miller]

We might want to think about the naming conventions for Lattice. As
with all words in mathematics, this one has multiple meanings. A
lattice can be a poset with a meet and a join, or it can be a free
abelian group with an inner product. Normally I wouldn't bring such a
thing up, but I'm working with a group thinking about implementing the
latter, and you have already (it seems) implemented the former.

On Apr 23, 12:48 pm, mhampton <[EMAIL PROTECTED]> wrote:
> I'm not really qualified to comment in detail, but I thought I would
> mention that I am interested in computing face lattices of polytopes
> as part of my polytope module.  Perhaps you could comment on whether
> there is (or could be) anything in your code that might help me out
> with that.
>
> I think its exciting that we are getting more sage-native
> functionality like this.
>
> Cheers,
> M. Hampton
>
> On Apr 23, 7:53 pm, "Franco Saliola" <[EMAIL PROTECTED]> wrote:
>
> > Dear all,
>
> > I've posted on trac the current version of my posets code.
> > There is still much to be done, some algorithms need
> > to be improved and others need to be implemented. (There
> > are no NotImplementedErrors.)
>
> >  http://trac.sagemath.org/sage_trac/ticket/2519
>
> > But before I continue working, I'd like some feedback. I've
> > made some decisions, and I don't know if they are the
> > best decisions. So please offer suggestions.
>
> > I've defined a HasseDiagram class that inherits from
> > DiGraph. A Hasse diagram are transitively-reduced, directed,
> > acyclic graph without loops or multiple edges. NOTE: We
> > assume that range(n) is a linear extension of the Hasse
> > diagram. This decision was taken in the hopes that it
> > increases the efficiency of algorithms.
>
> > There is a FinitePoset class that stores the list of
> > elements of the poset (_elements), the HasseDiagram
> > (_hasse_diagram, or hasse_diagram()), and maps
> > _element_to_vertex and _vertex_to_element. So FinitePoset is
> > just a vertex labelling of the HasseDiagram.
>
> > There is a constructor called Poset that takes various forms
> > of data describing a finite poset and returns a FinitePoset
> > object.
>
> > There are also Lattice, MeetSemilattice, JoinSemilattice...,
> > and PosetElement, LatticeElement,  So one create poset
> > elements and compare them with <, >, etc. And lattice
> > elements can by multiplied and added (for meet and join).
>
> > There are a few toy posets included (eventually there
> > should be a poset database): BooleanLattice, Chain,
> > Antichain, Pentagon, Diamond, PosetOfIntegerCompositions,
> > RandomPoset, SymmetricGroupBruhatOrder,
> > SymmetricGroupWeakOrder.
>
> > So what do you think?
>
> > Franco
>
> > --
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[sage-devel] Re: Sage 3.0 released

[mhampton]

Hi Mark!

I'm not sure what the problem is, probably William Stein or Michael
Abshoff will be able to answer that, but maybe its simplest to just
upgrade your gcc with the latest stuff from apple.  My gcc is build
5465; I'm not sure how they pick those version numbers.

I know you are (or were?) a fairly hardcore Mathematica user so I
wanted to write and encourage you to keep exploring sage.  It took me
a while to get over the learning curve but I think its worth it.

Cheers,
Marshall Hampton

On Apr 23, 9:23 pm, mark mcclure <[EMAIL PROTECTED]> wrote:
> On Apr 23, 1:08 pm, Robert Bradshaw <[EMAIL PROTECTED]>
> wrote:
>
> > >>  Are their binaries for OS X 10.4?
> > > NO.  And there won't be until somebody volunteers to make them.
> > > Can you make them?
>
> > Yes, do I just build and do sage -bdist?
>
> I attempted to compile sage 3.0 on my Mac G5 running OS X 10.4.10,
> but it failed with the errors below.  The gcc version is 4.0.1,
> build 5370.
>
> sage 3.0 compiled just fine on my Intel Mac with OS X 10.4.11.
> gcc version is 4.0.1, build 5367.
>
> The G5 errors are below.  I've never posted here before, so I'm
> not sure exactly what to report.  The compilation ran for a couple
> of hours and produced over 1000 lines in the install.log.  The
> stuff below is the last 75 lines.
>
> -
> gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-
> madd -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/
> mcmcclure/Desktop/sage-3.0/local/include/singular -I/Users/mcmcclure/
> Desktop/sage-3.0/local//include -I/Users/mcmcclure/Desktop/sage-3.0/
> local//include/csage -I/Users/mcmcclure/Desktop/sage-3.0/devel//sage/
> sage/ext -I/Users/mcmcclure/Desktop/sage-3.0/local/include/python2.5 -
> c sage/matrix/matrix_mpolynomial_dense.cpp -o build/temp.macosx-10.3-
> ppc-2.5/sage/matrix/matrix_mpolynomial_dense.o -w -w
> cc1plus: warning: command line option "-Wstrict-prototypes" is valid
> for C/ObjC but not for C++
> sage/matrix/matrix_mpolynomial_dense.cpp:39:21: error: factory.h: No
> such file or directory
> sage/matrix/matrix_mpolynomial_dense.cpp:40:25: error: libsingular.h:
> No such file or directory
> sage/matrix/matrix_mpolynomial_dense.cpp:225: error: ISO C++ forbids
> declaration of ‘polyrec’ with no type
> sage/matrix/matrix_mpolynomial_dense.cpp:225: error: expected ‘;’
> before ‘*’ token
> sage/matrix/matrix_mpolynomial_dense.cpp:978: error: ISO C++ forbids
> declaration of ‘ip_sring’ with no type
> sage/matrix/matrix_mpolynomial_dense.cpp:978: error: expected ‘;’
> before ‘*’ token
> sage/matrix/matrix_mpolynomial_dense.cpp:1839: error: ‘snumber’ has
> not been declared
> sage/matrix/matrix_mpolynomial_dense.cpp:1839: error: ‘ip_sring’ has
> not been declared
> sage/matrix/matrix_mpolynomial_dense.cpp:1840: error: ‘snumber’ has
> not been declared
> sage/matrix/matrix_mpolynomial_dense.cpp:1840: error: ‘ip_sring’ has
> not been declared
> sage/matrix/matrix_mpolynomial_dense.cpp:1841: error: ‘snumber’ has
> not been declared
> sage/matrix/matrix_mpolynomial_dense.cpp:1841: error: ‘ip_sring’ has
> not been declared
> sage/matrix/matrix_mpolynomial_dense.cpp:1842: error: ‘snumber’ has
> not been declared
> sage/matrix/matrix_mpolynomial_dense.cpp:1842: error: ‘ip_sring’ has
> not been declared
> sage/matrix/matrix_mpolynomial_dense.cpp:1843: error: ISO C++ forbids
> declaration of ‘snumber’ with no type
> sage/matrix/matrix_mpolynomial_dense.cpp:1843: error: expected ‘;’
> before ‘*’ token
> sage/matrix/matrix_mpolynomial_dense.cpp:1844: error: ISO C++ forbids
> declaration of ‘snumber’ with no type
> sage/matrix/matrix_mpolynomial_dense.cpp:1844: error: expected ‘;’
> before ‘*’ token
> sage/matrix/matrix_mpolynomial_dense.cpp:1845: error: ISO C++ forbids
> declaration of ‘snumber’ with no type
> sage/matrix/matrix_mpolynomial_dense.cpp:1845: error: expected ‘;’
> before ‘*’ token
> sage/matrix/matrix_mpolynomial_dense.cpp:1846: error: ISO C++ forbids
> declaration of ‘snumber’ with no type
> sage/matrix/matrix_mpolynomial_dense.cpp:1846: error: expected ‘;’
> before ‘*’ token
> sage/matrix/matrix_mpolynomial_dense.cpp:1847: error: ISO C++ forbids
> declaration of ‘snumber’ with no type
> sage/matrix/matrix_mpolynomial_dense.cpp:1847: error: expected ‘;’
> before ‘*’ token
> sage/matrix/matrix_mpolynomial_dense.cpp:1848: error: ‘snumber’ has
> not been declared
> sage/matrix/matrix_mpolynomial_dense.cpp:1848: error: ‘ip_sring’ has
> not been declared
> sage/matrix/matrix_mpolynomial_dense.cpp:1849: error: ISO C++ forbids
> declaration of ‘snumber’ with no type
> sage/matrix/matrix_mpolynomial_dense.cpp:1849: error: expected ‘;’
> before ‘*’ token
> sage/matrix/matrix_mpolynomial_dense.cpp:1850: error: ‘polyrec’ has
> not been declared
> sage/matrix/matrix_mpolynomial_dense.cpp: In function ‘PyObject*
> __pyx_pf_4sage_6matrix_24matrix_mpolynomial_dense_24Matrix_mpolynomial_dense__echelonize_gauss_bareiss(PyObject*,
> PyObject*)’:
> sage/matrix/ma

[sage-devel] Re: Sage 3.0 released

[mabshoff]

On Apr 23, 9:23 pm, mark mcclure <[EMAIL PROTECTED]> wrote:
> On Apr 23, 1:08 pm, Robert Bradshaw <[EMAIL PROTECTED]>
> wrote:
>
> > >>  Are their binaries for OS X 10.4?
> > > NO.  And there won't be until somebody volunteers to make them.
> > > Can you make them?
>
> > Yes, do I just build and do sage -bdist?
>
> I attempted to compile sage 3.0 on my Mac G5 running OS X 10.4.10,
> but it failed with the errors below.  The gcc version is 4.0.1,
> build 5370.
>
> sage 3.0 compiled just fine on my Intel Mac with OS X 10.4.11.
> gcc version is 4.0.1, build 5367.
>
> The G5 errors are below.  I've never posted here before, so I'm
> not sure exactly what to report.  The compilation ran for a couple
> of hours and produced over 1000 lines in the install.log.  The
> stuff below is the last 75 lines.

Hi,

> -
> gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-
> madd -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/
> mcmcclure/Desktop/sage-3.0/local/include/singular -I/Users/mcmcclure/
> Desktop/sage-3.0/local//include -I/Users/mcmcclure/Desktop/sage-3.0/
> local//include/csage -I/Users/mcmcclure/Desktop/sage-3.0/devel//sage/
> sage/ext -I/Users/mcmcclure/Desktop/sage-3.0/local/include/python2.5 -
> c sage/matrix/matrix_mpolynomial_dense.cpp -o build/temp.macosx-10.3-
> ppc-2.5/sage/matrix/matrix_mpolynomial_dense.o -w -w
> cc1plus: warning: command line option "-Wstrict-prototypes" is valid
> for C/ObjC but not for C++
> sage/matrix/matrix_mpolynomial_dense.cpp:39:21: error: factory.h: No
> such file or directory
> sage/matrix/matrix_mpolynomial_dense.cpp:40:25: error: libsingular.h:
> No such file or directory

This looks like Singular did not build properly.



Please post a link to the  whole install.log here so I can take a
look.

Cheers,

Michael
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[sage-devel] Re: Sage, Maxima, Lisp

[Robert Dodier]

On Apr 23, 1:08 pm, "Bill Page" <[EMAIL PROTECTED]> wrote:

> Perhaps you have other ideas about how to achieve this kind of
> interoperability? I could imagine for example linking Python directly
> into the Aldor C run-time system or maybe linking the Python into the
> lisp image that runs Axiom?

There is an implementation of Python in Lisp called CLPython.
There was a message from its developer a day or two ago that
he's thinking about porting CLPython to SBCL (it runs on
Allegro CL and Lispworks at present). If CLPython could run
on SBCL, it could be compiled into the same image as Maxima
and then Python could (I guess) be used as the user language
for Maxima. I would be interested to see what that's like.

FWIW

Robert Dodier

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[sage-devel] Re: rpy build script fails for sage-3.0

[mabshoff]

On Apr 23, 4:52 pm, strogdon <[EMAIL PROTECTED]> wrote:

Hi,

> On my Gentoo box I unpacked the subject tarball, changed to the sage
> directory and did a make with the results:
>
> gcc version 4.1.2 (Gentoo 4.1.2 p1.0.2)
> 
> 
> RHOMES= []
> DEBUG= True
> Setting RHOMES to  ['/usr/lib64/R']
> RHOMES= []
> DEBUG= True
> Setting RHOMES to  ['/usr/lib64/R']
> Traceback (most recent call last):
> Traceback (most recent call last):
>   File "setup.py", line 106, in 
>   File "setup.py", line 106, in 
>         RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
> RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
>   File "/local/sage-3.0/spkg/build/rpy-1.0.1.p1/src/rpy_tools.py",
> line 99, in get_R_VERSION
>   File "/local/sage-3.0/spkg/build/rpy-1.0.1.p1/src/rpy_tools.py",
> line 99, in get_R_VERSION
>         " `%s'.\n" % rexec )
> " `%s'.\n" % rexec )
> RuntimeErrorRuntimeError: : Couldn't execute the R interpreter `/usr/
> lib64/R/bin/R'.
> Couldn't execute the R interpreter `/usr/lib64/R/bin/R'.
>
> Error building RPY -- Python interface to R.
> Error building RPY -- Python interface to R.

Do you have R installed in the system? Is RHOMES set? Do you have the
build log?

> I tried several corrective measures and the only one that allowed sage
> to build was to issue:
>
> RHOMES="`pwd`/local/lib/R" make
>
> However, the following test failed:
>
> sage -t  devel/sage/sage/stats/test.py

What did fail? Can you post the log of only that test?

Cheers,

Michael
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[sage-devel] construction of finite fields GF(2^n)

[John Cremona]

There's a serious inefficiency in the construction of finite fields
GF(2^n) in Sage at the moment.
For n<=15 these are constructed of type
sage.rings.finite_field_givaro.FiniteField_givaro, about which I have
nothing to say now;  for n>=16 they have type
sage.rings.finite_field_ntl_gf2e.FiniteField_ntl_gf2e and are
constructed by wrapping the appropriate NTL class.

The problem lies with how the defining polynomial for te field is
chosen: any irreducible poly of degree n over GF(2) will do in
principle.

The code in sage/rings/finite_field_ntl_gf2e.pyx chooses random
polynomials of degree n until it finds an irreducible one, the n
passes it (actually its coefficients) to a wrapped NTL constructor.
Two problems:
(1) The random polynomials have expected number of terms n/2, so even
when one is found whcih is irreducuble it is inefficient to work with
(reduction mod f is faster if f is sparse);
(2) Many many trials may be needed before a polynomial is found, so
the constructor can take for ages (eg 15s for n=500, and 314 s for
n=600)

Some solutions:
(1) Use sparse polynomials only.  These are better to use as defining
polynomials.  Shoup says there are no known n for which there is no
known irreducible trinomial (x^n+x^k+1) or 5-term
(x^n+x^k1+x^k2+x^k3+1).
(2) In NTL suitable sparse polys are precomputed for n<2048;  we could
copy that list.   (It is called GF2X_irred_tab in GF2XFactring.c in
NTL)
(3) We could let NTL get the poly for us, using its
BuildSparseIrred() function.

I propose that (3) is best;  I can try to do that but it will be
harder than (1)+(2).  Shall I open a trac for this?  I should be able
to put in a patch based on (1)+(2) very easily.

John

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[sage-devel] Re: Initial support for posets

[mhampton]

I'm not really qualified to comment in detail, but I thought I would
mention that I am interested in computing face lattices of polytopes
as part of my polytope module.  Perhaps you could comment on whether
there is (or could be) anything in your code that might help me out
with that.

I think its exciting that we are getting more sage-native
functionality like this.

Cheers,
M. Hampton

On Apr 23, 7:53 pm, "Franco Saliola" <[EMAIL PROTECTED]> wrote:
> Dear all,
>
> I've posted on trac the current version of my posets code.
> There is still much to be done, some algorithms need
> to be improved and others need to be implemented. (There
> are no NotImplementedErrors.)
>
>  http://trac.sagemath.org/sage_trac/ticket/2519
>
> But before I continue working, I'd like some feedback. I've
> made some decisions, and I don't know if they are the
> best decisions. So please offer suggestions.
>
> I've defined a HasseDiagram class that inherits from
> DiGraph. A Hasse diagram are transitively-reduced, directed,
> acyclic graph without loops or multiple edges. NOTE: We
> assume that range(n) is a linear extension of the Hasse
> diagram. This decision was taken in the hopes that it
> increases the efficiency of algorithms.
>
> There is a FinitePoset class that stores the list of
> elements of the poset (_elements), the HasseDiagram
> (_hasse_diagram, or hasse_diagram()), and maps
> _element_to_vertex and _vertex_to_element. So FinitePoset is
> just a vertex labelling of the HasseDiagram.
>
> There is a constructor called Poset that takes various forms
> of data describing a finite poset and returns a FinitePoset
> object.
>
> There are also Lattice, MeetSemilattice, JoinSemilattice...,
> and PosetElement, LatticeElement,  So one create poset
> elements and compare them with <, >, etc. And lattice
> elements can by multiplied and added (for meet and join).
>
> There are a few toy posets included (eventually there
> should be a poset database): BooleanLattice, Chain,
> Antichain, Pentagon, Diamond, PosetOfIntegerCompositions,
> RandomPoset, SymmetricGroupBruhatOrder,
> SymmetricGroupWeakOrder.
>
> So what do you think?
>
> Franco
>
> --
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[sage-devel] Re: [fricas-devel] Re: [sage-devel] Re: FriCAS/Open-Axiom and SAGE

[Martin Rubey]

"Gary Furnish" <[EMAIL PROTECTED]> writes:

> I'd be interested in hearing which features of FriCAS/OpenAxiom has that
> might be useful in more detail.  

I'm not quite sure what you are interested in.  I attach some things that I
know to be working well or that I used recently below.

> My main technical concerns are that anything interacting through a pexpect
> interface is going to be slow and will not interact with Sage's internal
> coercion system (aside from the fact that adding another dependency to the
> standard core increases code complexity for symbolics dramatically).  I
> downloaded FriCAS to try to investigate, but I couldn't find a good
> introduction to the high level structure of the FriCAS code (at the file
> level).  Does such a thing exist?

I'll restrict myself to the algebra, i.e., the part that contains the math
algorithms.  Waldek already posted the more general structure.  The algebra is
located in the files src/algebra/*.spad.pamphlet.  The name "pamphlet" is (in
my opinion) an accident and really should be "nw" for noweb.

There are several ways to investigate the algebra:

1) the axiom book by Jenks & Sutor

2) hyperdoc

3) )wh th xxx (that is, )what things xxx)

I usually start with 3.  See an example of my workflow below.  But I think it's
better to start with the principal concept of types in FriCAS/OpenAxiom, since
I have no idea how much this matches Sage's idea of type.  Below I'll write
only FriCAS, but that's the same for all members of the Axiom family and also
for Aldor, of course.

FriCAS is statically typed.  At all time, every object must have a type.  In
order to make FriCAS usable, it comes with an "intelligent" interpreter, that
tries to "guess" a reasonable type for user input.  The algorithm is relatively
transparent and general, and can be easily overridden.

Types come in 3 flavours:

an object can be

* a category (eg., Field, Monoid, MultivariateTaylorSeriesCategory) 
 Important note: the concept "category" has (in my opinion) only
 superficially to do with mathematical categories.  Rather, they
 state which operations a domain satisfying the category has to
 provide.
* a domain (eg., Integer, Float, List Integer, Matrix Complex
Expression Integer, etc.)
* a member of a Domain (say, an integer like 3, a float like 2.7, a list of
integers, a Taylor series, etc.)

In principle, a function (which is a member of the domain Mapping) can return
an object of any type.  This ideal is not quite reached in FriCAS, but
completely implemented in Aldor.

Now, to explore FriCAS algebra, you need to have an idea what you are
interested in.  I believe, the best way is to look at some domains: go to
HyperDoc, browse, enter the name of a domain, eg., Set, click on "domains",
then a short description of Set should appear and a link named SET.spad.  Click
on it, if your FriCAS is correctly installed, some sort of editor or pager
should open with the source code of set in it.

Files ending with "cat.spad.pamphlet" contain most of the categories.  There
are some other naming schemas which are less consequent, like
int*.spad.pamphlet for integration.

I cannot claim to know all of the algebra.  I'd say I know roughly 20 percent -
mainly polynomials, matrices, and bits and pieces of expressions.  I guess that
a considerably large part deals with "Expressions": (I omit
.spad.pamphlet. WARNING: this list is probably incomplete and erroneous.)

the domain (and related domains) itself: fspace, expr, combfunc, kl, liouv,
 elemntry, trigcat
integration: defintef, defintrf, efstruc, intaf, intalg, intaux, intef,
 integrat, intpm, intrf, irexpand, laplace, rdesys, rderf, rdeef
series: efuls, efupxs, elfuts, expr2ups, fs2expxp, fs2ups
limits: limitps (Gruntz has been implemented by Waldek, but is not integrated
 yet)
ODEs: exprode
pattern matching: pattern, patmatch1, patmatch2
operators on expressions: op
drawing: draw, drawopt, drawpak
solving: transsolve

Is such a list what you had in mind?

Does this answer your question?

Martin

Recently I needed to do calculus with operators.  In the following I separate
comments from FriCAS in/output with lines full of "-".

I said:
---
(1) -> )wh th operator

Operations whose names satisfy the above pattern(s):

constantOperatoroperatoroperators   
quotedOperators 
   
  To get more information about an operation such as operators , 
  issue the command )display op operators 
--- Categories 

Categories with names matching patterns:
 operator 

 LODOCAT  LinearOrdinaryDifferentialOperatorCategory
 MLO  MonogenicLinearOperator
- Domains -

Domains with names matching patterns:
 op

[sage-devel] Re: Sage 3.0 released

[mark mcclure]

On Apr 23, 1:08 pm, Robert Bradshaw <[EMAIL PROTECTED]>
wrote:
> >>  Are their binaries for OS X 10.4?
> > NO.  And there won't be until somebody volunteers to make them.
> > Can you make them?
>
> Yes, do I just build and do sage -bdist?



I attempted to compile sage 3.0 on my Mac G5 running OS X 10.4.10,
but it failed with the errors below.  The gcc version is 4.0.1,
build 5370.

sage 3.0 compiled just fine on my Intel Mac with OS X 10.4.11.
gcc version is 4.0.1, build 5367.


The G5 errors are below.  I've never posted here before, so I'm
not sure exactly what to report.  The compilation ran for a couple
of hours and produced over 1000 lines in the install.log.  The
stuff below is the last 75 lines.

-
gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-
madd -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/
mcmcclure/Desktop/sage-3.0/local/include/singular -I/Users/mcmcclure/
Desktop/sage-3.0/local//include -I/Users/mcmcclure/Desktop/sage-3.0/
local//include/csage -I/Users/mcmcclure/Desktop/sage-3.0/devel//sage/
sage/ext -I/Users/mcmcclure/Desktop/sage-3.0/local/include/python2.5 -
c sage/matrix/matrix_mpolynomial_dense.cpp -o build/temp.macosx-10.3-
ppc-2.5/sage/matrix/matrix_mpolynomial_dense.o -w -w
cc1plus: warning: command line option "-Wstrict-prototypes" is valid
for C/ObjC but not for C++
sage/matrix/matrix_mpolynomial_dense.cpp:39:21: error: factory.h: No
such file or directory
sage/matrix/matrix_mpolynomial_dense.cpp:40:25: error: libsingular.h:
No such file or directory
sage/matrix/matrix_mpolynomial_dense.cpp:225: error: ISO C++ forbids
declaration of ‘polyrec’ with no type
sage/matrix/matrix_mpolynomial_dense.cpp:225: error: expected ‘;’
before ‘*’ token
sage/matrix/matrix_mpolynomial_dense.cpp:978: error: ISO C++ forbids
declaration of ‘ip_sring’ with no type
sage/matrix/matrix_mpolynomial_dense.cpp:978: error: expected ‘;’
before ‘*’ token
sage/matrix/matrix_mpolynomial_dense.cpp:1839: error: ‘snumber’ has
not been declared
sage/matrix/matrix_mpolynomial_dense.cpp:1839: error: ‘ip_sring’ has
not been declared
sage/matrix/matrix_mpolynomial_dense.cpp:1840: error: ‘snumber’ has
not been declared
sage/matrix/matrix_mpolynomial_dense.cpp:1840: error: ‘ip_sring’ has
not been declared
sage/matrix/matrix_mpolynomial_dense.cpp:1841: error: ‘snumber’ has
not been declared
sage/matrix/matrix_mpolynomial_dense.cpp:1841: error: ‘ip_sring’ has
not been declared
sage/matrix/matrix_mpolynomial_dense.cpp:1842: error: ‘snumber’ has
not been declared
sage/matrix/matrix_mpolynomial_dense.cpp:1842: error: ‘ip_sring’ has
not been declared
sage/matrix/matrix_mpolynomial_dense.cpp:1843: error: ISO C++ forbids
declaration of ‘snumber’ with no type
sage/matrix/matrix_mpolynomial_dense.cpp:1843: error: expected ‘;’
before ‘*’ token
sage/matrix/matrix_mpolynomial_dense.cpp:1844: error: ISO C++ forbids
declaration of ‘snumber’ with no type
sage/matrix/matrix_mpolynomial_dense.cpp:1844: error: expected ‘;’
before ‘*’ token
sage/matrix/matrix_mpolynomial_dense.cpp:1845: error: ISO C++ forbids
declaration of ‘snumber’ with no type
sage/matrix/matrix_mpolynomial_dense.cpp:1845: error: expected ‘;’
before ‘*’ token
sage/matrix/matrix_mpolynomial_dense.cpp:1846: error: ISO C++ forbids
declaration of ‘snumber’ with no type
sage/matrix/matrix_mpolynomial_dense.cpp:1846: error: expected ‘;’
before ‘*’ token
sage/matrix/matrix_mpolynomial_dense.cpp:1847: error: ISO C++ forbids
declaration of ‘snumber’ with no type
sage/matrix/matrix_mpolynomial_dense.cpp:1847: error: expected ‘;’
before ‘*’ token
sage/matrix/matrix_mpolynomial_dense.cpp:1848: error: ‘snumber’ has
not been declared
sage/matrix/matrix_mpolynomial_dense.cpp:1848: error: ‘ip_sring’ has
not been declared
sage/matrix/matrix_mpolynomial_dense.cpp:1849: error: ISO C++ forbids
declaration of ‘snumber’ with no type
sage/matrix/matrix_mpolynomial_dense.cpp:1849: error: expected ‘;’
before ‘*’ token
sage/matrix/matrix_mpolynomial_dense.cpp:1850: error: ‘polyrec’ has
not been declared
sage/matrix/matrix_mpolynomial_dense.cpp: In function ‘PyObject*
__pyx_pf_4sage_6matrix_24matrix_mpolynomial_dense_24Matrix_mpolynomial_dense__echelonize_gauss_bareiss(PyObject*,
PyObject*)’:
sage/matrix/matrix_mpolynomial_dense.cpp:2694: error: ‘intvec’ was not
declared in this scope
sage/matrix/matrix_mpolynomial_dense.cpp:2694: error: ‘__pyx_v_iv’ was
not declared in this scope
sage/matrix/matrix_mpolynomial_dense.cpp:2695: error: ‘ip_sideal’ was
not declared in this scope
sage/matrix/matrix_mpolynomial_dense.cpp:2695: error: ‘__pyx_v_res’
was not declared in this scope
sage/matrix/matrix_mpolynomial_dense.cpp:2696: error: ‘ip_smatrix’ was
not declared in this scope
sage/matrix/matrix_mpolynomial_dense.cpp:2696: error: ‘__pyx_v_i’ was
not declared in this scope
sage/matrix/matrix_mpolynomial_dense.cpp:2697: error: ‘__pyx_v_ii’ was
not declared in this scope
sage/matrix/matrix_mpolynomial_dense.cpp:2699: error: ‘ip_sring’ was
no

[sage-devel] Re: [fricas-devel] Re: Sage, Maxima, Lisp

[Bill Page]

2008/4/23 Waldek Hebisch wrote:
> ...
>  For FriCAS in longer run dropping Lisp is likely -- most Lisp code
>  is machine generated during FriCAS build.  With enough effort we
>  could directly generate C code.  Currently effort to drop Lisp would
>  be prohibitive, but the FriCAS code is constanly cleaned up and
>  simplified so in the future such change will be much easier.
>

I have a question that might at first seem heretical, but I think that
the answer might possibly be of some interest to the Sage
developers...

Both you and Gaby have discussed the possibility of defining an
abstract machine (aka. run-time system) to replace the role that Lisp
plays for Axiom. We also know that Aldor has already defined such a
machine called FOAM. FOAM can be implemented either in Lisp (for
interface with Axiom) or by a run-time system written entirely in C
for stand alone use. In fact this strategy is quite common and we here
a lot for example about the Java Virtual Machine.

Now it turns out that Python also has this notion of an abstract
virtual machine that is the target for the Python interpreter. There
are already some languages other than Python that can produce low
level code for the Python virtual machine. I believe that the current
Python virtual machine would very likely be adequate to support the
run time requirements of Axiom/Aldor. So my question is: Is there be
any possibility and interest in producing either an Axiom/Spad or
Aldor compiler that targets this same virtual machine?

In principle (and I admit that this is a big leap) this would allow
complete interoperability between Sage and Axiom or Aldor.

Perhaps you have other ideas about how to achieve this kind of
interoperability? I could imagine for example linking Python directly
into the Aldor C run-time system or maybe linking the Python into the
lisp image that runs Axiom?

What do you think? Is this crazy?

Regards,
Bill Page.

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[sage-devel] Re: [fricas-devel] Re: [sage-devel] Re: FriCAS/Open-Axiom and SAGE

[Bill Page]

On Wed, Apr 23, 2008 at 1:48 PM, Gary Furnish wrote:
> ...
> Right now, most functionality of the sage.calculus module is dictated
> strictly by how maxima is designed.  As we move to our own internal
> representation, this obviously will not be sufficient.

It is not immediately obvious to me that this is not sufficient. To
decide it might first be necessary to define more carefully exactly
what you want to be able to do in Sage.

> I'd be interested in hearing which features of FriCAS/OpenAxiom has
> that might be useful in more detail.

Here is a very short and personally biased summary:

I think a big difference between Maxima and Sage is that Maxima is
*untyped* or rather, there is really only one type of object in Maxima
- an expression - while Sage attempts to treat objects as belonging to
different mathematical categories. For example: a Polynomial is built
over some coefficient Ring, etc. Sage is like Axiom in this respect.
On the other hand Axiom has a domain called 'Expression' which fits
into the overall mathematical category struture in a well-defined
manner, i.e. it consists of a formal extension of the rational
functions (Fraction Polynomial). The Expression domain is very
different from simply being a "symbolic expression" in the sense used
in Maxima. Axiom has another domain called InputForm which is much
more like Maxima's symbolic expressions but in Axiom it is used only
for the internal representation of input to the interpreter. Very
little expression manipulation occurs in Axiom at this level although
some people have argued that Axiom should have better support of doing
this sort of thing.

Closely related to this is another set of domains in Axiom related to
pattern matching in Expression and other less highly structured
symbolic domains.

> My main technical concerns are that anything interacting
> through a pexpect interface is going to be slow and will not
> interact with Sage's internal coercion system (aside from the
> fact that adding another dependency to the standard core
> increases code complexity for symbolics dramatically).

Could you explain more about why you say this will not (can not?)
interact with Sage's coercion system?

> I downloaded FriCAS to try to investigate, but I couldn't
> find a good introduction to the high level structure of the
> FriCAS code (at the file level).  Does such a thing exist?
>

Do you really mean "structure of the code at the file level" or do you
want something more conceptual? For example: Have you looked at the
Axiom book (a little over 1000 pages). Chapters 11, 12 and 13 describe
the tools used to build the Axiom library. Have you tried hyperdoc to
navigate the mathematical structure?

If you really mean "at the file level", the files that you will
probably care most about are those found in the src/algebra directory.

Regards,
Bill Page.

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[sage-devel] Initial support for posets

[Franco Saliola]

Dear all,

I've posted on trac the current version of my posets code.
There is still much to be done, some algorithms need
to be improved and others need to be implemented. (There
are no NotImplementedErrors.)

  http://trac.sagemath.org/sage_trac/ticket/2519

But before I continue working, I'd like some feedback. I've
made some decisions, and I don't know if they are the
best decisions. So please offer suggestions.

I've defined a HasseDiagram class that inherits from
DiGraph. A Hasse diagram are transitively-reduced, directed,
acyclic graph without loops or multiple edges. NOTE: We
assume that range(n) is a linear extension of the Hasse
diagram. This decision was taken in the hopes that it
increases the efficiency of algorithms.

There is a FinitePoset class that stores the list of
elements of the poset (_elements), the HasseDiagram
(_hasse_diagram, or hasse_diagram()), and maps
_element_to_vertex and _vertex_to_element. So FinitePoset is
just a vertex labelling of the HasseDiagram.

There is a constructor called Poset that takes various forms
of data describing a finite poset and returns a FinitePoset
object.

There are also Lattice, MeetSemilattice, JoinSemilattice...,
and PosetElement, LatticeElement,  So one create poset
elements and compare them with <, >, etc. And lattice
elements can by multiplied and added (for meet and join).

There are a few toy posets included (eventually there
should be a poset database): BooleanLattice, Chain,
Antichain, Pentagon, Diamond, PosetOfIntegerCompositions,
RandomPoset, SymmetricGroupBruhatOrder,
SymmetricGroupWeakOrder.

So what do you think?

Franco

--

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[sage-devel] Re: [fricas-devel] Re: [sage-devel] Re: FriCAS/Open-Axiom and SAGE

[Gary Furnish]

No doubt the sage system is a bit too ad hoc.  However, this is something
that will be fixed in the symbolics rewrite.  While externally it will
maintain most backwards compatibility, internally it will be vastly
different (for example, elements (including variables) in the "symbolic
ring" (which is no longer even necessarily a ring!) no longer necessarily
commute, etc).  Care is being taken to make it significantly less ad hoc.
Right now, most functionality of the sage.calculus module is dictated
strictly by how maxima is designed.  As we move to our own internal
reperesentation, this obviously will not be sufficient.  I'd be interested
in hearing which features of FriCAS/OpenAxiom has that might be useful in
more detail.  My main technical concerns are that anything interacting
through a pexpect interface is going to be slow and will not interact with
Sage's internal coercion system (aside from the fact that adding another
dependency to the standard core increases code complexity for symbolics
dramatically).  I downloaded FriCAS to try to investigate, but I couldn't
find a good introduction to the high level structure of the FriCAS code (at
the file level).  Does such a thing exist?

-- Gary Furnish

On Wed, Apr 23, 2008 at 9:49 AM, Bill Page <[EMAIL PROTECTED]>
wrote:

>
> On Wed, Apr 23, 2008 at 4:28 AM, Michael.Abshoff wrote:
> >
> >  Martin Rubey wrote:
> >
> >  > I do not see how the problem of differing representations can be
> >  > resolved. Up to now I thought that Sage simply doesn't have an
> >  > "internal" representation, and just uses the one from the external
> >  > program - that's how my polymake interface for FriCAS/Axiom
> >  > works.
> >
> >  I am not 100% clear, but I believe for elements in a symbolic ring
> >  we do not yet have a Sage internal representation. It is being written
> >  in Cython since arithmetic is probably slowed down by a factor of
> > 10,000 by using pexpect+Maxima. That is largely the fault of pexpect.
> >
>
> I think that what Martin means is that if Sage has it's own internal
> representation of something then the problem of converting from one
> representation to another is unavoidable if the symbolic manipulation
> is done by an external program. This is independent of whether one
> uses the pexpect interface or not. Of course if symbolic manipulation
> is implemented in the Sage interpreter or compiled Cython code, then
> this conversion may not be necessary. However it is sometimes
> convenient also to change the internal representation depending on the
> type of manipulation to be done.
>
> So far as I can see Sage does have an internal representation for
> "Symbolic Ring".
>
> But the idea of a "Symbolic Ring" seems very strange to me. What is
> this from a mathematical point of view? How is it different from, say,
> a polynomial? Do you really mean that the variables of the ring do not
> commute as in the sense of a free algebra?
>
> http://en.wikipedia.org/wiki/Free_algebra
>
> I worry sometimes that the Sage type system is a little too ad hoc... :-(
>
> Anyway, here is an example computation that includes conversion from
> the internal Sage representation to the internal Axiom representation
> of a symbolic object:
>
> [EMAIL PROTECTED]:~# sage
> --
> | SAGE Version 3.0, Release Date: 2008-04-22 |
> | Type notebook() for the GUI, and license() for information.|
> --
>
> sage: # Construct some symbolic expression in Sage
> sage: var('a b c d')
> (a, b, c, d)
>
> sage: A = matrix([[a,b],[c,d]])
>
> sage: A
>
> [a b]
> [c d]
>
> sage: x=det(A)
>
> sage: x
> a*d - b*c
>
> sage: x.parent()
> Symbolic Ring
>
> sage: x?
> Type:   SymbolicArithmetic
> Base Class: 
> String Form:
>
>   a d - b c
> Namespace:  Interactive
> Docstring:
>
>Represents the result of an arithmetic operation on
>f and g.
>
> sage: # Convert it to an object in Axiom
> sage: y=axiom(x)
>
> sage: y
> a*d+(-b*c)
>
> sage: y.type()
> Polynomial Integer
>
> sage: y?
> Type:   AxiomElement
> Base Class: 
> String Form:a*d+(-b*c)
> Namespace:  Interactive
> Docstring:
>a*d+(-b*c)
>
> > ...
> >  So: What should you do:
> >
> >  a) wait a week or two for ecls and gdbm to become optional
> >  b) build an optional FriCAS/OpenAxiom spkg using ecls
> >  c) write a pexpect interface to use integration/ODE/guess if that
> >  is something where you see FriCAS/OpenAxiom as "better
> >  than anything else".
> >
> >  In parallel take a look at
> >
> >  http://wiki.sagemath.org/spkg/InclusionProcedure
> >
> >  and write some proposal *why* FriCAS/OpenAxiom should become
> >  part of standard Sage and *what* it should/can [via pexpect] do.
> >  ...
>
> Martin I would be interested in working with you on doing this (and
> anyone else who would like

[sage-devel] Re: Sage 3.0 released

[root]

I have a MAC OX X 10.4.4 build in process.
Its on a PowerPC (G4)
I'll make it available when it completes.

Tim

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[sage-devel] Re: Sage 3.0 released

[Robert Bradshaw]

On Apr 23, 2008, at 10:06 AM, William Stein wrote:
>
> On Wed, Apr 23, 2008 at 10:03 AM, Robert Bradshaw
> <[EMAIL PROTECTED]> wrote:
>>
>>  Are their binaries for OS X 10.4?
>
> NO.  And there won't be until somebody volunteers to make them.  See
> my long email about this a few minutes ago in Sage-support.
>
> Can you make them?

Yes, do I just build and do sage -bdist?

>
>>
>>  On Apr 23, 2008, at 4:58 AM, mabshoff wrote:
>>>
>>
>>
>>> [Note: If you are interested in announcements only please  
>>> subscribe to
>>> sage-announce. It is limited to roughly one email every ten days.]
>>>
>>> Hello folks,
>>>
>>> Sage 3.0 has been released on April 21st, 2008. It is available at
>>>
>>>http://sagemath.org/download.html
>>>
>>> * About Sage (http://www.sagemath.org)
>>>
>>> Sage is developed by volunteers and combines 71 open source  
>>> packages.
>>> It is available for download from sagemath.org and its mirrors in
>>> source or binary form. If you have any questions and/or problems
>>> please report them to the google groups sage-devel or sage-support.
>>> You can also drop by in #sage-devel or #sage-support in freenode.
>>>
>>>  
>>> -
>>>
>>> The following 48 people contributed to this release:
>>>
>>>  * Tim Abbott
>>>  * Michael Abshoff
>>>  * Martin Albrecht
>>>  * Nick Alexander
>>>  * Tom Boothby
>>>  * Robert Bradshaw
>>>  * Jason Brandlow
>>>  * Michael Brickenstein
>>>  * Dan Bump
>>>  * Craig Citro
>>>  * Ondrej Certik
>>>  * Timothy Clemans
>>>  * John Cremona
>>>  * Didier Deshommes
>>>  * Nathan Dunfield
>>>  * Dan Drake
>>>  * Alexander Dreyer
>>>  * Burin Erocal
>>>  * Gary Furnish
>>>  * Alex Ghitza
>>>  * Andrzej Giniewicz
>>>  * Jason Grout
>>>  * Marshall Hampton
>>>  * Mike Hansen
>>>  * David Harvey
>>>  * Geert Heldager Nielsen
>>>  * David Joyner
>>>  * Michael Kallweit
>>>  * Josh Kantor
>>>  * Simon King
>>>  * Emily Kirkman
>>>  * Robert Miller
>>>  * Minh Nguyen
>>>  * Willem Jan Palenstijn
>>>  * Clement Pernet
>>>  * Steffan Reidt
>>>  * David Roe
>>>  * Ryan Hinton
>>>  * Anne Schilling
>>>  * Harald Schilly
>>>  * William Stein
>>>  * Chris Swierczewski
>>>  * Nicolas Thiery
>>>  * Gonzalo Tornaria
>>>  * John Voight
>>>  * Yi Qiang
>>>  * Justin Walker
>>>  * Carl Witty
>>>
>>> Cheers,
>>>
>>> Binaries are available on the mirrors!
>>>
>>> Michael Abshoff (release chair), William Stein
>>>
>>> * Major Features, New Spkgs and Bugfixes
>>>
>>>  * Random Numbers
>>>  * GCC 4.3 Support
>>>  * New Default Binaries
>>>  * Boolean Polynomials
>>>  * Modular Abelian Varieties
>>>  * Increased Doctest Coverage
>>>  * R Pexpect Interface
>>>  * Crystals
>>>  * Laurent Polynomials
>>>
>>> For details see the Sage 3.0 Release Tour at
>>>
>>>   http://wiki.sagemath.org/sage-3.0
>>>
>>> * Known Issues with 3.0:
>>>
>>>  #2983: Singular interface problems in matrix_group.py on
>>> Itanium/Linux: We see a segfault in the doctest and
>>> will hopefully fix this in 3.0.1.
>>>  #2985: rubik.py's OptimalSolver() problem on Itanium/Linux:
>>> the doctest also segfaults with the "-long" option.
>>> This will hopefully be fixed in 3.0.1.
>>>
>>> * Bug Statistics
>>>
>>> We closed a record number of 277 tickets. For details see
>>>
>>>http://trac.sagemath.org/sage_trac/milestone/sage-3.0
>>>
>>> or check out the closed ticket section at the end of the
>>> announcement.
>>>
>>> * Upcoming Releases
>>>
>>> The next release will be 3.0.1, chaired by Michael Abshoff.
>>> The release is planned in about a week. It will be mostly a
>>> bug fix release to clear up issues from the 3.0 release.
>>>
>>> * Doctesting Coverage
>>>
>>> For 2.11 we had:
>>>
>>> Overall weighted coverage score:  48.9%
>>> Total number of functions:  18853
>>>
>>> We increased coverage by 2.6% in 3.0 while adding 661 functions:
>>>
>>> Overall weighted coverage score:  51.5%
>>> Total number of functions:  19514
>>>
>>> * Closed Tickets:
>>>
>>> Merged in final:
>>>
>>> #2979: Michael Abshoff, Andrzej Giniewicz: force "-O0" for
>>>clisp with gcc 4.3
>>> #2987: Tim Abbott: Debian build support for zn_poly
>>> #2988: William Stein: notebook -- issues with the CSS for the
>>>print display
>>> #2989: William Stein: notebook -- issue with how the notebook
>>>is run that breaks it sometimes; also fix a typo in pid.
>>> #2990: William Stein: sage-3.0.rc1: calculus/functions.py
>>>segfault on debian64 xeon vmware image
>>> #2991: William Stein: fix dsage testdoc problem
>>> #2994: Michael Abshoff: polybori.spkg - fix permission issue
>>>of the headers
>>>
>>> Merged in rc1:
>>>
>>> #2419: William Stein, Simon King: Gap interface and resultant
>>>destroy the Singular interface on some machines
>>> #2553: Yi Qiang, William Stein: dsage unit tests fail on linux
>>> #2928: Willem Jan Palenstijn: another p-adic extension segfault
>>> #2934: William Stein: doctesting files outsid

[sage-devel] Re: Sage 3.0 released

[William Stein]

On Wed, Apr 23, 2008 at 10:03 AM, Robert Bradshaw
<[EMAIL PROTECTED]> wrote:
>
>  Are their binaries for OS X 10.4?

NO.  And there won't be until somebody volunteers to make them.  See
my long email about this a few minutes ago in Sage-support.

Can you make them?

>
>  On Apr 23, 2008, at 4:58 AM, mabshoff wrote:
>  >
>
>
> > [Note: If you are interested in announcements only please subscribe to
>  > sage-announce. It is limited to roughly one email every ten days.]
>  >
>  > Hello folks,
>  >
>  > Sage 3.0 has been released on April 21st, 2008. It is available at
>  >
>  >http://sagemath.org/download.html
>  >
>  > * About Sage (http://www.sagemath.org)
>  >
>  > Sage is developed by volunteers and combines 71 open source packages.
>  > It is available for download from sagemath.org and its mirrors in
>  > source or binary form. If you have any questions and/or problems
>  > please report them to the google groups sage-devel or sage-support.
>  > You can also drop by in #sage-devel or #sage-support in freenode.
>  >
>  > -
>  >
>  > The following 48 people contributed to this release:
>  >
>  >  * Tim Abbott
>  >  * Michael Abshoff
>  >  * Martin Albrecht
>  >  * Nick Alexander
>  >  * Tom Boothby
>  >  * Robert Bradshaw
>  >  * Jason Brandlow
>  >  * Michael Brickenstein
>  >  * Dan Bump
>  >  * Craig Citro
>  >  * Ondrej Certik
>  >  * Timothy Clemans
>  >  * John Cremona
>  >  * Didier Deshommes
>  >  * Nathan Dunfield
>  >  * Dan Drake
>  >  * Alexander Dreyer
>  >  * Burin Erocal
>  >  * Gary Furnish
>  >  * Alex Ghitza
>  >  * Andrzej Giniewicz
>  >  * Jason Grout
>  >  * Marshall Hampton
>  >  * Mike Hansen
>  >  * David Harvey
>  >  * Geert Heldager Nielsen
>  >  * David Joyner
>  >  * Michael Kallweit
>  >  * Josh Kantor
>  >  * Simon King
>  >  * Emily Kirkman
>  >  * Robert Miller
>  >  * Minh Nguyen
>  >  * Willem Jan Palenstijn
>  >  * Clement Pernet
>  >  * Steffan Reidt
>  >  * David Roe
>  >  * Ryan Hinton
>  >  * Anne Schilling
>  >  * Harald Schilly
>  >  * William Stein
>  >  * Chris Swierczewski
>  >  * Nicolas Thiery
>  >  * Gonzalo Tornaria
>  >  * John Voight
>  >  * Yi Qiang
>  >  * Justin Walker
>  >  * Carl Witty
>  >
>  > Cheers,
>  >
>  > Binaries are available on the mirrors!
>  >
>  > Michael Abshoff (release chair), William Stein
>  >
>  > * Major Features, New Spkgs and Bugfixes
>  >
>  >  * Random Numbers
>  >  * GCC 4.3 Support
>  >  * New Default Binaries
>  >  * Boolean Polynomials
>  >  * Modular Abelian Varieties
>  >  * Increased Doctest Coverage
>  >  * R Pexpect Interface
>  >  * Crystals
>  >  * Laurent Polynomials
>  >
>  > For details see the Sage 3.0 Release Tour at
>  >
>  >   http://wiki.sagemath.org/sage-3.0
>  >
>  > * Known Issues with 3.0:
>  >
>  >  #2983: Singular interface problems in matrix_group.py on
>  > Itanium/Linux: We see a segfault in the doctest and
>  > will hopefully fix this in 3.0.1.
>  >  #2985: rubik.py's OptimalSolver() problem on Itanium/Linux:
>  > the doctest also segfaults with the "-long" option.
>  > This will hopefully be fixed in 3.0.1.
>  >
>  > * Bug Statistics
>  >
>  > We closed a record number of 277 tickets. For details see
>  >
>  >http://trac.sagemath.org/sage_trac/milestone/sage-3.0
>  >
>  > or check out the closed ticket section at the end of the
>  > announcement.
>  >
>  > * Upcoming Releases
>  >
>  > The next release will be 3.0.1, chaired by Michael Abshoff.
>  > The release is planned in about a week. It will be mostly a
>  > bug fix release to clear up issues from the 3.0 release.
>  >
>  > * Doctesting Coverage
>  >
>  > For 2.11 we had:
>  >
>  > Overall weighted coverage score:  48.9%
>  > Total number of functions:  18853
>  >
>  > We increased coverage by 2.6% in 3.0 while adding 661 functions:
>  >
>  > Overall weighted coverage score:  51.5%
>  > Total number of functions:  19514
>  >
>  > * Closed Tickets:
>  >
>  > Merged in final:
>  >
>  > #2979: Michael Abshoff, Andrzej Giniewicz: force "-O0" for
>  >clisp with gcc 4.3
>  > #2987: Tim Abbott: Debian build support for zn_poly
>  > #2988: William Stein: notebook -- issues with the CSS for the
>  >print display
>  > #2989: William Stein: notebook -- issue with how the notebook
>  >is run that breaks it sometimes; also fix a typo in pid.
>  > #2990: William Stein: sage-3.0.rc1: calculus/functions.py
>  >segfault on debian64 xeon vmware image
>  > #2991: William Stein: fix dsage testdoc problem
>  > #2994: Michael Abshoff: polybori.spkg - fix permission issue
>  >of the headers
>  >
>  > Merged in rc1:
>  >
>  > #2419: William Stein, Simon King: Gap interface and resultant
>  >destroy the Singular interface on some machines
>  > #2553: Yi Qiang, William Stein: dsage unit tests fail on linux
>  > #2928: Willem Jan Palenstijn: another p-adic extension segfault
>  > #2934: William Stein: doct

[sage-devel] Re: Sage 3.0 released

[Robert Bradshaw]

Are their binaries for OS X 10.4?

On Apr 23, 2008, at 4:58 AM, mabshoff wrote:
>
> [Note: If you are interested in announcements only please subscribe to
> sage-announce. It is limited to roughly one email every ten days.]
>
> Hello folks,
>
> Sage 3.0 has been released on April 21st, 2008. It is available at
>
>http://sagemath.org/download.html
>
> * About Sage (http://www.sagemath.org)
>
> Sage is developed by volunteers and combines 71 open source packages.
> It is available for download from sagemath.org and its mirrors in
> source or binary form. If you have any questions and/or problems
> please report them to the google groups sage-devel or sage-support.
> You can also drop by in #sage-devel or #sage-support in freenode.
>
> -
>
> The following 48 people contributed to this release:
>
>  * Tim Abbott
>  * Michael Abshoff
>  * Martin Albrecht
>  * Nick Alexander
>  * Tom Boothby
>  * Robert Bradshaw
>  * Jason Brandlow
>  * Michael Brickenstein
>  * Dan Bump
>  * Craig Citro
>  * Ondrej Certik
>  * Timothy Clemans
>  * John Cremona
>  * Didier Deshommes
>  * Nathan Dunfield
>  * Dan Drake
>  * Alexander Dreyer
>  * Burin Erocal
>  * Gary Furnish
>  * Alex Ghitza
>  * Andrzej Giniewicz
>  * Jason Grout
>  * Marshall Hampton
>  * Mike Hansen
>  * David Harvey
>  * Geert Heldager Nielsen
>  * David Joyner
>  * Michael Kallweit
>  * Josh Kantor
>  * Simon King
>  * Emily Kirkman
>  * Robert Miller
>  * Minh Nguyen
>  * Willem Jan Palenstijn
>  * Clement Pernet
>  * Steffan Reidt
>  * David Roe
>  * Ryan Hinton
>  * Anne Schilling
>  * Harald Schilly
>  * William Stein
>  * Chris Swierczewski
>  * Nicolas Thiery
>  * Gonzalo Tornaria
>  * John Voight
>  * Yi Qiang
>  * Justin Walker
>  * Carl Witty
>
> Cheers,
>
> Binaries are available on the mirrors!
>
> Michael Abshoff (release chair), William Stein
>
> * Major Features, New Spkgs and Bugfixes
>
>  * Random Numbers
>  * GCC 4.3 Support
>  * New Default Binaries
>  * Boolean Polynomials
>  * Modular Abelian Varieties
>  * Increased Doctest Coverage
>  * R Pexpect Interface
>  * Crystals
>  * Laurent Polynomials
>
> For details see the Sage 3.0 Release Tour at
>
>   http://wiki.sagemath.org/sage-3.0
>
> * Known Issues with 3.0:
>
>  #2983: Singular interface problems in matrix_group.py on
> Itanium/Linux: We see a segfault in the doctest and
> will hopefully fix this in 3.0.1.
>  #2985: rubik.py's OptimalSolver() problem on Itanium/Linux:
> the doctest also segfaults with the "-long" option.
> This will hopefully be fixed in 3.0.1.
>
> * Bug Statistics
>
> We closed a record number of 277 tickets. For details see
>
>http://trac.sagemath.org/sage_trac/milestone/sage-3.0
>
> or check out the closed ticket section at the end of the
> announcement.
>
> * Upcoming Releases
>
> The next release will be 3.0.1, chaired by Michael Abshoff.
> The release is planned in about a week. It will be mostly a
> bug fix release to clear up issues from the 3.0 release.
>
> * Doctesting Coverage
>
> For 2.11 we had:
>
> Overall weighted coverage score:  48.9%
> Total number of functions:  18853
>
> We increased coverage by 2.6% in 3.0 while adding 661 functions:
>
> Overall weighted coverage score:  51.5%
> Total number of functions:  19514
>
> * Closed Tickets:
>
> Merged in final:
>
> #2979: Michael Abshoff, Andrzej Giniewicz: force "-O0" for
>clisp with gcc 4.3
> #2987: Tim Abbott: Debian build support for zn_poly
> #2988: William Stein: notebook -- issues with the CSS for the
>print display
> #2989: William Stein: notebook -- issue with how the notebook
>is run that breaks it sometimes; also fix a typo in pid.
> #2990: William Stein: sage-3.0.rc1: calculus/functions.py
>segfault on debian64 xeon vmware image
> #2991: William Stein: fix dsage testdoc problem
> #2994: Michael Abshoff: polybori.spkg - fix permission issue
>of the headers
>
> Merged in rc1:
>
> #2419: William Stein, Simon King: Gap interface and resultant
>destroy the Singular interface on some machines
> #2553: Yi Qiang, William Stein: dsage unit tests fail on linux
> #2928: Willem Jan Palenstijn: another p-adic extension segfault
> #2934: William Stein: doctesting files outside of sage repo is
>completely broken
> #2972: William Stein: libSingular related segfault in
>laurent_polynomial_ring.py
> #2973: Michael Abshoff: RDF doctest failures on arch linux
> #2974: Mike Hansen: interfaces/r.py doctest failures on many
>linux machines
> #2975: William Stein: opening ports too conservative -- breaks
>on some os x systems
> #2977: Alex Ghitza: wronskian is broken on constants
> #2984: William Stein, Michael Abshoff: ITANIUM (RHEL 5) -- turn
>off all unaligned access messages
> #2986: Gonzalo Tornaria: Add atlas pretuning for Pentium D/64
>bits (ARCH=P4D64SSE3)
>
> Merged in rc0:
>
> #34: Craig Citro: 

[sage-devel] Re: notebook features discussion

[gerhard]

> What problems are you having? Beamer and SageTeX are largely orthogonal,
> but there are some tricky bits with verbatim environments

When I add a sageblock in a frame, e.g.,
\begin{sageblock}
  var('x')
  f = log(sin(x)/x)
\end{sageblock}

I get  the error message

Runaway argument?
! Paragraph ended before \next was complete.

\par


I installed the sagetex package directly from ctan.
The problem appears with bot sage 2.10.4 and 3.0.

-gerhard


> Dan
>
> --
> ---  Dan Drake <[EMAIL PROTECTED]>
> -  KAIST Department of Mathematical Sciences
> ---  http://math.kaist.ac.kr/~drake
>
>  signature.asc
> 1KDownload
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[sage-devel] Re: Sage build failure

[William Stein]

On Wed, Apr 23, 2008 at 9:46 AM,  <[EMAIL PROTECTED]> wrote:
>
>  The install.log file is at
>  
>

This fails with "internal compiler error":


'__pyx_pf_4sage_7modules_18real_double_vector_28RealDoubleVectorSpaceElement___init__':
sage/modules/real_double_vector.c:2014: internal compiler error: in
merge_alias_info, at tree-ssa-copy.c:235
Please submit a full bug report,
with preprocessed source if appropriate.
See http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccwUCwx8.out file, please attach
this to your bugreport.


I believe that error always indicates that there is a bug in the compiler;
i.e., it should be impossible to trigger with any program as input.

Your compiler is  "gcc version 4.1.0 20060304 (Red Hat 4.1.0-3)".

The compiler I use for building on RHEL5 is:
 gcc version 4.1.1 20070105

So to build Sage from source you will have to upgrade to gcc 4.1.1.

   -- William

-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-devel] Sage build failure

[daly]

The install.log file is at 



This fails on fedora 5

[EMAIL PROTECTED] sage-3.0]# uname -a
Linux localhost.localdomain 2.6.18-1.2239.fc5 #1 Fri Nov 10 13:04:06 EST 2006 
i686 i686 i386 GNU/Linux
You have new mail in /var/spool/mail/root
[EMAIL PROTECTED] sage-3.0]# cat /proc/cpuinfo
processor   : 0
vendor_id   : GenuineIntel
cpu family  : 6
model   : 14
model name  : Genuine Intel(R) CPU   T2050  @ 1.60GHz
stepping: 8
cpu MHz : 1595.293
cache size  : 2048 KB
fdiv_bug: no
hlt_bug : no
f00f_bug: no
coma_bug: no
fpu : yes
fpu_exception   : yes
cpuid level : 10
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat 
clflush dts acpi mmx fxsr sse sse2 ss nx constant_tsc pni
bogomips: 3233.79




building 'sage.modules.real_double_vector' extension
gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes 
-fPIC -DGSL_DISABLE_DEPRECATED=1 
-I/research/sage-3.0/local/lib/python2.5/site-packages/numpy/core/include/numpy 
-I/research/sage-3.0/local//include -I/research/sage-3.0/local//include/csage 
-I/research/sage-3.0/devel//sage/sage/ext 
-I/research/sage-3.0/local/include/python2.5 -c 
sage/modules/real_double_vector.c -o 
build/temp.linux-i686-2.5/sage/modules/real_double_vector.o -w -w
sage/modules/real_double_vector.c: In function 
'__pyx_pf_4sage_7modules_18real_double_vector_28RealDoubleVectorSpaceElement___init__':
sage/modules/real_double_vector.c:2014: internal compiler error: in 
merge_alias_info, at tree-ssa-copy.c:235
Please submit a full bug report,
with preprocessed source if appropriate.
See http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccwUCwx8.out file, please attach this to 
your bugreport.
error: command 'gcc' failed with exit status 1
sage: There was an error installing modified sage library code.

ERROR installing SAGE

real13m47.698s
user11m26.741s
sys 2m9.727s
sage: An error occurred while installing sage-3.0
Please email sage-devel http://groups.google.com/group/sage-devel
explaining the problem and send the relevant part of
of /research/sage-3.0/install.log.  Describe your computer, operating system, 
etc.
If you want to try to fix the problem, yourself *don't* just cd to
/research/sage-3.0/spkg/build/sage-3.0 and type 'make'.
Instead type "/research/sage-3.0/sage -sh"
in order to set all environment variables correctly, then cd to
/research/sage-3.0/spkg/build/sage-3.0
(When you are done debugging, you can type "exit" to leave the
subshell.)
make[1]: *** [installed/sage-3.0] Error 1
make[1]: Leaving directory `/research/sage-3.0/spkg'

real150m43.177s
user74m23.338s
sys 69m26.373s

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[sage-devel] Re: FriCAS/Open-Axiom and SAGE

[Bill Page]

On Wed, Apr 23, 2008 at 4:28 AM, Michael.Abshoff wrote:
>
>  Martin Rubey wrote:
>
>  > I do not see how the problem of differing representations can be
>  > resolved. Up to now I thought that Sage simply doesn't have an
>  > "internal" representation, and just uses the one from the external
>  > program - that's how my polymake interface for FriCAS/Axiom
>  > works.
>
>  I am not 100% clear, but I believe for elements in a symbolic ring
>  we do not yet have a Sage internal representation. It is being written
>  in Cython since arithmetic is probably slowed down by a factor of
> 10,000 by using pexpect+Maxima. That is largely the fault of pexpect.
>

I think that what Martin means is that if Sage has it's own internal
representation of something then the problem of converting from one
representation to another is unavoidable if the symbolic manipulation
is done by an external program. This is independent of whether one
uses the pexpect interface or not. Of course if symbolic manipulation
is implemented in the Sage interpreter or compiled Cython code, then
this conversion may not be necessary. However it is sometimes
convenient also to change the internal representation depending on the
type of manipulation to be done.

So far as I can see Sage does have an internal representation for
"Symbolic Ring".

But the idea of a "Symbolic Ring" seems very strange to me. What is
this from a mathematical point of view? How is it different from, say,
a polynomial? Do you really mean that the variables of the ring do not
commute as in the sense of a free algebra?

http://en.wikipedia.org/wiki/Free_algebra

I worry sometimes that the Sage type system is a little too ad hoc... :-(

Anyway, here is an example computation that includes conversion from
the internal Sage representation to the internal Axiom representation
of a symbolic object:

[EMAIL PROTECTED]:~# sage
--
| SAGE Version 3.0, Release Date: 2008-04-22 |
| Type notebook() for the GUI, and license() for information.|
--

sage: # Construct some symbolic expression in Sage
sage: var('a b c d')
(a, b, c, d)

sage: A = matrix([[a,b],[c,d]])

sage: A

[a b]
[c d]

sage: x=det(A)

sage: x
a*d - b*c

sage: x.parent()
Symbolic Ring

sage: x?
Type:   SymbolicArithmetic
Base Class: 
String Form:

   a d - b c
Namespace:  Interactive
Docstring:

Represents the result of an arithmetic operation on
f and g.

sage: # Convert it to an object in Axiom
sage: y=axiom(x)

sage: y
a*d+(-b*c)

sage: y.type()
Polynomial Integer

sage: y?
Type:   AxiomElement
Base Class: 
String Form:a*d+(-b*c)
Namespace:  Interactive
Docstring:
a*d+(-b*c)

> ...
>  So: What should you do:
>
>  a) wait a week or two for ecls and gdbm to become optional
>  b) build an optional FriCAS/OpenAxiom spkg using ecls
>  c) write a pexpect interface to use integration/ODE/guess if that
>  is something where you see FriCAS/OpenAxiom as "better
>  than anything else".
>
>  In parallel take a look at
>
>  http://wiki.sagemath.org/spkg/InclusionProcedure
>
>  and write some proposal *why* FriCAS/OpenAxiom should become
>  part of standard Sage and *what* it should/can [via pexpect] do.
>  ...

Martin I would be interested in working with you on doing this (and
anyone else who would like to join in), that is provided you are
willing to take the lead. :-)

>  Then eventually it will come down to the vote and if for example
>  FriCAS beats Maxima and the 4Ms at integration I would consider
>  it very like that it could make it in. FriCAS full [without gcl] weighs
>  in at 9MB, so if you can strip out unneeded parts for an initial bare
>  bone distribution it would be great.
>

Do you mean, for example eliminating the hyperdoc browser and Axiom
graphics? I think that trying to eliminate mathematical functionality
is not likely to save much in a "bare bones" distribution.

Regards,
Bill Page.

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[sage-devel] rpy build script fails for sage-3.0

[strogdon]

On my Gentoo box I unpacked the subject tarball, changed to the sage
directory and did a make with the results:

gcc version 4.1.2 (Gentoo 4.1.2 p1.0.2)


RHOMES= []
DEBUG= True
Setting RHOMES to  ['/usr/lib64/R']
RHOMES= []
DEBUG= True
Setting RHOMES to  ['/usr/lib64/R']
Traceback (most recent call last):
Traceback (most recent call last):
  File "setup.py", line 106, in 
  File "setup.py", line 106, in 
RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
  File "/local/sage-3.0/spkg/build/rpy-1.0.1.p1/src/rpy_tools.py",
line 99, in get_R_VERSION
  File "/local/sage-3.0/spkg/build/rpy-1.0.1.p1/src/rpy_tools.py",
line 99, in get_R_VERSION
" `%s'.\n" % rexec )
" `%s'.\n" % rexec )
RuntimeErrorRuntimeError: : Couldn't execute the R interpreter `/usr/
lib64/R/bin/R'.
Couldn't execute the R interpreter `/usr/lib64/R/bin/R'.


Error building RPY -- Python interface to R.
Error building RPY -- Python interface to R.

I tried several corrective measures and the only one that allowed sage
to build was to issue:

RHOMES="`pwd`/local/lib/R" make

However, the following test failed:

sage -t  devel/sage/sage/stats/test.py

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[sage-devel] Sage 3.0.1 Merge Cycle Opened - Game Plane

[mabshoff]

Hello folks,

since 3.0 is out the inevitable happens: 3.0.1 is next release. We
would like to do a mostly bug fix release, but that somehow depends on
how buggy 3.0 is. So far the issues with the notebook seems to be only
big issues reported so far.

I did talk to Robert in IRC earlier today and he stated that the
coercion system rewrite is another week or two away. So my plan is to
merge is possible only fixed that do not disturb the code base in that
area too much. Having said that: There are about 40 tickets with
patches in trac, so reviews are appreciated.

One  of the features that didn't make it into 3.0 are the FreeBSD and
OSX 10.5 64 bit build support. Since that does have little to no
impact on the coercion rewrite I will mostly work in that area and
hopefully get at least one of the above into good enough shape so
people not me can build it.

Another issues I am currently looking into are memory leaks in three
areas:

 * PolyBoRi
 * latin squares [Carlo contacted me already about those]
 * _fast_eval [I mentioned these to Robert already]

I am valgrinding 3.0.final on sage.math now and will have results once
I wake up ;)

Thoughts?

Cheers,

Michael


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[sage-devel] Sage 3.0 released

[mabshoff]

[Note: If you are interested in announcements only please subscribe to
sage-announce. It is limited to roughly one email every ten days.]

Hello folks,

Sage 3.0 has been released on April 21st, 2008. It is available at

   http://sagemath.org/download.html

* About Sage (http://www.sagemath.org)

Sage is developed by volunteers and combines 71 open source packages.
It is available for download from sagemath.org and its mirrors in
source or binary form. If you have any questions and/or problems
please report them to the google groups sage-devel or sage-support.
You can also drop by in #sage-devel or #sage-support in freenode.

-

The following 48 people contributed to this release:

 * Tim Abbott
 * Michael Abshoff
 * Martin Albrecht
 * Nick Alexander
 * Tom Boothby
 * Robert Bradshaw
 * Jason Brandlow
 * Michael Brickenstein
 * Dan Bump
 * Craig Citro
 * Ondrej Certik
 * Timothy Clemans
 * John Cremona
 * Didier Deshommes
 * Nathan Dunfield
 * Dan Drake
 * Alexander Dreyer
 * Burin Erocal
 * Gary Furnish
 * Alex Ghitza
 * Andrzej Giniewicz
 * Jason Grout
 * Marshall Hampton
 * Mike Hansen
 * David Harvey
 * Geert Heldager Nielsen
 * David Joyner
 * Michael Kallweit
 * Josh Kantor
 * Simon King
 * Emily Kirkman
 * Robert Miller
 * Minh Nguyen
 * Willem Jan Palenstijn
 * Clement Pernet
 * Steffan Reidt
 * David Roe
 * Ryan Hinton
 * Anne Schilling
 * Harald Schilly
 * William Stein
 * Chris Swierczewski
 * Nicolas Thiery
 * Gonzalo Tornaria
 * John Voight
 * Yi Qiang
 * Justin Walker
 * Carl Witty

Cheers,

Binaries are available on the mirrors!

Michael Abshoff (release chair), William Stein

* Major Features, New Spkgs and Bugfixes

 * Random Numbers
 * GCC 4.3 Support
 * New Default Binaries
 * Boolean Polynomials
 * Modular Abelian Varieties
 * Increased Doctest Coverage
 * R Pexpect Interface
 * Crystals
 * Laurent Polynomials

For details see the Sage 3.0 Release Tour at

  http://wiki.sagemath.org/sage-3.0

* Known Issues with 3.0:

 #2983: Singular interface problems in matrix_group.py on
Itanium/Linux: We see a segfault in the doctest and
will hopefully fix this in 3.0.1.
 #2985: rubik.py's OptimalSolver() problem on Itanium/Linux:
the doctest also segfaults with the "-long" option.
This will hopefully be fixed in 3.0.1.

* Bug Statistics

We closed a record number of 277 tickets. For details see

   http://trac.sagemath.org/sage_trac/milestone/sage-3.0

or check out the closed ticket section at the end of the
announcement.

* Upcoming Releases

The next release will be 3.0.1, chaired by Michael Abshoff.
The release is planned in about a week. It will be mostly a
bug fix release to clear up issues from the 3.0 release.

* Doctesting Coverage

For 2.11 we had:

Overall weighted coverage score:  48.9%
Total number of functions:  18853

We increased coverage by 2.6% in 3.0 while adding 661 functions:

Overall weighted coverage score:  51.5%
Total number of functions:  19514

* Closed Tickets:

Merged in final:

#2979: Michael Abshoff, Andrzej Giniewicz: force "-O0" for
   clisp with gcc 4.3
#2987: Tim Abbott: Debian build support for zn_poly
#2988: William Stein: notebook -- issues with the CSS for the
   print display
#2989: William Stein: notebook -- issue with how the notebook
   is run that breaks it sometimes; also fix a typo in pid.
#2990: William Stein: sage-3.0.rc1: calculus/functions.py
   segfault on debian64 xeon vmware image
#2991: William Stein: fix dsage testdoc problem
#2994: Michael Abshoff: polybori.spkg - fix permission issue
   of the headers

Merged in rc1:

#2419: William Stein, Simon King: Gap interface and resultant
   destroy the Singular interface on some machines
#2553: Yi Qiang, William Stein: dsage unit tests fail on linux
#2928: Willem Jan Palenstijn: another p-adic extension segfault
#2934: William Stein: doctesting files outside of sage repo is
   completely broken
#2972: William Stein: libSingular related segfault in
   laurent_polynomial_ring.py
#2973: Michael Abshoff: RDF doctest failures on arch linux
#2974: Mike Hansen: interfaces/r.py doctest failures on many
   linux machines
#2975: William Stein: opening ports too conservative -- breaks
   on some os x systems
#2977: Alex Ghitza: wronskian is broken on constants
#2984: William Stein, Michael Abshoff: ITANIUM (RHEL 5) -- turn
   off all unaligned access messages
#2986: Gonzalo Tornaria: Add atlas pretuning for Pentium D/64
   bits (ARCH=P4D64SSE3)

Merged in rc0:

#34: Craig Citro: Factoring for a subspace of ModularSymbols
 in general
#839: Harald Schilly, Mike Hansen, William Stein: R pexpect
  interface
#1642: William Stein: search for common Fortran compiles if
   no binary is present
#2344: Michael Abshoff: python -- upgrade to version 2.5.2
#2955: Michael Abshoff: GFortran autodection on Linux/Itanium
#2958: William Stein: twist.py -- doctest

[sage-devel] Re: FriCAS/Open-Axiom and SAGE

[Michael.Abshoff]

[this email will likely bounce somewhere, so if it doesn't show up in 
some place please forward]

Martin Rubey wrote:
> Dear Michael,

Hi Martin,

> just a short recap, whether I have understood things correctly:
> 
>the problem you currently face with external symbolic calculus is that the
>representation of the objects is not identical in SAGE and in the external
>progam (Maxima).
> 
>you are using something called "pexpect" which does the parsing.

pexpect is a mechanism to talk to other executables via a pseudo tty 
interface. It also does parsing.

> I do not see how the problem of differing representations can be resolved.  Up
> to now I thought that Sage simply doesn't have an "internal" representation,
> and just uses the one from the external program - that's how my polymake
> interface for FriCAS/Axiom works.

I am not 100% clear, but I believe for elements in a symbolic ring we do 
not yet have a Sage internal representation. It is being written in 
Cython since arithmetic is probably slowed down by a factor of 10,000 by 
  using pexpect+Maxima. That is largely the fault of pexpect.

For other code like Singular or pari we can either use the library 
interface or pexpect, depending if the operation is available in the 
library or nor. So if you are multiplying two polynomials over Q[x,y] 
with libSingular we use Singular's computational engine directly.

> If this is correct and if Sage insists on having an internal representation,
> then it probably only makes sense to have external programs for "large" jobs,
> where the time spent in parsing is not an issue.  Either, because the result 
> is
> not processed much further anyway, or because obtaining the result is much 
> more
> costly than the parsing.

Yes, that is the exact strategy that make sense. I gave the example with 
  arithmetic for GAP, but any high level algorithm with little input, 
little output and huge computational time is well suited for a pexpect 
interface.

> Thus, the obvious candidates for using FriCAS are integration (it beats the
> commercial CAS in the elementary case, by the way) and related stuff like
> solving ODE's, and guessing (ditto).

Interesting, I didn't know that ;)

> Please correct me, if I'm wrong.

So far you got it all right.

> ---
> 
> Apart from that, I would like to clarify a point, that might become a
> misunderstanding otherwise:
> 
> FriCAS (as far as I can control it) has a pragmatic approach what concerns the
> "target language" of it's compiler and the language it's interpreter is 
> written
> in.  Currently, it's lisp, because that works, works well, seems to be
> reasonably fast and works on many platforms, including MS Windows.  FriCAS
> builds on quite a few lisps, sbcl seems to be fastest.

Yes, that is what I have gathered so far. Gaby pointed out that sbcl 
does tend to fail on occasion on Windows since it needs contiguous 
memory and if some DLL is mapped into the wrong area its memory 
allocation will fail. We have been bitten by Sage+Cygwin by similar 
problems since the total memory available to Cygwin is limited to 
roughly 1.3GB  and since we build a massive amount of extension 
libraries [180 extension from Sage + others] you do have library address 
space collisions. You can work around that via a rebase tool for DLLs, 
but it is certainly a peculiar aspect of Windows.

> HOWEVER: FriCAS has (almost) no mathematics written in lisp, not even for
> bootstrapping.  We use bignums, arrays, floats, strings, symbols from lisp, 
> but
> that's about it.
> 
> The goals of FriCAS and open-axiom are quite similar, as far as I can tell.  I
> truly hope that the collaboration of the two will continue.

Yes. I was surprised "back then" when the Axiom for happened that it was 
followed by a second one. But this is certainly neither the time nor the 
place to get into this. My usual limit is one flame war per week ;)

> ---
> 
> Finally, concerning lisp: is it correct that Sage would not mind (for the
> moment) a default lisp, that builds the Sage way, but would use a "better
> suited" lisp, if available and installed on the target machine?  (in fact,
> that's how FriCAS and, as far as I know, open-axiom work currently, anyway.)

I had some off-list exchange with Robert Dodier and he will try to look 
into building Maxima on top of ecl [it was renamed from ecls and I 
didn't notice :)] - Michael Goffioul did some work in that direction in 
2005 and Robert will see how close that work and his own from roughly 
January 2008 will get him to a working Maxima. He also stated that he 
will likely spend more time on this during this weekend.

I just checked into some more details of ecl and Juan Jose Garcia-Ripoll 
   just posted the following to the ecls mailing list:

 > I have uploaded a copy of the talk I gave two days ago at the

[sage-devel] FriCAS/Open-Axiom and SAGE

[Martin Rubey]

Dear Michael,

just a short recap, whether I have understood things correctly:

   the problem you currently face with external symbolic calculus is that the
   representation of the objects is not identical in SAGE and in the external
   progam (Maxima).

   you are using something called "pexpect" which does the parsing.

I do not see how the problem of differing representations can be resolved.  Up
to now I thought that Sage simply doesn't have an "internal" representation,
and just uses the one from the external program - that's how my polymake
interface for FriCAS/Axiom works.

If this is correct and if Sage insists on having an internal representation,
then it probably only makes sense to have external programs for "large" jobs,
where the time spent in parsing is not an issue.  Either, because the result is
not processed much further anyway, or because obtaining the result is much more
costly than the parsing.

Thus, the obvious candidates for using FriCAS are integration (it beats the
commercial CAS in the elementary case, by the way) and related stuff like
solving ODE's, and guessing (ditto).

Please correct me, if I'm wrong.

---

Apart from that, I would like to clarify a point, that might become a
misunderstanding otherwise:

FriCAS (as far as I can control it) has a pragmatic approach what concerns the
"target language" of it's compiler and the language it's interpreter is written
in.  Currently, it's lisp, because that works, works well, seems to be
reasonably fast and works on many platforms, including MS Windows.  FriCAS
builds on quite a few lisps, sbcl seems to be fastest.

HOWEVER: FriCAS has (almost) no mathematics written in lisp, not even for
bootstrapping.  We use bignums, arrays, floats, strings, symbols from lisp, but
that's about it.

The goals of FriCAS and open-axiom are quite similar, as far as I can tell.  I
truly hope that the collaboration of the two will continue.

---

Finally, concerning lisp: is it correct that Sage would not mind (for the
moment) a default lisp, that builds the Sage way, but would use a "better
suited" lisp, if available and installed on the target machine?  (in fact,
that's how FriCAS and, as far as I know, open-axiom work currently, anyway.)

Martin


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