Re: [sage-combinat-devel] cristallographic takes two l

2013-06-01 Thread Frédéric Chapoton
Yes indeed, and that is what I have done in the patch. Sorry for the 
mistake here.

Le vendredi 31 mai 2013 22:44:37 UTC+2, Anne Schilling a écrit :

 Hi Frederic, 

 If you want the English spelling, I think it is crystallographic. 

 Best, 

 Anne 

 On 5/31/13 12:41 PM, Fr�d�ric Chapoton wrote: 
  And it is spelled in sage/combinat with just one ! 
  
  I have made a (little bomb) patch at 
 http://trac.sagemath.org/sage_trac/ticket/14673 
  
  turning everything to cristallographic 
  
  I think this is necessary, but I am afraid it may cause a lot of trouble 
 in the combinat queue 
  
  Opinions ? 
  
  Frederic 
  


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[sage-devel] Re: recompilation with sage -clone

2013-06-01 Thread leif

John H Palmieri wrote:

On Thursday, May 30, 2013 9:57:07 PM UTC-7, leif wrote:

leif wrote:
  Looks like reinstalling the Sage library spkg would meanwhile also
  trigger the rebuild of *all* extension modules; not sure since when
  though...  (seen with Sage 5.10.beta5 at least)

Yep.  This is because #14570, merged into Sage 5.10.beta4, completely
breaks sage-sync-build, which is also used in the Sage library's
spkg-install.  (sage -sync-build now removes all Cython-generated
files,
hence *all* have to get rebuilt afterwards.)


IMHO both issues (complete rebuild upon cloning and after
sage-sync-build) should be resolved before the final 5.10 gets out.


The rebuild is dealt with at #13245 (needs partial review).


I'll revisit #13245 now that you've changed the ticket's title... ;-)

[Avoiding also the rebuild of the fast_callable interpreters should be 
feasable by just copying a few more files in sage-clone (I /think/ I 
already did that), but I agree that's a minor issue, at least compared 
to rebuilding the whole Sage library.]




Is there a ticket for the sage-sync-build problem?


Not yet.  There are a couple of ways to (quickly or temporarily) fix this:

1) Unmerge #14570, which doesn't fix a bug, but only introduces a new 
(btw. non-configurable) feature.  [A bit odd, especially since #14570 
also patches the Cython spkg.]


2) Revert just #14570's change to setup.py, a one-liner (removing the 
build_dir parameter to cythonize()).  [Better than 1), although 
effectively the same -- feature vanishes until we reenable it on some 
follow-up ticket.]


3) Make the behaviour configurable (defaulting to the previous; little 
change to setup.py).  No breakage to ordinary users; people using the 
new feature are expected to know what they're doing, i.e., at least 
sage-sync-build [still] won't work for them.  [IMHO preferable for a 
temporary / quick fix; easy and safe.]


4) Minimally adapt sage-sync-build.py to reflect the (hard-coded) change 
by #14570.  [May be easy as well, but potentially unsafe.]



I'd personally prefer 2) or 3) for now, postponing a proper solution 
to a follow-up ticket which presumably won't make it into 5.10 (but 
hopefully 5.11.*), as sage-sync-build needs some rework* anyway, the 
Cython build directory (kind of VPATH) should IMHO be configurable, and 
#14570 might cause further issues we haven't noticed yet.



-leif

__
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[sage-devel] Re: recompilation with sage -clone

2013-06-01 Thread leif

leif wrote:

John H Palmieri wrote:

Is there a ticket for the sage-sync-build problem?


Not yet.  There are a couple of ways to (quickly or temporarily) fix
this:

1) Unmerge #14570, which doesn't fix a bug, but only introduces a new
(btw. non-configurable) feature.  [A bit odd, especially since #14570
also patches the Cython spkg.]

2) Revert just #14570's change to setup.py, a one-liner (removing the
build_dir parameter to cythonize()).  [Better than 1), although
effectively the same -- feature vanishes until we reenable it on some
follow-up ticket.]


diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -532,7 +532,7 @@
 ext_modules = cythonize(
 ext_modules,
 nthreads = int(os.environ.get('SAGE_NUM_THREADS', 0)),
-build_dir = 'build/cythonized',
+# build_dir = 'build/cythonized',
 force=force)

 open(version_file, 'w').write(Cython.__version__)


works for me (with Sage 5.10.rc0).



3) Make the behaviour configurable (defaulting to the previous; little
change to setup.py).  No breakage to ordinary users; people using the
new feature are expected to know what they're doing, i.e., at least
sage-sync-build [still] won't work for them.  [IMHO preferable for a
temporary / quick fix; easy and safe.]


Similar to the above change, but with (say)

diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -532,7 +532,7 @@
 ext_modules = cythonize(
 ext_modules,
 nthreads = int(os.environ.get('SAGE_NUM_THREADS', 0)),
-build_dir = 'build/cythonized',
+build_dir = 'build/cythonized' if 
os.environ.get(BREAK_SAGE_SYNC_BUILD, no)==yes else None,

 force=force)

 open(version_file, 'w').write(Cython.__version__)


which *optionally* enables building extension modules out of tree 
(they're in fact in the same tree, but one level deeper, still 
hard-coded location) at the expense of breaking (at least) 
sage-sync-build.  (Works for me, too.)



-leif


4) Minimally adapt sage-sync-build.py to reflect the (hard-coded) change
by #14570.  [May be easy as well, but potentially unsafe.]


I'd personally prefer 2) or 3) for now, postponing a proper solution
to a follow-up ticket which presumably won't make it into 5.10 (but
hopefully 5.11.*), as sage-sync-build needs some rework* anyway, the
Cython build directory (kind of VPATH) should IMHO be configurable, and
#14570 might cause further issues we haven't noticed yet.


-leif

__
* the usual can of worms



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[sage-devel] Re: 3 GSoC projects for Sage

2013-06-01 Thread mmarco
I know that this is not exactly about the windows port situation, but
still, it is closely related to the sage-on-windows issue:

On the project ideas suggestions that were proposed by sage, there was
one dedicated to writing a GUI to handle the sage installation in
windows. No student decided to propose such a project.

On the other hand, there are people working on a cygwin port. I
haven't tested it, but they claim to have obtained something usable.
So it is not true at all that the windows port has been abandoned.
What it is true, on the other hand, is that the prefered way to run
sage on windows is through the virtualbox appliance. This is maybe a
suboptimal solution, but it's a solution that works. So the statement
that we are ignoring the windows is far from being true.

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[sage-devel] Re: 3 GSoC projects for Sage

2013-06-01 Thread rjf


On Friday, May 31, 2013 3:21:06 AM UTC-7, Volker Braun wrote:

 On Friday, May 31, 2013 7:39:02 AM UTC+1, rjf wrote:

 Interesting perspective. Where did you get the $10k/year difference?



 http://www.indeed.com/salary?q1=Unix+System+Administratorq2=windows+System+Administrator
  

 This is an interesting resource.  Here's some more data from the same 
source.

Unix Systems Administrator$88,000.
Windows Systems Administrator $77,000. 
Lisp Programmer   $95,000.
Python Programmer $89,000

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[sage-devel] Re: 3 GSoC projects for Sage

2013-06-01 Thread rjf


On Friday, May 31, 2013 5:25:39 AM UTC-7, kcrisman wrote:


I think the mentor thing is a red herring, though; the number of 
 projects proposed on Windows probably would roughly match the number of 
 mentors (at least by proportion), because you wouldn't likely get 
 interested in Sage development in the first place unless you were on Linux 
 or Mac.


My assumption was that the number of mentors willing and capable of 
supervising a Windows port
was, most likely, zero.  It's the kind of expertise that is  probably not 
so common among mathematicians.
So I agree that the number might match, proportionally. 

My point was that Google goals were consistent with a possible 
(student-proposed)
project of porting Sage to native Windows framework.  

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[sage-devel] Re: 3 GSoC projects for Sage

2013-06-01 Thread rjf


On Saturday, June 1, 2013 6:16:59 AM UTC-7, mmarco wrote:



 On the other hand, there are people working on a cygwin port. I 
 haven't tested it, ... Why is it suboptimal?  (one guess: you can't

have a one-click windows installer?) 

I thought this had been done some time ago -- a cygwn solution.
It also seemed to me that there was an undercurrent of activity
to get a native windows version.  I'm not sure why this was viewed
as valuable -- certainly there are some neat things on Windows
that are not on Linux, but just as certainly Sage can't depend on
them... people would be upset if Sage on
windows had better features and could not be back-ported to Linux.

Anyway,  maybe we will all meet in the cloud.

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[sage-devel] Re: 3 GSoC projects for Sage

2013-06-01 Thread leif

rjf wrote:

On Friday, May 31, 2013 3:21:06 AM UTC-7, Volker Braun wrote:

On Friday, May 31, 2013 7:39:02 AM UTC+1, rjf wrote:

Interesting perspective. Where did you get the $10k/year difference?



http://www.indeed.com/salary?q1=Unix+System+Administratorq2=windows+System+Administrator

http://www.indeed.com/salary?q1=Unix+System+Administratorq2=windows+System+Administrator

This is an interesting resource.  Here's some more data from the same
source.

Unix Systems Administrator$88,000.
Windows Systems Administrator $77,000.
Lisp Programmer   $95,000.
Python Programmer $89,000


Demanding William's Lisp port of Sage even more.

(Although I have to admit I haven't checked whether there are figures 
for Cython programmers as well.)



-leif

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[sage-devel] Re: 3 GSoC projects for Sage

2013-06-01 Thread Harald Schilly


On Saturday, June 1, 2013 4:51:39 PM UTC+2, rjf wrote:

 Lisp Programmer   $95,000.


I raise you the VAX Mainframe: $100,000

http://www.indeed.com/salary?q1=vax+mainframe 

Welcome to the cloud!

Could we stop this pointless discussion please? 

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[sage-devel] LELA for matrices?

2013-06-01 Thread Volker Braun
I would like to have some discussion about the roadmap for matrices in 
Sage. It seems that linbox has essentially been forked by LELA 
(http://www.singular.uni-kl.de/lela). Since it optionally contains M4RI, 
one would think that it is a good fit for Sage, too. Has anybody given any 
thoughts to switching Sage from linbox to LELA? In particular, Burcin and 
Martin should have an opinion and it would be nice to hear from them ;-)

On a related note, sparse matrices in Sage suck (dictionary of keys). 
Sparse matrices in LELA only suck slightly less (list of lists). For fast 
computation one should implement compressed sparse row/column, I think.

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[sage-devel] Re: 3 GSoC projects for Sage

2013-06-01 Thread leif

rjf wrote:

On Friday, May 31, 2013 5:25:39 AM UTC-7, kcrisman wrote:


I think the mentor thing is a red herring, though; the number of
projects proposed on Windows probably would roughly match the number
of mentors (at least by proportion), because you wouldn't likely get
interested in Sage development in the first place unless you were on
Linux or Mac.


My assumption was that the number of mentors willing and capable of
supervising a Windows port
was, most likely, zero.  It's the kind of expertise that is  probably
not so common among mathematicians.
So I agree that the number might match, proportionally.

My point was that Google goals were consistent with a possible
(student-proposed)
project of porting Sage to native Windows framework.


Modulo the time frame.


-leif

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Re: [sage-devel] LELA for matrices?

2013-06-01 Thread Martin Albrecht
Hi,

as far as I know LELA does not support the same operations as LinBox, it's not 
a straight-forward fork but a re-implementation of a subset (that's my 
understanding, anyway). it has some advantages, i.e., that some bits nicely 
generic, i.e., it should be fairly easy to add new matrix types by adding 
stuff like matrix-matrix multiplication and e.g. PLE decomposition is handled 
generically.

Also, the main developer of LELA Bradford has left academia. He usually 
responds fairly quickly to e-mail and is up for helping out, but as far as I 
know nobody is actively developing LELA at the moment (I might be terribly 
wrong here!)

On Saturday 01 Jun 2013, Volker Braun wrote:
 I would like to have some discussion about the roadmap for matrices in
 Sage. It seems that linbox has essentially been forked by LELA
 (http://www.singular.uni-kl.de/lela). Since it optionally contains M4RI,
 one would think that it is a good fit for Sage, too. Has anybody given any
 thoughts to switching Sage from linbox to LELA? In particular, Burcin and
 Martin should have an opinion and it would be nice to hear from them ;-)
 
 On a related note, sparse matrices in Sage suck (dictionary of keys).
 Sparse matrices in LELA only suck slightly less (list of lists). For fast
 computation one should implement compressed sparse row/column, I think.

Cheers,
Martin

--
name: Martin Albrecht
_pgp: http://pgp.mit.edu:11371/pks/lookup?op=getsearch=0x6532AFB4
_otr: 47F43D1A 5D68C36F 468BAEBA 640E8856 D7951CCF
_www: http://martinralbrecht.wordpress.com/
_jab: martinralbre...@jabber.ccc.de


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Re: [sage-devel] LELA for matrices?

2013-06-01 Thread Charles Bouillaguet
My understanding is that only a very small subset of linbox is wired into Sage. 
In particular, all the iterative methods for the [rank/minpoly/charpoly/det] of 
sparse matrices are not accessible yet, but they are Linbox's strong point. 
Currently, sparse matrices are converted to dense ones, and very generic cython 
code is then used.

Recent versions of linbox have some support for (read-only) compressed row 
matrices.

---
Charles Bouillaguet
http://www.lifl.fr/~bouillaguet/



On Jun 1, 2013, at 6:48 PM, Martin Albrecht wrote:

 Hi,
 
 as far as I know LELA does not support the same operations as LinBox, it's 
 not 
 a straight-forward fork but a re-implementation of a subset (that's my 
 understanding, anyway). it has some advantages, i.e., that some bits nicely 
 generic, i.e., it should be fairly easy to add new matrix types by adding 
 stuff like matrix-matrix multiplication and e.g. PLE decomposition is handled 
 generically.
 
 Also, the main developer of LELA Bradford has left academia. He usually 
 responds fairly quickly to e-mail and is up for helping out, but as far as I 
 know nobody is actively developing LELA at the moment (I might be terribly 
 wrong here!)
 
 On Saturday 01 Jun 2013, Volker Braun wrote:
 I would like to have some discussion about the roadmap for matrices in
 Sage. It seems that linbox has essentially been forked by LELA
 (http://www.singular.uni-kl.de/lela). Since it optionally contains M4RI,
 one would think that it is a good fit for Sage, too. Has anybody given any
 thoughts to switching Sage from linbox to LELA? In particular, Burcin and
 Martin should have an opinion and it would be nice to hear from them ;-)
 
 On a related note, sparse matrices in Sage suck (dictionary of keys).
 Sparse matrices in LELA only suck slightly less (list of lists). For fast
 computation one should implement compressed sparse row/column, I think.
 
 Cheers,
 Martin
 
 --
 name: Martin Albrecht
 _pgp: http://pgp.mit.edu:11371/pks/lookup?op=getsearch=0x6532AFB4
 _otr: 47F43D1A 5D68C36F 468BAEBA 640E8856 D7951CCF
 _www: http://martinralbrecht.wordpress.com/
 _jab: martinralbre...@jabber.ccc.de

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[sage-devel] Re: recompilation with sage -clone and after sage -sync-build

2013-06-01 Thread leif

leif wrote:

leif wrote:

John H Palmieri wrote:

Is there a ticket for the sage-sync-build problem?


Not yet.  There are a couple of ways to (quickly or temporarily) fix
this:

1) Unmerge #14570, which doesn't fix a bug, but only introduces a new
(btw. non-configurable) feature.  [A bit odd, especially since #14570
also patches the Cython spkg.]

2) Revert just #14570's change to setup.py, a one-liner (removing the
build_dir parameter to cythonize()).  [Better than 1), although
effectively the same -- feature vanishes until we reenable it on some
follow-up ticket.]


diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -532,7 +532,7 @@
  ext_modules = cythonize(
  ext_modules,
  nthreads = int(os.environ.get('SAGE_NUM_THREADS', 0)),
-build_dir = 'build/cythonized',
+# build_dir = 'build/cythonized',
  force=force)

  open(version_file, 'w').write(Cython.__version__)


works for me (with Sage 5.10.rc0).



3) Make the behaviour configurable (defaulting to the previous; little
change to setup.py).  No breakage to ordinary users; people using the
new feature are expected to know what they're doing, i.e., at least
sage-sync-build [still] won't work for them.  [IMHO preferable for a
temporary / quick fix; easy and safe.]


Similar to the above change, but with (say)

diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -532,7 +532,7 @@
  ext_modules = cythonize(
  ext_modules,
  nthreads = int(os.environ.get('SAGE_NUM_THREADS', 0)),
-build_dir = 'build/cythonized',
+build_dir = 'build/cythonized' if
os.environ.get(BREAK_SAGE_SYNC_BUILD, no)==yes else None,
  force=force)

  open(version_file, 'w').write(Cython.__version__)


which *optionally* enables building extension modules out of tree
(they're in fact in the same tree, but one level deeper, still
hard-coded location) at the expense of breaking (at least)
sage-sync-build.  (Works for me, too.)


-leif


4) Minimally adapt sage-sync-build.py to reflect the (hard-coded) change
by #14570.  [May be easy as well, but potentially unsafe.]


Even that turns out to be non-trivial, AFAICS, i.e., the whole strategy 
would have to get changed, as opposed to just some file / directory 
names in a few places.



-leif


I'd personally prefer 2) or 3) for now, postponing a proper solution
to a follow-up ticket which presumably won't make it into 5.10 (but
hopefully 5.11.*), as sage-sync-build needs some rework* anyway, the
Cython build directory (kind of VPATH) should IMHO be configurable, and
#14570 might cause further issues we haven't noticed yet.


-leif

__
* the usual can of worms


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[sage-devel] Re: GSoC New decoding error-correcting codes algorithm for Sage

2013-06-01 Thread mmarco
Welcome on board, Veronica.

Please keep us up to date to your progress. I am your mentor, but i am
sure the rest of the sage community would like to have you involved.

Just a little clarification: Veronica has been selected under the
umbrella of lmonade, even thoigh her work will be focused on sage.

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[sage-devel] Re: 3 GSoC projects for Sage

2013-06-01 Thread mmarco

I  haven't tested it, ... Why is it suboptimal?

I used the word suboptimal to reffer to the virtualbox based
solution, not to the cygwin one.

If by native you mean without cygwin... i am afraid that that we
would be very far away from that. Not only from the sage side (at the
end of the day, most of the code writen by sage devs is portable
python/cython), but from the thirthd party pieces: Singular is not
natively ported to windows (runs under cygwin), GAP for windows uses
cygwin too, Pari/gp also runs under cygwin (and has limitations
compared to the linux version)...

So the native windows port of sage is really unlikely to happen in the
mid term. Considering that, Sage releases official versions that work
under windows (via virtualbox), and also a cygwin port is being worked
on (although it is true that, with the virtual machine available, this
has become a secondary effort).

And since you mention the one-click installer... that was pretty much
what the GUI project that we suggested was about. As i said, no
student showed interest in working on that. As i said, the statement
that the sage project is turning its back on windows system is far
from being true.

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Re: [sage-devel] Re: 3 GSoC projects for Sage

2013-06-01 Thread Eviatar
On Thursday, 30 May 2013 12:21:25 UTC-7, rjf wrote:

 I repeat. Generating random arguments is not sensible.  (Incidentally,
 you will still need to be able to generate the correct answers for these
 functions. This seems to have been overlooked.
  What do you do if your benchmark test shows slightly
 different answers from the systems?) 
  My point is that this is poorly formulated as a question, and the 
 proposed answer is also
 poorly thought out.


Hello,

Do you have any suggestions on how to benchmark the different backends 
other than pick random arguments from specified domains? I'm open to any 
suggestions. In any case, the benchmark framework is going to be a 
relatively minor part of the project.

Eviatar

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Re: [sage-devel] Re: 3 GSoC projects for Sage

2013-06-01 Thread William Stein
On Sat, Jun 1, 2013 at 3:47 PM, mmarco mma...@unizar.es wrote:

I  haven't tested it, ... Why is it suboptimal?

 I used the word suboptimal to reffer to the virtualbox based
 solution, not to the cygwin one.

 If by native you mean without cygwin... i am afraid that that we
 would be very far away from that. Not only from the sage side (at the
 end of the day, most of the code writen by sage devs is portable
 python/cython), but from the thirthd party pieces: Singular is not
 natively ported to windows (runs under cygwin), GAP for windows uses
 cygwin too, Pari/gp also runs under cygwin (and has limitations
 compared to the linux version)...

 So the native windows port of sage is really unlikely to happen in the
 mid term. Considering that, Sage releases official versions that work
 under windows (via virtualbox), and also a cygwin port is being worked
 on (although it is true that, with the virtual machine available, this
 has become a secondary effort).

 And since you mention the one-click installer... that was pretty much
 what the GUI project that we suggested was about. As i said, no
 student showed interest in working on that. As i said, the statement
 that the sage project is turning its back on windows system is far
 from being true.

One tidbit to add to this discussion (which has gone on way too long),
is that in my experience often compute intensive functions in Sage are
faster on Windows when run on a VM than when run under Cygwin or
natively.   There are many reasons for this, including LInux's
excellent memory management, special optimizations people writing code
make for the Linux version of some code, but don't make anywhere else,
etc.

 -- William


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

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