[sage-combinat-devel] GradedAlgebrasWithBasis

2011-12-21 Thread Martin Rubey
Hi gurus!

I just hadto implement a GradedAlgebrasWithBasis, the basis being
StandardTableaux() and the degree given by the size of the tableau (and
a peculiar multiplication).

Now, everything works fine except that the output of the elements is not
sorted by degree.

How could I accomplish that?  Or did I possibly make a mistake?

(my mouse is defunct, so I cannot easily copy paste.  If necessary, I
would, of course!)

Thanks,

Martin

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Re: [sage-combinat-devel] GradedAlgebrasWithBasis

2011-12-21 Thread Martin Rubey
Martin Rubey martin.ru...@math.uni-hannover.de writes:

 Hi gurus!

 I just hadto implement a GradedAlgebrasWithBasis, the basis being
 StandardTableaux() and the degree given by the size of the tableau (and
 a peculiar multiplication).

and another, more important, question: what I actually want to do is to
compute t - t^2 + t^3 - + ... for a certain element t.

Even computing t^3 takes far too long.  Fortunately, I am only
interested in low degree terms of the ressult.  Is there an easy trick
to compute only those?  (the real thing would be a lazy formal power
series ring, I suppose)

Many thanks,

Martin

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Re: [sage-combinat-devel] GradedAlgebrasWithBasis

2011-12-21 Thread Martin Rubey
Martin Rubey martin.ru...@math.uni-hannover.de writes:

 Martin Rubey martin.ru...@math.uni-hannover.de writes:

 Hi gurus!

 I just hadto implement a GradedAlgebrasWithBasis, the basis being
 StandardTableaux() and the degree given by the size of the tableau (and
 a peculiar multiplication).

 and another, more important, question: what I actually want to do is to
 compute t - t^2 + t^3 - + ... for a certain element t.

Please excuse me for answering my own question... LazyPowerSeriesRing
does both!

Thank you,

Martin

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[sage-devel] Re: genus() for Function Fields

2011-12-21 Thread syd.lavas...@gmail.com
Hi Maarten,

I see this in Florian Hess's codes

###
# Genus

GffDifferentDeg := function(K)
   local of, oi, df, di;
   of := GffOrderMaxFinite(K);
   oi := GffOrderMaxInfty(K);
   df := GffOrderDisc(of);
   di := GffOrderDisc(oi);

   return (PolyDeg(df) + InftyVal(di))/GffDimExactConstField(K);
end;


#GffGenus := function(K)
#   local d, dim, n;
#
#   n := GffDeg(K);
#   dim := 1;
#   d := GffDifferentDeg(K);
#
#   return d/2 - n/dim + 1;
#end;

Which basically uses Riemann-Hurwitz to compute the Genus. But I don't
think it's the fastest way to do it. I think analyzing the
singularities is faster than analyzing the ramification. (It might be
the reason that he commented GffGenus out)

Anyway, I sent him an email and asked him about his opinion.

First: I couldn't find the implementation for GffOrde... functions.
On 17 דצמבר, 04:12, Maarten Derickx m.derickx.stud...@gmail.com
wrote:
 It'shttp://trac.sagemath.org/sage_trac/ticket/12170.

 For Florian Hess ideas see my post 
 inhttps://groups.google.com/forum/#!searchin/sage-devel/function$20fiel...
 of wich you are probably already aware.

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Re: [sage-devel] Re: Statistics on Printouts of open source Sage books

2011-12-21 Thread Nicolas M. Thiery

Thanks William and Rob for your feedback!

Cheers,
Nicolas
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[sage-devel] Re: Help with automated testing of ECL

2011-12-21 Thread Volker Braun
On Wednesday, December 21, 2011 3:23:41 AM UTC, Dima Pasechnik wrote:

 That's what the Sage's patchbot does, pulls patches from Sage's trac, and 
 tests them.


Just for the record, this is a completely separate automated testing 
system: the build bot compiles potential releases on a variety of systems, 
the patch bot builds patches from the sage trac on a single system.

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[sage-devel] Re: Anyone developing Differential System and Cartan--Kaehler in sage?

2011-12-21 Thread Paul Leopardi
Back in 2008, I said I was interested in adding support for Clifford 
algebras / Geometric Algebra to Sage. Since then I have found out that 
there is some support available in Axiom. Now that there is renewed 
interest in Exterior algebras, I would like to better understand how to 
incorporate both the Exterior algebras and the Clifford algebras into Sage 
in a way that makes sense both in terms of coercion and in terms of 
Categories, Is there an existing structure we could bolt our 
implementations into, or do we need to define these ourselves? I would much 
prefer elegance and logical consistency over convention. I do know that 
there are lots of conventions hanging around Clifford algebras and spinors, 
but I don't want these to get in the way. 

As a prototype, I added a Python interface to GluCat http://glucat.sf.net, 
implemented via Cython code. (GluCat implements both the Clifford and the 
exterior product, as well as inner products and the left contraction.) I 
began the Python interface at Sage Days 10 in Nancy, and am still refining 
this interface in anticipation of Cython v0.16. I did not try to add this 
to Sage (1) because it only implements a special case (up to 64 generators, 
Real field via float, double, dd_real or qd_real), (2) because it employs 
its own convention for generators and basis elements (signed index sets), 
(3) because I did not understand coercion or Categories in Sage, (4) 
because my ARC grant applications which included this work were 
unsuccessful, but mostly (5) because I did not make the time to do this.

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[sage-devel] Re: @cached_method using strong references?

2011-12-21 Thread Simon King
Hi Volker,

On 21 Dez., 13:08, Volker Braun vbraun.n...@gmail.com wrote:
 You'll see that the size of __classcall__.cache increases dramatically.
 I've worked around this in my program by periodically purging stuff from
 the cache, but that shouldn't be the actual solution. I think
   * all unique objects should use weak refs

I strongly agree, and actually I am right now working on two related
tickets, namely #11521 (needs review, introducing weak references for
caching homsets) and #715 (needs a lot of work, eventually aiming at
using weak references for caching coerce maps).

   * @cached_method should also use weak refs
 Maybe there is any reason why this is not the case?

Because cached_method is supposed to work on anything that can be used
as a dictionary key -- on None, for example.

However, None and many other things do not allow weak references.

Also, what we need in the case of UniqueRepresentation is: Weak
references to the return value (not to the key). Again, this can't be
used in @cached_method by default.

But I think it would be a good idea to introduce weak variants of
@cached_method, and specifically a version @weak_value_cached_method.
I'll try to implement such thing on top of #5.

Do you have a ticket for the memory leak?

Best regards,
Simon

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[sage-devel] Re: @cached_method using strong references?

2011-12-21 Thread Simon King
Even with #11521, one gets

sage: import gc
sage: len(gc.get_objects())
164699
sage: for i in range(2,1000):
ring = ZZ.quotient(ZZ(i))
vectorspace = ring^2
:
sage: gc.collect()
63
sage: len(gc.get_objects())
375660

So, there is work to do.

However, I think using weak references in UniqueRepresentation would
not solve the problem:

sage: from sage.structure.unique_representation import
UniqueRepresentation
sage: len(UniqueRepresentation.__classcall__.cache.keys())
5136
sage: UniqueRepresentation.__classcall__.cache.clear()
sage: gc.collect()
18
sage: len(gc.get_objects())
335493

I think the strong references in the coercion cache are equally to
blame. So, I suggest to deal with #715 before introducing weak cached
methods.

Cheers,
Simon

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[sage-devel] Re: @cached_method using strong references?

2011-12-21 Thread Volker Braun
How about the following implementation: If the return values is 
weakref-able, we store a weakref. Otherwise, we just store the object. Upon 
lookup, if the value is a weakref it is dereferenced. 

I now understand that @cached_method might be useful to cache the result of 
a long computation even if nobody holds a reference to the result. But I'm 
feeling a bit uneasy that the cached value then remains alive 
unconditionally. Aging the cache to only keep the last n values would make 
me much happier. This could be implemented by a global ring buffer holding 
strong references to the last n (otherwise only weakly referenced) cache 
elements. 

Anyways, I haven't made a ticket yet.


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Re: [sage-devel] Re: Help with automated testing of ECL

2011-12-21 Thread Juan Jose Garcia-Ripoll
On Wed, Dec 21, 2011 at 4:23 AM, Dima Pasechnik dimp...@gmail.com wrote:

 do you like this to pull updates/patches from somewhere for testing, too?
 That's what the Sage's patchbot does, pulls patches from Sage's trac, and
 tests them.
 Or only full releases?


No, as I said in my original email, I would like to test the consistency of
the current git/CVS tree, or of a tagged release with Sage's buildbot. If
this does make sense at all, I really do not know.

Juanjo

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Re: [sage-devel] Re: Help with automated testing of ECL

2011-12-21 Thread Juan Jose Garcia-Ripoll
On Tue, Dec 20, 2011 at 3:27 PM, kcrisman kcris...@gmail.com wrote:

 Because Sage may sometimes have custom patches to ECL that weren't in
 upstream at the time but are now, I don't know if it can be done 100%
 automatically.


I really wonder what those patches are about. AFAIK they are related to
backporting changes to releases, but the need for this disappears
completely if the upstream sources are all the time consistent with Sage.


 But what you *could* do is the following:
 [...]
 and see what happens.


Hmm, again, it is not something that I would like to do on my own computer,
but rather provide a daily tarball or spkg to be tested in that bot.

However, I don't see that you'd be able to just test ECL inside of
 Sage, because of the very specific config and deleting of tons of
 stuff we don't use, and linking against Sage-specific things.


There is not so much stuff that you can delete: just the libraries that ECL
ships with it (GMP, Boehm-GC, libffi). Assuming that they are already
available in Sage, they are not even needed in a normal build -- for
instance, on my copy of Ubuntu, I rarely use the versions that come with
ECL, as the operating system already provides better versions --. The rest
is very much integrated and is what has to be tested.

Juanjo

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[sage-devel] Re: @cached_method using strong references?

2011-12-21 Thread Simon King
Hi Volker,

On 21 Dez., 14:22, Volker Braun vbraun.n...@gmail.com wrote:
 How about the following implementation: If the return values is
 weakref-able, we store a weakref. Otherwise, we just store the object. Upon
 lookup, if the value is a weakref it is dereferenced.

But that costs time, and I thus wouldn't like to make it the default.
What do other people think?

 I now understand that @cached_method might be useful to cache the result of
 a long computation even if nobody holds a reference to the result. But I'm
 feeling a bit uneasy that the cached value then remains alive
 unconditionally. Aging the cache to only keep the last n values would make
 me much happier. This could be implemented by a global ring buffer holding
 strong references to the last n (otherwise only weakly referenced) cache
 elements.

I'll first focus on #715, ...

 Anyways, I haven't made a ticket yet.

... and then perhaps a weak cache for UniqueRepresentation could be
discussed there.

Cheers,
Simon

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[sage-devel] Re: Help with automated testing of ECL

2011-12-21 Thread kcrisman


 I really wonder what those patches are about. AFAIK they are related to
 backporting changes to releases, but the need for this disappears
 completely if the upstream sources are all the time consistent with Sage.

Under the current development and testing model, that would be
extremely hard to do.

  But what you *could* do is the following:
  [...]
  and see what happens.

 Hmm, again, it is not something that I would like to do on my own computer,
 but rather provide a daily tarball or spkg to be tested in that bot.


Yeah, I don't know whether that could be 100% automated or not.
Possibly?

 There is not so much stuff that you can delete: just the libraries that ECL
 ships with it (GMP, Boehm-GC, libffi). Assuming that they are already
 available in Sage, they are not even needed in a normal build -- for
 instance, on my copy of Ubuntu, I rarely use the versions that come with
 ECL, as the operating system already provides better versions --. The rest
 is very much integrated and is what has to be tested.

Just for reference, here is what we delete, and a few other things.


== Special Update/Build Instructions ==
 * Deleting the following directories saves space: without doing
   this, the spkg can grow from under 2.5 megabytes to almost 7
   megabytes.  Deleting these files is done automatically by the
   `spkg-make` script.
   - The directory src/msvc/
   - The directory src/src/gc-unstable
   - The directory src/src/libffi
   - Most of the contents of the src/src/gmp directory:
 everything except install-sh, config.*, configfsf.*
   - The directory src/contrib/encodings/
   - The directory src/contrib/unicode/
 * The directories src/contrib/encodings/ and src/contrib/unicode/ may
   be removed because we build with --enable-unicode=no.
   Building with --enable-unicode=yes, the default in the latest ECL
   source, leads to problems with some strings in the Sage-Maxima-ECL
   interface.
 * Note: the way we configure Sage, CXX and CXXFLAGS are unused.
 * Do NOT quote SAGE_LOCAL when setting CPPFLAGS and/or LDFLAGS,
   in spkg-install as this caused the build to break. See
   http://trac.sagemath.org/sage_trac/ticket/10187#comment:117
 * TODO: Add the ECL test suite, and an spkg-check file to run it.
 * TODO: Make ECL use Sage's Boehm GC on MacOS X as well (but perhaps
   put some changes from ECL's into Sage's Boehm GC), then remove
   the src/src/gc directory, too.


The only current patch is from #9 [2]


diff -r -u src/src/c/ffi/libraries.d src.patched/src/c/ffi/libraries.d
--- src/src/c/ffi/libraries.d   2011-11-07 21:16:18.0 +0100
+++ src.patched/src/c/ffi/libraries.d   2011-11-15 11:13:42.0
+0100
@@ -70,6 +70,7 @@
 #endif /* ENABLE_DLOPEN */
 #include ecl/ecl-inl.h
 #include ecl/internal.h
+#include sys/stat.h

 cl_object
 ecl_make_codeblock()

This is for Cygwin.  We should only apply it then, but that was before
I knew how to do that.  Sorry we didn't report that upstream.

[1] http://cygwin.com/ml/cygwin/2011-04/msg00336.html
[2] http://trac.sagemath.org/sage_trac/ticket/9

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[sage-devel] plotting in sage-4.8.alpha5 is serious fubar'd

2011-12-21 Thread William Stein
Hi,

I've been trying to use sage-4.8.alpha5 for daily work during the last
few days. I don't know what was done to plotting in sage-4.8.alpha5,
but it is seriously messed up.Basically, something is broken so
that figsize doesn't work at all.  Often I have to set an aspect ratio
of 1000 just to see anything, etc.  Anybody have a clue what this is
about?

This is a BLOCKER for release, since it will cause massive trouble to
a lot of users.

Here's a simple example, in which both outputs looks fine in sage-4.7.2:

g = Graphics(); g += line([(0, 120.93), (1, 120.92)])
g.show()
g.show(figsize=[8,4])

To see this on a remote install, just use save('a.png') in place of show.

Even though the first show is broken, perhaps due to something being
set by default, the g.show(figsize=[8,4]) is supposed to produce an
8 inch by 4 inch figure, but instead it makes something that is 0
inches tall.  What's going on?  What broke stuff?

This is now blocker trac #12213.

William

P.S. And FUBAR is literally the right acronym to describe this.

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University of Washington
http://wstein.org

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attachment: b.png

Re: [sage-devel] plotting in sage-4.8.alpha5 is serious fubar'd

2011-12-21 Thread Jeroen Demeyer
On Wed, Dec 21, 2011 at 07:46:27AM -0800, William Stein wrote:
 I've been trying to use sage-4.8.alpha5 for daily work during the last
 few days.

Let me quote from
http://boxen.math.washington.edu/home/release/sage-4.8.alpha5/README.FIRST:

This version of Sage is under construction, it has not been officially
released.

There is no point in testing it.  In particular, you should *not* report
bugs for this version.  First of all, the issue might already be known
to the release manager, but more importantly: since the release can
still change, any bug reports might be difficult to reproduce.

 I don't know what was done to plotting in sage-4.8.alpha5,
 but it is seriously messed up.Basically, something is broken so
 that figsize doesn't work at all.  Often I have to set an aspect ratio
 of 1000 just to see anything, etc.  Anybody have a clue what this is
 about?
Probably the new matplotlib (#11915) which will *not* be merged in
sage-4.8.alpha5 but at some point I did include it.  So please check
your matplotlib version in your sage-4.8.alpha5

Jeroen.

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[sage-devel] Re: plotting in sage-4.8.alpha5 is serious fubar'd

2011-12-21 Thread Volker Braun
I'm pretty sure this is http://trac.sagemath.org/sage_trac/ticket/11963, 
which changed the aspect ratio handling. The default is now 1.0:

sage: Graphics().aspect_ratio()
1.0

If you request 'automatic' then you get a plot of the specified 
width/height:

sage: g.show(figsize=[8,4], aspect_ratio='automatic')

I don't have a strong opinion about what the best default aspect_ratio is, 
but a warning/error if it conflicts with the chosen aspect_ratio seems in 
order.

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[sage-devel] Re: plotting in sage-4.8.alpha5 is serious fubar'd

2011-12-21 Thread kcrisman


On Dec 21, 11:17 am, Volker Braun vbraun.n...@gmail.com wrote:
 I'm pretty sure this ishttp://trac.sagemath.org/sage_trac/ticket/11963,
 which changed the aspect ratio handling. The default is now 1.0:

 sage: Graphics().aspect_ratio()
 1.0

More precisely, when an empty graphics object is added to something
nonempty which would ordinarily have an 'automatic' aspect ratio, it
goes to the

g.set_aspect_ratio(other.aspect_ratio())

but maybe that's not the best solution.

Let's continue this discussion on ticket.

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Re: [sage-devel] plotting in sage-4.8.alpha5 is serious fubar'd

2011-12-21 Thread William Stein
On Wed, Dec 21, 2011 at 8:07 AM, Jeroen Demeyer jdeme...@cage.ugent.be wrote:
 On Wed, Dec 21, 2011 at 07:46:27AM -0800, William Stein wrote:
 I've been trying to use sage-4.8.alpha5 for daily work during the last
 few days.

 Let me quote from
 http://boxen.math.washington.edu/home/release/sage-4.8.alpha5/README.FIRST:

 This version of Sage is under construction, it has not been officially
 released.

 There is no point in testing it.  In particular, you should *not* report
 bugs for this version.  First of all, the issue might already be known
 to the release manager, but more importantly: since the release can
 still change, any bug reports might be difficult to reproduce.

 I don't know what was done to plotting in sage-4.8.alpha5,
 but it is seriously messed up.    Basically, something is broken so
 that figsize doesn't work at all.  Often I have to set an aspect ratio
 of 1000 just to see anything, etc.  Anybody have a clue what this is
 about?
 Probably the new matplotlib (#11915) which will *not* be merged in
 sage-4.8.alpha5 but at some point I did include it.  So please check
 your matplotlib version in your sage-4.8.alpha5

It's not 11915. This was caused by a bad ticket merged in
sage-4.8.alpha3.   I'm glad I found this issue, and am reporting it,
irregardless of that README quote.  I would hate for this to have been
released.

-- William


 Jeroen.

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University of Washington
http://wstein.org

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[sage-devel] Minor question about ask.sagemath settings

2011-12-21 Thread kcrisman
It turns out that askbot has two different possible settings for when
you click on unanswered questions.  It can mean no accepted
answers or no answers.  Currently, it's the former.  I sort of feel
like that is confusing and it should be the other way, but I'm not
strongly in favor of either option.

What do heavy users think?

See 
http://askbot.org/en/question/802/does-unanswered-just-give-backwards-sort-by-number
for context.

In other news, Evgeny says that our askbot is a bit out of date :) but
that he can fix that if we wish.

- kcrisman

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[sage-devel] Re: @cached_method using strong references?

2011-12-21 Thread Volker Braun
On Wednesday, December 21, 2011 2:03:36 PM UTC, Simon King wrote:

  Anyways, I haven't made a ticket yet. 
 ... and then perhaps a weak cache for UniqueRepresentation could be 
 discussed there. 


This is now http://trac.sagemath.org/sage_trac/ticket/12215


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[sage-devel] Re: @cached_method using strong references?

2011-12-21 Thread Simon King
Hi Volker,

On 21 Dez., 21:05, Volker Braun vbraun.n...@gmail.com wrote:
 This is nowhttp://trac.sagemath.org/sage_trac/ticket/12215

There are further tickets related with weak references
 * #11521 has already be mentioned
 * #715
 * #5970 (which is about the cache of polynomial rings).

I have patches for all three of them, but even with all of them
together, the following simple example is still leaking:

sage: for p in primes(2,100):
: print get_memory_usage()
: R.x,y,z = GF(p)[]

So, it seems to be a very complex problem.

Cheers,
Simon

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[sage-devel] Re: new flask notebook-please review

2011-12-21 Thread Jonathan
Please check for the following issue:
1) Can you logout when using FF?  I've seen problems with this on a Linux 
box.  Can anybody reproduce it?  Otherwise, everything looks good to me.

Also, questions about handling the Jmol update as I will have some time 
over the next week to work on that:

1) It appears that trac #11053 
(http://trac.sagemath.org/sage_trac/ticket/11503) as I've now modified it 
will update the version of Jmol and work.  

2) Since we were tracking changes to jmol_lib in mercurial the spkg 
installed (trac #11503) does not include the updated jmol_lib.  Might it be 
cleaner to include the jmol_lib in the spkg?

Jonathan

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[sage-devel] Re: Minor question about ask.sagemath settings

2011-12-21 Thread Jason Grout

On 12/21/11 12:48 PM, kcrisman wrote:

It turns out that askbot has two different possible settings for when
you click on unanswered questions.  It can mean no accepted
answers or no answers.  Currently, it's the former.  I sort of feel
like that is confusing and it should be the other way, but I'm not
strongly in favor of either option.

What do heavy users think?

See 
http://askbot.org/en/question/802/does-unanswered-just-give-backwards-sort-by-number
for context.

In other news, Evgeny says that our askbot is a bit out of date :) but
that he can fix that if we wish.


I think no answers should be the default, and I feel moderately 
strongly about this.  It seems that lots of times there are good 
answers, but the original author hasn't clicked the button to accept them.


Jason



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Re: [sage-devel] Re: @cached_method using strong references?

2011-12-21 Thread William Stein
On Wed, Dec 21, 2011 at 12:35 PM, Simon King simon.k...@uni-jena.de wrote:
 Hi Volker,

 On 21 Dez., 21:05, Volker Braun vbraun.n...@gmail.com wrote:
 This is nowhttp://trac.sagemath.org/sage_trac/ticket/12215

 There are further tickets related with weak references
  * #11521 has already be mentioned
  * #715
  * #5970 (which is about the cache of polynomial rings).

 I have patches for all three of them, but even with all of them
 together, the following simple example is still leaking:

 sage: for p in primes(2,100):
 :     print get_memory_usage()
 :     R.x,y,z = GF(p)[]

 So, it seems to be a very complex problem.

When I'm in a get-shite-done mood, and hence have temporarily given up
on dealing with the above sort of sad annoying memory leak crap, I
just use fork:

for p in primes(2,100):
 print get_memory_usage()
 @fork
 def f():
 R.x,y,z = GF(p)[]
 return (x-y+z)^p
 print f()



I don't want to encourage you to do this, because of course Sage is
benefiting a lot from you worrying about this problem.   But just
for the record, using @fork can be handy in some cases like this, when
you *need* to get work done.

By the way, @fork does not work well if you are using pexpect
interfaces, since it just resets them for the child.

 -- William

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Re: [sage-devel] Re: @cached_method using strong references?

2011-12-21 Thread Robert Bradshaw
On Wed, Dec 21, 2011 at 5:22 AM, Volker Braun vbraun.n...@gmail.com wrote:
 How about the following implementation: If the return values is
 weakref-able, we store a weakref. Otherwise, we just store the object. Upon
 lookup, if the value is a weakref it is dereferenced.

 I now understand that @cached_method might be useful to cache the result of
 a long computation even if nobody holds a reference to the result. But I'm
 feeling a bit uneasy that the cached value then remains alive
 unconditionally. Aging the cache to only keep the last n values would make
 me much happier. This could be implemented by a global ring buffer holding
 strong references to the last n (otherwise only weakly referenced) cache
 elements.

+1

It's unlikely that the key or the value for cached_method will
actually be referenced elsewhere to be useful, unlike e.g. unique
representation.

- Robert

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