[sage-devel] Re: numerical optimization in sage

2007-10-11 Thread medvall

The majority of TOMLAB (80%) is code developed in C and Fortran
(embedded for use in Matlab).

OpenOpt is definitely not equivalent to TOMLAB.

Best wishes, Marcus
Tomlab Optimization Inc.
http://tomopt.com/


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[sage-devel] Bug Day 4 Proposal: Oct. 20th, 2007

2007-10-11 Thread mabshoff

Hello,

it has been a while since the last Bug Day and the number of tickets
keep growing, so I figured it would be a good idea to do another one.
As most people now have to teach/attend class I would suggest the next
Sunday, Oct. 20th, instead of a weekday. Let me know what you think.

Cheers,

Michael


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[sage-devel] Re: Bug Day 4 Proposal: Oct. 20th, 2007

2007-10-11 Thread Martin Albrecht

On Thursday 11 October 2007, mabshoff wrote:
 Hello,

 it has been a while since the last Bug Day and the number of tickets
 keep growing, so I figured it would be a good idea to do another one.
 As most people now have to teach/attend class I would suggest the next
 Sunday, Oct. 20th, instead of a weekday. Let me know what you think.

+1


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


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[sage-devel] Re: Bug Day 4 Proposal: Oct. 20th, 2007

2007-10-11 Thread Jason Grout

mabshoff wrote:
 Hello,
 
 it has been a while since the last Bug Day and the number of tickets
 keep growing, so I figured it would be a good idea to do another one.
 As most people now have to teach/attend class I would suggest the next
 Sunday, Oct. 20th, instead of a weekday. Let me know what you think.

I wouldn't be able to participate in a bug day on Sunday, so I'd vote 
for a weekday or a Saturday, for whatever weight my vote holds.

Thanks,

Jason


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[sage-devel] Re: Introductory SAGE talk in Oslo

2007-10-11 Thread Georg Muntingh

I tied up the loose ends, and now you can find the PDF, ODP and HTML
files at my website, http://folk.uio.no/georgmu/ . Visuals can be
found in the directory http://folk.uio.no/georgmu/Writings/SAGE-Oslo/Graphics/
.


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[sage-devel] Re: Introductory SAGE talk in Oslo

2007-10-11 Thread mabshoff



On Oct 11, 3:26 pm, Georg Muntingh [EMAIL PROTECTED] wrote:
 I tied up the loose ends, and now you can find the PDF, ODP and HTML
 files at my website,http://folk.uio.no/georgmu/. Visuals can be
 found in the directoryhttp://folk.uio.no/georgmu/Writings/SAGE-Oslo/Graphics/
 .

Well, yes  but

Forbidden

You don't have permission to access /georgmu/Writings/SAGE-Oslo/
Graphics/ActiveLearning.jpg on this server.
Apache/2.2.4 (Unix) Server at folk.uio.no Port 80

:)

Cheers,

Michael


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[sage-devel] Re: Bug Day 4 Proposal: Oct. 20th, 2007

2007-10-11 Thread mabshoff



On Oct 11, 2:35 pm, Jason Grout [EMAIL PROTECTED] wrote:
 mabshoff wrote:
  Hello,

  it has been a while since the last Bug Day and the number of tickets
  keep growing, so I figured it would be a good idea to do another one.
  As most people now have to teach/attend class I would suggest the next
  Sunday, Oct. 20th, instead of a weekday. Let me know what you think.

 I wouldn't be able to participate in a bug day on Sunday,

The initial suggestion of Sundays for Bug Days came out of a
discussion at SD 5 and I think that William at least told me that he
wanted to not work on Sage on Saturdays. Weekdays are tougher,
especially with the huge time zone difference (at least for the
Europeans)

 so I'd vote
 for a weekday or a Saturday, for whatever weight my vote holds.


:), depending on your time zone at least some of us will start in
Saturday and leave early on Sunday. But there are usually a sufficient
number of people in IRC to do some bug hunting in a social setting.

 Thanks,

 Jason

Cheers,

Michael


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[sage-devel] Re: Introductory SAGE talk in Oslo

2007-10-11 Thread David Joyner

Excellent! Thanks. However, the pdf at
http://folk.uio.no/georgmu/Writings/SAGE-Oslo/
has some black pages. Do you know why this is?

+++

On 10/11/07, Georg Muntingh [EMAIL PROTECTED] wrote:

 I tied up the loose ends, and now you can find the PDF, ODP and HTML
 files at my website, http://folk.uio.no/georgmu/ . Visuals can be
 found in the directory http://folk.uio.no/georgmu/Writings/SAGE-Oslo/Graphics/
 .


 


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[sage-devel] Re: Introductory SAGE talk in Oslo

2007-10-11 Thread William Stein

On 10/11/07, David Joyner [EMAIL PROTECTED] wrote:

 Excellent! Thanks. However, the pdf at
 http://folk.uio.no/georgmu/Writings/SAGE-Oslo/
 has some black pages. Do you know why this is?

I suspect they are intentional -- a dramatic pause -- it was a very
stylish talk after all.

Anyway, thanks for the beautiful slides, which I've posted here:
http://sagemath.org/why.html

William


 +++

 On 10/11/07, Georg Muntingh [EMAIL PROTECTED] wrote:
 
  I tied up the loose ends, and now you can find the PDF, ODP and HTML
  files at my website, http://folk.uio.no/georgmu/ . Visuals can be
  found in the directory 
  http://folk.uio.no/georgmu/Writings/SAGE-Oslo/Graphics/
  .
 
 
  
 

 



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

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[sage-devel] Re: Introductory SAGE talk in Oslo

2007-10-11 Thread Georg Muntingh

Yes, that is on purpose. I use them when I change subject or when I
want the audience to look at me, instead of at the screen. It is quite
a smart trick. The following article neatly describes the effect of a
black screen: http://www.bertdecker.com/experience/2007/03/blog_entry_date.html

I agree that it looks strange outside the context of the presentation.


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[sage-devel] Re: Bug Day 4 Proposal: Oct. 20th, 2007

2007-10-11 Thread William Stein

On 10/11/07, mabshoff [EMAIL PROTECTED] wrote:
   it has been a while since the last Bug Day and the number of tickets
   keep growing, so I figured it would be a good idea to do another one.
   As most people now have to teach/attend class I would suggest the next
   Sunday, Oct. 20th, instead of a weekday. Let me know what you think.
 
  I wouldn't be able to participate in a bug day on Sunday,

 The initial suggestion of Sundays for Bug Days came out of a
 discussion at SD 5 and I think that William at least told me that he
 wanted to not work on Sage on Saturdays. Weekdays are tougher,
 especially with the huge time zone difference (at least for the
 Europeans)

  so I'd vote
  for a weekday or a Saturday, for whatever weight my vote holds.
 

 :), depending on your time zone at least some of us will start in
 Saturday and leave early on Sunday. But there are usually a sufficient
 number of people in IRC to do some bug hunting in a social setting.

I think doing it on Saturday instead does make a lot of sense.  There
are other people (besides Jason) who couldn't do it on Sunday, but
whose participation is critical.  So I propose next Saturday (not
this coming Saturday), i.e., Saturday October 20.

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

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[sage-devel] Fwd: ode_solver

2007-10-11 Thread Marshall Hampton

-- Forwarded message --
From: Marshall Hampton [EMAIL PROTECTED]
Date: Oct 10, 12:07 pm
Subject: ode_solver
To: sage-support


I have used cython to try to speed up my function evaluations.  The
computation that used to take about 2400 seconds (40 minutes) now
takes 38 seconds - a very nice improvement.  I can more or less live
with that, although as I noted before mathematica takes about 1.5
seconds, and its solution looks quite accurate.  So we can do better.
Josh Kantor has suggested that I try the scipy integrate command,
which I hope to do soon.   Maybe it will be faster.

To fix the interpolation problems, I just use the line command:

T = ode_solver()
# lots of stuff I am leaving out
t_data = T.solution
show(line([[x[0],x[1][2]] for x in tdata])

In case anyone is interested in the full details, I have put a text
file with a minimal version of my model up at:

http://www.d.umn.edu/~mhampton/Model1.txt

Marshall

On Oct 5, 10:14 am, William Stein [EMAIL PROTECTED] wrote:

 On 10/5/07, David Joyner [EMAIL PROTECTED] wrote:

  I think this was written by Josh Kantor, but possibly it was
  William Stein.

  I don't understand it either. Sorry.

 Josh wrote it.  It wraps gsl.  You might be defining a function whose
 evaluation is really slow, e.g., if it involves symbolic calculus in
 any way, it could be very slow, and that would slow down everything
 else.   So you might:
(1) make sure any functions involved evaluate very very quickly.
(2) consider using scipy's ode solving capabilities, which are quite fast.
(3) wait for Josh to make some helpful remarks -- but only expect that
 if you post complete details about what you're doing.

 William

  On 10/5/07, Hamptonio [EMAIL PROTECTED] wrote:
   I just moved an ODE model of mine over to sage from mathematica and I
   am trying to use ode_solver to deal with it.  Now that I am using it
   seriously I found a few issues.  I am happy to try to help solve them
   but I don't know the code well yet.

   1) Trivial documentation error: in runge-kutta-felhberg, fehlberg is
   misspelled.
   2) interpolate_solution acts a little funny.  I was using a 5000 point
   solution, and the interpolation seemed to be ignoring some points -
   i.e. perhaps it only uses a sample of the solution?  I have a rapidly
   oscillating solution, and the interpolation fails pretty badly.
   3) It is extremely slow.  I have a rather complicated system of three
   variables.  Mathematica's NDSolve takes about 1.5 seconds to solve it
   on one computer, and ode_solver takes about 2400 seconds on a better
   computer.  I will have to learn more pyrex I guess.  I was surprised
   by how bad the difference was.

   Marshall

   On Apr 1, 8:04 pm, David Joyner [EMAIL PROTECTED] wrote:
On 1/4/07, JoshuaKantor[EMAIL PROTECTED] wrote:

 In response to Williams sage-2.0 plan I wanted to describe what I had 
 done
 with using gsl to implement a numerical ode solver. I believe that the
 patch containing this  will be applied after
 doing a recent pull or upgrade but I'm not sure(is this true?). If not

..
 Ideas for extension:

 1. It would be nice if there was some facility for automatically
 converting a nth order ODE
 to a system of first order ones.

If an n-th order ODE is simply a function of the variables
x, y0=y, y1=y',...,yn = y^(n), then this is easy to write.
Should the n-th order ODEs form a class?

 2. It would be nice if there was some facility for automatically 
 computing
 the jacobian when the functions involved are rational functions and
 elementary functions.

Maxima has a function called hessian, as well as
a determinant. Together, I think they should do
what you want.

 3. Numerically computing the jacobian: For the algorithms that 
 require the
 jacobian It would be possible to numerically compute the jacobian,
 however I was wary of doing this by default. Does anyone have any 
 knowledge
 about
 the benefits of this, can it cause instability (using the numerical
 jacobian
 instead of the exact one).

I don't but I agree with you anyway.

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


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[sage-devel] DSage Zombie issue on sage.math

2007-10-11 Thread mabshoff

Hello,

zombies have taken over sage.math:

top - 09:48:46 up 36 days, 18:09, 17 users,  load average: 2.24, 1.79,
1.44
Tasks: 864 total,   3 running, 550 sleeping,   0 stopped, 311 zombie
Cpu(s):  8.1%us,  1.0%sy, 13.1%ni, 76.7%id,  1.2%wa,  0.0%hi,
0.0%si,  0.0%st

They all appear to be dsage jobs started by was yesterday. Any ideas
what happened?

Cheers,

Michael


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[sage-devel] Re: DSage Zombie issue on sage.math

2007-10-11 Thread Yi Qiang
Hi Michael,
I think there is a problem with the way the individual workers are restarted
which leaves them as zombie processes.  I'll look into this.

Cheers,
Yi
--
http://www.yiqiang.org

On 10/11/07, mabshoff [EMAIL PROTECTED]
wrote:


 Hello,

 zombies have taken over sage.math:

 top - 09:48:46 up 36 days, 18:09, 17 users,  load average: 2.24, 1.79,
 1.44
 Tasks: 864 total,   3 running, 550 sleeping,   0 stopped, 311 zombie
 Cpu(s):  8.1%us,  1.0%sy, 13.1%ni, 76.7%id,  1.2%wa,  0.0%hi,
 0.0%si,  0.0%st

 They all appear to be dsage jobs started by was yesterday. Any ideas
 what happened?

 Cheers,

 Michael


 


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[sage-devel] Re: DSage Zombie issue on sage.math

2007-10-11 Thread William Stein

On 10/11/07, Yi Qiang [EMAIL PROTECTED] wrote:
 Hi Michael,
 I think there is a problem with the way the individual workers are restarted
 which leaves them as zombie processes.  I'll look into this.

 Cheers,
 Yi

Yep.  I killed them all, since my entire huge job finished (yes!).
But yeah, it would be good to make sure zombies don't get created
in the future.

William

 --
  http://www.yiqiang.org


 On 10/11/07, mabshoff
 [EMAIL PROTECTED] wrote:
 
  Hello,
 
  zombies have taken over sage.math:
 
  top - 09:48:46 up 36 days, 18:09, 17 users,  load average: 2.24, 1.79,
  1.44
  Tasks: 864 total,   3 running, 550 sleeping,   0 stopped, 311 zombie
  Cpu(s):  8.1%us,  1.0%sy, 13.1%ni, 76.7%id,  1.2%wa,  0.0%hi,
  0.0%si,  0.0%st
 
  They all appear to be dsage jobs started by was yesterday. Any ideas
  what happened?
 
  Cheers,
 
  Michael
 
 
   
 



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

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[sage-devel] Re: Bug Day 4 Proposal: Oct. 20th, 2007

2007-10-11 Thread Mike Hansen

Saturday the 20th works for me.

--Mike

On 10/11/07, William Stein [EMAIL PROTECTED] wrote:

 On 10/11/07, mabshoff [EMAIL PROTECTED] wrote:
it has been a while since the last Bug Day and the number of tickets
keep growing, so I figured it would be a good idea to do another one.
As most people now have to teach/attend class I would suggest the next
Sunday, Oct. 20th, instead of a weekday. Let me know what you think.
  
   I wouldn't be able to participate in a bug day on Sunday,
 
  The initial suggestion of Sundays for Bug Days came out of a
  discussion at SD 5 and I think that William at least told me that he
  wanted to not work on Sage on Saturdays. Weekdays are tougher,
  especially with the huge time zone difference (at least for the
  Europeans)
 
   so I'd vote
   for a weekday or a Saturday, for whatever weight my vote holds.
  
 
  :), depending on your time zone at least some of us will start in
  Saturday and leave early on Sunday. But there are usually a sufficient
  number of people in IRC to do some bug hunting in a social setting.

 I think doing it on Saturday instead does make a lot of sense.  There
 are other people (besides Jason) who couldn't do it on Sunday, but
 whose participation is critical.  So I propose next Saturday (not
 this coming Saturday), i.e., Saturday October 20.

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

 


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[sage-devel] Re: numerical optimization in sage

2007-10-11 Thread William Stein

On 10/11/07, medvall [EMAIL PROTECTED] wrote:

 The majority of TOMLAB (80%) is code developed in C and Fortran
 (embedded for use in Matlab).

Does TOMLAB also have a Python interface?  If so, how much does
it cost?

Thanks for writing,

 William

 OpenOpt is definitely not equivalent to TOMLAB.

 Best wishes, Marcus
 Tomlab Optimization Inc.
 http://tomopt.com/


 



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

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[sage-devel] Re: [Pyrex] C-API implementation in Pyrex 0.9.6

2007-10-11 Thread William Stein

On 10/11/07, Stefan Behnel [EMAIL PROTECTED] wrote:
 the C-API support has been rewritten for integration in Pyrex, but not much to
...

Hi,

Can I ask a few naive questions about the C-API support, since I know that
me and _many_ of the people I work with are confused about what this support
provides?  I'll just ask a few naive questions, and maybe your answers would
be useful for me to add to the faq or documentation.

(1) Suppose I would like to define a cdef'd function in a module
arith.pyx that I want
to call from other .pyx files, e.g.,

cdef int fast_gcd(int a, int b):
   ...

Then I basically want to do this sort of thing from other .pyx files:
from arith cimport fast_gcd
int x = fast_gcd(5,7)

Definitely in Cython/Pyrex a few months ago the above wouldn't work.
Is there a way to make it work now?  And if so, what are the linking
requirements
(i.e. options to gcc or distutils)?

(2) Suppose I want to define a cdef'd function in a .pyx file, as above, but now
I want it to be callable from some external C file.  E.g.,

/* this is a C function in a .c file */
   int foo(blah) {
   fast_gcd(...)
   }

This is very natural to do because I might be mixing C and .pyx code,
and this provides a way to reach back and get at Python data directly
from C code.   Is there now a way to do this?

-- William


 However, I think the current implementation is a bad idea, as it pollutes the
 module namespace. What a user see now is a lot of module attributes that are
 nicely named like functions, but that cannot be called. Also, this means that
 the C-level view on the module gets exposed to the Python level, which can be
 rather confusing, depending on the naming scheme(s) in use. And given the fact
 that C APIs tend to be larger and more redundant than Python APIs, e.g. to
 reflect different function signatures, this is not a problem that I would want
 to see ignored.

 My original implementation was targeted to avoid exactly this problem, as it
 exported only a single PyCObject as entry point that pointed to a function
 table mapping string names to function pointers. It would have been easy to
 generate the import code based on this table instead, which would have
 provided the same level of binary independence.

 Greg, is there any chance you could revert your changes to make the generated
 modules less ugly and confusing?

 Stefan


 ___
 Pyrex mailing list
 [EMAIL PROTECTED]
 http://lists.copyleft.no/mailman/listinfo/pyrex



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

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[sage-devel] Re: Bug Day 4 Proposal: Oct. 20th, 2007

2007-10-11 Thread Robert Bradshaw

On Oct 11, 2007, at 5:35 AM, Jason Grout wrote:

 mabshoff wrote:
 Hello,

 it has been a while since the last Bug Day and the number of tickets
 keep growing, so I figured it would be a good idea to do another one.
 As most people now have to teach/attend class I would suggest the  
 next
 Sunday, Oct. 20th, instead of a weekday. Let me know what you think.

 I wouldn't be able to participate in a bug day on Sunday, so I'd vote
 for a weekday or a Saturday, for whatever weight my vote holds.

Same here.

- Robert


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[sage-devel] Re: Bug Day 4 Proposal: Oct. 20th, 2007

2007-10-11 Thread William Stein

On 10/11/07, Robert Bradshaw [EMAIL PROTECTED] wrote:
  I wouldn't be able to participate in a bug day on Sunday, so I'd vote
  for a weekday or a Saturday, for whatever weight my vote holds.

 Same here.


OK, Saturday October 20, 2007 it is:

http://wiki.sagemath.org/bug4

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[sage-devel] Fwd: [Pyrex] C-API implementation in Pyrex 0.9.6

2007-10-11 Thread William Stein

-- Forwarded message --
From: Stefan Behnel [EMAIL PROTECTED]
Date: Oct 11, 2007 11:19 AM
Subject: Re: [Pyrex] C-API implementation in Pyrex 0.9.6
To: William Stein [EMAIL PROTECTED]
Cc: sage-devel@googlegroups.com, Greg Ewing
[EMAIL PROTECTED], Pyrex ML [EMAIL PROTECTED]



William Stein wrote:
 Can I ask a few naive questions about the C-API support, since I know that
 me and _many_ of the people I work with are confused about what this support
 provides?  I'll just ask a few naive questions, and maybe your answers would
 be useful for me to add to the faq or documentation.

Sure. The main idea behind the C-API support for Pyrex/Cython is to
automate this:

http://docs.python.org/ext/using-cobjects.html


 (1) Suppose I would like to define a cdef'd function in a module
 arith.pyx that I want
 to call from other .pyx files, e.g.,

 cdef int fast_gcd(int a, int b):
...

 Then I basically want to do this sort of thing from other .pyx files:
 from arith cimport fast_gcd
 int x = fast_gcd(5,7)

 Definitely in Cython/Pyrex a few months ago the above wouldn't work.
 Is there a way to make it work now?

Yes. You can export the function from arith.pyx via the api keyword (in
Pyrex 0.9.6, Cython will follow here) and it will generate a file
arith_api.h and (if you want) a .pxd file that define it. Then the above
code should work.


  And if so, what are the linking
 requirements (i.e. options to gcc or distutils)?

No linking required, pure runtime access.


 (2) Suppose I want to define a cdef'd function in a .pyx file, as above, but 
 now
 I want it to be callable from some external C file.  E.g.,

 /* this is a C function in a .c file */
int foo(blah) {
fast_gcd(...)
}

 This is very natural to do because I might be mixing C and .pyx code,
 and this provides a way to reach back and get at Python data directly
 from C code.   Is there now a way to do this?

In exactly the same way, just with a little less automatism. The arith_api.h
files defines static function pointers for each exported function and a static
function that you can call to initialise the pointers based on the Python
module. So, #including the header file and calling that function is enough to
do the above.

To make my position regarding the Pyrex 0.9.6 implementation clear: I like the
Pyrex interface to this functionality, it is better and cleaner than my
original implementation, and Cython should follow here. I just dislike the
internal implementation that leaks too much into Python space, where it simply
does not belong at all.

Stefan



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

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[sage-devel] Re: Version of sage on sage.math on October 4th

2007-10-11 Thread mabshoff



On Oct 10, 1:07 am, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On Oct 9, 8:27 pm, William Stein [EMAIL PROTECTED] wrote:

  On 10/9/07, Iftikhar Burhanuddin [EMAIL PROTECTED] wrote:

   On Tue, 9 Oct 2007, William Stein wrote:
I think thememoryleaks that we identified before (which involve ntl
strings, etc.)
only *maybe* got fixed in Sage-2.8.6, and certainly weren't fixed in
sage-2.8.5.1,
so if you ran a computation with sage-2.8.5.1 you should expect 
thatmemory
leak.

 Hi Ifti,

   The level ofmemoryleaking in *unexpected* compared to previous versions
   of sage.

   I ran a SupersingularModule computation on September 18 (which is pre
   sage-2.8.5) and it ran for about a 2 weeks and consumed only about 20% on
  memoryon sage.math.

   Something seems to have changed in and around sage-2.8.5

 Well, as far as I know there is only  the ntl string leak. I assumed
 that the ntl rewrite would go in and fix the problem. So how about
 this in 2.8.7? Otherwise I will fix this temporarily until the ntl
 write goes in.

* A run of computation using the SupersingularModule on sage.math
running sage-2.?.? consumed 54.4% ofmemoryin 4512:26 seconds (75.2
hours) starting October 4th.

 I will rerun the computation with 2.8.6 and see if more leaks
 appeared.


Hi Ifti,

I reran SuperComp() from #501 with 5 iterations using a clean 2.8.6
installed from sources and the leak of 2.3MB was all in NTL glue code
via str() methods except for 240 bytes leaked via python's compiler/
interpreter. So when is the ntl update coming?

Cheers,

Michael



* A run of computation using the SupersingularModule on sage.math
running sage-2.8.6 consumed 11.8% ofmemoryin 2269:50 seconds (37.8
hours) starting October 7th.
   ps: I should start keeping track of version numbers in my long
   computations.

  This command helps with that:

  sage: version()
  'SAGE Version 2.8.6, Release Date: 2007-10-06'

   Do you have a log of when you installed new versions of sage on sage.math
   and what those versions were in the september-october time frame?

  Fortunately any Sage install is very good at tracking its entire upgrade
  history.  On sage.math do this:

 SNIP

 Cheers,

 Michael


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[sage-devel] Re: DSage Zombie issue on sage.math

2007-10-11 Thread Justin C. Walker


On Oct 11, 2007, at 10:19 AM, William Stein wrote:


 On 10/11/07, Yi Qiang [EMAIL PROTECTED] wrote:
 Hi Michael,
 I think there is a problem with the way the individual workers are  
 restarted
 which leaves them as zombie processes.  I'll look into this.

 Cheers,
 Yi

 Yep.  I killed them all, since my entire huge job finished (yes!).
 But yeah, it would be good to make sure zombies don't get created
 in the future.

FWIW, zombies are fairly light-weight processes :-}

They are really skeletons of what the process was: essentially enough  
state information so that the parent can reap them and collect the  
status information (I think it amounts to a process descriptor in the  
kernel), so even 300 of them shouldn't be a drain (despite  
Hollywood's unflattering depiction of them :-}).

It does pay to get rid of them, of course.

Justin

--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Absorption of Federal Funds

Men are from Earth.
Women are from Earth.
Deal with it.





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[sage-devel] Sage 2.8.6: doctest failures with cython.py on sage.math

2007-10-11 Thread mabshoff

The following happens on a compiled from source 2.8.6 on sage.math:

sage -t  devel/sage-main/sage/misc/cython.py
**
File cython.py, line 316:
sage: g = cython_lambda('double x, double y', 'x*x + y*y + x + y +
17*x + 3.2')
Exception raised:
Traceback (most recent call last):
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
doctest.py, line 1212, in __run
compileflags, 1) in test.globs
  File doctest __main__.example_4[1], line 1, in module
g = cython_lambda('double x, double y', 'x*x + y*y + x + y +
17*x + 3.2')###line 316:
sage: g = cython_lambda('double x, double y', 'x*x + y*y + x + y +
17*x + 3.2')
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
packages/sage/misc/cython.py, line 357, in cython_lambda
create_local_c_file=False)
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
packages/sage/server/support.py, line 303, in cython_import_all
create_local_c_file=create_local_c_file)
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
packages/sage/server/support.py, line 286, in cython_import
return __builtin__.__import__(name)
ImportError: /tmp/Work-mabshoff/sage-2.8.5.1/local/lib/
libcblas.so: undefined symbol: ATL_ctbmv
**
File cython.py, line 317:
sage: g(2,3)
Exception raised:
Traceback (most recent call last):
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
doctest.py, line 1212, in __run
compileflags, 1) in test.globs
  File doctest __main__.example_4[2], line 1, in module
g(Integer(2),Integer(3))###line 317:
sage: g(2,3)
NameError: name 'g' is not defined
**
File cython.py, line 319:
sage: g(0,0)
Exception raised:
Traceback (most recent call last):
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
doctest.py, line 1212, in __run
compileflags, 1) in test.globs
  File doctest __main__.example_4[3], line 1, in module
g(Integer(0),Integer(0))###line 319:
sage: g(0,0)
NameError: name 'g' is not defined
**
File cython.py, line 324:
sage: f = cython_lambda('double x', 'sage.math.sin(x) + sage.a')
Exception raised:
Traceback (most recent call last):
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
doctest.py, line 1212, in __run
compileflags, 1) in test.globs
  File doctest __main__.example_4[5], line 1, in module
f = cython_lambda('double x', 'sage.math.sin(x) +
sage.a')###line 324:
sage: f = cython_lambda('double x', 'sage.math.sin(x) + sage.a')
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
packages/sage/misc/cython.py, line 357, in cython_lambda
create_local_c_file=False)
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
packages/sage/server/support.py, line 303, in cython_import_all
create_local_c_file=create_local_c_file)
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
packages/sage/server/support.py, line 286, in cython_import
return __builtin__.__import__(name)
ImportError: /tmp/Work-mabshoff/sage-2.8.5.1/local/lib/
libcblas.so: undefined symbol: ATL_ctbmv
**
File cython.py, line 325:
sage: f(10)
Exception raised:
Traceback (most recent call last):
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
doctest.py, line 1212, in __run
compileflags, 1) in test.globs
  File doctest __main__.example_4[6], line 1, in module
f(Integer(10))###line 325:
sage: f(10)
TypeError: lambda() takes exactly 2 arguments (1 given)
**
File cython.py, line 328:
sage: f(10)
Exception raised:
Traceback (most recent call last):
  File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
doctest.py, line 1212, in __run
compileflags, 1) in test.globs
  File doctest __main__.example_4[8], line 1, in module
f(Integer(10))###line 328:
sage: f(10)
TypeError: lambda() takes exactly 2 arguments (1 given)
**
1 items had failures:
   6 of   9 in __main__.example_4

I haven't seen a ticket for this one. Should we open one?

Cheers,

Michael


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[sage-devel] Re: Sage 2.8.6: doctest failures with cython.py on sage.math

2007-10-11 Thread Mike Hansen

Weird.  cython.py passes all tests for me under an upgraded 2.8.5 -
2.8.6 from source install.

--Mike

On 10/11/07, mabshoff [EMAIL PROTECTED] wrote:

 The following happens on a compiled from source 2.8.6 on sage.math:

 sage -t  devel/sage-main/sage/misc/cython.py
 **
 File cython.py, line 316:
 sage: g = cython_lambda('double x, double y', 'x*x + y*y + x + y +
 17*x + 3.2')
 Exception raised:
 Traceback (most recent call last):
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
 doctest.py, line 1212, in __run
 compileflags, 1) in test.globs
   File doctest __main__.example_4[1], line 1, in module
 g = cython_lambda('double x, double y', 'x*x + y*y + x + y +
 17*x + 3.2')###line 316:
 sage: g = cython_lambda('double x, double y', 'x*x + y*y + x + y +
 17*x + 3.2')
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
 packages/sage/misc/cython.py, line 357, in cython_lambda
 create_local_c_file=False)
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
 packages/sage/server/support.py, line 303, in cython_import_all
 create_local_c_file=create_local_c_file)
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
 packages/sage/server/support.py, line 286, in cython_import
 return __builtin__.__import__(name)
 ImportError: /tmp/Work-mabshoff/sage-2.8.5.1/local/lib/
 libcblas.so: undefined symbol: ATL_ctbmv
 **
 File cython.py, line 317:
 sage: g(2,3)
 Exception raised:
 Traceback (most recent call last):
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
 doctest.py, line 1212, in __run
 compileflags, 1) in test.globs
   File doctest __main__.example_4[2], line 1, in module
 g(Integer(2),Integer(3))###line 317:
 sage: g(2,3)
 NameError: name 'g' is not defined
 **
 File cython.py, line 319:
 sage: g(0,0)
 Exception raised:
 Traceback (most recent call last):
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
 doctest.py, line 1212, in __run
 compileflags, 1) in test.globs
   File doctest __main__.example_4[3], line 1, in module
 g(Integer(0),Integer(0))###line 319:
 sage: g(0,0)
 NameError: name 'g' is not defined
 **
 File cython.py, line 324:
 sage: f = cython_lambda('double x', 'sage.math.sin(x) + sage.a')
 Exception raised:
 Traceback (most recent call last):
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
 doctest.py, line 1212, in __run
 compileflags, 1) in test.globs
   File doctest __main__.example_4[5], line 1, in module
 f = cython_lambda('double x', 'sage.math.sin(x) +
 sage.a')###line 324:
 sage: f = cython_lambda('double x', 'sage.math.sin(x) + sage.a')
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
 packages/sage/misc/cython.py, line 357, in cython_lambda
 create_local_c_file=False)
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
 packages/sage/server/support.py, line 303, in cython_import_all
 create_local_c_file=create_local_c_file)
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
 packages/sage/server/support.py, line 286, in cython_import
 return __builtin__.__import__(name)
 ImportError: /tmp/Work-mabshoff/sage-2.8.5.1/local/lib/
 libcblas.so: undefined symbol: ATL_ctbmv
 **
 File cython.py, line 325:
 sage: f(10)
 Exception raised:
 Traceback (most recent call last):
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
 doctest.py, line 1212, in __run
 compileflags, 1) in test.globs
   File doctest __main__.example_4[6], line 1, in module
 f(Integer(10))###line 325:
 sage: f(10)
 TypeError: lambda() takes exactly 2 arguments (1 given)
 **
 File cython.py, line 328:
 sage: f(10)
 Exception raised:
 Traceback (most recent call last):
   File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
 doctest.py, line 1212, in __run
 compileflags, 1) in test.globs
   File doctest __main__.example_4[8], line 1, in module
 f(Integer(10))###line 328:
 sage: f(10)
 TypeError: lambda() takes exactly 2 arguments (1 given)
 **
 1 items had failures:
6 of   9 in __main__.example_4

 I haven't seen a ticket for this one. Should we open one?

 Cheers,

 Michael


 


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[sage-devel] Re: DSage Zombie issue on sage.math

2007-10-11 Thread Yi Qiang
Yup, you are right.  The processes are dead but have an entry in the process
table.  I fixed this issue btw.

Cheers,
Yi
--
http://www.yiqiang.org

On 10/11/07, Justin C. Walker [EMAIL PROTECTED] wrote:



 On Oct 11, 2007, at 10:19 AM, William Stein wrote:

 
  On 10/11/07, Yi Qiang [EMAIL PROTECTED] wrote:
  Hi Michael,
  I think there is a problem with the way the individual workers are
  restarted
  which leaves them as zombie processes.  I'll look into this.
 
  Cheers,
  Yi
 
  Yep.  I killed them all, since my entire huge job finished (yes!).
  But yeah, it would be good to make sure zombies don't get created
  in the future.

 FWIW, zombies are fairly light-weight processes :-}

 They are really skeletons of what the process was: essentially enough
 state information so that the parent can reap them and collect the
 status information (I think it amounts to a process descriptor in the
 kernel), so even 300 of them shouldn't be a drain (despite
 Hollywood's unflattering depiction of them :-}).

 It does pay to get rid of them, of course.

 Justin

 --
 Justin C. Walker, Curmudgeon-At-Large
 Institute for the Absorption of Federal Funds
 
 Men are from Earth.
 Women are from Earth.
 Deal with it.
 




 


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[sage-devel] Re: Sage 2.8.6: doctest failures with cython.py on sage.math

2007-10-11 Thread mabshoff



On Oct 12, 2:05 am, Mike Hansen [EMAIL PROTECTED] wrote:
 Weird.  cython.py passes all tests for me under an upgraded 2.8.5 -
 2.8.6 from source install.

 --Mike

Hi Mike,

I just reran

[EMAIL PROTECTED]:/tmp/Work-mabshoff/sage-2.8.6$ ./sage -t  devel/sage-
main/sage/misc/cython.py
sage -t  devel/sage-main/sage/misc/cython.py
 [4.6 s]

--
All tests passed!
Total time for all tests: 4.6 seconds

And it works. For a reason see below.

Cheers,

Michael


 On 10/11/07, mabshoff [EMAIL PROTECTED] wrote:



  The following happens on a compiled from source 2.8.6 on sage.math:

  sage -t  devel/sage-main/sage/misc/cython.py
  **
  File cython.py, line 316:
  sage: g = cython_lambda('double x, double y', 'x*x + y*y + x + y +
  17*x + 3.2')
  Exception raised:
  Traceback (most recent call last):
File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
  doctest.py, line 1212, in __run
  compileflags, 1) in test.globs
File doctest __main__.example_4[1], line 1, in module
  g = cython_lambda('double x, double y', 'x*x + y*y + x + y +
  17*x + 3.2')###line 316:
  sage: g = cython_lambda('double x, double y', 'x*x + y*y + x + y +
  17*x + 3.2')
File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
  packages/sage/misc/cython.py, line 357, in cython_lambda
  create_local_c_file=False)
File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
  packages/sage/server/support.py, line 303, in cython_import_all
  create_local_c_file=create_local_c_file)
File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
  packages/sage/server/support.py, line 286, in cython_import
  return __builtin__.__import__(name)
  ImportError: /tmp/Work-mabshoff/sage-2.8.5.1/local/lib/
  libcblas.so: undefined symbol: ATL_ctbmv
  **
  File cython.py, line 317:
  sage: g(2,3)
  Exception raised:
  Traceback (most recent call last):
File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
  doctest.py, line 1212, in __run
  compileflags, 1) in test.globs
File doctest __main__.example_4[2], line 1, in module
  g(Integer(2),Integer(3))###line 317:
  sage: g(2,3)
  NameError: name 'g' is not defined
  **
  File cython.py, line 319:
  sage: g(0,0)
  Exception raised:
  Traceback (most recent call last):
File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
  doctest.py, line 1212, in __run
  compileflags, 1) in test.globs
File doctest __main__.example_4[3], line 1, in module
  g(Integer(0),Integer(0))###line 319:
  sage: g(0,0)
  NameError: name 'g' is not defined
  **
  File cython.py, line 324:
  sage: f = cython_lambda('double x', 'sage.math.sin(x) + sage.a')
  Exception raised:
  Traceback (most recent call last):
File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
  doctest.py, line 1212, in __run
  compileflags, 1) in test.globs
File doctest __main__.example_4[5], line 1, in module
  f = cython_lambda('double x', 'sage.math.sin(x) +
  sage.a')###line 324:
  sage: f = cython_lambda('double x', 'sage.math.sin(x) + sage.a')
File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
  packages/sage/misc/cython.py, line 357, in cython_lambda
  create_local_c_file=False)
File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
  packages/sage/server/support.py, line 303, in cython_import_all
  create_local_c_file=create_local_c_file)
File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/site-
  packages/sage/server/support.py, line 286, in cython_import
  return __builtin__.__import__(name)
  ImportError: /tmp/Work-mabshoff/sage-2.8.5.1/local/lib/
  libcblas.so: undefined symbol: ATL_ctbmv

Notice the 2.8.5.1 here -  I source sage-env from 2.8.5.1 and that
build has ATLAS installed. Why ./sage -testall doesn't see
LD_LIBRARY_PATH properly in this case I do not know. I have

[EMAIL PROTECTED]:/tmp/Work-mabshoff/sage-2.8.6$ env | grep LD_L
LD_LIBRARY_PATH=/tmp/Work-mabshoff/sage-2.8.5.1/local/lib/openmpi:/tmp/
Work-mabshoff/sage-2.8.5.1/local/lib/

before I start sage from the 2.8.6 directory.

Sorry for the noise.


 **
  File cython.py, line 325:
  sage: f(10)
  Exception raised:
  Traceback (most recent call last):
File /tmp/Work-mabshoff/sage-2.8.6/local/lib/python2.5/
  doctest.py, line 1212, in __run
  compileflags, 1) in test.globs
File doctest __main__.example_4[6], line 1, in module
  

[sage-devel] Fwd: [Pyrex] C-API implementation in Pyrex 0.9.6

2007-10-11 Thread William Stein

-- Forwarded message --
From: Greg Ewing [EMAIL PROTECTED]
Date: Oct 11, 2007 4:58 PM
Subject: Re: [Pyrex] C-API implementation in Pyrex 0.9.6
To: William Stein [EMAIL PROTECTED]
Cc: sage-devel@googlegroups.com, Pyrex ML [EMAIL PROTECTED]


William Stein wrote:
 (1) Suppose I would like to define a cdef'd function in a module
 arith.pyx that I want
 to call from other .pyx files, e.g.,

 cdef int fast_gcd(int a, int b):
...

 Then I basically want to do this sort of thing from other .pyx files:
 from arith cimport fast_gcd
 int x = fast_gcd(5,7)

Yes. You can do that by declaring fast_gcd in a .pxd file, e.g.

   # arith.pxd
   cdef int fast_gcd(int, int)

   # arith.pyx
   cdef int fast_gcd(int a, int b):
 ...

   # anothermodule.pyx
   from arith cimport fast_gcd
   x = fast_gcd(5,7)

That's all you need to do. No linking is required.

 (2) Suppose I want to define a cdef'd function in a .pyx file, as above, but 
 now
 I want it to be callable from some external C file.  E.g.,

 /* this is a C function in a .c file */
int foo(blah) {
fast_gcd(...)
}

1) Declare the function as api in the .pyx file:

   # arith.pyx
   cdef api int fast_gcd(int a, int b):
 ...

2) Include the generated header in your C code and call the
importing function:

   /* somefile.c */
   #include arith_api.h
   ...
  int x
  import_arith()
  x = fast_gcd(p, q)

In this case, the object file produced by compiling arith.pyx
needs to be linked against the object file produced by compiling
somefile.c, either statically or dynamically.

--
Greg


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

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[sage-devel] Re: Bug Day 4 Proposal: Oct. 20th, 2007

2007-10-11 Thread mabshoff



On Oct 12, 3:03 am, John Voight [EMAIL PROTECTED] wrote:
 Cool, count me in!  JV

Hello,

if you are going to participate please add yourself to the list of
participants at the bottom of

  http://wiki.sagemath.org/bug4

Cheers,

Michael


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[sage-devel] Re: hg

2007-10-11 Thread William Stein

On 10/11/07, John Voight [EMAIL PROTECTED] wrote:
 Is this supposed to happen?

That should definitely not happen.  It's likely a bug
of some sort.  Could you try just removing the file
/home/was/s/devel/sage-main/.hg/hgrc?
You should make your own ~jvoight/.hgrc file.
Please let me know if that works.   If so, I need to make
sure to remove .hg/hgrc from the sage distro.

Thanks for reporting this problem.

William


 [EMAIL PROTECTED]:~$ sage -clone voight
 Now cloning the current SAGE library branch...
 hg clone  sage sage-voight
 Not trusting file /home/was/s/devel/sage-main/.hg/hgrc from untrusted
 user was, group was
 abort: Permission denied: sage-voight
 Error cloning

 real0m0.094s
 user0m0.048s
 sys 0m0.044s

 (I was trying to follow along the Programming Guide to add the
 function nfbasis, which returns the basis and the discriminant:

 def nfbasis_d(self, long flag=0, p=0):
 cdef gen _p
 cdef GEN g, d
 if p != 0:
 _p = self.pari(p)
 g = _p.g
 else:
 g = GENNULL
 d = self.pari(0)
 _sig_on
 nfb = self.new_gen(nfbasis(self.g, d.g, flag, g))
 return nfb, d

 I wanted to test it out first before submitting a patch...)

 Yours,

 John Voight
 Assistant Professor of Mathematics
 University of Vermont
 [EMAIL PROTECTED]
 [EMAIL PROTECTED]
 http://www.cems.uvm.edu/~voight/



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

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