[sage-devel] Re: __new__ versus __cinit__ for cython classes

Robert Bradshaw wrote: > On Jun 30, 2009, at 11:16 PM, Jason Grout wrote: > >> I recently noticed that many, many places, cython classes in Sage are >> using __new__ to initialize their C data structures (i.e., malloc >> memory, etc.) rather than __cinit__: >> >> ~/sage/devel/sage/sage$ grep -r "

[sage-devel] Re: __new__ versus __cinit__ for cython classes

On Jun 30, 2009, at 11:16 PM, Jason Grout wrote: > I recently noticed that many, many places, cython classes in Sage are > using __new__ to initialize their C data structures (i.e., malloc > memory, etc.) rather than __cinit__: > > ~/sage/devel/sage/sage$ grep -r "def __cinit__" * | grep \\\.pyx

[sage-devel] graphics tutorial

Hi, The worksheets from a graphics tutorial (for people who know nothing about sage) which I'm giving today are posted here: http://wstein.org/talks/20090701-sage_graphics_tutorial/ -- William Stein Associate Professor of Mathematics University of Washington http://wstein.org --~--~-~-

[sage-devel] __new__ versus __cinit__ for cython classes

I recently noticed that many, many places, cython classes in Sage are using __new__ to initialize their C data structures (i.e., malloc memory, etc.) rather than __cinit__: ~/sage/devel/sage/sage$ grep -r "def __cinit__" * | grep \\\.pyx | wc -l 7 ~/sage/devel/sage/sage$ grep -r "def __new__" *

[sage-devel] Re: Cython and Libraries

On Jun 30, 2009, at 10:48 PM, Jason Grout wrote: > > Nathann Cohen wrote: >> Hello everybody !!! >> >> I have been trying for ages to post a clean patch for Cliquer, a >> software used to solve the Max Clique problem in Sage. It has been >> refused a lot of times for reasons I understand, but I s

[sage-devel] Re: Cython and Libraries

Nathann Cohen wrote: > Hello everybody !!! > > I have been trying for ages to post a clean patch for Cliquer, a > software used to solve the Max Clique problem in Sage. It has been > refused a lot of times for reasons I understand, but I still do not > know how to correct it. My problem is the fo

[sage-devel] Re: Cliquer spkg

Robert Miller wrote: >> There is another problem, which is that currently, the web page seems >> to indicate (although not directly) that the code is released under >> GPLv3. > > Wait a tic, the distribution itself has a LICENSE file which clearly > says that the code is GPLv2. One less thing, I

[sage-devel] Re: MPFR test failures in Sage (optimisation issue)

Dr. David Kirkby wrote: > I found that when trying to build Sage on t2.math.washington.edu there > are problems with 'mpfr', with 20 out of 148 test failures. > > I downloaded the mpfr 2.4.1 source, compiled that with the same gcc > optimisation level as used in Sage (-O2). Again mpfr failed 20

[sage-devel] Re: 3D using processing.js

On Tue, Jun 30, 2009 at 2:41 AM, Rob Beezer wrote: > > On Jun 29, 12:09 pm, William Cauchois wrote: >> At the behest of William I took a stab at implementing this very type >> of renderer in Sage. My work, [with patch], is available at >> for anyon

[sage-devel] Re: flint's use of the 'cp' command.

Jason Grout wrote: > Dr. David Kirkby wrote: >> William Stein wrote: >>> On Tue, Jun 30, 2009 at 5:05 PM, Dr. David >>> Kirkby wrote: I noticed a problem when building 'sage-4.1.alpha2.spkg'. It complains ld: fatal: library -lflint: not found But the flint package ind

[sage-devel] Re: flint's use of the 'cp' command.

Dr. David Kirkby wrote: > William Stein wrote: >> On Tue, Jun 30, 2009 at 5:05 PM, Dr. David >> Kirkby wrote: >>> I noticed a problem when building 'sage-4.1.alpha2.spkg'. It complains >>> >>> ld: fatal: library -lflint: not found >>> >>> >>> But the flint package indicates it was installed. Howev

[sage-devel] MPFR test failures in Sage (optimisation issue)

I found that when trying to build Sage on t2.math.washington.edu there are problems with 'mpfr', with 20 out of 148 test failures. I downloaded the mpfr 2.4.1 source, compiled that with the same gcc optimisation level as used in Sage (-O2). Again mpfr failed 20 tests. I can't say for sure they

[sage-devel] Re: vtk fails to build on Mac

On Tue, Jun 30, 2009 at 4:58 PM, Tim Lahey wrote: > > On Tue, Jun 30, 2009 at 6:47 PM, Ondrej Certik wrote: >> >> >> Do Mac systems have /usr/include/X11? the bsd.math has it. If generaly >> not, then I still need to tweak the configure to build without X11 at >> all, if that is possible (maybe no

[sage-devel] Re: vtk fails to build on Mac

On Tue, Jun 30, 2009 at 6:47 PM, Ondrej Certik wrote: > > > Do Mac systems have /usr/include/X11? the bsd.math has it. If generaly > not, then I still need to tweak the configure to build without X11 at > all, if that is possible (maybe not). Not always. The user has to explicitly install the X11

[sage-devel] Re: vtk fails to build on Mac

On Tue, Jun 30, 2009 at 4:00 PM, Brian Granger wrote: > > Ondrej, > >> Many thanks for this! Some comments below: >> >>> >>> Here is their main page for information about building VisIt: >>> >>> https://wci.llnl.gov/codes/visit/source.html >>> >>> Here is the "build_visit" shell script that will b

[sage-devel] Re: vtk fails to build on Mac

Ondrej, > Many thanks for this! Some comments below: > >> >> Here is their main page for information about building VisIt: >> >> https://wci.llnl.gov/codes/visit/source.html >> >> Here is the "build_visit" shell script that will build visit from >> source (check it out, it is 1 lines long and

[sage-devel] Re: vtk fails to build on Mac

On Tue, Jun 30, 2009 at 3:52 PM, Ondrej Certik wrote: > Hi Brian! > > On Tue, Jun 30, 2009 at 1:13 PM, Brian Granger wrote: >> >> Ondrej, >> >> So I heard back from the VisIt devs and thankfully, they keep really >> good records of how they build everything.  What they go through to >> build VisIt

[sage-devel] Re: sage fails to make on 64 bit fedora 11 when making Singular

I also encountered this, and the problem is actually GCC 4.4, which comes with Fedora 11. See http://trac.sagemath.org/sage_trac/ticket/6362 I installed the spkg from that page and built Sage flawlessly; I suspect it would fix your problem too. regards john perry On Jun 30, 4:45 pm, wn wrote:

[sage-devel] Re: vtk fails to build on Mac

Hi Brian! On Tue, Jun 30, 2009 at 1:13 PM, Brian Granger wrote: > > Ondrej, > > So I heard back from the VisIt devs and thankfully, they keep really > good records of how they build everything.  What they go through to > build VisIt is insane.  But here are the references that I think could > hel

[sage-devel] sage fails to make on 64 bit fedora 11 when making Singular

The fedora 10 binary failed after I updated to fedora 11 (I think because python has been updated). Making from source in Fedora 11 fails when making Singular. Kernel is 2.6.29.5-191.fc11.x86_64, gcc is gcc (GCC) 4.4.0 20090506 (Red Hat 4.4.0-4) Here are the relevant errors. make install in kern

[sage-devel] Re: Cython and Libraries

Yippieh, that's what I really love about Sage: you'll never walk alone! What about the following idea: let's create sage.libs.playground and, say, Cython (sub-)modules sage.libs.playground.exampleclib sage.libs.playground.examplecpplib which are amply documented despite their names, but in a s

[sage-devel] Re: vtk fails to build on Mac

Ondrej, So I heard back from the VisIt devs and thankfully, they keep really good records of how they build everything. What they go through to build VisIt is insane. But here are the references that I think could help you... Here is their main page for information about building VisIt: https

[sage-devel] Re: 4.1.alpha2 released

On Jun 30, 7:49 am, John H Palmieri wrote: > It would be nice to see timings on other systems. 64-bit Kubuntu 9.04 on dual-core Intel, reasonably new, but not extravagant hardware. 4.1.alpha2: sage: time s = search_src('matrix', interact=False) CPU times: user 0.01 s, sys: 0.00 s, total: 0.01 s

[sage-devel] Re: flint's use of the 'cp' command.

William Stein wrote: > On Tue, Jun 30, 2009 at 5:05 PM, Dr. David > Kirkby wrote: >> I noticed a problem when building 'sage-4.1.alpha2.spkg'. It complains >> >> ld: fatal: library -lflint: not found >> >> >> But the flint package indicates it was installed. However, when I tried >> to build flint

[sage-devel] Re: vtk fails to build on Mac

On Tue, Jun 30, 2009 at 6:53 PM, Ondrej Certik wrote: > > On Tue, Jun 30, 2009 at 10:43 AM, Brian Granger > wrote: >> >>> One important >>> thing to note is where the Framework goes.  It will be installed in >>> $SAGE_LOCAL/Frameworks.  The bin and lib directories (where >>> executables and site-

[sage-devel] Re: vtk fails to build on Mac

On Tue, Jun 30, 2009 at 10:43 AM, Brian Granger wrote: > >> One important >> thing to note is where the Framework goes.  It will be installed in >> $SAGE_LOCAL/Frameworks.  The bin and lib directories (where >> executables and site-packages) end up will be subdirectories of this. >> You will proba

[sage-devel] Re: vtk fails to build on Mac

> One important > thing to note is where the Framework goes. It will be installed in > $SAGE_LOCAL/Frameworks. The bin and lib directories (where > executables and site-packages) end up will be subdirectories of this. > You will probably need to point PATH to something like > $SAGE_LOCAL/Framewo

[sage-devel] Re: vtk fails to build on Mac

I am attaching my spkg-install script that I have used to generate a Framework build of Python 2.5.1. You might have to tweak it for later versions of Python, but this should get you started. One important thing to note is where the Framework goes. It will be installed in $SAGE_LOCAL/Frameworks.

[sage-devel] Re: vtk fails to build on Mac

On Jun 30, 2009, at 12:32 PM, Ondrej Certik wrote: > > Is Sage using nonframework Python build? I don't know. Yes, it's using a regular build. I think some people are looking at a framework build .spkg because it's necessary for any GUI work on OS X. Cheers, Tim. --- Tim Lahey PhD Candidate,

[sage-devel] Re: vtk fails to build on Mac

On Tue, Jun 30, 2009 at 10:06 AM, Brian Granger wrote: > > Ondrej, > > The traditional way of building VTK on a Mac is to build it as a Cocoa > or Carbon library.  This means a couple of things: > > * Python must be built as a framework. > * The Mac native GUI is used, not X11. > * You are using a

[sage-devel] Re: flint's use of the 'cp' command.

William Stein wrote: > On Tue, Jun 30, 2009 at 5:05 PM, Dr. David > Kirkby wrote: >> I noticed a problem when building 'sage-4.1.alpha2.spkg'. It complains >> >> ld: fatal: library -lflint: not found >> >> >> But the flint package indicates it was installed. However, when I tried >> to build flint

[sage-devel] Re: vtk fails to build on Mac

Ondrej, The traditional way of building VTK on a Mac is to build it as a Cocoa or Carbon library. This means a couple of things: * Python must be built as a framework. * The Mac native GUI is used, not X11. * You are using all of Apples OpenGL libraries. If you stick to these assumptions, gett

[sage-devel] Re: flint's use of the 'cp' command.

On Tue, Jun 30, 2009 at 5:05 PM, Dr. David Kirkby wrote: > > I noticed a problem when building 'sage-4.1.alpha2.spkg'. It complains > > ld: fatal: library -lflint: not found > > > But the flint package indicates it was installed. However, when I tried > to build flint again, I see this error messa

[sage-devel] flint's use of the 'cp' command.

I noticed a problem when building 'sage-4.1.alpha2.spkg'. It complains ld: fatal: library -lflint: not found But the flint package indicates it was installed. However, when I tried to build flint again, I see this error message: Deleting old FLINT Installing new library file cp: illegal opti

[sage-devel] Re: Documentation for enabling multicore Numpy support

> Is MATLAB actually 8 times faster than Sage at computing matrix > products and eigendecompositions than Sage on exactly the same > matrices? Not exactly the same matrixes since to save time I'm using random matrixes. For both 2048x2048 and 8192x8192 matrix multiplication (64- bit float), I'm se

[sage-devel] Re: 4.1.alpha2 released

On Tue, Jun 30, 2009 at 4:49 PM, John H Palmieri wrote: > > > > On Jun 30, 12:22 am, William Stein wrote: >> On Tue, Jun 30, 2009 at 3:11 AM, Dan Drake wrote: >> > On Mon, 29 Jun 2009 at 05:21PM -0700, John H Palmieri wrote: >> >> How about #6429: sagedoc: make search_src and friends less OS >> >

[sage-devel] Re: 4.1.alpha2 released

On Jun 30, 12:22 am, William Stein wrote: > On Tue, Jun 30, 2009 at 3:11 AM, Dan Drake wrote: > > On Mon, 29 Jun 2009 at 05:21PM -0700, John H Palmieri wrote: > >> How about #6429: sagedoc: make search_src and friends less OS > >> dependent?  This should fix the doctest failure for sagedoc.py o

[sage-devel] Re: Documentation for enabling multicore Numpy support

On Tue, Jun 30, 2009 at 3:11 PM, Ahmed Fasih wrote: > > Hi, Google has been bountiful in providing pieces of this puzzle (or > God has been stingy in giving me the brains to put them together), but > I write asking if there exists a coherent and unified document telling > me what to do to get mult

[sage-devel] Re: Fw: [mpir-devel] Strange problem on t2 - pari fails to build, but fine on my home machine.

William Stein wrote: > On Tue, Jun 30, 2009 at 4:39 AM, Dr. David > Kirkby wrote: >> Jason Moxham wrote: >>> - Original Message - From: "Jason Moxham" >>> >>> To: "mpir-devel" >>> Sent: Monday, June 29, 2009 8:46 PM >>> Subject: [mpir-devel] Re: Fwd: [sage-devel] Strange problem on t2 -

[sage-devel] Documentation for enabling multicore Numpy support

Hi, Google has been bountiful in providing pieces of this puzzle (or God has been stingy in giving me the brains to put them together), but I write asking if there exists a coherent and unified document telling me what to do to get multicore Numpy support in Sage. On 8-core Xeon, Matlab (which ap

[sage-devel] Re: SAGE reference

On Tue, Jun 30, 2009 at 2:52 PM, Massimo Corinaldesi wrote: > Hi, > > my name is Massimo. > > I’m writing a manual on SAGE (for newbies) in Italian language. > > I reference SAGE with: > > > > William Stein et al., Sage Mathematics Software (Version 4.0.2), > >    The Sage Development Team, 2009,

[sage-devel] Re: Cython and Libraries

An example spkg could be included as a test the same way that examples in documentation are now used as a test, so there need not be an issue of the example not working. Indeed, if it is required that the documentation is updated in tandem with the example spkg, then the documentation will also be

[sage-devel] Re: [Cython] OT: Sage build

On Tue, Jun 30, 2009 at 12:25 PM, Stefan Behnel wrote: > > Robert Bradshaw wrote: >> On Jun 29, 2009, at 5:45 AM, Dag Sverre Seljebotn wrote: >>> do you know if e.g. Sage builds are IO bound? >> >> Not sure, but that's certainly a big component. > > Now that you mention it, how do you parallelise

[sage-devel] Re: vtk fails to build on Mac

On 06/30/09 00:42, William Stein wrote: >> Oops, sage-4.0.2 doesn't build on bsd.math. Here is what I get after a >> long compile: > > For what it is worth, sage-4.0.2 does build fine on bsd.math. That's > where I build all the OS X 10.5 intel binaries.Since you didn't > actually post anythi

[sage-devel] Re: Improving QQ['x']

On Tue, Jun 30, 2009 at 3:04 AM, Bill Hart wrote: > > The current implementation of FLINT will not care which design choice > you make because integer polynomials are currently implemented with > all coefficients the same size anyway. So a common denominator is > absolutely fine. I also doubt that

[sage-devel] Re: 4.1.alpha2 released

On Tue, Jun 30, 2009 at 3:11 AM, Dan Drake wrote: > On Mon, 29 Jun 2009 at 05:21PM -0700, John H Palmieri wrote: >> How about #6429: sagedoc: make search_src and friends less OS >> dependent?  This should fix the doctest failure for sagedoc.py on ppc >> OS X 10.4 (I hope). > > I'd also like to see

[sage-devel] Re: /mpir-1.2.p4 has no entry for p4 is SPKG.txt

On Tue, Jun 30, 2009 at 4:29 AM, Craig Citro wrote: > >> The SPKG.txt for mpir-1.2.p4 shows: >> >> >> == Changelog == >> >> === mpir-1.2.p3 (Nick Alexander, June 9, 2009) === >>  * Update to latest MPIR 1.2 final release. >> >> === mpir-1.2.p2 (William Stein, June 4, 2009) === >>  * Update to late

[sage-devel] Re: Fw: [mpir-devel] Strange problem on t2 - pari fails to build, but fine on my home machine.

On Tue, Jun 30, 2009 at 4:39 AM, Dr. David Kirkby wrote: > > Jason Moxham wrote: >> >> - Original Message - From: "Jason Moxham" >> >> To: "mpir-devel" >> Sent: Monday, June 29, 2009 8:46 PM >> Subject: [mpir-devel] Re: Fwd: [sage-devel] Strange problem on t2 - pari >> fails to build, bu