[sage-devel] Sage 4.1.1.rc2 released
Hi folks, Sage 4.1.1.rc2 resolves issues caused by non-ASCII characters in a patch at ticket #5793. So the only ticket that has been merged in this release is #6674: Minh Van Nguyen: only use ASCII characters in patches [Reviewed by Nathann Cohen, Alex Ghitza] Source and binary are up at http://sage.math.washington.edu/home/mvngu/release/sage-4.1.1.rc2.tar http://sage.math.washington.edu/home/mvngu/release/sage-4.1.1.rc2-sage.math.washington.edu-x86_64-Linux.tar.gz and the upgrade path is http://sage.math.washington.edu/home/mvngu/release/sage-4.1.1.rc2/ As always, please test and report any problems. -- Regards Minh Van Nguyen --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Linear Programming -- First applications in Sage
Well, it should not O_o I applied it on a sage-4.1.1.rc1 and all wen fine. The only patch I applied before this one was the one removing non-ascii characters from Cliquer files ! :-/ Nathann On Aug 7, 5:54 am, Minh Nguyen wrote: > Hi Rado, > > On Fri, Aug 7, 2009 at 1:33 PM, Rado wrote: > > > r...@rado-desktop:~/sage-4.0.2/devel/sage-lp$ cat sage/numerical/ > > all.py.rej > > --- all.py > > +++ all.py > > @@ -1,3 +1,4 @@ > > from optimize import (find_root, find_maximum_on_interval, > > > find_minimum_on_interval,minimize,minimize_constrained, > > linear_program, find_fit) > > +from sage.numerical.mip import * > > It looks like the patch AllMIP.patch at ticket #6502 > > http://trac.sagemath.org/sage_trac/ticket/6502 > > depends on some other ticket or patch. As you know, the only failure > when applying that patch is this block of code: > > [mv...@sage numerical]$ cat all.py.rej > --- all.py > +++ all.py > @@ -1,3 +1,4 @@ > from optimize import (find_root, find_maximum_on_interval, > find_minimum_on_interval,minimize,minimize_constrained, > linear_program, find_fit) > +from sage.numerical.mip import * > > which is to be patched against the file > > sage/numerical/all.py > > As of Sage 4.1, the content of that file is > > [mv...@sage numerical]$ cat all.py > from optimize import (find_root, find_maximum_on_interval, > find_minimum_on_interval,minimize,minimize_constrained, > linear_program, find_fit) > > which is just one (long) line. However, from the file all.py.rej, it > looks like this line has been split off into more than one line. > > > what is rebase? anyways this seems simple enough to do by hand, but i > > want to learn mercurial, so I wouldn't might if any one can explain > > how to make hg patch work. > > Your attempt at patching failed because the patch you were trying to > apply depends on another patch or ticket. > > -- > Regards > Minh Van Nguyen --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Looking for Collaboration
I stumbled upon your math tool and it looks very interesting. It reminded me of a math environment that I designed for a grad class (although never implemented it). After seeing Sage, there are striking similarities and would relish the opportunity to discuss my ideas further. My background is computers science and math but I am a bit rusty in the programming department now that I teach math full- time. The vision of my environment involves an interface like Sage, but with a drop-down box where students can select an operation from a list. I also envision the environment being used to solve problems in multiple steps using multiple methods (more of a discovery tool). In my vision, there are more Web2.0-like features for collaboration with other students and teachers. And, there is a way to save steps to a library and to share with other students. If interested, please contact me about interesting directions for Sage. I have lots of vision, but little implementation skills. I think that an math tool that does not automatically provide the correct answer could be used by every math student! Thanks in advance, John Faig school: jdf2...@columbia.edu work: jf...@klht.org personal: johnfaig...@gmail.com twitter: johnfaig --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Linear Programming -- First applications in Sage
Hi Rado, On Fri, Aug 7, 2009 at 1:33 PM, Rado wrote: > > r...@rado-desktop:~/sage-4.0.2/devel/sage-lp$ cat sage/numerical/ > all.py.rej > --- all.py > +++ all.py > @@ -1,3 +1,4 @@ > from optimize import (find_root, find_maximum_on_interval, > > find_minimum_on_interval,minimize,minimize_constrained, > linear_program, find_fit) > +from sage.numerical.mip import * It looks like the patch AllMIP.patch at ticket #6502 http://trac.sagemath.org/sage_trac/ticket/6502 depends on some other ticket or patch. As you know, the only failure when applying that patch is this block of code: [mv...@sage numerical]$ cat all.py.rej --- all.py +++ all.py @@ -1,3 +1,4 @@ from optimize import (find_root, find_maximum_on_interval, find_minimum_on_interval,minimize,minimize_constrained, linear_program, find_fit) +from sage.numerical.mip import * which is to be patched against the file sage/numerical/all.py As of Sage 4.1, the content of that file is [mv...@sage numerical]$ cat all.py from optimize import (find_root, find_maximum_on_interval, find_minimum_on_interval,minimize,minimize_constrained, linear_program, find_fit) which is just one (long) line. However, from the file all.py.rej, it looks like this line has been split off into more than one line. > what is rebase? anyways this seems simple enough to do by hand, but i > want to learn mercurial, so I wouldn't might if any one can explain > how to make hg patch work. Your attempt at patching failed because the patch you were trying to apply depends on another patch or ticket. -- Regards Minh Van Nguyen --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Linear Programming -- First applications in Sage
r...@rado-desktop:~/sage-4.0.2/devel/sage-lp$ cat sage/numerical/ all.py.rej --- all.py +++ all.py @@ -1,3 +1,4 @@ from optimize import (find_root, find_maximum_on_interval, find_minimum_on_interval,minimize,minimize_constrained, linear_program, find_fit) +from sage.numerical.mip import * what is rebase? anyways this seems simple enough to do by hand, but i want to learn mercurial, so I wouldn't might if any one can explain how to make hg patch work. Rado On Aug 6, 10:23 pm, Minh Nguyen wrote: > Hi Rado, > > On Fri, Aug 7, 2009 at 1:06 PM, Rado wrote: > > > I hit sage -upgrade successfully, cloned sage and tried to patch but > > got this... > > > r...@rado-desktop:~/sage-4.0.2/devel/sage-lp$ hg patch AllMIP.patch > > applying AllMIP.patch > > patching file sage/numerical/all.py > > Hunk #1 FAILED at 0 > > 1 out of 1 hunks FAILED -- saving rejects to file sage/numerical/ > > all.py.rej > > abort: patch failed to apply > > > any ideas :/ > > What's the content of the following file? > > sage/numerical/all.py.rej > > A rebase of AllMIP.patch would solve the failure to patch. > > -- > Regards > Minh Van Nguyen --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: wiki.sagemath.org/ appears down
Hi David, On Fri, Aug 7, 2009 at 1:14 PM, David Kirkby wrote: > I just restarted the wiki. Can you please try again? -- Regards Minh Van Nguyen --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Linear Programming -- First applications in Sage
Hi Rado, On Fri, Aug 7, 2009 at 1:06 PM, Rado wrote: > > I hit sage -upgrade successfully, cloned sage and tried to patch but > got this... > > r...@rado-desktop:~/sage-4.0.2/devel/sage-lp$ hg patch AllMIP.patch > applying AllMIP.patch > patching file sage/numerical/all.py > Hunk #1 FAILED at 0 > 1 out of 1 hunks FAILED -- saving rejects to file sage/numerical/ > all.py.rej > abort: patch failed to apply > > any ideas :/ What's the content of the following file? sage/numerical/all.py.rej A rebase of AllMIP.patch would solve the failure to patch. -- Regards Minh Van Nguyen --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] wiki.sagemath.org/ appears down
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[sage-devel] Re: Linear Programming -- First applications in Sage
I hit sage -upgrade successfully, cloned sage and tried to patch but got this... r...@rado-desktop:~/sage-4.0.2/devel/sage-lp$ hg patch AllMIP.patch applying AllMIP.patch patching file sage/numerical/all.py Hunk #1 FAILED at 0 1 out of 1 hunks FAILED -- saving rejects to file sage/numerical/ all.py.rej abort: patch failed to apply any ideas :/ On Aug 6, 1:55 pm, Nathann Cohen wrote: > Of course not I mean not anymore, thank you for reminding me :-) > > I just created a new patch containing all you need. It is > onhttp://trac.sagemath.org/sage_trac/ticket/6502under the name > "AllMIP". > > You can also get it there > :http://trac.sagemath.org/sage_trac/attachment/ticket/6502/AllMIP.patch > > Nathann > > On Aug 6, 8:30 pm, Rado wrote: > > > I want to try it, but i have a newbie question, do i need to download > > and install all 8 patches fromhttp://trac.sagemath.org/sage_trac/ticket/6502 > > ? > > Can we get a master patch, (something along the way of hg diff > > baserv:lastrv should give a composite patch). > > > On Aug 6, 10:53 am, Nathann Cohen wrote: > > > > Hello everybody ! > > > > A new message about Linear Programming in Sage. Everything we talked > > > about a few weeks ago is now available in different places : > > > > The patch necessary to use Linear Programming > > > :http://trac.sagemath.org/sage_trac/ticket/6502 > > > The package GLPK ( first solver available, required ) : sage > > > -fhttp://www.sagemath.org/packages/optional/glpk-4.38.spkg > > > The package Coin-or/Cbc ( optional, but even faster than GLPK ) > > > :http://trac.sagemath.org/sage_trac/ticket/6501 > > > > Today I posted the first patches for Graph functions using Linear > > > Programming in Sage : > > > > Vertex/Edge coloring :http://trac.sagemath.org/sage_trac/ticket/6679 > > > A lot of others :http://trac.sagemath.org/sage_trac/ticket/6680 > > > > Those two tickets needs reviews, but if you do not intend to give it a > > > try it may just be interesting as a base of examples of what you can > > > do with Linear Programming in Sage ! > > > > I am aware that most of these functions can be rewritten in a > > > different specific way to make them more efficient, and I expect most > > > of them to be rewritten eventually. Linear Programming in Sage was the > > > laziest way I knew to write all these functions, but I thought Sage > > > really needed them and I hope you will find them efficient enough > > > compared to what we had, or compared to what you would expect to get > > > from such a general framework as LP. > > > > Finally, I spent a lot of time writing the docstrings for all of these > > > functions and for all the MIP-related functions, so learning how to > > > use them should be pretty quick for those familiar with LP, using just > > > MIP?, or using the question mark at the end of each function you'll > > > find > > > > Have fun, and thank you all again for your help ! ;-) > > > > Nathann > > --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 4.1.1.rc1 build halt
On Thu, Aug 6, 2009 at 10:32 PM, William Stein wrote: > > > 2009/8/6 David Joyner >> >> I tried >> >> export CC=/usr/bin/gcc-3.4 >> export CXX=/usr/bin/cpp-3.4 >> >> then removing the links gcc, cpp and relinking with >> >> sudo ln -s /usr/bin/gcc-3.4 /usr/bin/gcc >> sudo ln -s /usr/bin/cpp-3.4 /usr/bin/cpp >> >> The build failed at matplotlib. One error was that c++ was not >> installed on the system. > > Just for the record, I think GCC 3.4 couldn't work even on a correctly > configured system, because of ratpoints. I tried the same thing with 3.4 replaced by 4.2. The error this time was "too many input files". Then I tried replacing 4.2 by 4.3. Same error. I only have gcc-3.4, 4-4.2, -4.3, and -4.4 on this system, so I think I'm out of options for now. > > William > > > > > --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 4.1.1.rc1 build halt
2009/8/6 David Joyner > > I tried > > export CC=/usr/bin/gcc-3.4 > export CXX=/usr/bin/cpp-3.4 > > then removing the links gcc, cpp and relinking with > > sudo ln -s /usr/bin/gcc-3.4 /usr/bin/gcc > sudo ln -s /usr/bin/cpp-3.4 /usr/bin/cpp > > The build failed at matplotlib. One error was that c++ was not > installed on the system. Just for the record, I think GCC 3.4 couldn't work even on a correctly configured system, because of ratpoints. William --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 4.1.1.rc1 build halt
I tried export CC=/usr/bin/gcc-3.4 export CXX=/usr/bin/cpp-3.4 then removing the links gcc, cpp and relinking with sudo ln -s /usr/bin/gcc-3.4 /usr/bin/gcc sudo ln -s /usr/bin/cpp-3.4 /usr/bin/cpp The build failed at matplotlib. One error was that c++ was not installed on the system. On Thu, Aug 6, 2009 at 4:11 PM, Dr. David Kirkby wrote: > > J Elaych wrote: >>> I just upgraded to karmic and the exact same thing happened. >>> Please tell me (in terms an idiot can understand:-) how to get >>> the Sage make command to use a different gcc. >>> >>> >> >> Good question, and I hope somebody else can improve my response. >> I didn't find a gcc switching tool like I've used in the distant past, >> so I went to /usr/bin, did an 'ls -l gc*' and noted that gcc and >> something else (gcov?) pointed to the gcc-4.4 versions. There were >> also gcc-4.3 versions, so I just did > > > For what it is worth, I have built Sage 4.1.1.rc0 with gcc 4.4.0 on > SPARC. Pari built fine. > > In theory, setting > > CC=/path/to/what/C/compiler/you/want > CXX=/path/to/what/C++/compiler/you/want > SAGE_FORTRAN=/path/to/what/Fortran/compiler/you/want > > should allow you to use any gcc. > > But in practice I don't think it will. I've tried doing this with the > Sun compiler, and find that some parts of Sage build with gcc even > though CC is specified as the Sun compiler. Hence some parts of Sage are > ignoring whatever CC is set to. > > The only one I can see to use a specific version of gcc is to make sure > that version is the first gcc in your path. Then it will be found before > any other version. > > Dave > > > > --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: 3D using processing.js
Is there anyone who could referee #6447, my ticket to implement
canvas3d? I think this would be a neat feature to have in Sage.
Thanks,
Bill
On Fri, Jul 10, 2009 at 9:23 PM, Nick Alexander wrote:
>
I did hg_sage.apply("http://trac.sagemath.org/sage_trac/attachment/
ticket/6447/trac_6447-canvas3d.patch") and I didn't *think* I saw
anything that looked like and error message.
>
> It sounds like you haven't built sage (sage -b) before rerunning it.
> You might also try (from a fresh sage!) "sage -merge 6447", which
> should download, import, build, and test for you.
>
> Nick
>
> >
>
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[sage-devel] Re: What version of gcc is needed?
2009/8/6 Dr. David Kirkby > > The README.txt says > > > SUPPORTED COMPILERS: > * Sage builds with GCC >= 3.x and GCC >= 4.1.x. > * Sage will not build with GCC 2.9.x. > * WARNING: Don't build with GCC 4.0.0, which is very buggy. > * Sage has never been built without using GCC compiler. > > > Yet from what I gather, people on OS X are using 4.0.1 with success. True. > > I've also herd it said that gcc < 3.4 will not work. True. In fact, GCC 3.x will not work anymore for any value of x, due to ratpoints. This should be considered a bug... but it's still a fact, and as far as I know nobody is even working on fixing it. I wish we wouldn't have let ratpoints get through refereeing without this getting fixed. > > I'm trying to put some sensible tests for the compilers - the current > 'configure' script is lacking in places. I'll show you what I have to date. > > > My aim is to do these things. > > 1) Allows non-GNU compilers, but issues a warning when compilers are not > GNU > 2) Checks if gcc is version is 4.0.0 and if so exits > 3) Checks if version is less than 3.4.0 and if so exits. (but is 3.4.0 > the sensible number)? I don't think any 3.x works anymore. See above. > > 4) Checks if gcc4 is at least 4.0.1 > 5) Checks that if the C compiler is gcc, then the C++ compiler is g++, > and will now allow mixing compilers. > 6) Checks the versions of gcc and g++ are the same, if the GNU tools are > used. > > i.e. this throws an error > > checking gcc version... 3.4.3 > checking if gcc accepts -dumpversion option... yes > checking gxx version... 4.4.1 > configure: error: gcc and g++ must be the same version > > 7) I hope to extend this to fortran - somewhat more difficult to do in > fact. Awesome. That's a good step toward getting rid of shipping g95. > > > I'm defining: > > Buggy_gcc_version="4.0.0" > Sage_minimum_gcc3_version="3.4.0" > Sage_minimum_gcc4_version="4.0.1" > > Are those ok? If not, what should they be? Should they be different for > OS X? > > > This is what I have as a basic configure.ac (this uses M4 macros, do > don't try to build it, but you should get the idea what it does). > > I really need to know what compiler versions to accept, and what to > reject, as things that are said on sage-devel and things that it says in > README.txt are not the same. > > If we are going to permit 4.0.1 on OS X, but not anywhere else, then I'd > need to come up with a test for that. I can't recall why we wouldn't allow 4.0.1 on Linux... > > > > Dave > > AC_PREREQ(2.62) > AC_COPYRIGHT([GPL version 2]) > AC_INIT([Sage],[version], sage-devel@googlegroups.com) > AC_CONFIG_SRCDIR([Sage.c]) > > AM_INIT_AUTOMAKE([1.9.6 foreign]) > > #- > # Hardware architecture > # > AC_CANONICAL_HOST > > #- > # C/C++ compilers > > AC_LANG(C) > AC_LANG(C++) > AC_LANG(Fortran) > AC_PROG_CC() > AC_PROG_CXX() > AC_PROG_F77([gfortran g95]) > AC_PROG_CPP > > Buggy_gcc_version="4.0.0" > Sage_minimum_gcc3_version="3.4.0" > Sage_minimum_gcc4_version="4.0.1" > if test x$GCC = xyes > then > dnl Check if C++ compiler is g++. If not, there is a problem. > dnl as mixing GNU and non-GNU compilers is likely to cause problems. > if test x$GXX != xyes > then >AC_MSG_WARN([You are trying to use gcc but not g++]) >AC_MSG_ERROR([The mixing of GNU and non-GNU compilers is not > permitted]) > fi > dnl do likewise with the Fortran compiler (not working yet) > if test x$G77 != xyes > then >AC_MSG_WARN([You are trying to use gcc but not a GNU Fortran > compiler]) >AC_MSG_ERROR([The mixing of GNU and non-GNU compilers is not > permitted]) > fi > > dnl Thank you to Andrew W. Nosenko andrew.w.nose...@gmail.com who > answered my query about > dnl testing of gcc versions on the autoc...@gnu.org mailing list. > dnl AS_VERSION_COMPARE(ver-1, ver-2, [action-if-less], > [action-if-eq], [action-if-greater]) > AX_GCC_VERSION > AX_GXX_VERSION > AS_VERSION_COMPARE([$GCC_VERSION], [$GXX_VERSION], > [AC_MSG_ERROR([gcc and g++ must be the same version])], > [], > [AC_MSG_ERROR([gcc and g++ must be the same version])]) > > dnl Exit if the version of GCC is known to be buggy. > AS_VERSION_COMPARE([$GCC_VERSION], [$Buggy_gcc_version],[], > [ > AC_MSG_WARN([GCC $Buggy_gcc_version is very buggy and can not > build AC_PACKAGE_NAME. Please use]) > AC_MSG_WARN([a GCC 3.x version of at least > $Sage_minimum_gcc3_version or a GCC 4.x version]) > AC_MSG_WARN([of at least $Sage_minimum_gcc4_version. (GCC > $Buggy_gcc_version is too bug ridden)]) > AC_MSG_ERROR([Exiting due to the use of a buggy GCC]) > ] > , []) > dnl Exit if the version of GCC is known to be too old > AS_VERSION_COMPARE([$GCC_VERSION], [$Sage_minimum_gcc3_version],[ > AC_MSG_WARN([GCC $GCC
[sage-devel] Re: What version of gcc is needed?
Dr. David Kirkby wrote: > 5) Checks that if the C compiler is gcc, then the C++ compiler is g++, > and will now allow mixing compilers. Sorry, I want to stop people mixing GNU and non-GNU compilers, as that is bound to result in problems. --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] What version of gcc is needed?
The README.txt says SUPPORTED COMPILERS: * Sage builds with GCC >= 3.x and GCC >= 4.1.x. * Sage will not build with GCC 2.9.x. * WARNING: Don't build with GCC 4.0.0, which is very buggy. * Sage has never been built without using GCC compiler. Yet from what I gather, people on OS X are using 4.0.1 with success. I've also herd it said that gcc < 3.4 will not work. I'm trying to put some sensible tests for the compilers - the current 'configure' script is lacking in places. I'll show you what I have to date. My aim is to do these things. 1) Allows non-GNU compilers, but issues a warning when compilers are not GNU 2) Checks if gcc is version is 4.0.0 and if so exits 3) Checks if version is less than 3.4.0 and if so exits. (but is 3.4.0 the sensible number)? 4) Checks if gcc4 is at least 4.0.1 5) Checks that if the C compiler is gcc, then the C++ compiler is g++, and will now allow mixing compilers. 6) Checks the versions of gcc and g++ are the same, if the GNU tools are used. i.e. this throws an error checking gcc version... 3.4.3 checking if gcc accepts -dumpversion option... yes checking gxx version... 4.4.1 configure: error: gcc and g++ must be the same version 7) I hope to extend this to fortran - somewhat more difficult to do in fact. I'm defining: Buggy_gcc_version="4.0.0" Sage_minimum_gcc3_version="3.4.0" Sage_minimum_gcc4_version="4.0.1" Are those ok? If not, what should they be? Should they be different for OS X? This is what I have as a basic configure.ac (this uses M4 macros, do don't try to build it, but you should get the idea what it does). I really need to know what compiler versions to accept, and what to reject, as things that are said on sage-devel and things that it says in README.txt are not the same. If we are going to permit 4.0.1 on OS X, but not anywhere else, then I'd need to come up with a test for that. Dave AC_PREREQ(2.62) AC_COPYRIGHT([GPL version 2]) AC_INIT([Sage],[version], sage-devel@googlegroups.com) AC_CONFIG_SRCDIR([Sage.c]) AM_INIT_AUTOMAKE([1.9.6 foreign]) #- # Hardware architecture # AC_CANONICAL_HOST #- # C/C++ compilers AC_LANG(C) AC_LANG(C++) AC_LANG(Fortran) AC_PROG_CC() AC_PROG_CXX() AC_PROG_F77([gfortran g95]) AC_PROG_CPP Buggy_gcc_version="4.0.0" Sage_minimum_gcc3_version="3.4.0" Sage_minimum_gcc4_version="4.0.1" if test x$GCC = xyes then dnl Check if C++ compiler is g++. If not, there is a problem. dnl as mixing GNU and non-GNU compilers is likely to cause problems. if test x$GXX != xyes then AC_MSG_WARN([You are trying to use gcc but not g++]) AC_MSG_ERROR([The mixing of GNU and non-GNU compilers is not permitted]) fi dnl do likewise with the Fortran compiler (not working yet) if test x$G77 != xyes then AC_MSG_WARN([You are trying to use gcc but not a GNU Fortran compiler]) AC_MSG_ERROR([The mixing of GNU and non-GNU compilers is not permitted]) fi dnl Thank you to Andrew W. Nosenko andrew.w.nose...@gmail.com who answered my query about dnl testing of gcc versions on the autoc...@gnu.org mailing list. dnl AS_VERSION_COMPARE(ver-1, ver-2, [action-if-less], [action-if-eq], [action-if-greater]) AX_GCC_VERSION AX_GXX_VERSION AS_VERSION_COMPARE([$GCC_VERSION], [$GXX_VERSION], [AC_MSG_ERROR([gcc and g++ must be the same version])], [], [AC_MSG_ERROR([gcc and g++ must be the same version])]) dnl Exit if the version of GCC is known to be buggy. AS_VERSION_COMPARE([$GCC_VERSION], [$Buggy_gcc_version],[], [ AC_MSG_WARN([GCC $Buggy_gcc_version is very buggy and can not build AC_PACKAGE_NAME. Please use]) AC_MSG_WARN([a GCC 3.x version of at least $Sage_minimum_gcc3_version or a GCC 4.x version]) AC_MSG_WARN([of at least $Sage_minimum_gcc4_version. (GCC $Buggy_gcc_version is too bug ridden)]) AC_MSG_ERROR([Exiting due to the use of a buggy GCC]) ] , []) dnl Exit if the version of GCC is known to be too old AS_VERSION_COMPARE([$GCC_VERSION], [$Sage_minimum_gcc3_version],[ AC_MSG_WARN([GCC $GCC_VERSION is too old and can not build AC_PACKAGE_NAME. Please use]) AC_MSG_WARN([a GCC 3.x version of at least $Sage_minimum_gcc3_version or a GCC 4.x version]) AC_MSG_WARN([of at least $Sage_minimum_gcc4_version. (GCC $Buggy_gcc_version is too bug ridden)]) AC_MSG_ERROR([Exiting due to the use of a version of GCC that is too old]) ], [],[]) dnl AS_VERSION_COMPARE(ver-1, ver-2, [action-if-less], [action-if-eq], [action-if-greater]) else AC_MSG_WARN([You have a non-GNU compiler, but AC_PACKAGE_NAME has never been built]) AC_MSG_WARN([successfully with any compiler other than GCC, despite]) AC_MSG_WARN([some attempts made on Solaris to use
[sage-devel] Re: only use ASCII characters in patches
Hi Gonzalo, On Thu, Aug 6, 2009 at 12:21 PM, Gonzalo Tornaria wrote: > > On Wed, Aug 5, 2009 at 4:19 PM, wrote: >> >> On 2009-Aug-04 15:49:40 +0100, David Kirkby wrote: >>>I don't claim to know the most appropiate letter - it was just what it >>>looked like when I see it. But I would agree non-ASCII characters >>>should be removed - it causes many issues. >> >> I would see restricting Sage to ASCII-only as fairly limiting - >> English is one of about two languges that can be expressed using only >> ASCII. If Sage is going to be used (and accept contributions from) >> outside the English-speaking world then non-ASCII support is fairly >> important. >> >> The proposed patch might be the best solution for the short term but >> in the longer term, I believe Sage needs to look at how non-ASCII >> characters can be supported - UTF-8 is probably the best solution here >> since it is a proper superset of ASCII. > > +1 > > My students had very frustrating issues with loading code with > non-ascii characters or CRLF end of lines, just because they use > non-ascii letters in comments or they used an editor with DOS line > endings. > > This arises in the following setup: they write a .py or a .sage file, > which they upload to a sage worksheet. When they try to load the .py, > it gives useless errors if the file contains CRLF or non-ascii > letters. I think it is a bit better when loading .sage files. > > It's especially frustrating since UTF-8 in the notebook works > reasonably well --- can use non-ascii in comments, html cells, even > python strings, etc. (some quirks may remain, but it's pretty good --- > much better than back in march when my course started). > > Also, it'd be nice to be able to spell names properly in sage source > code (this one is way less important to me). I agree that restricting to ASCII only is a short-term option. The issue that started this thread is related to non-ASCII characters in a patch that modifies sage/graphs/graph.py Because of that patch, it has caused the reference manual to fail to build with Sage 4.1.1.rc1 and resulted in many doctest failures. The issue of non-ASCII characters should be revisited again after the release of Sage 4.1.1. Until then, only ASCII characters should be used in any patches that are to be merged in the 4.1.1 release cycle. -- Regards Minh Van Nguyen --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Cylindrical Algebraic Decomposition for Sage
Nick Alexander wrote: >> unfortunately, there is little support for QEPCAD for mac. In >> particular, it seems that my system mac os 10.4/ppc is not even >> supported by fink. See http://pdb.finkproject.org/pdb/package.php/qepcad > > I know nothing about this, but start with the spkg at > http://trac.sagemath.org/sage_trac/ticket/772 > and the patches (already merged?) at > http://trac.sagemath.org/sage_trac/ticket/3431 > .. Carl Witty and I (mostly Carl) worked on getting qepcad working with Sage. I don't know if the spkg works on 10.4. It works wonderfully in linux. I know we apply some patches to get it to compile on some systems, so the spkg may work even if qepcadb doesn't work on other systems. Carl has been working towards a native implementation of CAD in Sage for a very long time. From what I understand, some of his significant contributions (like QQbar, AA, etc.) were motivated by getting needed functionality for CAD into Sage. So I think it is just a matter of time, but it might be on the order of years before it is complete and native in Sage. Thanks, Jason --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Ubuntu 9.10 and gcc-4.4 failure
I think it might be some kind of bug in gcc-4.4.x, relating to amd64 weirdness; the pari people have had such gcc-4 issues before. What's pre-release is the Ubuntu 9.10 OS, and pre-release OSs sometimes in fact use lookahead prerelease packages, but not always. The actual gcc-4.4.1 they send out should be the same one everybody else gets. Of course, you don't just have to worry about the compiler what with all of the various utils and libs and stuff that get used, and the whole assortment may in fact be 'pre-release'. I don't have an earlier Ubuntu 9.04 to check out their gcc-4.4.1. And you're right about the pari mailing list: I _think_ I jumped through all the hoops to get my email sent, but then I never actually received it, so who knows how it all works. In any case, I'm updating 9.10 daily, and every day there are some libc6 / gcc / g++ updates, so I'll keep trying the pari build until they work. On Aug 6, 4:45 pm, William Stein wrote: > 2009/8/6 J Elaych > > > > > Hi all, > > > I've been working with the Sage / Python package which > > includes pari-2.3.4 and noticed that the build failed at > > the command > > > /usr/bin/gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. > > -I../src/headers -fPIC -o base3.o ../src/basemath/base3.c > > > when using the latest gcc-4.4. When I switched back to > > gcc-4.3 pari built fine. Unfortunately because of the way > > the Sage/Python packages are released, we need to be > > able to use the latest gcc's. I'm using the Ubuntu prerelease > > of 9.10. > > > I have found that the problem is completely reproducible > > from the pari-2.3.4.tar.gz and pari-2.4.2.alpha.tar.gz > > tarballs. With 'make -j2 all' the compile extends to > > init.c, where presumably the second thread halts. Using > > 'top' shows cc1 taking up 99% cpu and most of the > > memory, for hours until its interrupted. > > > I didn't find any gcc-4.4 related issues when I searched the > > mailing list archives, so I want to bring this issue to your > > attention if you don't already know about the problem. > > I don't think this is a bug in GCC-4.4 or 4.4.1 released versions. I > regularly build Sage on the Skynet cluster which had GCC 4.4.0 for a long > time, and lately has had GCC 4.4.1, and I haven't had any specific compiler > problems with building PARI. I just checked and my build with GCC 4.4.1 of > Sage-4.1.1.rc1 worked fine. Isn't your ubuntu GCC a prerelease or > something? Prerelease compilers almost never work to build Sage. > > Note that skynet only has Fedora, Suse, and Redhat boxes on it, and the GCC > on their was built by their sysadmin. It's > > [wst...@eno ~]$ gcc -v > Using built-in specs. > Target: x86_64-unknown-linux-gnu > Configured with: /usr/local/gcc-4.4.1/src/gcc-4.4.1/configure > --enable-languages=c,c++,fortran,java --with-gnu-as > --with-gnu-as=/usr/local/binutils-2.19.1/x86_64-Linux-fc-gcc-4.3.3/bin/as > --with-gnu-ld > --with-ld=/usr/local/binutils-2.19.1/x86_64-Linux-fc-gcc-4.3.3/bin/ld > --with-gmp=/usr/local/mpir-1.2.1/x86_64-Linux-core2-gcc-4.4.0 > --with-mpfr=/usr/local/mpfr-2.4.1/x86_64-Linux-core2-mpir-1.2.1-gcc-4.4.0 > --prefix=/usr/local/gcc-4.4.1/x86_64-Linux-core2-fc > Thread model: posix > gcc version 4.4.1 (GCC) > > (I'm not cc'ing this to the PARI list, since it is too difficult for me to > figure out how to post to their mailing list.) > > William --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage on the Sun website
Minh Nguyen wrote: > Hi Ondrej, > > On Fri, Aug 7, 2009 at 8:19 AM, Ondrej Certik wrote: >> On Wed, Aug 5, 2009 at 5:41 PM, William Stein wrote: >>> Hi, >>> >>> There is an article on the Sun website that mentions Sage: >>> >>> http://www.sun.com/customers/servers/univ_washington.xml >> Nice. Does Sage work on that machine? > > The latest release that's currently installed on the Sun SPARC T2 > machine is Sage 3.4.1. It's installed system-wide, so if you have an > account on t2 you can use that version of Sage. There's also *currently* a later Sage at /scratch/kirkby/sage-4.1.1.rc0/sage kir...@t2:[/scratch/kirkby/sage-4.1.1.rc0] $ ./sage -- | Sage Version 4.1.1.rc0, Release Date: 2009-07-29 | | Type notebook() for the GUI, and license() for information.| -- ** ** * Warning: this is a prerelease version, and it may be unstable. * ** ** sage: 12+45 57 However, Maxima is not built into this release of Sage. In order to get Maxima to build, I'd need to use the latest CVS source from both ECL and Maxima. Given both ECL and Maxima will make new official (stable) releases this month, it hardly seems worth the effort just now. --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Ubuntu 9.10 and gcc-4.4 failure
2009/8/6 J Elaych > Hi all, > > I've been working with the Sage / Python package which > includes pari-2.3.4 and noticed that the build failed at > the command > > /usr/bin/gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer-I. > -I../src/headers -fPIC -o base3.o ../src/basemath/base3.c > > when using the latest gcc-4.4. When I switched back to > gcc-4.3 pari built fine. Unfortunately because of the way > the Sage/Python packages are released, we need to be > able to use the latest gcc's. I'm using the Ubuntu prerelease > of 9.10. > > I have found that the problem is completely reproducible > from the pari-2.3.4.tar.gz and pari-2.4.2.alpha.tar.gz > tarballs. With 'make -j2 all' the compile extends to > init.c, where presumably the second thread halts. Using > 'top' shows cc1 taking up 99% cpu and most of the > memory, for hours until its interrupted. > > I didn't find any gcc-4.4 related issues when I searched the > mailing list archives, so I want to bring this issue to your > attention if you don't already know about the problem. > I don't think this is a bug in GCC-4.4 or 4.4.1 released versions. I regularly build Sage on the Skynet cluster which had GCC 4.4.0 for a long time, and lately has had GCC 4.4.1, and I haven't had any specific compiler problems with building PARI. I just checked and my build with GCC 4.4.1 of Sage-4.1.1.rc1 worked fine. Isn't your ubuntu GCC a prerelease or something? Prerelease compilers almost never work to build Sage. Note that skynet only has Fedora, Suse, and Redhat boxes on it, and the GCC on their was built by their sysadmin. It's [wst...@eno ~]$ gcc -v Using built-in specs. Target: x86_64-unknown-linux-gnu Configured with: /usr/local/gcc-4.4.1/src/gcc-4.4.1/configure --enable-languages=c,c++,fortran,java --with-gnu-as --with-gnu-as=/usr/local/binutils-2.19.1/x86_64-Linux-fc-gcc-4.3.3/bin/as --with-gnu-ld --with-ld=/usr/local/binutils-2.19.1/x86_64-Linux-fc-gcc-4.3.3/bin/ld --with-gmp=/usr/local/mpir-1.2.1/x86_64-Linux-core2-gcc-4.4.0 --with-mpfr=/usr/local/mpfr-2.4.1/x86_64-Linux-core2-mpir-1.2.1-gcc-4.4.0 --prefix=/usr/local/gcc-4.4.1/x86_64-Linux-core2-fc Thread model: posix gcc version 4.4.1 (GCC) (I'm not cc'ing this to the PARI list, since it is too difficult for me to figure out how to post to their mailing list.) William --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 4.1.1.rc1 released
Hi John, On Thu, Aug 6, 2009 at 6:48 AM, John H Palmieri wrote: > > On Aug 5, 1:44 pm, John H Palmieri wrote: >> On Aug 5, 12:57 pm, Minh Nguyen wrote: > > [snip] > >> On my ubuntu box, if I upgrade to Sphinx-0.6.2, for the file sage/ >> graphs/graph I get the message >> >> Sphinx error: >> 'ascii' codec can't decode byte 0xc3 in position 404: ordinal not in >> range(128) >> >> I'm trying to track this down now. (In other words, I don't think >> it's a Sphinx issue -- it's something wrong with the file graph.py.) > > Minh, does your patch at #6674 fix things? I suspect that the patch at #6674 http://trac.sagemath.org/sage_trac/ticket/6674 should fix the non-ASCII characters issue and some other problems as well. I'm currently testing my merge tree with that patch applied. -- Regards Minh Van Nguyen --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage on the Sun website
On Thu, Aug 6, 2009 at 4:34 PM, Robert Bradshaw wrote: > On Thu, 6 Aug 2009, Ondrej Certik wrote: > >> >> On Wed, Aug 5, 2009 at 5:41 PM, William Stein wrote: >>> Hi, >>> >>> There is an article on the Sun website that mentions Sage: >>> >>> http://www.sun.com/customers/servers/univ_washington.xml >> >> Nice. Does Sage work on that machine? You were describing how easy it >> is to test in parallel, so I was curious if you were talking about the >> sun machine, or sage.math. >> >> Ondrej > > sage.math (as well as geom, mod, boxen, and the file server) are all Sun > machines. Of course, David Kirkby is making a lot of progress on getting > Sage to run on t2 as well, but that's not what they're talking about here. > > They managed to put a very positive spin on their hardware without > bending the truth... of course the fact that they gave us a very sweet > deal on some very sweet machines helped :). One thing that is missing is > they barely mentioned doing actually mathematical computation on the > machines--it was mostly about developing and supporting Sage. Ah, I got it -- I forgot that sage.math is from Sun too. So it makes perfect sense now. Ondrej --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage on the Sun website
On Thu, 6 Aug 2009, Ondrej Certik wrote: > > On Wed, Aug 5, 2009 at 5:41 PM, William Stein wrote: >> Hi, >> >> There is an article on the Sun website that mentions Sage: >> >> ?? http://www.sun.com/customers/servers/univ_washington.xml > > Nice. Does Sage work on that machine? You were describing how easy it > is to test in parallel, so I was curious if you were talking about the > sun machine, or sage.math. > > Ondrej sage.math (as well as geom, mod, boxen, and the file server) are all Sun machines. Of course, David Kirkby is making a lot of progress on getting Sage to run on t2 as well, but that's not what they're talking about here. They managed to put a very positive spin on their hardware without bending the truth... of course the fact that they gave us a very sweet deal on some very sweet machines helped :). One thing that is missing is they barely mentioned doing actually mathematical computation on the machines--it was mostly about developing and supporting Sage. - Robert --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage on the Sun website
Hi Ondrej, On Fri, Aug 7, 2009 at 8:19 AM, Ondrej Certik wrote: > > On Wed, Aug 5, 2009 at 5:41 PM, William Stein wrote: >> Hi, >> >> There is an article on the Sun website that mentions Sage: >> >> http://www.sun.com/customers/servers/univ_washington.xml > > Nice. Does Sage work on that machine? The latest release that's currently installed on the Sun SPARC T2 machine is Sage 3.4.1. It's installed system-wide, so if you have an account on t2 you can use that version of Sage. > You were describing how easy it > is to test in parallel, so I was curious if you were talking about the > sun machine, or sage.math. The machine sage.math is a Sun server machine running an Ubuntu server distribution. So most likely the article is talking about sage.math. -- Regards Minh Van Nguyen --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage on the Sun website
On Wed, Aug 5, 2009 at 5:41 PM, William Stein wrote: > Hi, > > There is an article on the Sun website that mentions Sage: > > http://www.sun.com/customers/servers/univ_washington.xml Nice. Does Sage work on that machine? You were describing how easy it is to test in parallel, so I was curious if you were talking about the sun machine, or sage.math. Ondrej --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 4.1.1.rc1 build halt
J Elaych wrote: >> I just upgraded to karmic and the exact same thing happened. >> Please tell me (in terms an idiot can understand:-) how to get >> the Sage make command to use a different gcc. >> >> > > Good question, and I hope somebody else can improve my response. > I didn't find a gcc switching tool like I've used in the distant past, > so I went to /usr/bin, did an 'ls -l gc*' and noted that gcc and > something else (gcov?) pointed to the gcc-4.4 versions. There were > also gcc-4.3 versions, so I just did For what it is worth, I have built Sage 4.1.1.rc0 with gcc 4.4.0 on SPARC. Pari built fine. In theory, setting CC=/path/to/what/C/compiler/you/want CXX=/path/to/what/C++/compiler/you/want SAGE_FORTRAN=/path/to/what/Fortran/compiler/you/want should allow you to use any gcc. But in practice I don't think it will. I've tried doing this with the Sun compiler, and find that some parts of Sage build with gcc even though CC is specified as the Sun compiler. Hence some parts of Sage are ignoring whatever CC is set to. The only one I can see to use a specific version of gcc is to make sure that version is the first gcc in your path. Then it will be found before any other version. Dave --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: pictures in the reference manual?
On Aug 5, 6:16 pm, Pat LeSmithe wrote: > John H Palmieri wrote: > > Should we allow the inclusion of pictures in the reference manual? We > > could have a directory > > > SAGE_ROOT/devel/sage/doc/en/reference/pictures > > > and then in docstrings in the Sage library code, a line like > > > .. image:: ../../pictures/sphere.png > > > would include the picture in the reference manual. (This is for a > > file in sage/sage/MODULE/FILE.py; adjust the number of "../"s for > > files in sage/sage/MODULE/SUBDIRECTORY/FILE.py, etc.) I haven't > > figured out how to get the pictures to appear when you view the > > docstrings in the notebook, but I haven't worked at it very much. > > I think one way to go, as we do already for HTML files, is to make the > image directory accessible to Sphinx on disk for the reference manual > proper, but also to map the directory to some server address, in twist.py. If they are included in the reference manual by ".. image:: blah.png" directives, then when the docs are built, the images are all copied to sage/doc/output/html/en/reference/_images, and since these are viewable in the live and static versions of the documentation, the pictures should be accessible already. In the cached html version of the docstring (in .sage/sage_worksheets/doc), I can edit the path for the image, putting in "http://localhost:8000/doc/static/reference/ _images/blah.png", and the image appears. So for notebook introspection, we need to replace the old path with the appropriate URL; then the issue is that the images may get renamed when the docs are built. For example, I was imagining that the "pictures" directory would have subdirectories, for example, one from each Sage module. If there are files "pictures/homology/simplex.png" and "pictures/geometry/simplex.png", each used in docstrings somewhere in the Sage library, then these would be copied to something like "reference/_images/simplex.png" and "reference/_images/simplex1.png", and I don't know how to keep track of which one goes with which docstring (other than scanning the html version of the reference manual). I guess the other issue is that if there are pictures in functions which are not included in the reference manual (__init__, for example), then they would not be available. [snip] > I think the command-line output would, if we left it alone, contain the > source line. Perhaps we can process that, too, in some way? Should the > docstring not make essential use of the image? I think that would be best. For example, in the file plot.py, a docstring could look like EXAMPLES: We construct a plot involving several graphics objects:: sage: G = plot(cos, -5, 5, thickness=5, rgbcolor=(0.5,1,0.5)) sage: P = polygon([[1,2], [5,6], [5,0]], rgbcolor=(1,0,0)) sage: G + P # show it .. image:: ../../pictures/plot/cos_and_triangle.png (The last line is the only change from the existing docstring.) Then in the notebook or the reference manual, you see a nice picture; from the command-line, you either see the ".. image" command, or we could remove it (via the detex function). The command-line version would then look just like it does now. John --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Linear Programming -- First applications in Sage
Of course not I mean not anymore, thank you for reminding me :-) I just created a new patch containing all you need. It is on http://trac.sagemath.org/sage_trac/ticket/6502 under the name "AllMIP". You can also get it there : http://trac.sagemath.org/sage_trac/attachment/ticket/6502/AllMIP.patch Nathann On Aug 6, 8:30 pm, Rado wrote: > I want to try it, but i have a newbie question, do i need to download > and install all 8 patches fromhttp://trac.sagemath.org/sage_trac/ticket/6502 > ? > Can we get a master patch, (something along the way of hg diff > baserv:lastrv should give a composite patch). > > On Aug 6, 10:53 am, Nathann Cohen wrote: > > > Hello everybody ! > > > A new message about Linear Programming in Sage. Everything we talked > > about a few weeks ago is now available in different places : > > > The patch necessary to use Linear Programming > > :http://trac.sagemath.org/sage_trac/ticket/6502 > > The package GLPK ( first solver available, required ) : sage > > -fhttp://www.sagemath.org/packages/optional/glpk-4.38.spkg > > The package Coin-or/Cbc ( optional, but even faster than GLPK ) > > :http://trac.sagemath.org/sage_trac/ticket/6501 > > > Today I posted the first patches for Graph functions using Linear > > Programming in Sage : > > > Vertex/Edge coloring :http://trac.sagemath.org/sage_trac/ticket/6679 > > A lot of others :http://trac.sagemath.org/sage_trac/ticket/6680 > > > Those two tickets needs reviews, but if you do not intend to give it a > > try it may just be interesting as a base of examples of what you can > > do with Linear Programming in Sage ! > > > I am aware that most of these functions can be rewritten in a > > different specific way to make them more efficient, and I expect most > > of them to be rewritten eventually. Linear Programming in Sage was the > > laziest way I knew to write all these functions, but I thought Sage > > really needed them and I hope you will find them efficient enough > > compared to what we had, or compared to what you would expect to get > > from such a general framework as LP. > > > Finally, I spent a lot of time writing the docstrings for all of these > > functions and for all the MIP-related functions, so learning how to > > use them should be pretty quick for those familiar with LP, using just > > MIP?, or using the question mark at the end of each function you'll > > find > > > Have fun, and thank you all again for your help ! ;-) > > > Nathann --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 4.1.1.rc1 build halt
> > I just upgraded to karmic and the exact same thing happened. > Please tell me (in terms an idiot can understand:-) how to get > the Sage make command to use a different gcc. > > Good question, and I hope somebody else can improve my response. I didn't find a gcc switching tool like I've used in the distant past, so I went to /usr/bin, did an 'ls -l gc*' and noted that gcc and something else (gcov?) pointed to the gcc-4.4 versions. There were also gcc-4.3 versions, so I just did cd /usr/bin sudo rm gcc gcov sudo ln -s gcc-4.3 gcc sudo ln -s gcov-4.3 gcov The problem is that then Sage dies with some make error [255] in the Atlas build, and rather than to keep mucking around with earlier gcc versions I'm going to ping the pari mailing list. The raw pari.tar downloads show the same problems reproducibly, so of course they should be made aware. I also tried a bunch of different -f flags on gcc-4.4 in the pari tar files and nothing helped. --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Linear Programming -- First applications in Sage
I want to try it, but i have a newbie question, do i need to download and install all 8 patches from http://trac.sagemath.org/sage_trac/ticket/6502 ? Can we get a master patch, (something along the way of hg diff baserv:lastrv should give a composite patch). On Aug 6, 10:53 am, Nathann Cohen wrote: > Hello everybody ! > > A new message about Linear Programming in Sage. Everything we talked > about a few weeks ago is now available in different places : > > The patch necessary to use Linear Programming > :http://trac.sagemath.org/sage_trac/ticket/6502 > The package GLPK ( first solver available, required ) : sage > -fhttp://www.sagemath.org/packages/optional/glpk-4.38.spkg > The package Coin-or/Cbc ( optional, but even faster than GLPK ) > :http://trac.sagemath.org/sage_trac/ticket/6501 > > Today I posted the first patches for Graph functions using Linear > Programming in Sage : > > Vertex/Edge coloring :http://trac.sagemath.org/sage_trac/ticket/6679 > A lot of others :http://trac.sagemath.org/sage_trac/ticket/6680 > > Those two tickets needs reviews, but if you do not intend to give it a > try it may just be interesting as a base of examples of what you can > do with Linear Programming in Sage ! > > I am aware that most of these functions can be rewritten in a > different specific way to make them more efficient, and I expect most > of them to be rewritten eventually. Linear Programming in Sage was the > laziest way I knew to write all these functions, but I thought Sage > really needed them and I hope you will find them efficient enough > compared to what we had, or compared to what you would expect to get > from such a general framework as LP. > > Finally, I spent a lot of time writing the docstrings for all of these > functions and for all the MIP-related functions, so learning how to > use them should be pretty quick for those familiar with LP, using just > MIP?, or using the question mark at the end of each function you'll > find > > Have fun, and thank you all again for your help ! ;-) > > Nathann --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage on Solaris - I've managed to build it with gcc 4.4.0 !!
2009/8/4 David Kirkby : > 2009/8/4 William Stein : > >> Once Sage builds on t2 (or disk.math), I can look into the notebook issue. >> >> William > > As soon as it does, I'll let you know. > > Dave > Sods law said the notebook would work on 't2'. Perhaps if I create you an account on my SPARC, you could take a look on there and see if you can see why it does not work on my SPARC. I think once the Maxima and ECL issues are resolved, Sage should build without too much hassle on SPARC. Then perhaps is the time to ask some more people to test it. There is still the issue with the pari header file though. We could either tell people to edit it manually, or I make a change to the .spkg to apply a patch on Solaris. I know it would be a hack, but I can't work out what's wrong. It would be good to get someone else to help on that issue. Dave --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] A suggestion to use other titles in emails about a release
When a new release is made, the person releasing that will generally start an email with the subject "Sage x.y.z is released" or similar. and then give a link to the release. 99% of people asking questions about the release, or reporting problems, simply reply to that, so the subject remains the same. Would it not be more sensible if people used a title such as * Sage x.y.x has 10 doctest failues with on OS X * "Sage x.y.z dumps core on Redhat linux" * MPIR a.b.c in Sage x.y.z refuses to build on Solaris" or something else a bit more informative? In othe words, put the version of Sage in the title, but make the rest of the subject a bit more informative that just "Sage x.y.z released" It would make finding things of interst a lot easier, if the titles were a bit more informative. Dave --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 4.1.1.rc0 finally builds on the Sun T5240 (t2).
2009/8/6 William Stein : > > > On Wed, Aug 5, 2009 at 6:02 PM, Dr. David Kirkby > wrote: >> >> In /scratch/kirkby/sage-4.1.1.rc0 there is a build of sage: >> >> >> kir...@t2:[/scratch/kirkby/sage-4.1.1.rc0] $ ./sage >> -- >> | Sage Version 4.1.1.rc0, Release Date: 2009-07-29 | >> | Type notebook() for the GUI, and license() for information. | >> -- >> ** >> * * >> * Warning: this is a prerelease version, and it may be unstable. * >> * * >> ** >> Setting permissions of DOT_SAGE directory so only you can read and write >> it. >> sage: factorial(100) >> >> 9332621544394415268169923885626670049071596826438162146859296389521753229915608941463976156518286253697920827223758251185210916864 >> sage: quit >> Exiting SAGE (CPU time 0m0.31s, Wall time 0m12.58s). >> Exiting spawned Gap process. >> kir...@t2:[/scratch/kirkby/sage-4.1.1.rc0] $ >> >> The really annoying thing is that the notebook appears to work. > > :-) Yeah! Great work getting Sage to build. > >> >> I've not >> connected a browser to it, but when I telnet to the local host on port >> 8000, so I can get a connection. But on my machine I can't. >> >> This was build with gcc 4.2.4, but I have also built Sage 4.1.1.rc0 with >> gcc 4.4.0 >> >> At one point in the build process on 't2' I had to temporarily rename >> /opt/SUNWspro to something else, as something in Sage is looking for the >> Sun C++ compiler and finding it there. I thought SCons was the reason, >> but I've hacked SCons so that should not find it. >> >> I'm going to bed now (it's 2 AM here). If anyone wants to have a play, >> or set some tests running, please do. I've changed the permissions on >> /scratch/kirkby to 777, and all files below it are 777 too. So anyone >> can write to them. (Naturally I have made a backup of this too, so I can >> restore it). > > > I typed "make test"... > > William I've checked the log and see a list of failed tests (see below). Note Maxima was not built, so anything using that would have failed. As soon as official releases of Maxima and ECL are released, I'll create packages using them. At the moment ECL is building from CVS, but it not really doing much in Sage if only Maxima uses it. Dave -- The following tests failed: sage -t "devel/sage/doc/en/constructions/linear_algebra.rst" sage -t "devel/sage/doc/en/constructions/calculus.rst" sage -t "devel/sage/doc/en/constructions/interface_issues.rst" sage -t "devel/sage/doc/en/constructions/polynomials.rst" sage -t "devel/sage/doc/en/constructions/plotting.rst" sage -t "devel/sage/doc/en/bordeaux_2008/nf_introduction.rst" sage -t "devel/sage/doc/en/bordeaux_2008/birds_other.rst" sage -t "devel/sage/doc/en/tutorial/tour_algebra.rst" sage -t "devel/sage/doc/en/tutorial/interfaces.rst" sage -t "devel/sage/doc/en/a_tour_of_sage/index.rst" sage -t "devel/sage/doc/fr/tutorial/interfaces.rst" sage -t "devel/sage/doc/fr/tutorial/tour_algebra.rst" sage -t "devel/sage/sage/graphs/graph.py" sage -t "devel/sage/sage/matrix/matrix_symbolic_dense.pyx" sage -t "devel/sage/sage/matrix/matrix2.pyx" sage -t "devel/sage/sage/matrix/matrix1.pyx" sage -t "devel/sage/sage/interfaces/tests.py" sage -t "devel/sage/sage/interfaces/maxima.py" sage -t "devel/sage/sage/interfaces/expect.py" sage -t "devel/sage/sage/schemes/elliptic_curves/ell_generic.py" sage -t "devel/sage/sage/schemes/elliptic_curves/ell_rational_field.py" sage -t "devel/sage/sage/server/simple/twist.py" sage -t "devel/sage/sage/misc/citation.pyx" sage -t "devel/sage/sage/misc/functional.py" sage -t "devel/sage/sage/misc/latex.py" sage -t "devel/sage/sage/gsl/interpolation.pyx" sage -t "devel/sage/sage/gsl/integration.pyx" sage -t "devel/sage/sage/calculus/desolvers.py" sage -t "devel/sage/sage/calculus/calculus.py" sage -t "devel/sage/sage/calculus/tests.py" sage -t "devel/sage/sage/calculus/wester.py" sage -t "devel/sage/sage/calculus/functional.py" sage -t "devel/sage/sage/calculus/test_sympy.py" sage -t "devel/sage/sage/combinat/combinat.py" sage -t "devel/sage/sage/modular/overconvergent/genus0.py" sage -t "devel/sage/sage/modular/overconvergent/weightspace.py" sage -t "devel/sage/sage/tests/benchmark.py"
[sage-devel] sage fat build , trac ticket 6246
Hi I think I know what is wrong here , if someone can point me to the 32bit virtual machine on sage.math.was.. I can have a go at fixing it Thanks Jason --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Linear Programming -- First applications in Sage
Hello everybody ! A new message about Linear Programming in Sage. Everything we talked about a few weeks ago is now available in different places : The patch necessary to use Linear Programming : http://trac.sagemath.org/sage_trac/ticket/6502 The package GLPK ( first solver available, required ) : sage -f http://www.sagemath.org/packages/optional/glpk-4.38.spkg The package Coin-or/Cbc ( optional, but even faster than GLPK ) : http://trac.sagemath.org/sage_trac/ticket/6501 Today I posted the first patches for Graph functions using Linear Programming in Sage : Vertex/Edge coloring : http://trac.sagemath.org/sage_trac/ticket/6679 A lot of others : http://trac.sagemath.org/sage_trac/ticket/6680 Those two tickets needs reviews, but if you do not intend to give it a try it may just be interesting as a base of examples of what you can do with Linear Programming in Sage ! I am aware that most of these functions can be rewritten in a different specific way to make them more efficient, and I expect most of them to be rewritten eventually. Linear Programming in Sage was the laziest way I knew to write all these functions, but I thought Sage really needed them and I hope you will find them efficient enough compared to what we had, or compared to what you would expect to get from such a general framework as LP. Finally, I spent a lot of time writing the docstrings for all of these functions and for all the MIP-related functions, so learning how to use them should be pretty quick for those familiar with LP, using just MIP?, or using the question mark at the end of each function you'll find Have fun, and thank you all again for your help ! ;-) Nathann --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 4.1.1.rc1 build halt
On Wed, Aug 5, 2009 at 9:34 PM, J Elaych wrote: > > I went into spkg/build and tried different flags. Surprisingly > with MAKE=make it systematically died at the same place, > base3.c, but with MAKE="make -j2" it continued on until > it reached init.c, and stopped there. Ubuntu is updating > gcc-4.4 just about every day, so maybe soon it will work. > > I backed out of gcc-4.4 and pointed gcc -> gcc-4.3, and sure > enough the sage build has passed through pari just fine. > I'd be interested in other Ubuntu user's experiments with > gcc-4.4. I just upgraded to karmic and the exact same thing happened. Please tell me (in terms an idiot can understand:-) how to get the Sage make command to use a different gcc. > > > On Aug 5, 5:19 pm, William Stein wrote: >> On Wed, Aug 5, 2009 at 5:12 PM, J Elaych wrote: >> >> > I'm on Ubuntu 9.10 beta with amd64 x2 and the >> > gcc version 4.4.1 (Ubuntu 4.4.1-1ubuntu1). The >> > build just stops at base3, for hours so far, though >> > 'top' shows cc1 using 99% cpu. I can't find any >> > related info by searching the group but that doesn't >> > mean there isn't a fix. Does anybody have any >> > suggestions about how I might muck around with >> > my compilers on Ubuntu? >> >> > Here's the latest terminal window: >> >> > ... >> > cd ../src/desc && /usr/bin/perl gen_proto highlevel pari.desc > >> > highlvl-linux-x86_64-29561.tmp >> > mv ../src/desc/highlvl-linux-x86_64-29561.tmp ../src/gp/highlvl.h >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -DDL_DFLT_NAME=NULL -o highlvl.o ../src/gp/highlvl.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -o whatnow.o ../src/gp/whatnow.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -I../src/graph -o plotport.o ../src/graph/plotport.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -o plotnull.o ../src/graph/plotnull.c >> > cat ../src/kernel/gmp/mp.c ../src/kernel/none/cmp.c ../src/kernel/none/ >> > gcdll.c ../src/kernel/none/ratlift.c ../src/kernel/none/invmod.c ../ >> > src/kernel/gmp/gcd.c ../src/kernel/none/mp_indep.c ../src/kernel/none/ >> > add.c > mp.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -fPIC - >> > I. -I../src/headers -I/home/jlh/wrk/sage-4.1.1.rc1/local/include -o >> > mp.o mp.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -fPIC -o mpinl.o ../src/kernel/none/mpinl.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -fPIC -o Flx.o ../src/basemath/Flx.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -fPIC -o Qfb.o ../src/basemath/Qfb.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -fPIC -o RgX.o ../src/basemath/RgX.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -fPIC -o alglin1.o ../src/basemath/alglin1.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -fPIC -o alglin2.o ../src/basemath/alglin2.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -fPIC -o arith1.o ../src/basemath/arith1.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -fPIC -o arith2.o ../src/basemath/arith2.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -fPIC -o base1.o ../src/basemath/base1.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -fPIC -o base2.o ../src/basemath/base2.c >> > gcc -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -I. - >> > I../src/headers -fPIC -o base3.o ../src/basemath/base3.c >> >> I have never ever seen or heard of anything like this before, and have no >> clue what could cause this, except a compiler bug. Can you install a more >> stable (or different) version of GCC and use that instead? >> >> -- William > > > --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage and medical imaging (i.e. pynifti)
I have a proposed experimental pynifti package, tracked as ticket #6678: http://trac.sagemath.org/sage_trac/ticket/6678 -Marshall On Aug 5, 10:23 pm, Marshall Hampton wrote: > Maybe this was some sort of path issue I don't understand, but when I > tried things again it seemed to work, i.e. if I go into my SAGE_ROOT > folder and use either sage or the sage python, the "import nifti" > works. So what I described above seems to be sufficient, and this > could be made into an spkg. I will give that a try tomorrow if I can > find the time. > > -Marshall Hampton > > On Aug 5, 10:12 pm, William Stein wrote: > > > On Wed, Aug 5, 2009 at 8:09 PM, Marshall Hampton wrote: > > > > I gave this a shot but it seems its not trivial to install. > > > > 1) I installed pymvpa with: > > > > pymvpa-0.4.2: sage -python setup.py build_ext > > > > 2) I installed the nifti c libraries with: > > > > nifticlib-1.1.0: make all > > > > 2b) then I copied everything in the bin, lib, and include directories > > > into the corresponding SAGE_LOCAL places. > > > > 3) Then I tried to install pynifti but had trouble. Going into a sage > > > shell: > > > > pynifti-0.20090303.1: sage -sh > > > > building with: > > > > pynifti-0.20090303.1: python setup.py build > > > > and installing with: > > > > pynifti-0.20090303.1: python setup.py install > > > > seems to go OK but when I try to test I get an error: > > > > pynifti-0.20090303.1: sage -python > > > Python 2.6.2 (r262:71600, Jul 16 2009, 10:01:32) > > > [GCC 4.0.1 (Apple Inc. build 5465)] on darwin > > > Type "help", "copyright", "credits" or "license" for more information. > > > >>> import nifti > > > Traceback (most recent call last): > > > File "", line 1, in > > > File "nifti/__init__.py", line 21, in > > >from nifti.image import NiftiImage, MemMappedNiftiImage > > > File "nifti/image.py", line 27, in > > >import nifti.clib as ncl > > > ImportError: No module named clib > > > > ...I'm not sure how to proceed. > > > I recommend emailing the developers of pynifti and see if they care about > > getting it to install into Sage.If so, obviously they could install Sage > > and try the above, but with their added knowledge of pynifti, they might > > succeed... > > > -- William > > > > This looks like a nice opportunity for Sage to become more relevant in > > > biomedical imaging. > > > > -Marshall Hampton > > > > On Aug 5, 1:46 pm, Harald Schilly wrote: > > > > On Aug 5, 8:36 pm, Arvid wrote: > > > > > > Will it be possible to incorporate access to NIfTI and ANALYZE files > > > > > in SAGE through PyNIfTI (http://niftilib.sourceforge.net/pynifti/)? > > > > > Hi, I can't access the sourceforge website right now, but it is "easy" > > > > to install additional python packages in sage. They don't need to be > > > > included or packaged. Just go into the "sage environment" with "sage - > > > > sh" and install the package there. Background: Sage has it's own > > > > python and you have to install it there, not system wide python > > > > installation. > > > > Your actual problem seems to be that additional C/C++ software is > > > > missing, it can be installed in the same way. > > > > And, I don't think this will be included in sage, soon. The general > > > > process is, to first create an experimental or optional package, that > > > > can be downloaded and installed. Once many users need it and after a > > > > voting it is included as a standard package. > > > > > H > > > -- > > William Stein > > Associate Professor of Mathematics > > University of Washingtonhttp://wstein.org --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Some problems on Trac...
On Thu, Aug 6, 2009 at 2:53 AM, Nathann Cohen wrote: > > Hello everybody !!! > > Am I the only one who is unable to download patches on Trac ? > > > http://trac.sagemath.org/sage_trac/raw-attachment/ticket/6674/trac_6674-use-ascii.patch > > I constantly get errors such that : > > Attachment 'trac_6674-use-ascii.patch' not found > > or > > Trac detected an internal error: > > IOError: [Errno 24] Too many open files: u'/home/sage/wiki/trac/ > sage_trac/attachments/ticket/6674/trac_6674-use-ascii.patch' > > Hi, I raised the default number of allowed open files per user on the trac server to 1 by adding this line to /etc/security/limits.conf * - nofile 1 I then stopped all wiki / trac servers that I server, and restarted them with this new limit in effect. This fixed the problem. I have noticed similar "too many open files" problems with sagenb.org when I have a large number of users at once (e.g., during a demo in Barcelona with around 30 users on a humble desktop at the front of the room serving everybody). So, this is good to be aware of. I'm also raising the limit as above for *.sagenb.org and restarting those servers, so we won't have a similar problem with sagenb.org. -- William --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Memory management with @parallel('multiprocessing'), or, how do I use Heapy?
This may be relevant to the question: http://bugs.python.org/issue6653
'Potential memory leak in multiprocessing'
Opened yesterday.
On Aug 5, 9:07 pm, Ahmed Fasih wrote:
> I started writing this post asking for assistance on using Heapy for
> studying my Sage application's memory usage. But I think that a more
> important question relates to my use of @parallel('multiprocessing').
> So here goes.
>
> Section 1.
> On an 8-core machine, I kick off a function (which has been decorated
> with @parallel('multiprocessing')) with 16 arguments. (BTW, Sage
> outrocks all---the sirens of multicore have given Matlab-addicted
> colleagues weeks of impotent rage; me, only a couple of hours of
> searching and finding "parallel?". The creators of Sage will have a
> special place in heaven.)
>
> Anyway, 16 arguments are kicked to this parallel function (which
> creates large vectors and reduces them to a scalar), I see 8 or so
> sage processes in "top", but one of them stands out: it's memory
> footprint steadily increases in small 1-3% increments to about 12% of
> memory. It stays at 12% after the sage script finishes. If I kicked
> off 100 parallel runs, I get MemoryErrors due to excessive RAM use
> (and Sage doesn't recover---it hangs, and Control-C kicks off
> KeyboardErrors but never cleanly goes down, I have to kill the
> screen).
>
> But if I decorate my function with @parallel('reference'), that is, to
> force serial execution, the Sage process at the end of many parallel
> runs only takes 1.5% memory. (It just takes a lot more time.)
>
> Is there an issue with @parallel with multiprocessing and garbage
> collection? Why would Sage sop up so much memory after parallel runs
> of a function that solely returns a scalar? (The function does take as
> its input a small compound object, deepcopy's it, modifies the copy,
> generates large vectors from the original and modified objects and
> reduces them to a scalar, which it returns. I haven't tried making
> Python explicitly garbage-collect the intermediate variables it
> generates because that sounds risky.)
>
> Section 2.
> In a bid to figure out what Python objects are taking so much RAM, I
> installed Guppy and am trying to use Heapy (http://guppy-
> pe.sourceforge.net/heapy_tutorial.html). I cannot understand its
> output, and "from guppy import hpy; hp=hpy(); hp.heap()" tells me that
> my 12% memory usage (of 8 GB RAM) is using just 40 MB of memory. If
> anyone knows how to interpret it's output, I'd be much obliged:
>
> sage: hp.heap()
>
> Partition of a set of 390118 objects. Total size = 42345660 bytes.
> Index Count % Size % Cumulative % Kind (class / dict of
> class)
> 0 168567 43 24633284 58 24633284 58 str
> 1 93441 24 3740796 9 28374080 67 tuple
> 2 1593 0 2051016 5 30425096 72 dict of module
> 3 14869 4 2022184 5 32447280 77 dict of
> numpy.core.defmatrix.matrix
> 4 25218 6 1714824 4 34162104 81 types.CodeType
> 5 24449 6 1369144 3 35531248 84 function
> 6 2518 1 1281712 3 36812960 87 dict of type
> 7 2301 1 1167912 3 37980872 90 dict (no owner)
> 8 2520 1 1094184 3 39075056 92 type
> 9 14869 4 832664 2 39907720 94
> numpy.core.defmatrix.matrix
> <839 more rows. Type e.g. '_.more' to view.>
>
> Thanks very much!
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[sage-devel] Re: Getting started with my own branch
Georg, Thanks. My situation is a bit unique (as William fully understands). Copying the sage source from sagemath.org is not an option that I have. Our sysadmins get the source and then build it and make a built directory available to us on the system. I have to proceed from there. Victor On Aug 6, 7:02 am, gsw wrote: > On 5 Aug., 19:15, VictorMiller wrote: > > > > > > > Ok, I think I've found the problem. Perhaps this should point to the > > need for making clear and complete instructions about creating your > > own copy. > > > I found that in my local copy there was a sage script that pointed to > > the systemwide sage. When I changed that I now get my local copy. So > > perhaps the instructions should say: > > > Copy the whole directory tree. Inside the top level directory there > > is a script called sage. Edit that so that SAGE_ROOT points to your > > local copy, and use that version of sage to run sage (e.g. by making a > > symbolic link to it in one of your local directories in search order > > ahead of the system wide copy). > > > So, another question -- it seems that sage -ba didn't regerenate the > > individual doc files, since if I do something like > > > EllipticCurve?? > > > the path that it displays is in the systemwide directories. Should > > sage -ba do that? How do I regenerate these files? > > > Victor > > Hi Victor, > > a) > Just to be sure --- this sounds like the "Guess 1" from William > (second message in this thread) turned out to be 100% correct, or am I > missing something? > And if "Guess 1" was correct, how could we have phrased it better / > more understandable? > > b) > Regarding the EllipticCurve?? issue. Sorry for asking --- but did you > do "sage -ba" again, after having adressed the $SAGE_ROOT problem? > > c) > Generally speaking, the way of "copying" an existing Sage tree, and > then starting to develop, is a way rarely used. So there might be > lurking even more pitfalls yet to be discovered. > On the other hand, building Sage from source is spectacularly easy: > > - download the single tar file with all sources for the current Sage > release from sagemath.org > - unpack the tar file in the directory of your choice > - cd into the newly created "Sage root" directory (after possibly > moving and/or renaming it, if you wish so) > - type "make" (and wait a few hours) > > You then have the setup / the environment Sage is developed in, and > where certainly fewer such issues as you report are to be expected. > And *if* any problems should occur during the build/install as > described above, it's likely that they will be sorted out even faster, > once reported here to sage-devel. > > Cheers, > Georg --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Getting started with my own branch
On 5 Aug., 19:15, VictorMiller wrote: > Ok, I think I've found the problem. Perhaps this should point to the > need for making clear and complete instructions about creating your > own copy. > > I found that in my local copy there was a sage script that pointed to > the systemwide sage. When I changed that I now get my local copy. So > perhaps the instructions should say: > > Copy the whole directory tree. Inside the top level directory there > is a script called sage. Edit that so that SAGE_ROOT points to your > local copy, and use that version of sage to run sage (e.g. by making a > symbolic link to it in one of your local directories in search order > ahead of the system wide copy). > > So, another question -- it seems that sage -ba didn't regerenate the > individual doc files, since if I do something like > > EllipticCurve?? > > the path that it displays is in the systemwide directories. Should > sage -ba do that? How do I regenerate these files? > > Victor > Hi Victor, a) Just to be sure --- this sounds like the "Guess 1" from William (second message in this thread) turned out to be 100% correct, or am I missing something? And if "Guess 1" was correct, how could we have phrased it better / more understandable? b) Regarding the EllipticCurve?? issue. Sorry for asking --- but did you do "sage -ba" again, after having adressed the $SAGE_ROOT problem? c) Generally speaking, the way of "copying" an existing Sage tree, and then starting to develop, is a way rarely used. So there might be lurking even more pitfalls yet to be discovered. On the other hand, building Sage from source is spectacularly easy: - download the single tar file with all sources for the current Sage release from sagemath.org - unpack the tar file in the directory of your choice - cd into the newly created "Sage root" directory (after possibly moving and/or renaming it, if you wish so) - type "make" (and wait a few hours) You then have the setup / the environment Sage is developed in, and where certainly fewer such issues as you report are to be expected. And *if* any problems should occur during the build/install as described above, it's likely that they will be sorted out even faster, once reported here to sage-devel. Cheers, Georg --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Some problems on Trac...
Hello everybody !!! Am I the only one who is unable to download patches on Trac ? http://trac.sagemath.org/sage_trac/raw-attachment/ticket/6674/trac_6674-use-ascii.patch I constantly get errors such that : Attachment 'trac_6674-use-ascii.patch' not found or Trac detected an internal error: IOError: [Errno 24] Too many open files: u'/home/sage/wiki/trac/ sage_trac/attachments/ticket/6674/trac_6674-use-ascii.patch' Nathann --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Deprecation Warning on twisted after starting notebook().
On Thu, Aug 6, 2009 at 12:58 AM, Dr. David Kirkby wrote: > > I don't know if this is particular to Solaris or not, but I found when I > started 'notebook()', which is likely to be the first command someone > runs, I immediately get a message that the 'md5 module is deprecated; > use hashlib instead' This issue is tracked and fixed here:http://twistedmatrix.com/trac/ticket/2763 It's part of the Python2.6 milestone for Twisted: http://twistedmatrix.com/trac/query?component=core&milestone=Python-2.6 so my understanding is that this will go into Twisted's next release, and it is already in the Twisted trunk. -Alex > > It gives the wrong impression to me, despite the fact I'm expect it is > perfectly functional. If I get a warning like that as soon as I start a > program, it does not give me a good impression. > > I stuck this as > > http://sagetrac.org/sage_trac/ticket/6676 > > Perhaps someone more knowledgeable than me about this bit of code could > fix it. Or is it an issue in 'twisted' itself, which need reporting > upstream? > > PS The tests are still running on 't2', but the Maxima ones are > obviously failing, since Maxima was not installed, as I stated. > > > Dave > > > > -- Alex Clemesha clemesha.org --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Deprecation Warning on twisted after starting notebook().
I don't know if this is particular to Solaris or not, but I found when I started 'notebook()', which is likely to be the first command someone runs, I immediately get a message that the 'md5 module is deprecated; use hashlib instead' It gives the wrong impression to me, despite the fact I'm expect it is perfectly functional. If I get a warning like that as soon as I start a program, it does not give me a good impression. I stuck this as http://sagetrac.org/sage_trac/ticket/6676 Perhaps someone more knowledgeable than me about this bit of code could fix it. Or is it an issue in 'twisted' itself, which need reporting upstream? PS The tests are still running on 't2', but the Maxima ones are obviously failing, since Maxima was not installed, as I stated. Dave --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
