Re: [sage-devel] Re: Is the valgrind spkg broken? Debugging help needed...

2014-09-05 Thread Jeroen Demeyer
On 2014-09-04 22:38, Simon King wrote: And how can one build the debug version? I recall that one had to export SAGE_DEBUG=yes before building, and I had several Sage versions on my machine, all built from sources. But now, with git, I only have *one* Sage install. Is it possible to switch back

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Jori Mantysalo
On Thu, 4 Sep 2014, Volker Braun wrote: ls -al /lib /lib64 ls: cannot access /lib64 : No such file or directory You don't have a 64-bit system, it seems.  What the hell... I have just mechanically copied output without thinkin. I have 64-bit system where /lib64 is symlink to

Re: [sage-devel] Re: speed regression testing

2014-09-05 Thread Clement Pernet
Hi Jean-Pierre and all, Grat! At some point, I pushed patches on linbox-devel (or something like that), but never got any reply. IIRC they were just tiny patches to ease ocmpilation on unusual archs. I did not check recently, but one year ago or so they did not make it upstream. It would

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Volker Braun
The missing symbol is in libgfortran: $ readelf -aW /usr/lib64/libgfortran.so.3 | grep _gfortran_transfer_integer_write@@GFORTRAN_1.4 676: 000e1f40 5 FUNCGLOBAL DEFAULT 12 _gfortran_transfer_integer_write@@GFORTRAN_1.4 So it seems that we don't link libf77blas against

[sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-05 Thread Nathann Cohen
Permutation groups used to only handle permutations of 1,..n, and the methods permute_rows and friends of matrices coped with this with an ugly and potentially confusing shift by 1. EVERYBODY is using those -1 and +1 everywhere. Those 1-based permutations are just hell for whoever uses

[sage-devel] Re: Is the valgrind spkg broken? Debugging help needed...

2014-09-05 Thread Simon King
Hi Jeroen, On 2014-09-05, Jeroen Demeyer jdeme...@cage.ugent.be wrote: On 2014-09-04 22:38, Simon King wrote: And how can one build the debug version? I recall that one had to export SAGE_DEBUG=yes before building, and I had several Sage versions on my machine, all built from sources. But

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Jori Mantysalo
On Fri, 5 Sep 2014, Volker Braun wrote: So it seems that we don't link libf77blas against libgfortran. Whats the output of  sage -sh -c ldd local/lib/libf77blas.so linux-vdso.so.1 = (0x7fffad3fe000) libatlas.so.3 =

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Jean-Pierre Flori
On Friday, September 5, 2014 11:42:21 AM UTC+2, Jori Mantysalo wrote: On Fri, 5 Sep 2014, Volker Braun wrote: So it seems that we don't link libf77blas against libgfortran. Whats the output of sage -sh -c ldd local/lib/libf77blas.so linux-vdso.so.1 =

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Francois Bissey
What is very curious is that you have a compilation error, yet you say that setting LD_LIBRARY_PATH solve the problem. That variable shouldn't influence compilation/linking, unlike LD_RUN_PATH or LDFLAGS. Are you using gold for linking? François On 5/09/2014, at 21:42, Jori Mantysalo

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Jori Mantysalo
On Fri, 5 Sep 2014, Jean-Pierre Flori wrote: Btw, I just installed a clean Fedora 20. At least yum install patch m4 is needed before compiling. Might be worth writing up somewhere the packages that are needed to compile. http://www.sagemath.org/doc/installation/source.html

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Volker Braun
The erroneous dependency on patch was fixed in #16794 On Friday, September 5, 2014 10:42:21 AM UTC+1, Jori Mantysalo wrote: On Fri, 5 Sep 2014, Volker Braun wrote: So it seems that we don't link libf77blas against libgfortran. Whats the output of sage -sh -c ldd

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Jori Mantysalo
On Fri, 5 Sep 2014, Francois Bissey wrote: What is very curious is that you have a compilation error, yet you say that setting LD_LIBRARY_PATH solve the problem. That variable shouldn't influence compilation/linking, unlike LD_RUN_PATH or LDFLAGS. Are you using gold for linking? I have never

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Francois Bissey
In /home/jm58660/r-compile-test/sage-6.3/local/var/tmp/sage/build/r-3.1.1.p0/src/src/main What does gcc -std=gnu99 -Wl,--export-dynamic -fopenmp -L/home/jm58660/r-compile-test/sage-6.3/local/lib/ -o R.bin Rmain.o -L../../lib -lR -Wl,--verbose says. Furthermore, does gcc -std=gnu99

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Volker Braun
On Friday, September 5, 2014 11:30:44 AM UTC+1, Jori Mantysalo wrote: I have never needed to think about what linker I am using. If gold is installed as a default on Fedora, then I am using it. Its not. -- You received this message because you are subscribed to the Google Groups

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Jori Mantysalo
On Fri, 5 Sep 2014, Francois Bissey wrote: In /home/jm58660/r-compile-test/sage-6.3/local/var/tmp/sage/build/r-3.1.1.p0/src/src/main What does gcc -std=gnu99 -Wl,--export-dynamic -fopenmp -L/home/jm58660/r-compile-test/sage-6.3/local/lib/ -o R.bin Rmain.o -L../../lib -lR -Wl,--verbose

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Francois Bissey
Sorry you should have started a sage shell first /home/jm58660/r-compile-test/sage-6.3/sage -sh On 5/09/2014, at 23:00, Jori Mantysalo jori.mantys...@uta.fi wrote: On Fri, 5 Sep 2014, Francois Bissey wrote: In

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Jori Mantysalo
On Fri, 5 Sep 2014, Francois Bissey wrote: Sorry you should have started a sage shell first /home/jm58660/r-compile-test/sage-6.3/sage -sh And then cd and gcc? Here: (sage-sh) jm58660@localhost:sage-6.3$ cd

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Francois Bissey
You appear to have bits of another gnu compiler in /usr/local. You don't appear to have the binaries but some libs. Do you also have libgfortran under /usr/local/lib64? François On 5/09/2014, at 23:14, Jori Mantysalo jori.mantys...@uta.fi wrote: found libstdc++.so.6 at

Re: [sage-devel] Re: Compiling sage on Fedora

2014-09-05 Thread Jori Mantysalo
On Fri, 5 Sep 2014, Francois Bissey wrote: You appear to have bits of another gnu compiler in /usr/local. You don't appear to have the binaries but some libs. Do you also have libgfortran under /usr/local/lib64? Yes. And of course /usr/local/* is checked before / and /usr. I have no idea

[sage-devel] Sage's debug version

2014-09-05 Thread Simon King
Hi! I just tried to build a debug version of Sage on my openSuse 12.3 laptop. However, with SAGE_DEBUG=yes, the Singular spkg fails to build. I know that in order to get a debug version a couple of years ago, we had to add some patch to the Singular spkg. However, it *used* to work with that

[sage-devel] About typechecking

2014-09-05 Thread Jori Mantysalo
Here is the code for is_isomorphic() on class FinitePoset: if hasattr(other,'hasse_diagram'): return . . . else: raise ValueError('The input is not a finite poset.') So for example Posets.PentagonPoset().is_isomorphic(Hello everyone!) gives the error

Re: [sage-devel] About typechecking

2014-09-05 Thread William A Stein
On Fri, Sep 5, 2014 at 7:22 AM, Jori Mantysalo jori.mantys...@uta.fi wrote: Here is the code for is_isomorphic() on class FinitePoset: if hasattr(other,'hasse_diagram'): return . . . else: raise ValueError('The input is not a finite poset.') So for

[sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-05 Thread Dima Pasechnik
I just had a quick look at it, and the following looks downright scary: +For backward compatibility, if a permutation group element +acts on the integers `\{1,\ldots,n\}` or a subset thereof, +the columns are considered as being numbered from `1`:: + +

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-05 Thread Nathann Cohen
I just had a quick look at it, and the following looks downright scary: It is one of this code's many wonders. Also, note that : sage: Permutation([1,2,3]) [1, 2, 3] sage: Permutation((1,2,3)) [2, 3, 1] I hate that code. Nathann -- You received this message because you are subscribed to the

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-05 Thread Viviane Pons
Your last example makes petgect sense in terms of mathematics: the first one is a petmutation as a word and the second one is a permutation as a group element. We need BOTH and we need both to be simple. The diff between brackets and parenthesis is quite natural AND consistent with mathematic

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-05 Thread David Joyner
On Fri, Sep 5, 2014 at 11:00 AM, Nathann Cohen nathann.co...@gmail.com wrote: I just had a quick look at it, and the following looks downright scary: It is one of this code's many wonders. Also, note that : sage: Permutation([1,2,3]) [1, 2, 3] sage: Permutation((1,2,3)) [2, 3, 1] I hate

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-05 Thread Nathann Cohen
And I must add that even so it is annoying for code, we do need the 1-starting permutations. All the combinatorists I know do not even think a permutation can start at 0. It makes things more complicated for us and we need to put extra care in code and documentation but we do need to print and

[sage-devel] Re: Sage's debug version

2014-09-05 Thread Jean-Pierre Flori
On Friday, September 5, 2014 3:47:53 PM UTC+2, Volker Braun wrote: I don't know of a ticket, feel free to fix it. All relevant files are in build/pkgs/singular. It seems that the debug patches conflict with the cygwin patch. Also, the debug patches should probably be applied strictly

[sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-05 Thread Volker Braun
The whole 0 vs. 1 based permutations (Python vs. Matlab :-) is always confusing. And there is good reason and history in both conventions, so we should IMHO accept that we'll have to live with it. Its not something that can be solved satisfactorily by trying to guess the user's intentions, you

[sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-05 Thread Dima Pasechnik
On 2014-09-05, Nathann Cohen nathann.co...@gmail.com wrote: I just had a quick look at it, and the following looks downright scary: It is one of this code's many wonders. Also, note that : sage: Permutation([1,2,3]) [1, 2, 3] sage: Permutation((1,2,3)) [2, 3, 1] this actually makes

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-05 Thread Viviane Pons
The Permutation0 might be a good idea, I don't know... It wouldn't change the tuple vs. list thing which is used to distinguish between the cycle notation and the word notation. I agree some of the syntax could be improved. But I do think backward compatibility is important. It's really annoying

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-05 Thread David Joyner
On Fri, Sep 5, 2014 at 5:48 PM, Viviane Pons vivianep...@gmail.com wrote: The Permutation0 might be a good idea, I don't know... It wouldn't change the tuple vs. list thing which is used to distinguish between the cycle notation and the word notation. I agree some of the syntax could be

Re: [sage-devel] Re: #16577: enable 0-based row/column permutation of matrices

2014-09-05 Thread Nathann Cohen
The Permutation0 might be a good idea, I don't know... It wouldn't change the tuple vs. list thing which is used to distinguish between the cycle notation and the word notation. The cycle notation is incorrect too, as a permutation is a collection of cycles. It also removes the need to

[sage-devel] Please review #16745

2014-09-05 Thread Volker Braun
http://trac.sagemath.org/ticket/16745 -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to