[sage-devel] Re: Memory leaks on matrix creation?

2015-07-13 Thread Ralf Stephan
On Monday, July 13, 2015 at 9:44:01 AM UTC+2, Jori Mäntysalo wrote: Is there anything I can do for these? (Other than running the code part-by-part.) As quick hint I would use valgrind for the search. http://wiki.sagemath.org/ValgrindingSage -- You received this message because you are

[sage-devel] Re: Memory leaks on matrix creation?

2015-07-13 Thread Volker Braun
For every matrix dimension there is a parent (MatrixSpace). You are most likely seeing those. Use @fork / @parallel. On Monday, July 13, 2015 at 9:44:01 AM UTC+2, Jori Mäntysalo wrote: I was asked to make a code that iterates over all matrices of given type and size. And once again I

[sage-devel] Heuristics to approximate matrix bandwidth

2015-07-13 Thread michele . borassi
Hi all! My name is Michele Borassi, and I recently entered this great community for a Google Summer of Code project. Among other works, I am including in Sage an algorithm for computing the Cuthill-McKee and the King orderings [1,2], which are heuristics used to approximate the bandwidth of a

[sage-devel] Re: Memory leaks on matrix creation?

2015-07-13 Thread Volker Braun
True, but in practice its easy to have a matrix result hang off an @cached_method. On Monday, July 13, 2015 at 12:15:07 PM UTC+2, Simon King wrote: Hi Volker and Jori, On 2015-07-13, Volker Braun vbrau...@gmail.com javascript: wrote: For every matrix dimension there is a parent

[sage-devel] local failure of tests/startup.py doctest

2015-07-13 Thread Ralf Stephan
What could be the reason for File src/sage/tests/startup.py, line 17, in sage.tests.startup Failed example: print test_executable([sage, --python], cmd)[0] # long time Expected: False Got: BLANKLINE which happens here in the two latest devel versions, not sure when it started, I

Re: [sage-devel] Re: Memory leaks on matrix creation?

2015-07-13 Thread Jori Mäntysalo
On Mon, 13 Jul 2015, Volker Braun wrote: For every matrix dimension there is a parent (MatrixSpace). You are most likely seeing those. But they have the same size. 7 x 7 on my example code. -- Jori Mäntysalo

[sage-devel] Re: local failure of tests/startup.py doctest

2015-07-13 Thread Ralf Stephan
On Monday, July 13, 2015 at 10:45:20 AM UTC+2, Volker Braun wrote: Never seen that before. What do you get when you run it manually? Python 2.7.9 (default, May 28 2015, 07:15:13) [GCC 4.8.3 20140627 [gcc-4_8-branch revision 212064]] on linux2 Type help, copyright, credits or license for more

[sage-devel] Re: Memory leaks on matrix creation?

2015-07-13 Thread Nils Bruin
On Monday, July 13, 2015 at 10:51:09 AM UTC+2, Nils Bruin wrote: so I'd think there's a leak in constructing univar_pd. My guess would be a cached routine that shouldn't be cached. A little bisection shows that the leak is caused by calling eigenvalues. However L=[c for c in

Re: [sage-devel] Re: a sage bug

2015-07-13 Thread Volker Braun
Tor works in China (you might have to manually configure a bridge https://bridges.torproject.org). It also works great for circumventing censorship by European and American universities for that matter. On Monday, July 13, 2015 at 12:08:02 PM UTC+2, Simon King wrote: Hi Volker, On

[sage-devel] Re: Memory leaks on matrix creation?

2015-07-13 Thread Nils Bruin
On Monday, July 13, 2015 at 10:39:17 AM UTC+2, Ralf Stephan wrote: As quick hint I would use valgrind for the search. http://wiki.sagemath.org/ValgrindingSage Does valgrind understand python memory layout? most leaks in sage are due to lingering references and hence are detectable by python.

[sage-devel] Re: local failure of tests/startup.py doctest

2015-07-13 Thread Volker Braun
Do you have pdb directory in your current working directory, or something like that? On Monday, July 13, 2015 at 11:12:20 AM UTC+2, Ralf Stephan wrote: Oops, rather: from sage.all import * Traceback (most recent call last): File stdin, line 1, in module File

[sage-devel] Re: local failure of tests/startup.py doctest

2015-07-13 Thread Ralf Stephan
On Monday, July 13, 2015 at 1:49:25 PM UTC+2, Volker Braun wrote: Do you have pdb directory in your current working directory, or something like that? Ah yes, I had pdb.py and pdb.pyc from earlier unrelated sessions. Quite an accident, but you can see it happens. -- You received this

[sage-devel] Re: local failure of tests/startup.py doctest

2015-07-13 Thread Volker Braun
Never seen that before. What do you get when you run it manually? $ sage --python Python 2.7.9 (default, Jul 5 2015, 10:21:02) [GCC 5.1.1 20150618 (Red Hat 5.1.1-4)] on linux2 Type help, copyright, credits or license for more information. from sage.all import * print('IPython' in sys.modules)

[sage-devel] Re: Server Relocation

2015-07-13 Thread William Stein
On Monday, July 13, 2015, R. Andrew Ohana andrew.oh...@gmail.com wrote: On Sun, Jul 12, 2015 at 6:02 AM, Jeroen Demeyer jdeme...@cage.ugent.be javascript:_e(%7B%7D,'cvml','jdeme...@cage.ugent.be'); wrote: On 2015-07-12 03:40, R. Andrew Ohana wrote: In addition, boxen.math.washington.edu

[sage-devel] Re: Memory leaks on matrix creation?

2015-07-13 Thread Simon King
Hi Volker and Jori, On 2015-07-13, Volker Braun vbraun.n...@gmail.com wrote: For every matrix dimension there is a parent (MatrixSpace). You are most=20 likely seeing those. Use @fork / @parallel. MatrixSpace is supposed to use a weak cache. Hence, if you drop all matrices of a given dimension

Re: [sage-devel] Re: Memory leaks on matrix creation?

2015-07-13 Thread Jori Mäntysalo
On Mon, 13 Jul 2015, Nils Bruin wrote: A little bisection shows that the leak is caused by calling eigenvalues. Can you make a ticket with minimal example demonstrating bug? -- Jori Mäntysalo

[sage-devel] Re: local failure of tests/startup.py doctest

2015-07-13 Thread Ralf Stephan
Oops, rather: from sage.all import * Traceback (most recent call last): File stdin, line 1, in module File /home/ralf/sage/local/lib/python2.7/site-packages/sage/all.py, line 84, in module from sage.misc.all import * # takes a while File

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Jori Mäntysalo
On Mon, 13 Jul 2015, mmarco wrote: Related to that, i think the current 17? digits are way too much for a visually nice representation. I would prefear to see 1.4142... than 1.414213562373095?  inside an expression. OK for me. But I would like to have a setting for default length; I have

Re: [sage-devel] Re: Build system changes in 6.8.beta7

2015-07-13 Thread mmarco
In gentoo, for instance, there is a file that you edit to add the licenses that you accept. That way the package manager knows which packages can be installed and which can't. I don't know if that kind of system would work for sage, but it does work pretty well for gentoo. -- You received

[sage-devel] Sage in Mac OSX 11.11 (El Capitan)

2015-07-13 Thread Juan Luis Varona
I have try to install sage (the current stable version 6.7) in Mac OSX 11.11 (El Capitan), public beta (the final version will be available after the summer). I have tried with both *sage-6.7-x86_64-Darwin-OSX_10.10_x86_64.dmg

[sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Simon King
Hi! On 2015-07-13, Nathann Cohen nathann.co...@gmail.com wrote: sage: sqrt(2) # a symbolic ring element sqrt(2) sage: QQbar(sqrt(2)) # an algebraic value 1.414213562373095? It is true that this final '?' sounds more like a '...', as if some additional digits were hidden in

[sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread mmarco
I agree with Simon, although finding a nice expression like sqrt(2)+3^(1/3) can be very costly deppending on how the algebraic number was constructed. Anyways we could have such an expression for the cases where it is evident from the number construction. Related to that, i think the current

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Nathann Cohen
I agree with Simon, although finding a nice expression like sqrt(2)+3^(1/3) can be very costly deppending on how the algebraic number was constructed. Yepyep. As Simon said we cannot always express algebraic numbers in such a nice way, though. Well, if you want to build such an object *in

[sage-devel] Re: sage 6.7 failed to load jmol to display 3d object

2015-07-13 Thread Volker Braun
Confirmed, this is http://trac.sagemath.org/ticket/18891 Run sage -i jmol to fix it for now. On Monday, July 13, 2015 at 7:14:03 PM UTC+2, rt. wrote: this is a newly built version together with gentoo, while the other functions works well with only 3d plot failed. As I excute the following

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread John Cremona
Jonas -- the implementation of QQbar elements is precisely via real intervals and a polynomial satisfied by the number (not always the min poly unless that is forced, since that can be expensive). This I think that the only issue is in how real interval field elements are represented. No-one (or

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Dima Pasechnik
On Monday, 13 July 2015 18:49:48 UTC+1, William wrote: On Mon, Jul 13, 2015 at 10:15 AM, Simon King simon...@uni-jena.de javascript: wrote: Hi! On 2015-07-13, Nathann Cohen nathan...@gmail.com javascript: wrote: sage: sqrt(2) # a symbolic ring element sqrt(2)

Re: [sage-devel] Re: a sage bug

2015-07-13 Thread Dima Pasechnik
On Monday, 13 July 2015 11:08:02 UTC+1, Simon King wrote: Hi Volker, On 2015-07-13, Volker Braun vbrau...@gmail.com javascript: wrote: You can use tor (https://www.torproject.org) to access the entire internet or gmane (http://dir.gmane.org/gmane.comp.mathematics.sage.devel)

Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object

2015-07-13 Thread Francois Bissey
Hi rt, sage-on-gentoo bugs are best discussed in a github issue unless you can reproduce it in a “vanilla” sage build. Github issue for sage-on-gentoo: https://github.com/cschwan/sage-on-gentoo/issues Funny that your message lead Volker to something that was wrong in vanilla when your problem

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Volker Braun
¿¡Qué estás diciendo!? On Monday, July 13, 2015 at 9:14:51 PM UTC+2, Dima Pasechnik wrote: On Monday, 13 July 2015 18:49:48 UTC+1, William wrote: On Mon, Jul 13, 2015 at 10:15 AM, Simon King simon...@uni-jena.de wrote: Hi! On 2015-07-13, Nathann Cohen nathan...@gmail.com wrote:

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Vincent Delecroix
On 13/07/15 19:15, Simon King wrote: Hi! On 2015-07-13, Nathann Cohen nathann.co...@gmail.com wrote: sage: sqrt(2) # a symbolic ring element sqrt(2) sage: QQbar(sqrt(2)) # an algebraic value 1.414213562373095? It is true that this final '?' sounds more like a '...', as if

[sage-devel] sage 6.7 failed to load jmol to display 3d object

2015-07-13 Thread rt.
this is a newly built version together with gentoo, while the other functions works well with only 3d plot failed. As I excute the following command: sage: var('x,y') sage: plot3d(sin(x*y), (x, -pi, pi), (y, -pi, pi)) it returns :

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Jonas Jermann
On 13.07.2015 19:33, Nathann Cohen wrote: I agree with Simon, although finding a nice expression like sqrt(2)+3^(1/3) can be very costly deppending on how the algebraic number was constructed. Yepyep. As Simon said we cannot always express algebraic numbers in such a nice way, though.

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread William Stein
On Mon, Jul 13, 2015 at 10:15 AM, Simon King simon.k...@uni-jena.de wrote: Hi! On 2015-07-13, Nathann Cohen nathann.co...@gmail.com wrote: sage: sqrt(2) # a symbolic ring element sqrt(2) sage: QQbar(sqrt(2)) # an algebraic value 1.414213562373095? It is true that this

Re: [sage-devel] Heuristics to approximate matrix bandwidth

2015-07-13 Thread Thierry Dumont
Le 13/07/2015 10:36, michele.bora...@imtlucca.it a écrit : Hi all! My name is Michele Borassi, and I recently entered this great community for a Google Summer of Code project. Among other works, I am including in Sage an algorithm for computing the Cuthill-McKee and the King orderings [1,2],

[sage-devel] Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Nathann Cohen
Hello everybody! In a recent thread [1], Nils Bruin mentionned that the default representation of algebraic numbers does not really inspire trust: sage: sqrt(2) # a symbolic ring element sqrt(2) sage: QQbar(sqrt(2)) # an algebraic value 1.414213562373095? It is true that this

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Jeroen Demeyer
On 2015-07-13 21:55, Bill Hart wrote: The elements of QQbar are the solutions of algebraic equations. As you probably know, the solutions of algebraic equations of degree 4 can, in general, not be expressed that nicely. This is slightly incorrect. The general quintic can be solved

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Bill Hart
On Monday, 13 July 2015 22:07:46 UTC+2, Jeroen Demeyer wrote: On 2015-07-13 21:55, Bill Hart wrote: The elements of QQbar are the solutions of algebraic equations. As you probably know, the solutions of algebraic equations of degree 4 can, in general, not be expressed

[sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Bill Hart
On Monday, 13 July 2015 19:15:40 UTC+2, Simon King wrote: Hi! On 2015-07-13, Nathann Cohen nathan...@gmail.com javascript: wrote: sage: sqrt(2) # a symbolic ring element sqrt(2) sage: QQbar(sqrt(2)) # an algebraic value 1.414213562373095? It is true that

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Vincent Delecroix
On 13/07/15 19:48, Jonas Jermann wrote: On 13.07.2015 19:33, Nathann Cohen wrote: I agree with Simon, although finding a nice expression like sqrt(2)+3^(1/3) can be very costly deppending on how the algebraic number was constructed. Yepyep. As Simon said we cannot always express algebraic

Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Dima Pasechnik
On Monday, 13 July 2015 20:30:34 UTC+1, Volker Braun wrote: ¿¡Qué estás diciendo!? So that '¿' indicates the beginning of the questionable part! -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop

[sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)

2015-07-13 Thread Simon King
Hi Bill, On 2015-07-13, Bill Hart goodwillh...@googlemail.com wrote: On Monday, 13 July 2015 19:15:40 UTC+2, Simon King wrote: On 2015-07-13, Nathann Cohen nathan...@gmail.com javascript: wrote: sage: sqrt(2) # a symbolic ring element sqrt(2) sage: QQbar(sqrt(2)) # an

Re: [sage-devel] Building Sage 6.8.beta8 from source; singular build errors

2015-07-13 Thread Francois Bissey
This is ticket http://trac.sagemath.org/ticket/18892 and it has been solved earlier today and incidentally in April in sage-on-gentoo. You can just copy the patch

[sage-devel] Re: sage 6.7 failed to load jmol to display 3d object

2015-07-13 Thread rt.
this seems not to be my case, as François said, this problem should have been posted for sage-on-gentoo, while I haven't realized it before. Thank you all the same! 在 2015年7月14日星期二 UTC+8上午1:37:06,Volker Braun写道: Confirmed, this is http://trac.sagemath.org/ticket/18891 Run sage -i jmol to fix

Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object

2015-07-13 Thread rt.
It's strange that all the file in the directory is empty,and I find scene.spt.zip in the subdirectory,but when try to display it directly with Jmol: jmol /root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip

Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object

2015-07-13 Thread Francois Bissey
First I would try to use sage as your regular user, then we can talk about any problems arising. François On 14/07/2015, at 13:27, rt. rtgisk...@gmail.com wrote: It's strange that all the file in the directory is empty,and I find scene.spt.zip in the subdirectory,but when try to display

Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object

2015-07-13 Thread Francois Bissey
I think your problem is because you are running sage as root, but from a normal user session. The big clue is that your $DOT_SAGE folder is “/root/.sage”. Please try as a normal user. François On 14/07/2015, at 13:14, rt. rtgisk...@gmail.com wrote: this seems not to be my case, as François

Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object

2015-07-13 Thread rt.
I just switch to a normal user, it still returns the same error. And before this, I am always using root to do the daily job, and sage works well. (just for convinience, these days I'm considering rearrange my system, and maybe, a normal user will be applied to do the daily job) thanks! :) 在

Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object

2015-07-13 Thread Francois Bissey
What about posting /root/.sage/temp/rt./12958/tmp_KGOIjb.txt” or its equivalent when run as a normal user? I will only be able to test this tomorrow when I get physical access to a machine with sage-on-gentoo. François On 14/07/2015, at 13:35, rt. rtgisk...@gmail.com wrote: I just switch

Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object

2015-07-13 Thread rt.
when excuted as a regular user, this file still comes with empty contents. It's indeed no easy to diagnose sage-on-gentoo with no sage-on-gentoo on the computer, now that I have got to know the more appropriate place to report the bug, I'd better to file bugs there later. thanks! :) 在

Re: [sage-devel] Announcing $0M in new funding for the SageMathCloud over the next 3 years

2015-07-13 Thread Dima Pasechnik
On Sunday, 12 July 2015 20:59:40 UTC+1, Nathann Cohen wrote: We, European devs, have benefited from NSF funding for Sage in numerous occasions (Sage days, visits, ...) when we had no funding here. You are speaking in your own name only. You are not the Europeans Devs, are are not

Re: [sage-devel] Server Relocation

2015-07-13 Thread R. Andrew Ohana
On Sun, Jul 12, 2015 at 6:02 AM, Jeroen Demeyer jdeme...@cage.ugent.be wrote: On 2015-07-12 03:40, R. Andrew Ohana wrote: In addition, boxen.math.washington.edu http://boxen.math.washington.edu will finally be going offline, and due to lack of space won't be coming back (at least for now).

Re: [sage-devel] Announcing $0M in new funding for the SageMathCloud over the next 3 years

2015-07-13 Thread Dima Pasechnik
On Monday, 13 July 2015 08:11:45 UTC+1, Dima Pasechnik wrote: On Sunday, 12 July 2015 20:59:40 UTC+1, Nathann Cohen wrote: We, European devs, have benefited from NSF funding for Sage in numerous occasions (Sage days, visits, ...) when we had no funding here. You are speaking in

Re: [sage-devel] Announcing $0M in new funding for the SageMathCloud over the next 3 years

2015-07-13 Thread Nathann Cohen
Nicolas did not put 'the' after 'we'; do not twist his words please. What he wrote is a correct statement. You are amazing, guys. Nathann -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails

Re: [sage-devel] Re: a sage bug

2015-07-13 Thread Volker Braun
You can use tor (https://www.torproject.org) to access the entire internet or gmane (http://dir.gmane.org/gmane.comp.mathematics.sage.devel) specifically for sage-devel. Realistically, the Chinese government is always going to block mass communication utilities that are not under their

[sage-devel] Memory leaks on matrix creation?

2015-07-13 Thread Jori Mäntysalo
I was asked to make a code that iterates over all matrices of given type and size. And once again I see a memory leak. Here's an example code n = 7 m = Integer(n*(n-1)/2) for i in IntegerRange(2^m): d = i.digits(base=2, padto=m) l = [[1]+[0]*(n-1)] for j in range(n-1):

Re: [sage-devel] Announcing $0M in new funding for the SageMathCloud over the next 3 years

2015-07-13 Thread Nathann Cohen
there were unconfirmed reports of an 1-person demonstration in front of the US Embassy in Paris, with a banner saying Sage Days are a waste of US taxpayer's money! Stop them now! Don't trust anybody who claims to have seen me in Paris. They are liars. Though on the other hand that would