[sage-devel] Re: Memory leaks on matrix creation?
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 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: Memory leaks on matrix creation?
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 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): l.append( d[(j+1)*j/2:(j+1)*(j+2)/2]+ [1] + [0]*(n-j-2) ) M = Matrix(l) eig = sorted((M*M.transpose()).eigenvalues())[0] if eig = 0: print Foobar These kind of codes, where I make millions of small objects, compute something and discard the object, seems to eat memory. Not much, but so much that otherwise reasonable computable thing - say, something to run for two days - will be impossible to do directly. Is there anything I can do for these? (Other than running the code part-by-part.) This was ran on newest beta version. -- Jori Mäntysalo -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Heuristics to approximate matrix bandwidth
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 graph [3] (ticket 18876, [4]). Since the bandwidth of a graph is the bandwidth of its adjacency matrix, maybe these algorithms might be useful also in the matrix context. However, before including them, since I work with graphs and I know very little about matrix algorithms, I have some doubts: - Are these algorithm really interesting for matrix analysis? - In case, where and how should I include these algorithms? - If it is more complicated than this), could you provide more information? For instance, if you need related routines, like permuting rows and columns according to these orderings, or maybe you would like to integrate this work with other algorithms. In case, I might open a new ticket that takes care of all these things. For any other comment, doubt, or suggestion, please feel free to contact me! Thank you very much for your help! Best, Michele [1] https://en.wikipedia.org/wiki/Cuthill%E2%80%93McKee_algorithm [2] http://www.boost.org/doc/libs/1_58_0/libs/graph/doc/king_ordering.html [3] https://en.wikipedia.org/wiki/Graph_bandwidth [4] http://trac.sagemath.org/ticket/18876 -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: Memory leaks on matrix creation?
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 (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 and base ring, then the corresponding matrix space is supposed to be deallocated. If it isn't, then it's a bug. Best regards, Simon -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] local failure of tests/startup.py doctest
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 don't want to recompile half a dozen versions. System is OpenSuSE. -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Memory leaks on matrix creation?
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
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 information.
print('IPython' in sys.modules)
Traceback (most recent call last):
File stdin, line 1, in module
NameError: name 'sys' is not defined
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[sage-devel] Re: Memory leaks on matrix creation?
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 gc.get_objects() if type(c) is sage.rings.polynomial.polynomial_compiled.univar_pd] objgraph.show_backrefs(L[1000],filename=test.png) seems to show that the only reference that's findable by python's gc is the one from L! So the leak in this case might be due to a refcounting error (or a reference to a python object held by something outside the scope of the python memory manager). Or I've overlooked some subtle issue. -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: a sage bug
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 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) specifically for sage-devel. I wouldn't be surprised if they blocked tor, too (and of course anybody who uses tor automatically becomes suspect). And I have seen at several European and US-American universities that the web is configured in such a way that using gmane via slrn doesn't work (but I don't know if they just block slrn or also block using gmane in a web browser). Best regards, Simon -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: Memory leaks on matrix creation?
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. If I run:
import gc
from collections import Counter
gc.collect()
pre={id(c) for c in gc.get_objects()}
n = 5
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):
l.append( d[(j+1)*j/2:(j+1)*(j+2)/2]+ [1] + [0]*(n-j-2) )
M = Matrix(l)
eig = sorted((M*M.transpose()).eigenvalues())[0]
if eig = 0:
print Foobar
gc.collect()
post=Counter(type(o) for o in gc.get_objects() if id(o) not in pre)
sorted(post.iteritems(),key=lambda t: t[1])
I find:
...
[(type 'set', 1),
(type 'generator', 1),
(type 'builtin_function_or_method', 1),
(class '_ast.Attribute', 1),
(class 'sage.rings.qqbar.AlgebraicPolynomialTracker', 1),
(class 'sage.rings.qqbar.ANRoot', 1),
(type 'enumerate', 1),
(class '_ast.Interactive', 1),
(class '_ast.comprehension', 1),
(type 'function', 1),
(type 'instancemethod', 1),
(class
'sage.rings.polynomial.polynomial_element_generic.Polynomial_generic_dense_field',
1),
(type 'listiterator', 1),
(class '_ast.Assign', 1),
(type 'sage.rings.complex_interval.ComplexIntervalFieldElement', 1),
(class '_ast.Compare', 1),
(class '_ast.GeneratorExp', 1),
(class '_ast.Module', 1),
(type 'weakref', 3),
(class '_ast.Call', 4),
(type 'frame', 6),
(type 'sage.rings.rational.Rational', 6),
(type 'sage.rings.real_mpfi.RealIntervalFieldElement', 6),
(class 'sage.rings.qqbar.ANRational', 6),
(class 'sage.rings.qqbar.AlgebraicNumber', 7),
(class '_ast.Name', 9),
(type 'tuple', 11),
(type 'list', 29),
(type 'dict', 32),
(type 'sage.rings.polynomial.polynomial_compiled.univar_pd', 6273)]
...
so I'd think there's a leak in constructing univar_pd. My guess would be a
cached routine that shouldn't be cached.
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[sage-devel] Re: local failure of tests/startup.py doctest
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 /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 /home/ralf/sage/local/lib/python2.7/site-packages/sage/misc/all.py, line 4, in module from misc import (alarm, cancel_alarm, File /home/ralf/sage/local/lib/python2.7/site-packages/sage/misc/misc.py, line 2002, in module import pdb File pdb.py, line 2, in module pdb.set_trace() AttributeError: 'module' object has no attribute 'set_trace' -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: local failure of tests/startup.py doctest
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 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: local failure of tests/startup.py doctest
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)
False
On Monday, July 13, 2015 at 10:36:21 AM UTC+2, Ralf Stephan wrote:
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 don't want to recompile half
a dozen versions. System is OpenSuSE.
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[sage-devel] Re: Server Relocation
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 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). Important question: what will happen with the data currently stored on boxen? Will you transfer it to the new machine? It depends on what you mean by data currently on boxen. Do you mean things under /home? If so then that will still be accessible on geom.math.washington.edu and mod.math.washington.edu for the time being, as it actually a network filesystem being exported from another machine. My plan is to mount it as read only for a bit on the new machines, but after a period of time (probably a couple of months) the storage machine of the current/old sage cluster will be repurposed as a backup machine, at which point I'll make a final snapshot of the /home directory on an external usb drive. Anything lying on the root and scratch filesystems on boxen will be wiped. Don't wipe it. Instead archive it to an external usb drive. I have a bunch of large Ian drives in my office. -- 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 javascript:_e(%7B%7D,'cvml','sage-devel%2bunsubscr...@googlegroups.com'); . To post to this group, send email to sage-devel@googlegroups.com javascript:_e(%7B%7D,'cvml','sage-devel@googlegroups.com');. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. -- Andrew -- 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 javascript:_e(%7B%7D,'cvml','sage-devel%2bunsubscr...@googlegroups.com'); . To post to this group, send email to sage-devel@googlegroups.com javascript:_e(%7B%7D,'cvml','sage-devel@googlegroups.com');. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. -- Sent from my massive iPhone 6 plus. -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: Memory leaks on matrix creation?
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 and base ring, then the corresponding matrix space is supposed to be deallocated. If it isn't, then it's a bug. Best regards, Simon -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Memory leaks on matrix creation?
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
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 /home/ralf/sage/local/lib/python2.7/site-packages/sage/misc/all.py, line 4, in module from misc import (alarm, cancel_alarm, File /home/ralf/sage/local/lib/python2.7/site-packages/sage/misc/misc.py, line 2002, in module import pdb File pdb.py, line 2, in module pdb.set_trace() AttributeError: 'module' object has no attribute 'set_trace' -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 done some computations where differences arise, for example, about tenth digit. Not a big deal, thought. -- Jori Mäntysalo
Re: [sage-devel] Re: Build system changes in 6.8.beta7
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 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Sage in Mac OSX 11.11 (El Capitan)
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 ftp://ftp.fu-berlin.de/unix/misc/sage/osx/sage-6.7-x86_64-Darwin-OSX_10.10_x86_64.dmg* and *sage-6.7-x86_64-Darwin-OSX_10.10_x86_64-app.dmg ftp://ftp.fu-berlin.de/unix/misc/sage/osx/sage-6.7-x86_64-Darwin-OSX_10.10_x86_64-app.dmg* without success. None of them can be used due to an error. I have not found any information about it in any sage page, so I report it. This is the error message: Last login: Tue Jul 14 02:29:58 on ttys001 AirTeXano:~ jvarona$ /Applications/sage/sage ; exit; ┌┐ │ SageMath Version 6.7, Release Date: 2015-05-17 │ │ Type notebook() for the browser-based notebook interface.│ │ Type help() for help.│ └┘ The Sage installation tree has moved from /Users/buildslave-sage/slave/sage_git/build to /Applications/sage Updating various hardcoded paths... (Please wait at most a few minutes.) DO NOT INTERRUPT THIS. Done updating paths. Traceback (most recent call last): File /Applications/sage/src/bin/sage-ipython, line 7, in module from sage.repl.interpreter import SageTerminalApp File /Applications/sage/local/lib/python2.7/site-packages/sage/__init__.py, line 3, in module from sage.repl.ipython_extension import load_ipython_extension File /Applications/sage/local/lib/python2.7/site-packages/sage/repl/ipython_extension.py, line 59, in module from IPython.core.magic import Magics, magics_class, line_magic File /Applications/sage/local/lib/python2.7/site-packages/IPython/__init__.py, line 45, in module from .config.loader import Config File /Applications/sage/local/lib/python2.7/site-packages/IPython/config/__init__.py, line 6, in module from .application import * File /Applications/sage/local/lib/python2.7/site-packages/IPython/config/application.py, line 9, in module import json File /Applications/sage/local/lib/python/json/__init__.py, line 108, in module from .decoder import JSONDecoder File /Applications/sage/local/lib/python/json/decoder.py, line 5, in module import struct File /Applications/sage/local/lib/python/struct.py, line 1, in module from _struct import * ImportError: dlopen(/Applications/sage/local/lib/python2.7/lib-dynload/_struct.so, 2): Symbol not found: _PyUnicodeUCS4_AsEncodedString Referenced from: /Applications/sage/local/lib/python2.7/lib-dynload/_struct.so Expected in: flat namespace in /Applications/sage/local/lib/python2.7/lib-dynload/_struct.so logout Saving session...completed. [Proceso completado] -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 a value stored as a float/double. Yet it is exact. How could we replace it? Ideally, that would be a 'sqrt(2)' but can we always provide such a representation cheaply? Could we display it as 'sqrt(2)' at least when it is free to do so? 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. But it seems like an appealing idea to show a nice expression for algebraic numbers of degree up to 4. If we cannot get rid totally of this numerical representation, what would you think of replacing this '?' by a 'alg', which would be (slightly) more informative, e.g.: 1.4142134... looks exact to me: ... seems to suggest that Sage knows all (potentially infinitely many) digits but can't show them all, whereas ? seems to suggest that the last shown digit is questionable (i.e., subject to rounding errors), i.e., ? seems to suggest that Sage doesn't know the exact value. So, I'd prefer to display elements of QQbar as floating point numbers (what default precision?), always rounded DOWN to the last digit that is displayed, and followed by ... (not ?) unless the displayed value is exact. So, what is displayed is an initial part of the potentially infinite sequence of digits. Best regards, Simon -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 17? digits are way too much for a visually nice representation. I would prefear to see 1.4142... than 1.414213562373095? inside an expression. El lunes, 13 de julio de 2015, 19:15:40 (UTC+2), Simon King escribió: 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 this final '?' sounds more like a '...', as if some additional digits were hidden in a value stored as a float/double. Yet it is exact. How could we replace it? Ideally, that would be a 'sqrt(2)' but can we always provide such a representation cheaply? Could we display it as 'sqrt(2)' at least when it is free to do so? 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. But it seems like an appealing idea to show a nice expression for algebraic numbers of degree up to 4. If we cannot get rid totally of this numerical representation, what would you think of replacing this '?' by a 'alg', which would be (slightly) more informative, e.g.: 1.4142134... looks exact to me: ... seems to suggest that Sage knows all (potentially infinitely many) digits but can't show them all, whereas ? seems to suggest that the last shown digit is questionable (i.e., subject to rounding errors), i.e., ? seems to suggest that Sage doesn't know the exact value. So, I'd prefer to display elements of QQbar as floating point numbers (what default precision?), always rounded DOWN to the last digit that is displayed, and followed by ... (not ?) unless the displayed value is exact. So, what is displayed is an initial part of the potentially infinite sequence of digits. Best regards, Simon -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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* then you must describe your value somehow, and it is also stored internally somewhere.. And I wonder how, and whether we can base the representation on this internal version of the value :-) Anyways we could have such an expression for the cases where it is evident from the number construction. +1 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. +1. It would also lessen the odds of having people believe that it is stored as a float (with possibly many, but finitely many, digits) 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 from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: sage 6.7 failed to load jmol to display 3d object
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 command:
sage: var('x,y')
sage: plot3d(sin(x*y), (x, -pi, pi), (y, -pi, pi))
it returns :
/usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:561:
RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol
failed to create file '/root/.sage/temp/rt./12958/dir_W9ZHtR/preview.png',
see '/root/.sage/temp/rt./12958/tmp_KGOIjb.txt' for details
RichReprWarning,
Graphics3d Object
Not knowing what's going wrong, I have rebuild Jmol, but it changed nothing
maybe I can find the solution or reason here, and just around these days,
thanks to any help very much.
If needed, more information would be provided (as now I don't know what's
neesded.
Thanks very much!
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Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 almost) has ever liked the current form ending in a ? which does of course have a logic behind it but is *very* hard to explain (and to remember). The sqrt() - style representation is only really practical for number of degree 2 -- in principle one could do more general radical expressions, and sqrt(2)+sqrt(3) looks rather nicer than sage: QQbar(2).sqrt()+QQbar(3).sqrt() 3.146264369941973? but that is (a) expensive and (b) only applies to rather special algebraic numbers. John On 13 July 2015 at 18:49, William Stein wst...@gmail.com wrote: 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 final '?' sounds more like a '...', as if some additional digits were hidden in a value stored as a float/double. Yet it is exact. How could we replace it? Ideally, that would be a 'sqrt(2)' but can we always provide such a representation cheaply? Could we display it as 'sqrt(2)' at least when it is free to do so? 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. But it seems like an appealing idea to show a nice expression for algebraic numbers of degree up to 4. If we cannot get rid totally of this numerical representation, what would you think of replacing this '?' by a 'alg', which would be (slightly) more informative, e.g.: 1.4142134... looks exact to me: ... seems to suggest that Sage knows all (potentially infinitely many) digits but can't show them all, whereas ? seems to suggest that the last shown digit is questionable (i.e., subject to rounding errors), i.e., ? seems to suggest that Sage doesn't know the exact value. Yes. Also, with interval arithmetic, that is precisely what it means: sage: RealIntervalField(53)(sqrt(2)) 1.414213562373095? sage: QQbar(sqrt(2)) 1.414213562373095? It's certainly not good that the above two print in the same way. The (mysterious [1]) person who made those design choices -- Carl Witty -- isn't contributing anymore, or I'd ask his opinion. [1] http://stackoverflow.com/users/684532/carl-witty So, I'd prefer to display elements of QQbar as floating point numbers (what default precision?), always rounded DOWN to the last digit that is displayed, and followed by ... (not ?) unless the displayed value is exact. So, what is displayed is an initial part of the potentially infinite sequence of digits. Best regards, Simon -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. -- William (http://wstein.org) -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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) 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 a value stored as a float/double. Yet it is exact. How could we replace it? Ideally, that would be a 'sqrt(2)' but can we always provide such a representation cheaply? Could we display it as 'sqrt(2)' at least when it is free to do so? 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. But it seems like an appealing idea to show a nice expression for algebraic numbers of degree up to 4. If we cannot get rid totally of this numerical representation, what would you think of replacing this '?' by a 'alg', which would be (slightly) more informative, e.g.: 1.4142134... looks exact to me: ... seems to suggest that Sage knows all (potentially infinitely many) digits but can't show them all, whereas ? seems to suggest that the last shown digit is questionable (i.e., subject to rounding errors), i.e., ? seems to suggest that Sage doesn't know the exact value. Yes. Also, with interval arithmetic, that is precisely what it means: sage: RealIntervalField(53)(sqrt(2)) 1.414213562373095? sage: QQbar(sqrt(2)) 1.414213562373095? It's certainly not good that the above two print in the same way. The (mysterious [1]) person who made those design choices -- Carl Witty -- isn't contributing anymore, or I'd ask his opinion. As we now allow unicode, we can probably find a better character than '?'. Say ⇘, or ↴, or even ¿. [1] http://stackoverflow.com/users/684532/carl-witty So, I'd prefer to display elements of QQbar as floating point numbers (what default precision?), always rounded DOWN to the last digit that is displayed, and followed by ... (not ?) unless the displayed value is exact. So, what is displayed is an initial part of the potentially infinite sequence of digits. Best regards, Simon -- 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+...@googlegroups.com javascript:. To post to this group, send email to sage-...@googlegroups.com javascript:. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. -- William (http://wstein.org) -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: a sage bug
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) specifically for sage-devel. I wouldn't be surprised if they blocked tor, too (and of course anybody who uses tor automatically becomes suspect). And I have seen at several European and US-American universities that the web is configured in such a way that using gmane via slrn doesn't work (but I don't know if they just block slrn or also block using gmane in a web browser). I have only seen NNTP port (119) blocked (the one needed by the classical Usenet readers such as slrn). And this is mostly out of ignorance - I managed a couple of times to get it open just by emailing sysadmins. Best regards, Simon -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object
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 is unrelated. Volker's advice is not applicable
to your install since “sage -i” doesn’t exist in sage-on-gentoo.
Can you post /root/.sage/temp/rt./12958/tmp_KGOIjb.txt” so I can try
to figure it out.
François
On 14/07/2015, at 04:50, rt. rtgisk...@gmail.com 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 command:
sage: var('x,y')
sage: plot3d(sin(x*y), (x, -pi, pi), (y, -pi, pi))
it returns :
/usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:561:
RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol
failed to create file '/root/.sage/temp/rt./12958/dir_W9ZHtR/preview.png',
see '/root/.sage/temp/rt./12958/tmp_KGOIjb.txt' for details
RichReprWarning,
Graphics3d Object
Not knowing what's going wrong, I have rebuild Jmol, but it changed nothing
maybe I can find the solution or reason here, and just around these days,
thanks to any help very much.
If needed, more information would be provided (as now I don't know what's
neesded.
Thanks very much!
--
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Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
¿¡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: 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 a value stored as a float/double. Yet it is exact. How could we replace it? Ideally, that would be a 'sqrt(2)' but can we always provide such a representation cheaply? Could we display it as 'sqrt(2)' at least when it is free to do so? 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. But it seems like an appealing idea to show a nice expression for algebraic numbers of degree up to 4. If we cannot get rid totally of this numerical representation, what would you think of replacing this '?' by a 'alg', which would be (slightly) more informative, e.g.: 1.4142134... looks exact to me: ... seems to suggest that Sage knows all (potentially infinitely many) digits but can't show them all, whereas ? seems to suggest that the last shown digit is questionable (i.e., subject to rounding errors), i.e., ? seems to suggest that Sage doesn't know the exact value. Yes. Also, with interval arithmetic, that is precisely what it means: sage: RealIntervalField(53)(sqrt(2)) 1.414213562373095? sage: QQbar(sqrt(2)) 1.414213562373095? It's certainly not good that the above two print in the same way. The (mysterious [1]) person who made those design choices -- Carl Witty -- isn't contributing anymore, or I'd ask his opinion. As we now allow unicode, we can probably find a better character than '?'. Say ⇘, or ↴, or even ¿. [1] http://stackoverflow.com/users/684532/carl-witty So, I'd prefer to display elements of QQbar as floating point numbers (what default precision?), always rounded DOWN to the last digit that is displayed, and followed by ... (not ?) unless the displayed value is exact. So, what is displayed is an initial part of the potentially infinite sequence of digits. Best regards, Simon -- 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+...@googlegroups.com. To post to this group, send email to sage-...@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. -- William (http://wstein.org) -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 some additional
digits were hidden in a value stored as a float/double. Yet it is exact.
How could we replace it? Ideally, that would be a 'sqrt(2)' but can we always
provide such a representation cheaply? Could we display it as 'sqrt(2)' at least
when it is free to do so?
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. But it seems like an appealing
idea to show a nice expression for algebraic numbers of degree up to 4.
If we cannot get rid totally of this numerical representation, what would you
think of replacing this '?' by a 'alg', which would be (slightly) more
informative, e.g.:
1.4142134... looks exact to me: ... seems to suggest that Sage knows all
(potentially infinitely many) digits but can't show them all, whereas ? seems
to suggest that the last shown digit is questionable (i.e., subject to rounding
errors), i.e., ? seems to suggest that Sage doesn't know the exact value.
+1
It is consistent with
sage: words.FibonacciWord([0,1])
word: 0100101001001010010100100101001001010010...
sage: continued_fraction(pi)
[3; 7, 15, 1, 292, 1, 1, 1, 2, 1, 3, 1, 14, 2, 1, 1, 2, 2, 2, 2, ...]
sage: IntegerRange(0,+Infinity,2)
{0, 2, ...}
Vincent
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[sage-devel] sage 6.7 failed to load jmol to display 3d object
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 :
/usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:561:
RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol
failed to create file '/root/.sage/temp/rt./12958/dir_W9ZHtR/preview.png',
see '/root/.sage/temp/rt./12958/tmp_KGOIjb.txt' for details
RichReprWarning,
Graphics3d Object
Not knowing what's going wrong, I have rebuild Jmol, but it changed nothing
maybe I can find the solution or reason here, and just around these days,
thanks to any help very much.
If needed, more information would be provided (as now I don't know what's
neesded.
Thanks very much!
--
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Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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. Well, if you want to build such an object *in Sage* then you must describe your value somehow, and it is also stored internally somewhere.. And I wonder how, and whether we can base the representation on this internal version of the value :-) Anyways we could have such an expression for the cases where it is evident from the number construction. -1 I definitely prefer a uniform output. If you want a symbolic representation then convert the element to one from SR (symbolic ring). This is basically what you are asking with where it is evident anyway... Of course you could add a function which tries to do exactly that but in my opinion the default output should have a uniform look for a given parent. That way you also realize (better) over what parent you are working with currently. Sidenote: Another useful representation is the minimal polynomial + exact bounds (maybe interval field element?) for a root location. I implemented a proof of concept of such a field once where all elements were displayed as their minimal polynomial + bounds for the root location. Arithmetic operations like addition or multiplication can be defined for the root polynomial. What is harder are the root location bounds (+ irreducible parts of the polynomial) which have to be recalculated I suppose. Best Jonas -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 final '?' sounds more like a '...', as if some additional digits were hidden in a value stored as a float/double. Yet it is exact. How could we replace it? Ideally, that would be a 'sqrt(2)' but can we always provide such a representation cheaply? Could we display it as 'sqrt(2)' at least when it is free to do so? 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. But it seems like an appealing idea to show a nice expression for algebraic numbers of degree up to 4. If we cannot get rid totally of this numerical representation, what would you think of replacing this '?' by a 'alg', which would be (slightly) more informative, e.g.: 1.4142134... looks exact to me: ... seems to suggest that Sage knows all (potentially infinitely many) digits but can't show them all, whereas ? seems to suggest that the last shown digit is questionable (i.e., subject to rounding errors), i.e., ? seems to suggest that Sage doesn't know the exact value. Yes. Also, with interval arithmetic, that is precisely what it means: sage: RealIntervalField(53)(sqrt(2)) 1.414213562373095? sage: QQbar(sqrt(2)) 1.414213562373095? It's certainly not good that the above two print in the same way. The (mysterious [1]) person who made those design choices -- Carl Witty -- isn't contributing anymore, or I'd ask his opinion. [1] http://stackoverflow.com/users/684532/carl-witty So, I'd prefer to display elements of QQbar as floating point numbers (what default precision?), always rounded DOWN to the last digit that is displayed, and followed by ... (not ?) unless the displayed value is exact. So, what is displayed is an initial part of the potentially infinite sequence of digits. Best regards, Simon -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. -- William (http://wstein.org) -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Heuristics to approximate matrix bandwidth
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], which are heuristics used to approximate the bandwidth of a graph [3] (ticket 18876, [4]). Since the bandwidth of a graph is the bandwidth of its adjacency matrix, maybe these algorithms might be useful also in the matrix context. However, before including them, since I work with graphs and I know very little about matrix algorithms, I have some doubts: * Are these algorithm really interesting for matrix analysis? * In case, where and how should I include these algorithms? * If it is more complicated than this), could you provide more information? For instance, if you need related routines, like permuting rows and columns according to these orderings, or maybe you would like to integrate this work with other algorithms. In case, I might open a new ticket that takes care of all these things. Hi, These methods have been widely used for the solution of large linear systems one encounter in the discretization of Partial Differential Equations; these systems are sparse (O(n) non zeros for an order n); the factorizations (LU, Cholesky) create new non zeros terms inside the band. So reducing the band width is a necessity. Nowadays, direct methods for sparse systems (SuperLU, Mumps) are based on more sophisticated ideas (like nested dissection). The Cuthill-Mac Kee algorithm (actually the reverse Cuthill-Mac Kee version) is implemented in scipy (scipy.sparse.csgraph improvements). I think this is the right place for this. Yours t.d. For any other comment, doubt, or suggestion, please feel free to contact me! Thank you very much for your help! Best, Michele [1] https://en.wikipedia.org/wiki/Cuthill%E2%80%93McKee_algorithm [2] http://www.boost.org/doc/libs/1_58_0/libs/graph/doc/king_ordering.html [3] https://en.wikipedia.org/wiki/Graph_bandwidth [4] http://trac.sagemath.org/ticket/18876 -- 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 mailto:sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com mailto:sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. attachment: tdumont.vcf
[sage-devel] Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 final '?' sounds more like a '...', as if some additional digits were hidden in a value stored as a float/double. Yet it is exact. How could we replace it? Ideally, that would be a 'sqrt(2)' but can we always provide such a representation cheaply? Could we display it as 'sqrt(2)' at least when it is free to do so? If we cannot get rid totally of this numerical representation, what would you think of replacing this '?' by a 'alg', which would be (slightly) more informative, e.g.: sage: QQbar(sqrt(2)) # still not very trust-inspiring 1.414213562373095alg Thaaanks, Nathann P.S.: If you know a word which means that inspires trust, please share it (in private :-P) [1] https://groups.google.com/d/msg/sage-support/b6OinTC9mdk/Y_SLTILRI9kJ -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 in terms of Jacobi theta functions, the general sextic in terms of Kampe de Feriet functions, amongst others. In general Mellin integrals, Fuchsian functions and theta functions can be used to solve general equations of degree n. ...which proves the original poster's point about not be expressed that nicely. -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 that nicely. This is slightly incorrect. The general quintic can be solved in terms of Jacobi theta functions, the general sextic in terms of Kampe de Feriet functions, amongst others. In general Mellin integrals, Fuchsian functions and theta functions can be used to solve general equations of degree n. ...which proves the original poster's point about not be expressed that nicely. The formulas for the quintic in terms of Jacobi functions, for example, don't look that much more frightening than those for the quartic in terms of radicals. I don't see any explosion in complexity. Perhaps it is a matter of taste. -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 this final '?' sounds more like a '...', as if some additional digits were hidden in a value stored as a float/double. Yet it is exact. How could we replace it? Ideally, that would be a 'sqrt(2)' but can we always provide such a representation cheaply? Could we display it as 'sqrt(2)' at least when it is free to do so? 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 in terms of Jacobi theta functions, the general sextic in terms of Kampe de Feriet functions, amongst others. In general Mellin integrals, Fuchsian functions and theta functions can be used to solve general equations of degree n. Bill. -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 numbers in such a nice way, though. Well, if you want to build such an object *in Sage* then you must describe your value somehow, and it is also stored internally somewhere.. And I wonder how, and whether we can base the representation on this internal version of the value :-) Anyways we could have such an expression for the cases where it is evident from the number construction. -1 I definitely prefer a uniform output. Me too. I would really much prefer uniform output and uniform storage... If somebody input sum(QQbar(i).sqrt() for i in range(100)) do we really want to output 1 + sqrt(2) + sqrt(3) + etc I guess not. And we do not want to slow down the computation of numbers in QQbar because one can potentially have a nicer output form. If you want a symbolic representation then convert the element to one from SR (symbolic ring). This is basically what you are asking with where it is evident anyway... Of course you could add a function which tries to do exactly that but in my opinion the default output should have a uniform look for a given parent. That way you also realize (better) over what parent you are working with currently. That is a different matter and we already have #17516 for that. Vincent -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: Algebraic numbers: the '?' could be more informative (e.g.: 1.4142?)
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 algebraic value 1.414213562373095? It is true that this final '?' sounds more like a '...', as if some additional digits were hidden in a value stored as a float/double. Yet it is exact. How could we replace it? Ideally, that would be a 'sqrt(2)' but can we always provide such a representation cheaply? Could we display it as 'sqrt(2)' at least when it is free to do so? 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. For an appropriate notion of such a representation resp. that nicely, my statement is correct :-) Indeed, I replied to a message that was about representation of elements of QQbar in terms of square (generally n-th) roots. Best regards, Simon -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Building Sage 6.8.beta8 from source; singular build errors
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 https://raw.githubusercontent.com/cschwan/sage-on-gentoo/master/sci-mathematics/singular/files/singular-3.1.7-use_cxx_for_linking.patch in build/pkgs/singular/patches/ and you should be good to go. François On 14/07/2015, at 12:53, Brenton Horne brentonhorn...@gmail.com wrote: Hi, I attempted to build Sage 6.8.beta8 by cloning the git SageMath repo, i.e., running: git clone git://git.sagemath.org/sage.git then running: cd sage make This runs without issue until the ~/sage directory reaches 1.5 GB in size then I received the error: make[2]: *** [/home/fusion809/sage/local/var/lib/sage/installed/singular-3.1.7p1.p0] Error 1 make[2]: Leaving directory '/home/fusion809/sage/build' Makefile:418: recipe for target 'all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory '/home/fusion809/sage/build' real 6m16.285s user 5m44.756s sys 0m19.516s *** Error building Sage. The following package(s) may have failed to build: package: singular-3.1.7p1.p0 log file: /home/fusion809/sage/logs/pkgs/singular-3.1.7p1.p0.log build directory: /home/fusion809/sage/local/var/tmp/sage/build/singular-3.1.7p1.p0 The build directory may contain configuration files and other potentially helpful information. WARNING: if you now run 'make' again, the build directory will, by default, be deleted. Set the environment variable SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this. Makefile:19: recipe for target 'build' failed make: *** [build] Error 1 I have attempted to build sage 6.7 from source tarballs and I received the same error, so I doubt it's unique to git. My operating system is 32 bit Ubuntu 15.04 (although I have switched to a 4.0.0 kernel, but I experienced this same error before I switched the kernel too). My RAM is 3.8 GB, CPU is 4 x Intel Core (TM) i5 CPU M 460 @ 2.53GHz. Thanks for your time, Brenton -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. singular-3.1.7p1.p0.log -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Re: sage 6.7 failed to load jmol to display 3d object
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 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 command:
sage: var('x,y')
sage: plot3d(sin(x*y), (x, -pi, pi), (y, -pi, pi))
it returns :
/usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:561:
RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol
failed to create file '/root/.sage/temp/rt./12958/dir_W9ZHtR/preview.png',
see '/root/.sage/temp/rt./12958/tmp_KGOIjb.txt' for details
RichReprWarning,
Graphics3d Object
Not knowing what's going wrong, I have rebuild Jmol, but it changed
nothing
maybe I can find the solution or reason here, and just around these days,
thanks to any help very much.
If needed, more information would be provided (as now I don't know what's
neesded.
Thanks very much!
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Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object
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
splash_image=jar:file:/usr/share/sage-jmol-bin/lib/Jmol.jar!/org/openscience/jmol/app/images/Jmol_splash.jpg
history file is /root/.jmol/history
(C) 2012 Jmol Development
Jmol Version: 14.2.11_2015.01.20 2015-01-20 12:29
java.vendor: Java: Oracle Corporation
java.version: Java 1.7.0_79
os.name: Linux
Access: ALL
memory: 44.5/97.4
processors available: 4
useCommandThread: false
User macros dir: /root/.jmol/macros
exists: false
isDirectory: false
Executing script: load
/root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip;
FileManager.getAtomSetCollectionFromFile(/root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip)
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
FileManager opening 2 /root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
The Resolver thinks Xyz
line cannot be read for XYZ atom data: -3 -2.84615 0.0919047
line cannot be read for XYZ atom data: -3 -2.69231 0.806228
...
line cannot be read for XYZ atom data: 2.69231 -1.61538 1.4976
line cannot be read for XYZ atom data: 2.69231 2.69231 1.49328
line cannot be read for XYZ atom data: 2.84615 1.46154 -1.48303
line cannot be read for XYZ atom data: 2.84615 2.53846 1.49646
line cannot be read for XYZ atom data: 1521
line cannot be read for XYZ atom data: 1
line cannot be read for XYZ atom data: 41
line cannot be read for XYZ atom data: 40
...
I'm wondering is there something wrong with the data file
在 2015年7月14日星期二 UTC+8上午3:28:16，François写道：
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 is unrelated. Volker's advice is not
applicable
to your install since “sage -i” doesn’t exist in sage-on-gentoo.
Can you post /root/.sage/temp/rt./12958/tmp_KGOIjb.txt” so I can try
to figure it out.
François
On 14/07/2015, at 04:50, rt. rtgi...@gmail.com javascript: 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 command:
sage: var('x,y')
sage: plot3d(sin(x*y), (x, -pi, pi), (y, -pi, pi))
it returns :
/usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:561:
RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol
failed to create file '/root/.sage/temp/rt./12958/dir_W9ZHtR/preview.png',
see '/root/.sage/temp/rt./12958/tmp_KGOIjb.txt' for details
RichReprWarning,
Graphics3d Object
Not knowing what's going wrong, I have rebuild Jmol, but it changed
nothing
maybe I can find the solution or reason here, and just around these
days, thanks to any help very much.
If needed, more information would be provided (as now I don't know
what's neesded.
Thanks very much!
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Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object
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 it directly with Jmol:
jmol /root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip
splash_image=jar:file:/usr/share/sage-jmol-bin/lib/Jmol.jar!/org/openscience/jmol/app/images/Jmol_splash.jpg
history file is /root/.jmol/history
(C) 2012 Jmol Development
Jmol Version: 14.2.11_2015.01.20 2015-01-20 12:29
java.vendor: Java: Oracle Corporation
java.version: Java 1.7.0_79
os.name: Linux
Access: ALL
memory: 44.5/97.4
processors available: 4
useCommandThread: false
User macros dir: /root/.jmol/macros
exists: false
isDirectory: false
Executing script: load /root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip;
FileManager.getAtomSetCollectionFromFile(/root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip)
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
FileManager opening 2 /root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
cacheGet file://root/.sage/temp/rt./29736/dir_fz8ajw/scene.spt.zip false
The Resolver thinks Xyz
line cannot be read for XYZ atom data: -3 -2.84615 0.0919047
line cannot be read for XYZ atom data: -3 -2.69231 0.806228
...
line cannot be read for XYZ atom data: 2.69231 -1.61538 1.4976
line cannot be read for XYZ atom data: 2.69231 2.69231 1.49328
line cannot be read for XYZ atom data: 2.84615 1.46154 -1.48303
line cannot be read for XYZ atom data: 2.84615 2.53846 1.49646
line cannot be read for XYZ atom data: 1521
line cannot be read for XYZ atom data: 1
line cannot be read for XYZ atom data: 41
line cannot be read for XYZ atom data: 40
...
I'm wondering is there something wrong with the data file
在 2015年7月14日星期二 UTC+8上午3:28:16，François写道：
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 is unrelated. Volker's advice is not applicable
to your install since “sage -i” doesn’t exist in sage-on-gentoo.
Can you post /root/.sage/temp/rt./12958/tmp_KGOIjb.txt” so I can try
to figure it out.
François
On 14/07/2015, at 04:50, rt. rtgi...@gmail.com 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 command:
sage: var('x,y')
sage: plot3d(sin(x*y), (x, -pi, pi), (y, -pi, pi))
it returns :
/usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:561:
RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol
failed to create file '/root/.sage/temp/rt./12958/dir_W9ZHtR/preview.png',
see '/root/.sage/temp/rt./12958/tmp_KGOIjb.txt' for details
RichReprWarning,
Graphics3d Object
Not knowing what's going wrong, I have rebuild Jmol, but it changed nothing
maybe I can find the solution or reason here, and just around these days,
thanks to any help very much.
If needed, more information would be provided (as now I don't know what's
neesded.
Thanks very much!
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Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object
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 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 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 command:
sage: var('x,y')
sage: plot3d(sin(x*y), (x, -pi, pi), (y, -pi, pi))
it returns :
/usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:561:
RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol
failed to create file '/root/.sage/temp/rt./12958/dir_W9ZHtR/preview.png',
see '/root/.sage/temp/rt./12958/tmp_KGOIjb.txt' for details
RichReprWarning,
Graphics3d Object
Not knowing what's going wrong, I have rebuild Jmol, but it changed nothing
maybe I can find the solution or reason here, and just around these days,
thanks to any help very much.
If needed, more information would be provided (as now I don't know what's
neesded.
Thanks very much!
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Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object
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 2015年7月14日星期二 UTC+8上午9:23:17，François写道：
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. rtgi...@gmail.com javascript: wrote:
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 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 command:
sage: var('x,y')
sage: plot3d(sin(x*y), (x, -pi, pi), (y, -pi, pi))
it returns :
/usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:561:
RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol
failed to create file '/root/.sage/temp/rt./12958/dir_W9ZHtR/preview.png',
see '/root/.sage/temp/rt./12958/tmp_KGOIjb.txt' for details
RichReprWarning,
Graphics3d Object
Not knowing what's going wrong, I have rebuild Jmol, but it changed
nothing
maybe I can find the solution or reason here, and just around these
days, thanks to any help very much.
If needed, more information would be provided (as now I don't know
what's neesded.
Thanks very much!
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Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object
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 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 2015年7月14日星期二 UTC+8上午9:23:17，François写道：
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. rtgi...@gmail.com wrote:
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 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 command:
sage: var('x,y')
sage: plot3d(sin(x*y), (x, -pi, pi), (y, -pi, pi))
it returns :
/usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:561:
RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol
failed to create file '/root/.sage/temp/rt./12958/dir_W9ZHtR/preview.png',
see '/root/.sage/temp/rt./12958/tmp_KGOIjb.txt' for details
RichReprWarning,
Graphics3d Object
Not knowing what's going wrong, I have rebuild Jmol, but it changed nothing
maybe I can find the solution or reason here, and just around these days,
thanks to any help very much.
If needed, more information would be provided (as now I don't know what's
neesded.
Thanks very much!
--
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Re: [sage-devel] sage 6.7 failed to load jmol to display 3d object
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 2015年7月14日星期二 UTC+8上午9:39:44，François写道：
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. rtgi...@gmail.com javascript: wrote:
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 2015年7月14日星期二 UTC+8上午9:23:17，François写道：
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. rtgi...@gmail.com wrote:
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 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 command:
sage: var('x,y')
sage: plot3d(sin(x*y), (x, -pi, pi), (y, -pi, pi))
it returns :
/usr/lib64/python2.7/site-packages/sage/repl/rich_output/display_manager.py:561:
RichReprWarning: Exception in _rich_repr_ while displaying object: Jmol
failed to create file '/root/.sage/temp/rt./12958/dir_W9ZHtR/preview.png',
see '/root/.sage/temp/rt./12958/tmp_KGOIjb.txt' for details
RichReprWarning,
Graphics3d Object
Not knowing what's going wrong, I have rebuild Jmol, but it changed
nothing
maybe I can find the solution or reason here, and just around these
days, thanks to any help very much.
If needed, more information would be provided (as now I don't know
what's neesded.
Thanks very much!
--
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Re: [sage-devel] Announcing $0M in new funding for the SageMathCloud over the next 3 years
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 entitled to speak in their name. Nicolas did not put 'the' after 'we'; do not twist his words please. What he wrote is a correct statement. 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 from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Server Relocation
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). Important question: what will happen with the data currently stored on boxen? Will you transfer it to the new machine? It depends on what you mean by data currently on boxen. Do you mean things under /home? If so then that will still be accessible on geom.math.washington.edu and mod.math.washington.edu for the time being, as it actually a network filesystem being exported from another machine. My plan is to mount it as read only for a bit on the new machines, but after a period of time (probably a couple of months) the storage machine of the current/old sage cluster will be repurposed as a backup machine, at which point I'll make a final snapshot of the /home directory on an external usb drive. Anything lying on the root and scratch filesystems on boxen will be wiped. -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. -- Andrew -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Announcing $0M in new funding for the SageMathCloud over the next 3 years
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 your own name only. You are not the Europeans Devs, are are not entitled to speak in their name. Nicolas did not put 'the' after 'we'; do not twist his words please. What he wrote is a correct statement. and, by the way, Nathann, you do use Sage code that was developed with NFS funding, and thus benefit from it, so your point is really, really moot... 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 from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Announcing $0M in new funding for the SageMathCloud over the next 3 years
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 from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: a sage bug
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 control; So if gmane is not blocked then thats only because they are too small to be noticed. On Sunday, July 12, 2015 at 11:39:20 PM UTC+2, William wrote: Thanks Ralf! By the way, does anybody know what the deal is with: Please forgive me to send it to you for I am in China and have a problem to access Google groups. Do most people in China really not have access to Google groups? If so, that's a very good reason for us to consider at least some sort of alternative way to access the groups. -- William On Sun, Jul 12, 2015 at 12:08 PM, Ralf Stephan gtr...@gmail.com javascript: wrote: On Sunday, July 12, 2015 at 2:34:56 PM UTC+2, Stein William wrote: -- Forwarded message -- From: ruiming zhang ruimin...@outlook.com Date: Sunday, July 12, 2015 Subject: a sage bug To: wst...@math.washington.edu ... e=x+1=x-2 e*(-1) -x-1=-x+2, This is known and has a fix. Only the review is missing. If someone wants to review the fix, please see this ticket: http://trac.sagemath.org/ticket/7660 Regards, -- 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+...@googlegroups.com javascript:. To post to this group, send email to sage-...@googlegroups.com javascript:. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout. -- William (http://wstein.org) -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Memory leaks on matrix creation?
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): l.append( d[(j+1)*j/2:(j+1)*(j+2)/2]+ [1] + [0]*(n-j-2) ) M = Matrix(l) eig = sorted((M*M.transpose()).eigenvalues())[0] if eig = 0: print Foobar These kind of codes, where I make millions of small objects, compute something and discard the object, seems to eat memory. Not much, but so much that otherwise reasonable computable thing - say, something to run for two days - will be impossible to do directly. Is there anything I can do for these? (Other than running the code part-by-part.) This was ran on newest beta version. -- Jori Mäntysalo
Re: [sage-devel] Announcing $0M in new funding for the SageMathCloud over the next 3 years
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 prove one point: that anybody can voice his/her own opinion, and yet be heard. There is no need of indirect representation here as everybody can post freely, and so I do not want to be made to talk against my will, encompassed in the set of european developers, developers of combinatorics code, or whatever may come next. I do not trust representatives (least of all self-appointed), and with good reasons. I would be surprised if most of you did (*). Have fun, Nathann (*) In France they believe that the people wants to be monitored US-style, nowadays. Who wouldn't? -- 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 sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
