[sage-combinat-devel] Question on a doctest
Hi! Working on some patch, I get the following doctest errors in combinat/ sf/dual.py File /mnt/local/king/SAGE/broken/devel/sage-main/sage/combinat/sf/ dual.py, line 185: sage: l(f._to_self_cache) # note: this may depend on possible previous computations! Expected: [([1, 1], [([1, 1], 2), ([2], 1)]), ([2], [([1, 1], 1), ([2], 1)])] Got: [([], [([], 1)]), ([1, 1], [([1, 1], 2), ([2], 1)]), ([2], [([1, 1], 1), ([2], 1)])] ** File /mnt/local/king/SAGE/broken/devel/sage-main/sage/combinat/sf/ dual.py, line 187: sage: l(f._from_self_cache) Expected: [([1, 1], [([1, 1], 1), ([2], -1)]), ([2], [([1, 1], -1), ([2], 2)])] Got: [([], [([], 1)]), ([1, 1], [([1, 1], 1), ([2], -1)]), ([2], [([1, 1], -1), ([2], 2)])] It states that this may depend on possible previous computations. Is there really no work around? Such as, using an object that is not considered in any other doc test? Is the new result correct? Shouldn't both tests better be marked as random? Best regards, Simon -- You received this message because you are subscribed to the Google Groups sage-combinat-devel group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: Categorification of sage/rings/ring.pyx
On Fri, Apr 01, 2011 at 12:07:36AM -0700, Simon King wrote: On 31 Mrz., 21:35, Simon King simon.k...@uni-jena.de wrote: Once again, I forgot to include __init__.py in a patch. I will update it on trac tomorrow. Done. I don't know why, but aparently mercurial will not include an empty file in the patch. So, I filled __init__.py with a comment. Yup; that's a know shortcoming of standard patches. You can request git-style patches by throwing this in your .hgrc: [diff] git=1 Cheers, Nicolas -- Nicolas M. Thiéry Isil nthi...@users.sf.net http://Nicolas.Thiery.name/ -- You received this message because you are subscribed to the Google Groups sage-combinat-devel group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] #11111: Add features to FiniteDimensional(Modules/Algebras)WithBasis
Hi Franco, Florent, ... There are a bunch of patches (in particular from you) on the sage-combinat queue adding features to finite dimensional modules/algebras with basis. I further refactored/added quite some stuff. Do you mind if I take over those patches, merge them together, and try to get them ready for merging into Sage? This includes: echelon_form_of_module_elements-fs.patch fin_dim_algebra_example-fs.patch fin_dim_algebra_radical-fs.patch fin_dim_algebra_center-fs.patch cache-on-radical-nt.patch # to be folded in the two previous ones fin_dim_algebra_radical_char_p-fs.patch bigmess-nt.patch And possibly: module_morphism_function_extend-fh.patch Any others? I got a cool ticket number for that :-) Cheers, Nicolas -- Nicolas M. Thiéry Isil nthi...@users.sf.net http://Nicolas.Thiery.name/ -- You received this message because you are subscribed to the Google Groups sage-combinat-devel group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: sage-combinat queue broken
Hi! On Thu, Mar 31, 2011 at 11:22:18PM -0700, Anne Schilling wrote: On 3/31/11 5:59 PM, Daniel Bump wrote: It seems that your patch has a problem to be applied to the current sage 4.6.2. The patch was tested with 4.7.alphas (because we hope for it to be merged soon). The syntax of classical_crystals.py at the top of the file has changed since 4.6.2. So it doesn't merge. One possibility would be to guard the patch so that it only applies to more recent versions. I'm cc:ing Nicolas to ask his advice. Which patch are you talking about? The #7922 patches (Weyl character rings) did not apply smoothly due to a trivial import conflict with trac_10446_schuetzenberger_involution-as.patch I am writting a quick reviewer patch on #10466 that make them commute. By the way, it avoids importing parent code (RootSystems, WeylGroups) in category code, to reduce risks of import loops. I'll push that in a couple minutes. Cheers, Nicolas -- Nicolas M. Thiéry Isil nthi...@users.sf.net http://Nicolas.Thiery.name/ -- You received this message because you are subscribed to the Google Groups sage-combinat-devel group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: sage-combinat queue broken
On Fri, Apr 01, 2011 at 03:18:04PM +0200, Nicolas M. Thiery wrote: I'll push that in a couple minutes. Done. I used the occasion to polish a tiny bit the corresponding doctests. Please check, and if you are happy, fold and upload on trac. Cheers, Nicolas -- Nicolas M. Thiéry Isil nthi...@users.sf.net http://Nicolas.Thiery.name/ -- You received this message because you are subscribed to the Google Groups sage-combinat-devel group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] #11111: Add features to FiniteDimensional(Modules/Algebras)WithBasis
On Fri, Apr 01, 2011 at 02:48:22PM +0200, Nicolas M. Thiery wrote: Hi Franco, Florent, ... There are a bunch of patches (in particular from you) on the sage-combinat queue adding features to finite dimensional modules/algebras with basis. I further refactored/added quite some stuff. Do you mind if I take over those patches, merge them together, and try to get them ready for merging into Sage? Go for it ! Sorry for not pushing them to their conclusion. Florent -- You received this message because you are subscribed to the Google Groups sage-combinat-devel group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-devel] Re: Parallel builds
On Mar 31, 2011, at 21:24 , Volker Braun wrote: I agree that the number of make -jN threads should be a good deal larger than the number of physical cores. Also, make sure that you set export SAGE_PARALLEL_SPKG_BUILD=yes or you'll see mostly a slow single-threaded configure followed by a lightning-fast compile phase. This should be really the default by now but unfortunately it is not. In my case, that environment variable was set to 'yes'. J -- Justin C. Walker, Curmudgeon at Large Institute for the Absorption of Federal Funds --- My wife 'n kids 'n dogs are gone, I can't get Jesus on the phone, But Ol' Milwaukee's Best is my best friend. --- -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Difference between conversion and coercion?
Hi! I hope sage-devel is the right place to ask a very basic question on the coercion model. sage.structure.parent.Parent has methods register_conversion and register_coercion. What is the difference between conversion and coercion? I see that there are different caches for the two. In what situation is a coercion used, and in what situation a conversion? BTW, I think a method that tells whether there is already a conversion resp. a coercion from a ring R is cached, would be quite handy. I could not find such method (returning R in self._coerce_from_hash resp. R in in self._convert_from_hash). Is there anything, or shall I implement it myself? Best regards, Simon -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Fixed: Decorators ruining documentation
Hi everyone Can someone please review ticket #9976; its patch has been there for ~6 months now. It fixes a problem with decorators and Sphinx: as it is now, most decorated functions will get a generic signature in the Sphinx documentation. Notable examples include most of the plot commands, e.g. http://sagemath.org/doc/reference/sage/plot/plot.html#sage.plot.plot.plot as well as any function decorated with the deprecated-decorator (used for deprecating named arguments). The ticket introduces a new way of handling this by slightly patching Sphinx and including extra information in the sage_wraps decorator. The latter is an extension of the pure Python wraps decorator, which is already mandatory to use in decorators meant to decorate top-level callables. Cheers, Johan -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Difference between conversion and coercion?
On Thu, Mar 31, 2011 at 11:25 PM, Simon King simon.k...@uni-jena.de wrote: Hi! I hope sage-devel is the right place to ask a very basic question on the coercion model. sage.structure.parent.Parent has methods register_conversion and register_coercion. What is the difference between conversion and coercion? I see that there are different caches for the two. In what situation is a coercion used, and in what situation a conversion? A conversion is like a cast, which tries to make the object if it makes sense at all. This is useful, for example, during construction. E.g. there's a conversion QQ - ZZ, list - QQ[x], or even str - ZZ. They are invoked with __call__. Coercions are the set of conversions that happen automatically and implicitly, e.g. during arithmetic. We don't want to support str + ZZ, and ZZ coerces to QQ but not the other way around. BTW, I think a method that tells whether there is already a conversion resp. a coercion from a ring R is cached, would be quite handy. I could not find such method (returning R in self._coerce_from_hash resp. R in in self._convert_from_hash). Is there anything, or shall I implement it myself? No, I don't think there's anything like that yet. - Robert -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] lcalc code quality
An idea that may be on the constructive side. John could you convince/help Micheal to upload his current code in a hg repo on google code like you did with eclib? Rather than whining we could contribute and take a snapshot when it is satisfactory. Francois This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information. -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: lcalc code quality
On Thu, Mar 31, 2011 at 12:09 PM, kcrisman kcris...@gmail.com wrote: And I agree that we should communicate with the author politely. I was addressing the Sage developers that use lcalc, and I think that its allowable to use a more colloquial tone in that case. I would submit that we should be as polite as possible whenever discussing component pieces of Sage. We depend on them to make it work great. This is especially true when discussing something fairly technical to a large proportion of Sage developers, I would guess, and certainly to the many users who subscribe or visit this on the web in the hopes of learning something. This is a public forum, even if it often doesn't seem like it because we get to know one another to some extent at Sage Days and on the list. As a separate issue, I realize that not everyone will agree on what acronyms/cuss words are appropriate for this forum, so I won't push this too strongly. But my guess is that the public Mma lists, or Mapleprimes, wouldn't be too hot on this as a customer relations strategy. (I also realize that now someone will prove me wrong by finding a much worse example on one of those sites!) Colloquially yours, - kcrisman +1, to all of the above. What I was trying to say is that we should focus on getting the (very sophisticated and useful) code to compile and work again, rather than complain about the number of compiler warnings it gives. Getting it into a public repository would be a great step forward for those who care about cross-platform compatibility and compiler workings to contribute. - Robert -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Is this the most trivial patch? It needs review!!!
If anyone has a minute, http://trac.sagemath.org/sage_trac/ticket/0 needs review. There was an unneeded file .#spkg-install which was just a link to someone's email address. I just removed it, documented it in SPKG.txt and created a new package It should not take anyone too long to review. -- A: Because it messes up the order in which people normally read text. Q: Why is top-posting such a bad thing? A: Top-posting. Q: What is the most annoying thing in e-mail? Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: lcalc code quality
On 04/ 1/11 09:53 AM, Robert Bradshaw wrote: +1, to all of the above. What I was trying to say is that we should focus on getting the (very sophisticated and useful) code to compile and work again, rather than complain about the number of compiler warnings it gives. Getting it into a public repository would be a great step forward for those who care about cross-platform compatibility and compiler workings to contribute. - Robert A possible (probable?) problem will be that it will be very difficult for someone to know what changes to make. The current lcalc code in Sage is not valid C++, so trying to know what the author intended would be difficult and I feel attempting to clean it up would be more likely to break the code than improve it. BTW, what is the full name of the author? SPKG.txt says Rishikesh, yet people here talk of Risi and Mike. I've fixed many portability issues in the past, when it was clear what the author intended and one can see his mistakes. This is probably not so with 'lcalc' - at least based on what I can see just now. Obviously if revised code is much better then it may be possible for someone to clean it up further. Sympow was another case similar. I don't think anyone could clean up Sympow, as it's not valid C, so hard to know what the author was trying to do. I only managed to fix a bug in that as a result of finding a reference to a paper, reading the paper, then I was able to work out what the author intended. But I believe cleaning up Sympow would be dangerous rather than constructive. The big advantage here with lcalc is the author is still available, although busy just now. It might be safer to leave him to do it. If the Sun compiler was installed, this would give him the chance to turn it into valid C++. Then it would be much more maintainable. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Parallel builds
On 1 April 2011 05:24, Volker Braun vbraun.n...@gmail.com wrote: I agree that the number of make -jN threads should be a good deal larger than the number of physical cores. Also, make sure that you set export SAGE_PARALLEL_SPKG_BUILD=yes or you'll see mostly a slow single-threaded configure followed by a lightning-fast compile phase. This should be really the default by now but unfortunately it is not. It only needs a patch to make this the default. I agree with you. I created a ticket a week or so ago to update the instructions on building Sage from source http://trac.sagemath.org/sage_trac/ticket/11081 Currently these instructions are outdated, misleading and in one case I feel dangerous. One thing I did do there was to remove the comment that SAGE_PARALLEL_SPKG_BUILD=yes is experimental. This seems to be very stable now, so that comment is removed. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Debugging some cython code / Pynac
On Fri, 01 Apr 2011 00:37:46 +0100 Dr. David Kirkby david.kir...@onetel.net wrote: I've built Sage 64-bit on OpenSolaris but it crashes at startup. I've run gdb and find the bit of code that's causing the crash is this. ./devel/sage-main/sage/symbolic/function.cpp /* sage/symbolic/function.pyx:109 * raise ValueError, real_fname + parameter must be callable * * if not self._is_registered(): # * self._register_function() * */ snip allows Sage to run. It's not 100% stable, but much better than before. snip Can anyone see if there might be something wrong with this code, which is causing Sage to segfault? It might be due to the linker initializing the library in a different order. Can you post a backtrace so we can see which function it is trying to construct? Moving the lines # This must come before Calculus -- it initializes the Pynac library. import sage.symbolic.pynac in sage/all.py higher in the file might work around this problem. The correct solution would be to import the offending function lazily or locally. Cheers, Burcin -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Updating the instructions on building Sage from source.
I've created a ticket http://trac.sagemath.org/sage_trac/ticket/11081 to update the instructions on building Sage from source http://www.sagemath.org/doc/installation/source.html which are very outdated and therefore inaccurate. I'd appreciate any comments on the ticket, and hopefully a positive review at some point. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Parallel builds
Your storage might be slow, too, but I guess you got a reasonable SSD with your system so that shouldn't be a concern. Though I'm not surprised that a significant fraction of the build time is spent in various (single-threaded) configure scripts. If I exclude ATLAS, I can build Sage in about 30 minutes. Although I haven't tried to benchmark it, a good part of it seems to be non-parallelizeable. So there are some diminishing returns as you throw more cores at it. -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Parallel builds
On 1 April 2011 03:31, Justin C. Walker jus...@mac.com wrote: Hi, all, I've just upgraded my home system, to a Mac Pro (Dual 6-core Xeon, 24GB memory), and figured (hoped) I'd see 24 processes hammering away during the build test of a Sage release. Turns out not to happen. For the record, these new cores from Intel sport 2 threads each, which act almost like separate cores, capable on this system of running 24 processes at a time. However, both for the build itself, and the test, there are generally at most 12 runnable processes at any time. Anyone have any idea why the parallelism is limited this way? FWIW, I started with -j24, and when I saw only half the threads active, talked with Apple about it. Their suggestion (based on their experience with kernel builds) is to request double the number of available threads. I reran the build/test with -j48, and saw no improvement: the number of runnable threads remained at ~12. Thoughts? Justin If you look in the Makefile, there's a comment that the number should be limited to 8, so I'm surprised you see 12. The reason this was introduced was the assumption that any machine with 8+ cores is a multi-user machine, not owned by one individual, so he/she should not be able to accidentally cause havoc by having too many threads. So they need to specifically edit the Makefile. On t2.math for example, there are 128 threads. If one was to compile Sage with 128or 256, it would run out of memory. Hence Sage has a bit of a safety factor built in. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Parallel builds
On 1 April 2011 13:33, Volker Braun vbraun.n...@gmail.com wrote: Your storage might be slow, too, but I guess you got a reasonable SSD with your system so that shouldn't be a concern. Though I'm not surprised that a significant fraction of the build time is spent in various (single-threaded) configure scripts. If I exclude ATLAS, I can build Sage in about 30 minutes. Although I haven't tried to benchmark it, a good part of it seems to be non-parallelizeable. So there are some diminishing returns as you throw more cores at it. Another issue is the size of some of the source files. sqlite for example has a single C source file of 3.7 MB. I think now with multi-core CPUs being the norm rather than the exception, authors of code should try to split large files so it is possible to compile more than one bit of a package at once. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] #11111: Add features to FiniteDimensional(Modules/Algebras)WithBasis
Hi Franco, Florent, ... There are a bunch of patches (in particular from you) on the sage-combinat queue adding features to finite dimensional modules/algebras with basis. I further refactored/added quite some stuff. Do you mind if I take over those patches, merge them together, and try to get them ready for merging into Sage? This includes: echelon_form_of_module_elements-fs.patch fin_dim_algebra_example-fs.patch fin_dim_algebra_radical-fs.patch fin_dim_algebra_center-fs.patch cache-on-radical-nt.patch # to be folded in the two previous ones fin_dim_algebra_radical_char_p-fs.patch bigmess-nt.patch And possibly: module_morphism_function_extend-fh.patch Any others? I got a cool ticket number for that :-) Cheers, Nicolas -- Nicolas M. Thiéry Isil nthi...@users.sf.net http://Nicolas.Thiery.name/ -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Parallel builds
On 1 April 2011 14:31, Volker Braun vbraun.n...@gmail.com wrote: The NUM_THREADS variable in the main Makefile is only used for parallel testing, that is, when you run make ptest. I consider it a bug that it doesn't respect the MAKE=make -jN environment variable setting. But then, you can always run sage -tp N to set the number of threads to anything you want. Or edit the Makefile, which will be a nice test for the new sage-root repository scripts if you ever try to upgrade Sage. For the build target, make will use as many threads as you specify in $MAKE. Sorry, I don't know what I was thinking when I wrote that. dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Debugging some cython code / Pynac
On 1 April 2011 12:54, Burcin Erocal bur...@erocal.org wrote: On Fri, 01 Apr 2011 00:37:46 +0100 Dr. David Kirkby david.kir...@onetel.net wrote: I've built Sage 64-bit on OpenSolaris but it crashes at startup. I've run gdb and find the bit of code that's causing the crash is this. ./devel/sage-main/sage/symbolic/function.cpp /* sage/symbolic/function.pyx:109 * raise ValueError, real_fname + parameter must be callable * * if not self._is_registered(): # * self._register_function() * */ snip allows Sage to run. It's not 100% stable, but much better than before. snip Can anyone see if there might be something wrong with this code, which is causing Sage to segfault? It might be due to the linker initializing the library in a different order. Can you post a backtrace so we can see which function it is trying to construct? Moving the lines # This must come before Calculus -- it initializes the Pynac library. import sage.symbolic.pynac in sage/all.py higher in the file might work around this problem. The correct solution would be to import the offending function lazily or locally. Cheers, Burcin I just started to download 4.7.alpha3. Once I have that downloaded and built it, I'll post a backtrace. If it helps, I'm willing to give you an account on the machine hawk which is used by the buildbot. Unlike t2.math, it is pretty quick (quad core 3.33 GHz Xeon). Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] #11108: Improve class_graph
Hi!
While preparing a (short) talk about Categories in Sage [1], I improved a
bit the ``class_graph`` function to supports a class or object as input [2].
It turns out that the result is currently not a graph, but a
dictionary that you then have to convert to a graph using DiGraph. In
practice, I find this a bit inconvenient. Besides, ``class_graph`` is used
nowhere in the Sage sources. So, does anyone care if I change
``class_graph`` to directly return a graph, as its name states?
That's somewhat backward compatible since DiGraph is idempotent.
{{{
EXAMPLES:
We construct the inheritance graph of the classes within a given module::
sage: from sage.rings.polynomial.padics import
polynomial_padic_capped_relative_dense, polynomial_padic_flat
sage: G = class_graph(sage.rings.polynomial.padics); G
Digraph on 4 vertices
sage: G.vertices()
['Polynomial_generic_dense', 'Polynomial_generic_domain',
'Polynomial_padic_capped_relative_dense', 'Polynomial_padic_flat']
We construct the inheritance graph of a given class::
sage: class_graph(Parent).edges(labels=False)
[('CategoryObject', 'SageObject'), ('Parent', 'CategoryObject'),
('SageObject', 'object')]
We construct the inheritance graph of the class of an object::
sage: class_graph([1,2,3]).edges(labels=False)
[('list', 'object')]
}}}
Beware: Nathann is a fast reviewer. So the vote is only open until
tomorrow :-)
Cheers,
Nicolas
[1] Slides 87- of http://www.nicolas.thiery.name/Talks/2011-03-31-LRI.pdf
[2] http://trac.sagemath.org/sage_trac/ticket/11108
--
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http://Nicolas.Thiery.name/
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URL: http://www.sagemath.org
Re: [sage-devel] Re: Parallel builds
On Apr 1, 2011, at 05:33 , Volker Braun wrote: Your storage might be slow, too, but I guess you got a reasonable SSD with your system so that shouldn't be a concern. I actually have only the standard (7200 rpm) drive, no SSD. Though I'm not surprised that a significant fraction of the build time is spent in various (single-threaded) configure scripts. If I exclude ATLAS, I can build Sage in about 30 minutes. Although I haven't tried to benchmark it, a good part of it seems to be non-parallelizeable. So there are some diminishing returns as you throw more cores at it. This is Mac OS X, so Atlas takes ~0.0 seconds to build :-} Justin -- Justin C. Walker, Curmudgeon at Large Director Institute for the Enhancement of the Director's income --- -- They said it couldn't be done, but sometimes, it doesn't work out that way. - Casey Stengel -- -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Spam tickets on Trac
On Thu, Mar 31, 2011 at 9:00 PM, Minh Nguyen nguyenmi...@gmail.com wrote: On Fri, Apr 1, 2011 at 1:20 PM, kcrisman kcris...@gmail.com wrote: See (or don't) #11102 and #11103. Now they're creating new tickets, not just comments. Hopefully someone can get rid of them. They're closed as invalid and the corresponding accounts deleted. But it would be bad to go back to the email William for an account days... We need a better recaptcha plugin. The current one seems to be broken somehow. I have been dealing with spam accounts on a daily basis for months now, but it was only recently that I found myself dealing with more spam tickets than usual. It sounds like it might be less work for you if we switch to email Minh for an account? Anyway, no matter how good the recaptcha plugin is, a human spammer can still trivially get an account. -- William -- Regards Minh Van Nguyen -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org -- William Stein Professor of Mathematics University of Washington http://wstein.org -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Debugging some cython code / Pynac
On 04/ 1/11 12:54 PM, Burcin Erocal wrote:
On Fri, 01 Apr 2011 00:37:46 +0100
Dr. David Kirkbydavid.kir...@onetel.net wrote:
I've built Sage 64-bit on OpenSolaris but it crashes at startup. I've
run gdb and find the bit of code that's causing the crash is this.
./devel/sage-main/sage/symbolic/function.cpp
/* sage/symbolic/function.pyx:109
* raise ValueError, real_fname + parameter must
be callable *
* if not self._is_registered(): #
* self._register_function()
*
*/
snip
allows Sage to run. It's not 100% stable, but much better than before.
snip
Can anyone see if there might be something wrong with this code,
which is causing Sage to segfault?
It might be due to the linker initializing the library in a different
order. Can you post a backtrace so we can see which function it is
trying to construct?
Here's a backtrace
drkirkby@hawk:~/64/sage-4.7.alpha3$ ./sage -gdb
Building Sage on Solaris in 64-bit mode
Creating SAGE_LOCAL/lib/sage-64.txt since it does not exist
Detected SAGE64 flag
Building Sage on Solaris in 64-bit mode
--
| Sage Version 4.7.alpha3, Release Date: 2011-03-31 |
| Type notebook() for the GUI, and license() for information.|
--
**
**
* Warning: this is a prerelease version, and it may be unstable. *
**
**
/export/home/drkirkby/64/sage-4.7.alpha3/local/bin/sage-ipython
GNU gdb 6.8
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type show copying
and show warranty for details.
This GDB was configured as i386-pc-solaris2.11...
warning: Lowest section in /lib/amd64/libdl.so.1 is .dynamic at 00b0
Python 2.6.4 (r264:75706, Apr 1 2011, 15:07:52)
[GCC 4.5.0] on sunos5
Type help, copyright, credits or license for more information.
warning: Lowest section in /lib/amd64/libintl.so.1 is .dynamic at
00b0
warning: Lowest section in /lib/amd64/libpthread.so.1 is .dynamic at
00b0
Program received signal SIGSEGV, Segmentation fault.
0x003eb0a5 in ?? ()
(gdb) bt
#0 0x003eb0a5 in ?? ()
#1 0xfd7fff2ac5d1 in _Unwind_RaiseException_Body () from /lib/64/libc.so.1
#2 0xfd7fff2ac855 in _Unwind_RaiseException () from /lib/64/libc.so.1
#3 0xfd7ff91d6729 in __cxa_throw (obj=value optimized out, tinfo=value
optimized out, dest=value optimized out)
at ../../../../../gcc-4.5.0/libstdc++-v3/libsupc++/eh_throw.cc:78
#4 0xfd7fcec6d5ff in GiNaC::function::find_function (name=@0x4a359b0,
nparams=2) at function.cpp:1446
#5 0xfd7fce9454ad in
__pyx_f_4sage_8symbolic_8function_15BuiltinFunction__is_registered
(__pyx_v_self=0x4a142f0) at sage/symbolic/function.cpp:7301
#6 0xfd7fce950755 in __pyx_pf_4sage_8symbolic_8function_8Function___init__
(__pyx_v_self=0x4a142f0, __pyx_args=value optimized out,
__pyx_kwds=value optimized out) at sage/symbolic/function.cpp:2374
#7 0xfd7fffde7a70 in ?? ()
#8 0x0016745f5f63 in ?? ()
#9 0x04a0e5a8 in ?? ()
#10 0x04a142f0 in ?? ()
#11 0x000b in ?? ()
#12 0x04a0e5a8 in ?? ()
#13 0x02c913e8 in ?? ()
#14 0xfd7fd76c2b30 in module_members () from
/export/home/drkirkby/64/sage-4.7.alpha3/local/lib//libpython2.6.so.1.0
#15 0x002752657572 in ?? ()
#16 0xfd7fd76d5c60 in ?? () from
/export/home/drkirkby/64/sage-4.7.alpha3/local/lib//libpython2.6.so.1.0
#17 0x28004052 in ?? ()
#18 0xfd7fd76d5920 in ?? () from
/export/home/drkirkby/64/sage-4.7.alpha3/local/lib//libpython2.6.so.1.0
#19 0x0005 in ?? ()
#20 0x049e4db8 in ?? ()
---Type return to continue, or q return to quit---
#21 0x in ?? ()
The line starting:
__pyx_t_2 = ((struct __pyx_vtabstruct_4sage_8symbolic_8function_Function *)
below is sage/symbolic/function.cpp line 2374
/* sage/symbolic/function.pyx:109
* raise ValueError, real_fname + parameter must be callable
*
* if not self._is_registered(): #
* self._register_function()
*
*/
__pyx_t_2 = ((struct __pyx_vtabstruct_4sage_8symbolic_8function_Function
*)((struct __pyx_obj_4sage_8symbolic_8function_Function
*)__pyx_v_self)-__pyx_vtab)-_is_registered(((struct
__pyx_obj_4sage_8symbolic_8function_Function *)__pyx_v_self)); if
(unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 109;
Re: [sage-devel] Re: lcalc code quality
BTW, what is the full name of the author? SPKG.txt says Rishikesh, yet people here talk of Risi and Mike. Rishikesh is Mike Rubenstein's graduate student. That is his entire name; Rishi is an abbreviation. Mike is an abbreviation of Michael. I will suggest to Mike within the next hour about putting lcalc onto googlecode, just as I did with eclib. In fact, what made me put eclib onto google code was following Mike's example http://code.google.com/p/lmfdb/ John -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Parallel builds
On Apr 1, 2011, at 06:31 , Volker Braun wrote: The NUM_THREADS variable in the main Makefile is only used for parallel testing, that is, when you run make ptest. I consider it a bug that it doesn't respect the MAKE=make -jN environment variable setting. But then, you can always run sage -tp N to set the number of threads to anything you want. Or edit the Makefile, which will be a nice test for the new sage-root repository scripts if you ever try to upgrade Sage. For the build target, make will use as many threads as you specify in $MAKE. I think I knew about NUM_THREADS, but I keep forgetting... So, I have MAKE=make -j48, but I don't see much parallelism in the build; perhaps that means that with dependencies, we're at a max around 10 processors/threads (so throwing more at the problem doesn't help). With testing, I sure saw a difference. With NUM_THREADS=24, all 24 threads were pinned, so the Activity Monitor's CPU Meter was solid on. With this setting, the testing time dropped from 900 seconds to 600 seconds. Whee! Of course, with 24 threads, this pushes the per-UID process count way up. I had to change the setting (ulimit) to get the testing to complete without seeing a batch of EAGAIN errors. Now I just have to remember how to get this to happen from boot time... Thanks for the help! Justin -- Justin C. Walker, Curmudgeon-At-Large Institute for the Absorption of Federal Funds Men are from Earth. Women are from Earth. Deal with it. -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Make check fails for sage 4.6.2 build
Hi,
I was building sage 4.6.2 on a Sun Fire 4450 server (called parsley) running
Redhat linux, and the there was a preparser failure when running make check.
Is this something I should be concerned about? I thought that the new sage
builds are automatically tested on this architecture, so how can make check
fail?
Thanks,
-Jon
=)
jonhanke@[~/my_sage_dir/SAGE_parsley_Build_Testing/sage-4.6.2]: make check
...
--
The following tests failed:
sage -t -force_lib devel/sage/sage/misc/preparser.py
Total time for all tests: 6133.0 seconds
Please see /home/jonhanke/.sage//tmp/test.log for the complete log from this
test.
jonhanke@[~/my_sage_dir/SAGE_parsley_Build_Testing/sage-4.6.2]: sage -t
-force_lib devel/sage/sage/misc/preparser.py
sage -t -force_lib devel/sage/sage/misc/preparser.py
Non-default server settings detected:
Incoming Server = http://hg.sagemath.org (default)
Outgoing Server = ssh://
jonha...@sage.math.washington.edu/sage-4.1.1/devel
**
File
/sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/sage/misc/preparser.py,
line 1386:
sage: sage.misc.preparser.is_loadable_filename('foo.m')
Expected:
True
Got:
False
**
File
/sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/sage/misc/preparser.py,
line 1403:
sage: load_attach_path()
Exception raised:
Traceback (most recent call last):
File /usr/local/sage-4.6/local/bin/ncadoctest.py, line 1231, in
run_one_test
self.run_one_example(test, example, filename, compileflags)
File /usr/local/sage-4.6/local/bin/sagedoctest.py, line 38, in
run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File /usr/local/sage-4.6/local/bin/ncadoctest.py, line 1172, in
run_one_example
compileflags, 1) in test.globs
File doctest __main__.example_19[2], line 1, in module
load_attach_path()###line 1403:
sage: load_attach_path()
NameError: name 'load_attach_path' is not defined
**
...
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[sage-devel] Re: sage notebook with many Jmol viewers
Dan, I'm glad you like most of what has been done. If you manage to get anything to fail please report that as well. As to the speed, there's not a lot we can do. That is limited by how fast information is passed from the server and how fast your computer is. Jmol is doing quite a bit of computation to produce the live figures. Because of JavaVM memory constraints within browsers things do not work well if more than one applet is loading at once. This means that each applet has to finish loading before the next one can start. One thought is to make it clearer what is happening. Would a pop-up progress window indicating which applet is loading help with the way it feels? Long term, I will probably make it so that old pages load with all the applets replaced by static images, but this requires changes to the plot3d functions. I was worrying about the interface first. Jonathan On Mar 31, 8:44 pm, Dan Drake dr...@kaist.edu wrote: On Thu, 31 Mar 2011 at 06:08AM -0700, Jonathan wrote: If you want to see what is coming down the pike in the next few weeks, take a look at the published samples on my test server: http:///141.233.197.45:. I could really use some comments on how it works. I'm using Firefox 4.0 on Ubuntu 10.10 with the Sun/Oracle Java andhttp://141.233.197.45:/home/pub/0/is working great. I really like the new controls -- putting it in a new window, changing the size, turning the spin on and off. The sleeping/interactive thing is also nice. The only slight problem is that it did take quite a long time for all the applets to load, but I suppose it's better to get things working first before we worry about speed. I tried the lots of applets worksheet, and tried to get every applet interactive and spinning. I see that some will automatically sleep, rather than have too many applets running. That's nice. Excellent work! Thanks so much for your efforts. Jmol is absolutely essential to me when I teach multivariable calc. Dan -- --- Dan Drake - http://mathsci.kaist.ac.kr/~drake --- signature.asc 1KViewDownload -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Just a reminder to deprecate...
I have to admit I would have been caught by this in any case; Sage 4.0 has been out for a long time, before the deprecation policy, and I should have checked ahead of time. But it did look unprofessional in class today when I tried to use quadratic_nonresidue on an old worksheet and it didn't work! See http://trac.sagemath.org/sage_trac/ticket/5834 - I actually think the new name is an improvement in any case :-) So just a reminder that (especially, not exclusively) things imported into the global namespace should have some deprecation period if removed. Thanks! - kcrisman -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Make check fails for sage 4.6.2 build
On 1 April 2011 18:43, Jonathan Hanke jonha...@gmail.com wrote:
Hi,
I was building sage 4.6.2 on a Sun Fire 4450 server (called parsley) running
Redhat linux, and the there was a preparser failure when running make check.
Is this something I should be concerned about? I thought that the new sage
builds are automatically tested on this architecture, so how can make check
fail?
Thanks,
-Jon
=)
jonhanke@[~/my_sage_dir/SAGE_parsley_Build_Testing/sage-4.6.2]: make check
...
--
The following tests failed:
sage -t -force_lib devel/sage/sage/misc/preparser.py
Total time for all tests: 6133.0 seconds
Please see /home/jonhanke/.sage//tmp/test.log for the complete log from this
test.
jonhanke@[~/my_sage_dir/SAGE_parsley_Build_Testing/sage-4.6.2]: sage -t
-force_lib devel/sage/sage/misc/preparser.py
sage -t -force_lib devel/sage/sage/misc/preparser.py
Non-default server settings detected:
Incoming Server = http://hg.sagemath.org (default)
Outgoing Server =
ssh://jonha...@sage.math.washington.edu/sage-4.1.1/devel
**
File
/sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/sage/misc/preparser.py,
line 1386:
sage: sage.misc.preparser.is_loadable_filename('foo.m')
Expected:
True
Got:
False
**
File
/sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/sage/misc/preparser.py,
line 1403:
sage: load_attach_path()
Exception raised:
Traceback (most recent call last):
File /usr/local/sage-4.6/local/bin/ncadoctest.py, line 1231, in
run_one_test
self.run_one_example(test, example, filename, compileflags)
File /usr/local/sage-4.6/local/bin/sagedoctest.py, line 38, in
run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File /usr/local/sage-4.6/local/bin/ncadoctest.py, line 1172, in
run_one_example
compileflags, 1) in test.globs
File doctest __main__.example_19[2], line 1, in module
load_attach_path()###line 1403:
sage: load_attach_path()
NameError: name 'load_attach_path' is not defined
**
We are not regularly testing on Redhat Linux on x86 - see
http://wiki.sagemath.org/SupportedPlatforms
for what we test on.
Can you run the test again
./sage -t
/sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/sage/misc/preparser.py
if the failure is reproducible, then it should be added to the trac
server as a bug. Please state the exact version of Redhat though.
Dave
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Re: [sage-devel] Re: Parallel builds
A single 7200 rpm drive in a dual 6-core Xeon? Did you also go with the default 4GB ram? ;-) -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
One thought is to make it clearer what is happening. Would a pop-up progress window indicating which applet is loading help with the way it feels? Long term, I will probably make it so that old pages load Yes. But that can be added after this. Let's make sure your valuable improvements actually make it in before adding more stuff. with all the applets replaced by static images, but this requires changes to the plot3d functions. I was worrying about the interface first. Can you expand on this? Do you mean that any given page would have a static image, and it would only turn into an applet if one clicked on it (or evaluated it)? Or do you mean that only pages produced before this change would do so, or ...? - kcrisman -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Parallel builds
On 1 Apr, 2011, at 11:38 AM, Volker Braun wrote: A single 7200 rpm drive in a dual 6-core Xeon? Did you also go with the default 4GB ram? ;-) Actually, no. I have 2x2TB(7200rpm) drives and 24GB of ram. After all, these new processors like about 1GB/thread, right? But, you've shamed me. I'm thinking of getting a SSD as well. Maybe two. One for paging. On the off chance that I actually page on this system... :-} J -- Justin C. Walker, Curmudgeon at Large Institute for the Absorption of Federal Funds --- I'm beginning to like the cut of his jibberish. --- -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
On Apr 1, 1:49 pm, kcrisman kcris...@gmail.com wrote: with all the applets replaced by static images, but this requires changes to the plot3d functions. I was worrying about the interface first. Can you expand on this? Do you mean that any given page would have a static image, and it would only turn into an applet if one clicked on it (or evaluated it)? Or do you mean that only pages produced before this change would do so, or ...? What I'm thinking about is that when re-opening a worksheet the 3-D plots would initially load as static images each with a Make Interactive button. This would increase load speed. Then only the plots the user wants to interact with would have to load applets. I think that when the output cell contents are created by an evaluate call it should default to a live Jmol. This will require some reworking of how 3-D plots are generated. Jonathan -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
On Apr 1, 4:35 pm, Jonathan gu...@uwosh.edu wrote: On Apr 1, 1:49 pm, kcrisman kcris...@gmail.com wrote: with all the applets replaced by static images, but this requires changes to the plot3d functions. I was worrying about the interface first. Can you expand on this? Do you mean that any given page would have a static image, and it would only turn into an applet if one clicked on it (or evaluated it)? Or do you mean that only pages produced before this change would do so, or ...? What I'm thinking about is that when re-opening a worksheet the 3-D plots would initially load as static images each with a Make Interactive button. This would increase load speed. Then only the plots the user wants to interact with would have to load applets. I think that when the output cell contents are created by an evaluate call it should default to a live Jmol. This will require some reworking of how 3-D plots are generated. As you said. But not a bad idea. -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: Parallel builds
On 04/ 1/11 07:38 PM, Volker Braun wrote: A single 7200 rpm drive in a dual 6-core Xeon? Did you also go with the default 4GB ram? ;-) I think the technician at Sun who assembled my Sun must have thought it a bit odd. I ordered it with a 3.33 GHz quad core Xeon CPU (over £1000 at the time), a graphics card which was over £600, but only had 2 GB RAM and a single 500 GB disk. I then bought another 10 GB of third-party RAM, another 500 GB disk and a pair of 2 TB disks. -- A: Because it messes up the order in which people normally read text. Q: Why is top-posting such a bad thing? A: Top-posting. Q: What is the most annoying thing in e-mail? Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: Make check fails for sage 4.6.2 build
Dear Dave,
That's weird. Now the test seems to pass. I had tried it several
times before I wrote, but now it consistently passes. I'm now a
little worried about the stability of my system... Any ideas about
what can cause these problems (and tests I can run to detect them)?
Thanks,
-Jon
=)
P.S. /proc/version tells me:
Linux version 2.6.18-164.6.1.el5 (mockbuild@ls20-
bc2-14.build.redhat.com) (gcc version 4.1.2 20080704 (Red Hat
4.1.2-46)) #1 SMP Tue Oct 27 11:28:30 EDT 2009
=
jonhanke@[~/my_sage_dir/SAGE_parsley_Build_Testing/sage-4.6.2]: ./sage
-t /sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/
sage/misc/preparser.py
sage -t /sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/
sage/sage/misc/preparser.py
[7.2 s]
--
All tests passed!
Total time for all tests: 7.2 seconds
On Apr 1, 2:32 pm, David Kirkby david.kir...@onetel.net wrote:
On 1 April 2011 18:43, Jonathan Hanke jonha...@gmail.com wrote:
Hi,
I was building sage 4.6.2 on a Sun Fire 4450 server (called parsley) running
Redhat linux, and the there was a preparser failure when running make check.
Is this something I should be concerned about? I thought that the new sage
builds are automatically tested on this architecture, so how can make check
fail?
Thanks,
-Jon
=)
jonhanke@[~/my_sage_dir/SAGE_parsley_Build_Testing/sage-4.6.2]: make check
...
--
The following tests failed:
sage -t -force_lib devel/sage/sage/misc/preparser.py
Total time for all tests: 6133.0 seconds
Please see /home/jonhanke/.sage//tmp/test.log for the complete log from this
test.
jonhanke@[~/my_sage_dir/SAGE_parsley_Build_Testing/sage-4.6.2]: sage -t
-force_lib devel/sage/sage/misc/preparser.py
sage -t -force_lib devel/sage/sage/misc/preparser.py
Non-default server settings detected:
Incoming Server =http://hg.sagemath.org (default)
Outgoing Server =
ssh://jonha...@sage.math.washington.edu/sage-4.1.1/devel
**
File
/sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/sage/misc/
preparser.py,
line 1386:
sage: sage.misc.preparser.is_loadable_filename('foo.m')
Expected:
True
Got:
False
**
File
/sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/sage/misc/
preparser.py,
line 1403:
sage: load_attach_path()
Exception raised:
Traceback (most recent call last):
File /usr/local/sage-4.6/local/bin/ncadoctest.py, line 1231, in
run_one_test
self.run_one_example(test, example, filename, compileflags)
File /usr/local/sage-4.6/local/bin/sagedoctest.py, line 38, in
run_one_example
OrigDocTestRunner.run_one_example(self, test, example, filename,
compileflags)
File /usr/local/sage-4.6/local/bin/ncadoctest.py, line 1172, in
run_one_example
compileflags, 1) in test.globs
File doctest __main__.example_19[2], line 1, in module
load_attach_path()###line 1403:
sage: load_attach_path()
NameError: name 'load_attach_path' is not defined
**
We are not regularly testing on Redhat Linux on x86 - see
http://wiki.sagemath.org/SupportedPlatforms
for what we test on.
Can you run the test again
./sage -t
/sage/jonhanke/SAGE_parsley_Build_Testing/sage-4.6.2/devel/sage/sage/misc/p
reparser.py
if the failure is reproducible, then it should be added to the trac
server as a bug. Please state the exact version of Redhat though.
Dave
--
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[sage-devel] Re: sage notebook with many Jmol viewers
On 4/1/11 1:18 PM, Jonathan wrote: Dan, I'm glad you like most of what has been done. If you manage to get anything to fail please report that as well. As to the speed, there's not a lot we can do. That is limited by how fast information is passed from the server and how fast your computer is. Jmol is doing quite a bit of computation to produce the live figures. Because of JavaVM memory constraints within browsers things do not work well if more than one applet is loading at once. This means that each applet has to finish loading before the next one can start. One thought is to make it clearer what is happening. Would a pop-up progress window indicating which applet is loading help with the way it feels? If we end up doing a pop-up progress window, how about instead a little spinning icon in the place of the jmol applet, like a typical circular thing chasing its tail, or a progress bar loader. If it's in the place of the applets that haven't loaded yet, it's not intrusive on the experience, whereas a pop-up progress window I think intrudes too much on the user. I agree that we should get something in that we've been testing a long time first, and then we can worry more about adding additional things on. Thanks, Jason -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Debugging some cython code / Pynac
On Fri, 01 Apr 2011 17:20:57 +0100 Dr. David Kirkby david.kir...@onetel.net wrote: On 04/ 1/11 12:54 PM, Burcin Erocal wrote: On Fri, 01 Apr 2011 00:37:46 +0100 Dr. David Kirkbydavid.kir...@onetel.net wrote: I've built Sage 64-bit on OpenSolaris but it crashes at startup. I've run gdb and find the bit of code that's causing the crash is this. ./devel/sage-main/sage/symbolic/function.cpp /* sage/symbolic/function.pyx:109 * raise ValueError, real_fname + parameter must be callable * * if not self._is_registered(): # * self._register_function() * */ snip allows Sage to run. It's not 100% stable, but much better than before. snip Can anyone see if there might be something wrong with this code, which is causing Sage to segfault? It might be due to the linker initializing the library in a different order. Can you post a backtrace so we can see which function it is trying to construct? Here's a backtrace snip Program received signal SIGSEGV, Segmentation fault. 0x003eb0a5 in ?? () (gdb) bt #0 0x003eb0a5 in ?? () #1 0xfd7fff2ac5d1 in _Unwind_RaiseException_Body () from /lib/64/libc.so.1 #2 0xfd7fff2ac855 in _Unwind_RaiseException () from /lib/64/libc.so.1 #3 0xfd7ff91d6729 in __cxa_throw (obj=value optimized out, tinfo=value optimized out, dest=value optimized out) at ../../../../../gcc-4.5.0/libstdc++-v3/libsupc++/eh_throw.cc:78 #4 0xfd7fcec6d5ff in GiNaC::function::find_function (name=@0x4a359b0, nparams=2) at function.cpp:1446 #5 0xfd7fce9454ad in __pyx_f_4sage_8symbolic_8function_15BuiltinFunction__is_registered (__pyx_v_self=0x4a142f0) at sage/symbolic/function.cpp:7301 #6 0xfd7fce950755 in __pyx_pf_4sage_8symbolic_8function_8Function___init__ (__pyx_v_self=0x4a142f0, __pyx_args=value optimized out, __pyx_kwds=value optimized out) at sage/symbolic/function.cpp:2374 #7 0xfd7fffde7a70 in ?? () the stack is corrupted so the rest is useless David gave me an account on the machine. Here is the Python call stack: File /export/home/burcin/sage-4.7.alpha3/local/bin/sage-ipython, line 21, in module ipy_sage = IPython.Shell.start() File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/Shell.py, line 1233, in start return shell(user_ns = user_ns) File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/Shell.py, line 78, in __init__ debug=debug,shell_class=shell_class) File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/ipmaker.py, line 644, in make_IPython force_import(profmodname) File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/ipmaker.py, line 66, in force_import __import__(modname) File ipy_profile_sage.py, line 7, in module import sage.all_cmdline File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/all_cmdline.py, line 14, in module from sage.all import * File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/all.py, line 75, in module from sage.schemes.allimport * File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/all.py, line 25, in module from hyperelliptic_curves.all import * File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/all.py, line 1, in module from constructor import HyperellipticCurve File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/constructor.py, line 11, in module from sage.schemes.generic.all import ProjectiveSpace File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/all.py, line 4, in module from affine_space import AffineSpace, is_AffineSpace File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/affine_space.py, line 24, in module import algebraic_scheme File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/algebraic_scheme.py, line 143, in module import toric_variety File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/toric_variety.py, line 236, in module from sage.geometry.cone import Cone, is_Cone File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/geometry/cone.py, line 174, in module from sage.combinat.posets.posets import FinitePoset File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/combinat/posets/posets.py, line 24, in module from sage.graphs.all import DiGraph File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/graphs/all.py, line 16, in module from
Re: [sage-devel] Debugging some cython code / Pynac
On Fri, Apr 1, 2011 at 3:46 PM, Burcin Erocal bur...@erocal.org wrote: On Fri, 01 Apr 2011 17:20:57 +0100 Dr. David Kirkby david.kir...@onetel.net wrote: On 04/ 1/11 12:54 PM, Burcin Erocal wrote: On Fri, 01 Apr 2011 00:37:46 +0100 Dr. David Kirkbydavid.kir...@onetel.net wrote: I've built Sage 64-bit on OpenSolaris but it crashes at startup. I've run gdb and find the bit of code that's causing the crash is this. ./devel/sage-main/sage/symbolic/function.cpp /* sage/symbolic/function.pyx:109 * raise ValueError, real_fname + parameter must be callable * * if not self._is_registered(): # * self._register_function() * */ snip allows Sage to run. It's not 100% stable, but much better than before. snip Can anyone see if there might be something wrong with this code, which is causing Sage to segfault? It might be due to the linker initializing the library in a different order. Can you post a backtrace so we can see which function it is trying to construct? Here's a backtrace snip Program received signal SIGSEGV, Segmentation fault. 0x003eb0a5 in ?? () (gdb) bt #0 0x003eb0a5 in ?? () #1 0xfd7fff2ac5d1 in _Unwind_RaiseException_Body () from /lib/64/libc.so.1 #2 0xfd7fff2ac855 in _Unwind_RaiseException () from /lib/64/libc.so.1 #3 0xfd7ff91d6729 in __cxa_throw (obj=value optimized out, tinfo=value optimized out, dest=value optimized out) at ../../../../../gcc-4.5.0/libstdc++-v3/libsupc++/eh_throw.cc:78 #4 0xfd7fcec6d5ff in GiNaC::function::find_function (name=@0x4a359b0, nparams=2) at function.cpp:1446 #5 0xfd7fce9454ad in __pyx_f_4sage_8symbolic_8function_15BuiltinFunction__is_registered (__pyx_v_self=0x4a142f0) at sage/symbolic/function.cpp:7301 #6 0xfd7fce950755 in __pyx_pf_4sage_8symbolic_8function_8Function___init__ (__pyx_v_self=0x4a142f0, __pyx_args=value optimized out, __pyx_kwds=value optimized out) at sage/symbolic/function.cpp:2374 #7 0xfd7fffde7a70 in ?? () the stack is corrupted so the rest is useless David gave me an account on the machine. Here is the Python call stack: File /export/home/burcin/sage-4.7.alpha3/local/bin/sage-ipython, line 21, in module ipy_sage = IPython.Shell.start() File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/Shell.py, line 1233, in start return shell(user_ns = user_ns) File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/Shell.py, line 78, in __init__ debug=debug,shell_class=shell_class) File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/ipmaker.py, line 644, in make_IPython force_import(profmodname) File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/IPython/ipmaker.py, line 66, in force_import __import__(modname) File ipy_profile_sage.py, line 7, in module import sage.all_cmdline File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/all_cmdline.py, line 14, in module from sage.all import * File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/all.py, line 75, in module from sage.schemes.all import * File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/all.py, line 25, in module from hyperelliptic_curves.all import * File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/all.py, line 1, in module from constructor import HyperellipticCurve File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/hyperelliptic_curves/constructor.py, line 11, in module from sage.schemes.generic.all import ProjectiveSpace File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/all.py, line 4, in module from affine_space import AffineSpace, is_AffineSpace File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/affine_space.py, line 24, in module import algebraic_scheme File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/algebraic_scheme.py, line 143, in module import toric_variety File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/schemes/generic/toric_variety.py, line 236, in module from sage.geometry.cone import Cone, is_Cone File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/geometry/cone.py, line 174, in module from sage.combinat.posets.posets import FinitePoset File /export/home/burcin/sage-4.7.alpha3/local/lib/python2.6/site-packages/sage/combinat/posets/posets.py, line 24, in module from sage.graphs.all import DiGraph File
Re: [sage-devel] Spam tickets on Trac
Hi William, On Sat, Apr 2, 2011 at 3:07 AM, William Stein wst...@gmail.com wrote: It sounds like it might be less work for you if we switch to email Minh for an account? I can't say it would be less work for me. I check trac very often for over two years now. Creating trac accounts even on a daily basis would be normal routine for me. If you want, I would assume that role and manage the creation of new trac accounts. That is, anyone wishing to create/modify/delete or otherwise manage their trac account should contact me or someone with relevant privileges on trac. -- Regards Minh Van Nguyen -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
