[sage-devel] Memory leak (quite bad)
This slowly and inexorably goes on. Computing `sqrt(T2)` leaks 32 bytes
each and every time (asymptotically).
Found by a student who, through no fault of himself, brought down our
server (unable to ssh in until the OOM triggered -- but since the leak is
slow it takes a while to trash 16G of swap).
===
$ cat memleak.py
from sage.all import sqrt
T2 = sqrt(2)
import psutil
ps = psutil.Process()
base = ps.memory_info().rss
for a in range(1, 10):
for b in range(num := 100_000):
C = sqrt(T2)
mem = ps.memory_info().rss - base
print(f"{mem/1e6 :.2f} MB ({mem/a/num :.2f} bytes/iter)")
$ sage memleak.py
2.70 MB (27.03 bytes/iter)
5.95 MB (29.74 bytes/iter)
9.19 MB (30.64 bytes/iter)
12.44 MB (31.09 bytes/iter)
15.41 MB (30.82 bytes/iter)
18.65 MB (31.09 bytes/iter)
21.90 MB (31.28 bytes/iter)
25.14 MB (31.43 bytes/iter)
28.39 MB (31.54 bytes/iter)
===
Replace the 10 in the outer loop by something larger at your own peril
(each outer iteration will take 3.2M so 10_000 should kill a laptop in an
hour or two).
This is with system sagemath 10.0 but it also happens with 9.6, 9.7, 9.8
and 10.0 in cocalc.com.
Best,
Gonzalo
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Re: [sage-devel] sage is slowding down PARI/GP by factor x2 (roughly)
See https://trac.sagemath.org/ticket/34850#comment:65. Do I get that beer in Luminy? Best, Gonzalo On Friday, December 16, 2022 at 5:47:46 PM UTC-3 dim...@gmail.com wrote: > On Fri, Dec 16, 2022 at 4:58 PM David Lowry-Duda > wrote: > > > > On Thu, Dec 15, 2022 at 12:19:28PM +, Dima Pasechnik wrote: > > >On Thu, Dec 15, 2022 at 12:05 PM John Cremona > wrote: > > >> > > >> A propos, which Sage developers will be in Luminy for the COUNT > > >> meeting? I will. > > >> > > >I'm still waiting to hear from them. Or perhaps they don't notify > > >people who haven't made it on the list, I have no idea. > > >I should form a 1-person union and declare myself on strike w.r.t., > > >quoting their announcement, "informal collaboration and for coding > > >projects related to PARI/GP, SageMath,..." :-) > > > > > >Dima > > > > I'm also waiting to hear from them. But in principle, I'd like to be > > there too. > > > > we're now on the list, as far as I can see: > > > https://www.cirm-math.fr/Listes/liste_pre_verif.php?id_renc=2805_semaine=0 > > Cheers > Dima > > > - DLD > > > > -- > > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/Y5yjk1mCDBY9kkIL%40icerm-dld. > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/3488c44b-07ac-458e-8c13-79abcba96db1n%40googlegroups.com.
Re: [sage-devel] Re: What does it mean for a ticket to be closed?
Maybe you could append a Fixes: #x to the commit message (similar to the Signed-of-by lines that are used in the linux kernel), then have an hook in the official repo close the ticket. This way the ticket is automatically closed iff and when the fix is merged to the official development branch. Best, Gonzalo On Thu, Dec 19, 2013 at 10:01 AM, Volker Braun vbraun.n...@gmail.comwrote: On Thursday, December 19, 2013 11:42:23 AM UTC, Jeroen Demeyer wrote: You could consider closing a ticket only *after* testing it on the buildbot (that was what I did) when it is as good as certain that it will actually be merged. Yes, I've been doing both depending on how probable it seemed that the ticket can break something. Still trying to get a feel for the best workflow -- 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/groups/opt_out. -- 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/groups/opt_out.
Re: [sage-devel] Re: Changing branch on a trac ticket
More reading and some comments: a. Linus et al on git rebase: http://yarchive.net/comp/linux/git_rebase.html. b. An article in LWN about the topic: http://lwn.net/Articles/328436/ c. In the first reference there are a couple of comments by Linus on revert -- including a recipe using rebase that seems natural. d. to revert without rewriting history, I belive git revert does the trick. With respect to the allow rewriting history vs. don't allow rewriting history, p lease have a look at the comments by Linus from (a) above. I think he knows what he's talking about. One thing that Linus stresses is that rebasing affects more the people downstream than the people upstream. For instance: if a group is working on some module, we push a series of patches (but I'm still working on subsequent ones), and somewhere in the path between us and the final merge the patches get rewritten, then our work after that may be seriously screwed (meaning: we have to work to adjust, and we don't have history to tell us *how* or *where* the divergence with our codebase. On Tue, Nov 5, 2013 at 10:20 AM, Simon King simon.k...@uni-jena.de wrote: If the commit history was like A: Basic implementation of a duck (quacks, swims) B: Added duckumentation C: Added feature duck flies D: Remove trailing whitespace E: Fix bad doc formatting then I believe to *some* extent it makes sense to re-group these commits (like: (A+C+D)-(B+E)), since, as we have seen, rebasing of dependent branches does not become more difficult. As Linus says I wouldn't argue for hard rules and this may be an exception under some circumstances, but as a general rule I can think of different scenarios where it's ok and where it's not ok to rewrite. In particular I think this is only ok if all A-E have been writing by the same person or a group with tight synchronization, and I guess it also depends on time elapsed between A and E, etc. Example: 1. A, B are posted in ticket 2. purple-sage (or sage-next, or whatever) gets interested in ducks, and decides to merge these experimentally 3. C is posted in ticket 4. review of ticket requests D, E 5. author rewrites history to (A+C+D) , (B+E) 6. merged in master sage as rewritten 7. now purple-sage is screwed up wrt master sage Of course it wouldn't be too bad to resolve this issue for a few tickets, but doing it for a number of them may be quite boring. I would assume one of the features of switching to git would be to ease the exchange of code between sage and other efforts like purple-sage, and/or allow having a sage-next branch, or ... (other ideas people may come up with). Different scenario: A is completely broken so no way it can be merged (e.g. breaks compilation); then A is never merged, the author is requested to redo the feature, a new patch A' is posted by the author (based on A, fine) and that's merged. In this scenario purple-sage wouldn't have merged A either (due to compilation broken) or would want it removed anyway. -- As a general rule I would argue for: a. no rewriting of other people patches b. no rewriting of own patches that have been published c. adopt a sensible definition of published which allows *some* rewriting that people may want d. empower developers with easy ways to share feature development branches which are not published e. allow sensible exceptions when truly necessary For (d) feature branches should be based on stable points anyway and refrain from frequent pulls/merges with master until the feature is merged, etc. Best, Gonzalo -- 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/groups/opt_out.
Re: [sage-devel] Re: Changing branch on a trac ticket
On Tue, Nov 5, 2013 at 12:32 PM, Simon King simon.k...@uni-jena.de wrote: Hi Gonzalo, On 2013-11-05, Gonzalo Tornaria torna...@math.utexas.edu wrote: Example: 1. A, B are posted in ticket 2. purple-sage (or sage-next, or whatever) gets interested in ducks, and decides to merge these experimentally 3. C is posted in ticket 4. review of ticket requests D, E 5. author rewrites history to (A+C+D) , (B+E) 6. merged in master sage as rewritten 7. now purple-sage is screwed up wrt master sage Of course it wouldn't be too bad to resolve this issue for a few tickets, but doing it for a number of them may be quite boring. Wait a second. If purple-sage branches off at 2. (hence, if it only knows about A and B), then it eventually needs to be rebased anyway, because we now also have C, D, E. It doesn't need to be rebased. As a general rule, C-D-E would be pulled on top of B and merged with whatever other changes that happened in purple-sage after B. Merging is much more convenient than rebasing because it keeps history around. A practical reason why history is important: merging. To do a proper automatic or assisted merge of two versions of a file, you need a common base version to do 3-way merge (think about it, it really cannot work without a common base version -- how would you distinguish blocks of code that where added in version A from blocks of code that where removed in version B?). If we rewrite history (e.g. doing a rebase instead of a merge) then we complicate merges further down the line. (This is besides all the other good reasons to not rewrite history, e.g. git annotate/blame or git bisect, etc) That's why I argued: If rebasing of purple-sage with respect to (A+C+D)-(B+E) is not more difficult than rebasing of purple-sage with respect to A-B-C-D-E, and since rebasing of purple-sage is certainly necessary because of the existence of C, D and E in the master branch, then why do people keep argueing that changing the history causes trouble? It does not cause the trouble, and it does not increase trouble (at least in this and the previously discussed examples). To say it clearly: In the scenario above, you *have* to rebase, with or without a change of history, and the rebase (if I understand correctly) is the same effort with or without a change of history. Hence, saying that we need to rebase dependent work is just not an argument against rewriting history. Best, Gonzalo -- 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/groups/opt_out.
Re: [sage-devel] Re: Changing branch on a trac ticket
Relevant article by Linus Torvalds: http://lwn.net/Articles/328438/ Best, Gonzalo On Mon, Nov 4, 2013 at 4:33 PM, David Roe roed.m...@gmail.com wrote: I agree with Volker: any plan which involves rewriting the history of your branch to make it nicer is a very bad idea. Once you push changes to trac, you really should not go back and rewrite your commits. Even if you decide you don't want some code that you introduced, you should introduce a new commit that deletes the code rather than removing old commits and force-pushing your branch. This is a fundamental difference between using patches and using revision control properly. You just can't do this kind of thing without causing anyone else who's based work on your ticket a lot of pain. And you won't even know who they are: they may not have pushed their work to a trac ticket yet. TLDR; don't rewrite history. David On Mon, Nov 4, 2013 at 9:55 AM, Volker Braun vbraun.n...@gmail.com wrote: git blame already does cumulative blame over a range of commits. By mashing commits together you don't gain anything. But you invalidate all branches that were based on the un-mashed commits. If you absolutely can't live with others noticing that you are human after all, then you can still squash your history locally before pushing it to trac. But IMHO thats just OCD and nothing that we should teach people to do by default. TLDR; lots of pain for absolutely no gain. On Monday, November 4, 2013 6:15:19 AM UTC, Nils Bruin wrote: That's good to know. However, when trying to figure out the history of code, it's usually not so much the question what has changed, but more when and (more importantly) why. git blame does that, and hopefully the log entry for the relevant commit tells you where to look further. If that commit reads third iteration of typo correction and rollback of latest change it's not so helpful and you need to go and look in the log for commits close by that are more instructive. -- 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/groups/opt_out. -- 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/groups/opt_out. -- 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/groups/opt_out.
Re: [sage-devel] Re: VectorSpaces vs tuples
On Tue, Dec 11, 2012 at 10:38 PM, Robert Bradshaw rober...@math.washington.edu wrote: Not requiring a coercion allows statements like sage: 4/2 in ZZ True when there's no coercion from QQ to ZZ. I'm all for a better heuristic. (Perhaps require a coercion or injective coercion inverse into the target parent?) It gets even trickier for inexact parents. And of course who knows how much other stuff this will break. OTOH: sage: 4/2 in ZZ True sage: 4/2 in GF(3) False sage: 4/3 in ZZ False sage: 4/3 in GF(3) --- ZeroDivisionError Traceback (most recent call last) ... ZeroDivisionError: Inverse does not exist. Best, Gonzalo -- You received this message because you are subscribed to the Google Groups sage-devel group. To post to this group, send email to sage-devel@googlegroups.com. To unsubscribe from this group, send email to sage-devel+unsubscr...@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en.
Re: [sage-devel] Re: Fwd: NaN = Not A Number ???
On Thu, Mar 22, 2012 at 4:14 PM, Robert Bradshaw rober...@math.washington.edu wrote: ... This is horrendous. Better to not have this constant (at least not in the global namespace) than behavior like this. The top level NaN, if we want one, could be in RR (precision doesn't really matter for this value). Agreed, that's my point. Working on a completely unrelated project, I was hit by a different and unrelated bug regarding NaN: sage: RR(NaN) float(1e-10) True Also, I point out that the usual definition of NaN includes the fact that NaN == NaN should be false. Sage doesn't behave consistently: sage: float(NaN) == float(NaN) False sage: RR(NaN) == RR(NaN) True sage: NaN == NaN NaN == NaN sage: bool(_) True (this property is handy to test whether a value is nan) Gonzalo -- 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] Fwd: NaN = Not A Number ???
In sage 4.8: sage: NaN - NaN sage: 0 sage: NaN + NaN 2*NaN sage: NaN * NaN NaN^2 not what I expected... RR(NaN) seems to work better sage: RR(NaN) - RR(NaN) NaN sage: RR(NaN) + RR(NaN) NaN sage: RR(NaN) * RR(NaN) NaN Still some weirdness: sage: RR(NaN) + x x sage: RR(NaN) * x NaN*x Gonzalo -- 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: Eigen-stuff in Sage
On Thu, Jun 23, 2011 at 4:49 PM, Rob Beezer goo...@beezer.cotse.net wrote: Proposal: For matrices over QQ (or implicitly ZZ) with eigenvalues outside QQ, make the default output like the second example above, while retaining the current output as optional behavior via a keyword. What's wrong with: sage: B = matrix(ZZ, [[-87, -1, 1], [17, 2, -6], [-1, -2, 7]]) sage: B.eigenvectors_right() [(-86.80242042716417?, [(1, -0.190991066220052?, 0.006588506615773?)], 1), (0.12344763849958892?, [(1, -122.6499594923977?, -35.52651185389811?)], 1), (8.67897278866459?, [(1, -43.93682721916003?, 51.74214556950456?)], 1)] ? And what if the output of B.eigenspaces_right() is a bit confusing? I'd argue that's actually a feature, because it will make the student *think* about it, get a glimpse of some interesting mathematics, and maybe open a door to a new world. We can just tell students to use the eigenvectors_* methods, and challenge them to figure out how to read the output of the eigenspaces_* methods. Best, Gonzalo -- 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] Question about coercion
In sage/structure/parent_base.pyx there is a function check_old_coerce with the following definition: cdef inline check_old_coerce(parent.Parent p): if p._element_constructor is not None: raise RuntimeError, %s still using old coercion framework % p This function is called from a few methods in class ParentWithBase (e.g. from _richcmp, from _coerce_c_impl, and from base_extend). In my class (which inherits from ParentWithBase) I've defined _element_constructor_ instead, but the init for ParentWithBase insist on copying this method onto _element_constructor -- thus the check_old_coerce function always fails... It's impossible to avoid!!! What is the base class that one is supposed to use instead of ParentWithBase? The only reference for the coercion model that I was able to find is http://www.sagemath.org/doc/reference/coercion.html#example, which even shows an example, but the example inherits from Ring, which ultimately inherits from ParentWithBase anyway. Gonzalo -- 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: Question about coercion
On Tue, Jun 7, 2011 at 5:18 PM, Simon King simon.k...@uni-jena.de wrote: Hi Gonzalo, On 7 Jun., 21:25, Gonzalo Tornaria torna...@math.utexas.edu wrote: What is the base class that one is supposed to use instead of ParentWithBase? I think it is Parent. The Parent.__init__ accepts an argument base. Here is a small example: Thanks for the example. I'll try it. One caveat, though. The standard Ring and Algebra parents both inherit from the ParentWithBase. Am I allowed to mix an element class derived from AlgebraElements with a parent class derived from Parent? Also, is it my impression or this model seems to require a lot of boilerplate if I wanted to implement it fully (with categories, functors, etc)? Gonzalo -- 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: AbelianGroup constructor can't handle its own elements
On Sun, May 8, 2011 at 3:34 PM, John Cremona john.crem...@gmail.com wrote: I forwarded this thread to sage-algebra. Thanks John. I'm actually not subscribed to sage-algebra. Is it undesirable to discuss this here? Gonzalo -- 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] AbelianGroup constructor can't handle its own elements
sage: G = AbelianGroup(1,[2]) sage: ZG = GroupAlgebra(G) sage: f = ZG(G.gen()) sage: f in ZG True sage: ZG(f) ... TypeError: Don't know how to create an element of Group algebra of group Multiplicative Abelian Group isomorphic to C2 over base ring Integer Ring from f -- Proposed fix: --- a/sage/algebras/group_algebra.pyFri May 06 15:29:53 2011 -0700 +++ b/sage/algebras/group_algebra.pySun May 08 14:40:24 2011 -0700 @@ -234,6 +234,8 @@ sage: ZG = GroupAlgebra(G) sage: ZG(f) f +sage: ZG(f) == ZG(ZG(f)) +True sage: ZG(1) == ZG(G(1)) True sage: ZG(FormalSum([(1,f), (2, f**2)])) @@ -305,7 +307,10 @@ if not hasattr(x, 'parent'): x = IntegerRing()(x) # occasionally coercion framework tries to pass a Python int -if isinstance(x, FormalSum): +if parent is x.parent(): +self._fs = x._fs + +elif isinstance(x, FormalSum): if check: for c,d in x._data: if d.parent() != self.parent().group(): -- 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] default __hash__
On Mon, Apr 18, 2011 at 10:24 PM, William Stein wst...@gmail.com wrote: ... I think it is worth revisiting this design decision. I did a little poking, and in Python and Cython, a class by default has a hash, which is the location in memory of the object, e.g., Only so long as the class doesn't define __eq__ or __cmp__. That makes sense, because the default equality comparision in python is that two objects are equal if and only if they are the same instance. Thus, the basic assumption on hashes is not broken (equal objects should have the same hash). If a class defines a comparision, the default hash is to raise an exception So the main issue I pointed out above, namely that SageObject has a __hash__ defined, is really a non-issue, since that's the standard default convention in Python anyways. No, the basic assumptions about hashes in Python are: 1. the hash of an object never changes 2. two objects that compare equal should have the same hash bad things happen if either assumption is broken (a third assumption would be that hash collisions are uncommon, but that only affects performance, not semantics). So, as you suggested in the OP, the right thing is to have the __hash__ method removed from the SageObject class, and define it for subclasses as needed (and only for immutable classes!) Note that the class Element (sage.structure.element.Element) also has a similar default definition for __hash__. Gonzalo -- 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] default __hash__
http://thedailywtf.com/Articles/The-Nondeterministic-Hash.aspx Gonzalo On Mon, Apr 18, 2011 at 4:13 PM, William Stein wst...@gmail.com wrote: Hi, I was just explaining to a student in my Sage course how I had stupidly defined a default __hash__ method for SageObject, which was -- stupidly -- to just hash the string representation. This was of course silly and dangerous since only immutable objects should have a __hash__ method. I then of course pointed out that we must have fixed this years ago! But amazingly we didn't: sage: S = SageObject(); S type 'sage.structure.sage_object.SageObject' sage: hash(S) -7904861314369208036 sage: S.__hash__?? File: /sagenb/flask/sage-4.6.2/devel/sage/sage/structure/sage_object.pyx Source Code (starting at line 156): def __hash__(self): return hash(self.__repr__()) Thoughts? -- William -- 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 -- 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] VMware image -- bug with an easy fix
On Wed, Mar 30, 2011 at 7:52 PM, William Stein wst...@gmail.com wrote: There is an easy fix though. The problem was that the default network interface got renamed by udev to eth6, but the file /etc/network/interfaces only lists eth1-eth4. So whoever (?) is maintaining the vmware image should just add a bunch more lines to that file, say with all interfaces up to eth10 searched for. Also worth looking at the persistent rules for net devices udev. E.g. in debian, they are in /etc/udev/rules.d/70-persistent-net.rules Cleaning up the rules may help to keep the name of the eth interface to eth0 or eth1. I presume vmware is showing a device with a different MAC for each vm, so each time the image is run in a new vm a new rule is added with a new interface name. HTH Gonzalo -- 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: Adjoint of a matrix
On Thu, Dec 9, 2010 at 10:03 PM, Rob Beezer goo...@beezer.cotse.net wrote: Is there any objection to deprecating the current .adjoint() function (which returns a matrix of cofactors) and renaming it as the adjugate? With all the usual procedures and warnings for the deprecation. That would begin the process to free up adjoint for something else (ideally the conjugate-transpose). I've been unable to reply on this before, and today after receiving a comment on ticket #10501 I commented right there, which was possibly a bit unpolite given the lapse of time and that I didn't post that commentto this thread (if so I apologize). Anyway, here's a copy of my post, in case it's helpful: I already stated some objections, but I'll repeat: On deprecating adjoint meaning matrix of cofactors 1. it's standard terminology and has meant this in sage for long 2. adjugate is newer and (IMO) less standard terminology -- in particular it has no obvious translations On using adjoint meaning conjugate transpose 3. conjugate transpose is easy to say, and it's really what is meant 4. the adjoint operator for a matrix seems ill-defined, because a matrix is not an operator but only a representation of an operator in some basis. Moreover, if there are two colliding usages of the name adjoint, I would find it more reasonable to keep the usage that is already traditional in Sage. The usage of adjoint is ubiquitous in relation to quadratic forms afaict (and, as John Cremona pointed out, is where the term originates with Gauss on ternary quadratic forms). I also pointed out a reference to Bourbaki which I already posted above. I still haven't found a reference for adjugate which satisfies me (I mean, where does it originate?) or a good reference for how to use adjoint of a matrix as meaning conjugate transpose in reference to adjoint operators without eventually causing some pain when using it in the real world where not all bases are orthogonal (not even all vector spaces have inner product). OTOH, I do certainly appreciate that transpose and conjugate transpose is used quite a lot, and thus I think it really deserves all the shortcuts proposed (T, H, star, etc). Gonzalo -- 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] Adjoint of a matrix
On Thu, Dec 2, 2010 at 7:16 AM, John Cremona john.crem...@gmail.com wrote:
What you call the classical adjoint is really the adjugate. That is
abbreviated to adj, and since there is also an adjoint, it is a common
error to call the adjugate the adjoint.
Do you have a reference for this convention? I had never seen the word
adjugate before.
--
Something interesting:
if T : V -- V is an operator, it naturally induces a graded operator
T* in the exterior algebra of V. If V is of finite dimension n, there
are two pieces of the exterior algebra which are isomorphic to V,
namely
1. Lambda_1(V) = the dual space of V
2. Lambda_{n-1}(V) = the space of (n-1)-multivectors of V
Then the restriction of T* to Lambda_1(V) is the adjoint (or dual)
operator, but the dual space is not canonically isomorphic to V. Given
a duality (inner product) then you get the adjoint operator acting in
V. The matrix depends on the choice of basis.
On the other hand, Lambda_{n-1}(V) is naturally isomorphic to V (the
isomorphism is given by the determinant), and
so the restriction of T* to Lambda_{n-1}(V) naturally induces an
operator on V, which is precisely what I would call adj T. Since
this is natural, an adjoint operation for matrices can be defined in
terms of this.
In summary, both notions of adjointness are quite related. The simple
one is just duality, and makes more sense for operators in inner
product spaces. The seemingly not-so-simple one is natural, makes
sense for operators or matrices, is usually expressed in terms of
matrices, and appears often in relation to quadratic forms.
However: the first ever occurrence of what I just said is really the
adjugate is in Gauss's Disquisitiones Mathematicae in Art. 267 (page
293 of the modern Springer translation), where he calls it the
adjoint! But this is in a very special case: symmetric 3x3 integer
matrices, representing ternary quadratic forms, and Gauss does not use
our standard matrix notation. So he is defining the adjoint of
ternary quadratic forms rather than matrices.
+1 to Gauss :-)
[he reduces ternary quadratic forms by alternating a binary reduction
step on the form itself and a binary reduction step on the adjoint, so
he may have invented adjoints for this purpose]
Gonzalo
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Re: [sage-devel] Re: Adjoint of a matrix
On Fri, Dec 3, 2010 at 12:59 AM, kcrisman kcris...@gmail.com wrote: Do you have a reference for this convention? I had never seen the word adjugate before. At least in an older edition of Lay's Linear Algebra book (fairly widely used) uses this, and points out there is a real adjoint which is not covered in his text. With a bit of help of books.google.com I can see adjugate is used in this book (adjoint matrix is not used, though); however it doesn't seem to contain any reference to where this word came from. Do you know? On the other hand, searching for The adjoint of a square matrix bourbaki in books.google.com, yields the following passage: The adjoint of a square matrix X of order n over A is the matrix X = (det (A')) of minors of A of order n — 1. (bourbaki, elements, book 2, chapter III, section 11, exercise 9 -- the term also shows at the index of terminology) Best, Gonzalo -- 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] Supported platforms - once again
On Mon, Oct 25, 2010 at 12:09 PM, David Kirkby david.kir...@onetel.net wrote: Since Minh has been using an external server (I think run by GNU) for Debian, we can probably add Debian at some point if we can get permission to run a buildbot slave there. 1. Is there a reason for not running debian on a vm on boxen? 2. what is needed to run a buildbot? (it would feel pretty awkward not to support debian) Gonzalo -- 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: sage 4.5.1 unpack
On Tue, Jul 20, 2010 at 3:43 AM, 3DRaven 3dra...@gmail.com wrote: Yes. I do not speak English. I use a translator of Google. Why unpacking: sage-4.5-linux-32bit-ubuntu_10.04_lts-i686- Linux.tar.lzma I get the message about the impossibility of creating hard links? I just checked the file and I don't see any hard links in the tarball. Can you copy *exactly* what command you are using to uncompress, and what error message you get? Gonzalo PS: maybe your hard drive is full / running out of inodes. That is possible since there are 69k files in the tarball. You can check your disk space and inodes with df -h and df -i respectively. -- 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: talk on Sage...
On Mon, May 10, 2010 at 9:41 AM, William Stein wst...@gmail.com wrote: On Monday, May 10, 2010, Tim Joseph Dumol t...@timdumol.com wrote: I have the same problem. I see color noise instead of 3d plots. There is no support in the sage notebook for printing 3d plots. I'm a little surprised you guys didn't know this... It does, if one uses tachyon as the viewer, doesn't it? Would it make sense to have a global way to select the 3d viewer and a checkbox at the top of the worksheet to change the 3d viewer (kind of like the typeset checkbox). I find myself using the same worksheets usually on a java-less browser, but sometimes I use a java-enabled browser for presentations and I actually want to use jmol applet, so a solution like that would be useful. Best, Gonzalo -- 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: GCC-4.5.0
On Thu, May 6, 2010 at 7:58 PM, Dr. David Kirkby david.kir...@onetel.net wrote: ... The recent case of gcc accepting the macro INFINITY even when code was not compiled in C99 mode was just one example. INFINITY was not defined until the C99 standard. ... I must admit, I find it somewhat annoying that gcc is still not fully C99 compliant, despite it is 12 years since the standard was released! ... LOL! I hope the C99 standard doesn't specify the behaviour when code is NOT compiled in C99 mode... :-) Gonzalo PS: If it is possible to touch a clock without stopping it, then it should be possible to start a clock without touching 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] Fwd: [mpir-devel] New MPIR-related project
On Fri, Apr 30, 2010 at 4:11 AM, Sergey Bochkanov sergey.bochka...@alglib.net wrote: Hello, William. In Sage we (=mostly Gonzalo Tornaria) spent an enormous amount of time writing two very efficient C functions, one to convert from mpz to Python ints, and one to convert back. Yes, writing this code is a lot of work. But no, the resulting code is not slow. Just because something is hard doesn't mean we can't do it. If you want this code, I bet Gonzalo would be OK with letting you have it under another license (it's GPL v2+ right now); it's not long, just tricky to write. That would be nice. Currently X-MPIR is licensed under LGPL, but I think that the same automatic codegen technology may be applied to other projects under different licenses. So having this code under something BSD-like would be important step in Python support. Although I'm more of a GPL (v2) type, and I wouldn't write BSD code unless I had a very good reason, I could consider relicensing some interface code like this. I've actually relicensed this code to LGPL v2+ (for gmpy), but I'm not sure I can go farther than that, since my code was based on GMP code (itself LGPL v2+ at the time). See the forwarded message below for details. Best, Gonzalo -- Forwarded message -- From: Gonzalo Tornaria torna...@math.utexas.edu Date: Tue, Sep 8, 2009 at 10:58 PM Subject: Re: mpmath and files To: William Stein wst...@gmail.com Cc: casevh cas...@gmail.com, mpm...@googlegroups.com On Tue, Sep 8, 2009 at 8:54 PM, William Steinwst...@gmail.com wrote: On Tue, Sep 8, 2009 at 4:38 PM, casevhcas...@gmail.com wrote: On Sep 7, 5:00 pm, William Stein wst...@gmail.com wrote: I think there is very complicated highly optimized code somewhere in Sage (http://sagemath.org) for conversion between Python longs and GMP mpz_t's. If this is what you need, it could be dug up. I maintain gmpy, the Python wrapper for GMP or MPIR, and I would like to look at including Sage's conversion code. I'm currently using mpz_import and mpz_export and am always looking for faster code. Case Van Horsen Hi, Look in the src and include directories here: http://sage.math.washington.edu/home/wstein/build/sage-4.1.1/devel/sage/c_lib/ Would there be any licensing issues since gmpy is LGPL2+? Yes, there is a problem since the code is licensed GPL2+. However, I've cc'd the author -- Gonzalo Tornaria -- and I bet he would be willing to contribute a LGPL2+ version of the code to gmpy. I certainly endorse that! I can definitely contribute the mpz--pylong conversion code to gmpy under LGPL2+. You want to look at the files mpn_pylong.c and mpz_pylong.c. The high level interface (mpz - pylong) is given by functions mpz_get_pylong() and mpz_set_pylong(). There's also a function mpz_pythonhash() which computes a python-compatible hash of mpz integers. The function mpz_get_pyintlong() is a variation of mpz_get_pylong() written by David Harvey --- you should ask him about that one. Note also that the base conversion code used in mpn_get_pylong() is based on GMP code --- I think GMP was LGPLv2+ at the time, so it should be fine. Let me know if you have any issues with using this code in gmpy. If you use the code, can you add a comment to the files along these lines: Originally written for sage (http://sagemath.org) -- if you improve these functions, please contribute them back to sage by posting to sage-devel@googlegroups.com or sending me an email. Best, Gonzalo -- 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: norm of a complex number
2010/4/27 Johan Grönqvist johan.gronqv...@gmail.com: The definition of norm on vectors is consistent with definitions of norm according to wikipedia [0] and the springer encyclopedia of mathematics [1], and (I believe) any book I have ever used. Those did not even mention that there is an alternative definition of norm used in number theory. Here it is: http://en.wikipedia.org/wiki/Field_norm The norm on complex numbers is not consistent with viewing the complex numbers as a two-dimensional real vector space, according to the definitions mentioned above. One caveat: the norm of a two-dimensional real vector space is not canonical. In contrast, the norm of a two-dimensional field extension is uniquely defined. In the case of Sage, the norm of complex numbers is defined as the norm for the field extension C over R. Gonzalo -- 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] norm of a complex number
On Mon, Apr 26, 2010 at 4:26 PM, John Cremona john.crem...@gmail.com wrote: In number theory it is very useful to have this norm-alisation, as well as the square root one also called abs. It's a special case of the algebraic concept of norm(a) = product of conjugates of a. And the determinant of the action of a on C (as an R-vector space of dimension 2) by complex multiplication. However, this doesn't seem correct: sage: sqrt(-3).norm() -3 (I think the problem is with conjugates) --- Anyhow, the norm for complex numbers is fine as is, but for the symbolic ring, it makes me uneasy, e.g. sage: SR(2).norm() 4 sage: CC(2).norm() 4.00 sage: QQ(2).norm() 2 sage: ZZ(2).norm() ... AttributeError: 'sage.rings.integer.Integer' object has no attribute 'norm' sage: RR(2).norm() ... AttributeError: 'sage.rings.real_mpfr.RealNumber' object has no attribute 'norm' Gonzalo -- 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: Translation of coercion
On Fri, Apr 23, 2010 at 11:07 PM, Nathan O'Treally not.rea...@online.de wrote: [...] A coercion from one parent to another must be defined on the whole domain, and always succeeds. As it may be invoked implicitly, it should be obvious and natural (in both the mathematically rigorous and colloquial sense of the word). [...] There are situations where I would relax that and raise an exception e.g. if a specific value can't be implicitly converted because it has no representation in the target domain. For conversions in Sage it is said that success might depend on the actual values (as opposed to their types). I think one of the cases, we argued about it a lot (SD4 and later), is whether the canonical partial map QQ -- GF(p) should be an (automatic) coercion or not. This is for the defined on the whole domain part. Also, the == doesn't fail part seems to force this, since it would be even more awkward to hide the coercion failure. I'd rather have sage: 1/3 == GF(3)(1) raise a ZeroDivisionError, and sage: 1/4 == GF(3)(1) True sage: 1/5 == GF(3)(1) False but others didn't agree with me. You may have a point with the exact domain -- inexact domain coercions being partial. I think the reasoning is that as long as you only coerce from the exact domain into the inexact domain, there shouldn't be problems. Also, inexact domains are NOT rings, so you don't require the coercions to be ring homomorphisms. With respect to NaN, it seems to me sage gets it wrong... sage: 0.0/0.0 == 0.0/0.0 True Gonzalo -- 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 relocation (bug?)
On Sun, Apr 25, 2010 at 2:07 PM, Gonzalo Tornaria torna...@math.utexas.edu wrote: I'm having an issue with sage relocation, and wonder if this is known or not. [...] Moreover, if I move the directory /scratch/tornaria/sage-4.3.3 away, and restart sage, it works perfectly, and sqlite and freetype are loaded from my home. With risk of being a little obnoxious, I did the following experiment: In addition to moving the directory from the scratch build of sage, I also moved away the libsqlite* files in my home install of sage, since I have libsqlite3-0 3.5.9-6 installed (from debian lenny, i.e. stable). Now sage runs without a hitch mapping the system libraries: $ cat /proc/3283/maps | grep libsqlite 7f95db986000-7f95db9fa000 r-xp fe:01 918139 /usr/lib/libsqlite3.so.0.8.6 7f95db9fa000-7f95dbbfa000 ---p 00074000 fe:01 918139 /usr/lib/libsqlite3.so.0.8.6 7f95dbbfa000-7f95dbbfc000 rw-p 00074000 fe:01 918139 /usr/lib/libsqlite3.so.0.8.6 The same works for libfreetype (also with the version from debian stable). --- Update: using the system wide sqlite, all tests pass except one test in devel/sage/sage/graphs/graph_database.py, and the difference looks like one of ordering (i.e. seems a query for a list of graphs returns in a different order for the system wide sqlite). Gonzalo -- 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: Translation of coercion
On Sun, Apr 25, 2010 at 1:26 PM, Nathan O'Treally not.rea...@online.de wrote: On 25 Apr., 17:11, Gonzalo Tornaria torna...@math.utexas.edu wrote: I'd rather have sage: 1/3 == GF(3)(1) raise a ZeroDivisionError, and I'd prefer TypeError (or coercion error, incompatible types, not yet existent I guess) I think you may be missing my point. I'm not arguing about incompatible types raising an error instead of returning false. I'm arguing that there should (IMO) be a canonical coercion QQ --- GF(3) defined in the natural way: a / b |--- GF(3)(a / b) and since GF(3)(1 / 3) raises a ZeroDivisionError, it makes more sense IMO. sage: 1/4 == GF(3)(1) True sage: 1/5 == GF(3)(1) False but others didn't agree with me. I think I won't either. ;-) Well, indeed 1/4 == 1 and 1/5 != 1 in GF(3). In fact, I don't think anybody disagrees with that, and sage: GF(3)(1/4) == GF(3)(1) True sage: GF(3)(1/5) == GF(3)(1) False actually works. The point in question is whether this explicit conversion from QQ to GF(3) as above should also be an implicit coercion. You may have a point with the exact domain -- inexact domain coercions being partial. I think the reasoning is that as long as you only coerce from the exact domain into the inexact domain, there shouldn't be problems. Why? Or did you mean coercing from the *in*exact domain to the exact one? I mean the reasoning in the coercion model of sage is: when you operate between an exact domain and an inexact domain, it only makes sense to work in the inexact domain. Coercing from an inexact domain to an exact domain makes nosense at all, don't you think?. Gonzalo -- 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: Sage relocation (bug?)
On Sun, Apr 25, 2010 at 2:59 PM, Nathan O'Treally not.rea...@online.de wrote: On 25 Apr., 19:07, Gonzalo Tornaria torna...@math.utexas.edu wrote: This is actually a security issue, too. (Imagine e.g. a Sage bdist was compiled in /tmp: Everybody could place arbitrary code in a fake library there. Or he could even look into the Sage binary and find appropriate directories to create and put malware libs into.) Yikes! You are right... :-( I hope that somebody has a better idea of how to fix this bug. At least chmod og-r on all binaries, too (on a multiuser/open system). I don't see how that fixes anything (that isn't fixed by just moving away the build directory or building in a random location). Did you open a ticket for that? No, I didn't. I hoped to get some comments before. Gonzalo -- 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: How to doc-test tab completion, revisited
On Fri, Apr 2, 2010 at 12:31 PM, Simon King simon.k...@nuigalway.ie wrote: Hi John! On 2 Apr., 17:10, John Cremona john.crem...@gmail.com wrote: On your local machine running linux (which is the only thing I know about) I type ssh selmer -L 8123:localhost:8000 and I get the usual prompt on selmer *and* now in my browser I can go tohttps://localhost:8123 and get selmer's Sage login page, since ssh magically transforms port 8123 on localhost to port 8000 on selmer. Cool! Two problems though: - My netbook got Windows. - When I want to ssh to the computer in my office, the university forces me to use a Cisco AnyConnect VPN client on my netbook. The interesting thing is that I am unable to open *any* webpage located at my university while the VPN client is running. If you can ssh into your office computer in some way, you should be able to tunnel connections through it. For instance, using putty on windows: http://www.cs.uu.nl/technical/services/ssh/putty/puttyfw.html Gonzalo -- 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 To unsubscribe, reply using remove me as the subject.
Re: [sage-devel] Does sage.math have stack protection?
On Mon, Mar 29, 2010 at 11:04 AM, Dr. David Kirkby david.kir...@onetel.net wrote: When I try the same program on sage.math, it dumps core there too. So I don't know if sage.math has protection of the stack enabled. If it does, then it is strange that SELinux has problems, whereas sage.math does not. The stack is not executable by default (on NX hardware, I assume). You can make your program work by adding something like this: mprotect((void*)((long)a ~0xfff), 0x1000, PROT_READ|PROT_WRITE|PROT_EXEC); before the call to fnptr(), which will make the page where a lives executable. I don't think SELinux is installed on sage.math. Gonzalo -- 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 To unsubscribe from this group, send email to sage-devel+unsubscribegooglegroups.com or reply to this email with the words REMOVE ME as the subject.
Re: [sage-devel] Does sage.math have stack protection?
On Mon, Mar 29, 2010 at 5:41 PM, Dr. David Kirkby david.kir...@onetel.net wrote: I'm just puzzled why SELinux is indicating problems with code trying to execute the stack, whereas there are no such complaints on sage.math, despite the fact attempting to execute the stacks dumps core on sage.math. No, it doesn't if you do it properly. Did you try (at least read) what I wrote? Gonzalo -- 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 To unsubscribe from this group, send email to sage-devel+unsubscribegooglegroups.com or reply to this email with the words REMOVE ME as the subject.
Re: [sage-devel] Re: Bug: Elliptic Curve Point Counting
On Sun, Mar 28, 2010 at 3:13 AM, William Stein wst...@gmail.com wrote: We should definitely move to PARI 2.4. We haven't only because it is indeed a monumental task. Perhaps I'll do the move, since I wrote most of the Sage wrapper of PARI anyways, and surely porting is much less work than writing the whole wrapper in the first place. If anybody wants to help, please volunteer. For starters: I'm willing to help, but not lead, on this effort. * What is the relevant trac ticket? * Whoever tried last (Nick?), can they summarize some of the issues they encountered. Yes, please do. What's so significative about the API changes in pari 2.4? It could be worth moving straight to the pari 2.4 series for Sage-5.0. +1 If api changes are indeed relevant, syncing the changes with a 5.0 release of sage seems very sensible. Note that the latest released version of pari is 2.4.2.alpha, dated dec/2007... is this what we should aim for, or the svn HEAD? In case there is confusion, I had some long chats about Pari 2.4 versus 2.3 with Karim Belebas (lead Pari dev) last time I was in Bordeaux. The Pari 2.4 series is the one anybody should use if they can use it. It's meant to be solid for normal research applications. The reason it is called unstable is because the C API is not stable, i.e., the PARI devs reserve the right to change the C API from version to version. If the C API is not stable, changes they do may bite the Sage interface at some point? Gonzalo -- 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 To unsubscribe from this group, send email to sage-devel+unsubscribegooglegroups.com or reply to this email with the words REMOVE ME as the subject.
Re: [sage-devel] Does sage.math have stack protection?
On Mon, Mar 29, 2010 at 8:16 PM, Dr. David Kirkby david.kir...@onetel.net wrote: I don't know how practical it is going to be for a Sage developer to change the the source code of PARI, NTL and whatever else has this problem, to add mprotect() where needed. I suspect that might be a bit difficult, and perhaps slow the code. uh? The reason I used that code was to check if executing the stack caused a problem. As such, there was little point in me adding mprotect - it rather defeated the object of the program. I presume that the software which wants to execute code in the stack makes the call the mprotect as needed. The proper code (with the call to mprotect) shows that executing the stack doesn't cause a problem, if you follow the posix standard [ stack is not executable by default (only this wasn't enforced before cpus had NX support). ] YMMV, but you didn't post any evidence on the contrary. Did you try the fixed code (i.e. with call to mprotect) both in a non-SELinux and a SELinux enabled kernel to see if there actually is a difference? Running the code under strace(1) may help know what is going on. I'd guess that SELinux will return EACCESS in the mprotect call... Gonzalo -- 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 To unsubscribe from this group, send email to sage-devel+unsubscribegooglegroups.com or reply to this email with the words REMOVE ME as the subject.
Re: [sage-devel] Re: Category for IntegerModRing(n)
On Sat, Mar 20, 2010 at 11:52 AM, Rob Beezer goo...@beezer.cotse.net wrote: (2) IntegerModRing(n) is always in CommutativeRings() IMO this is the one that makes sense, by the same reasons why: sage: parent(2/1) Rational Field IOW, IntegerModRing should be a map from ZZ to CommutativeRings() This is the only natural definition, as the only possible generic property you know about IntegerModRing(n) is that it is commutative. This seems to lead to IntegerModRing(0) returning a ZZ in category CommutativeRings(). I don't know if that's right or even possible. You would have the same issue for R.quotient(I) where R is a ring and I is an R-ideal... You wouldn't want having to check properties of I and make inconsistent definitions for different R, etc. (3) Same thing, unless the user specifies the category: IntegerModRing(5, Fields()) Although in that case, he might as well call GF(5). I think it's ok to add a category=other argument, again for consistency with the case: R.quotient(I, category=blah) where you may not have an alternate notation as the GF(p) one. (4) IntegerModRing(n) always do a primality test, unless the user specifies himself the category. No way as already explained by others in this thread. (5) When n is not too big, IntegerModRing(n) checks the primality of n, and sets the category accordingly. Otherwise it always uses CommutativeRings(). (6) When n is not too big, IntegerModRing(n) checks the primality of n, and returns GF(n) or a plain IntegerModRing(n) accordingly. Making things depend on when n is not too big is as far away as I can possibly imagine from a categorical approach :-) Gonzalo -- 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 To unsubscribe from this group, send email to sage-devel+unsubscribegooglegroups.com or reply to this email with the words REMOVE ME as the subject.
Re: syntax support for _sig_on / _sig_off in cython (Re: [sage-devel] Re: Memory leak)
On Mon, Mar 15, 2010 at 3:57 PM, Brian Granger ellisonbg@gmail.com wrote: Thanks for describing this better, it helps me to understand what the current _sig_on/_sig_off does. Because of the licensing issues, I am not looking at the code in Sage until it has been officially re-licensed. Once that has been done, I will dig into the code to see what it actually does. Wow, you are serious about licensing. I don't think it would be a problem for you t look at it --- everybody agreed to relicense anyway... PPS: this seems to be very ingrained with the sage inners for library interfaces, and it's already in there, so it's hard to make a list of reasons we want to use (e.g. issues we would have otherwise, features we want it to support, etc). Since you are coming from a different camp, maybe you can try to list your reasons -- what problems do you think this would fix for you, and what enhancements would this bring up. [ok, I know some reasons for sage, but I'm not listing any to avoid biasing you... ] I am not sure I am following what you are asking. Can you elaborate on this question? Sorry. I'll rephrase: What are your reasons for needing this _sig_on/_sig_off stuff. What problems do you have that you think this would fix for you, and what enhancements you think this would this bring up. It will be helpful to have the perspective of somebody outside of sage. Gonzalo -- 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: syntax support for _sig_on / _sig_off in cython (Re: [sage-devel] Re: Memory leak)
On Sat, Mar 13, 2010 at 7:22 PM, Robert Bradshaw rober...@math.washington.edu wrote: On Mar 13, 2010, at 4:04 PM, Gonzalo Tornaria wrote: What are the options for supporting this (either the decorator/function attribute or the with-clause)? We can support both. We could support custom signal handlers via something like @cython.setup_signal_handler(some_func_ptr, other_data, ...) def blah(...): ... Great. How does that actually work? Is the decorator somehow modifying the code of blah at compile time, or is a python wrapper produced? Minimal overhead would be if the only difference in the C code is that calls to _sig_on/_sig_off are added in the entry/exit code, etc. for ultimate flexibility. It would also help if they were documented explained better--my understanding of _sig_on and _sig_off is very shallow: one needs them to be able to interrupt C code, they need to come in pairs, and doing Python stuff while holding the signal is dangerous (though I think we do it all the time). On that last note, we can actually enforce pure C inside a sig_on/sig_off block. I'm going to try to write a summary documentation of what's the issue, why we want this, and how it works in original /current / proposed implementation. Keep tuned (it could take me a while, but I don't want to hold this message). There's also the question of naming--sig_on probably isn't the clearest name. Definitely. Maybe something like with trap_signals, since that's more in line with the desired effect: we want certain signals which may be raised during execution of c code to be trapped and raised as exceptions to python. Gonzalo -- 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: syntax support for _sig_on / _sig_off in cython (Re: [sage-devel] Re: Memory leak)
On Sun, Mar 14, 2010 at 9:21 PM, Brian Granger ellisonbg@gmail.com wrote: Gonzalo, Thanks for starting this discussion. I am willing to help with this effort as I definitely need this capability. Part of the challenge will be figuring out how to do this on Windows. Not necessarily. I think signals(2) is part of C89, and setjmp(3) / longjmp(3) are as well, so they should work on windows (although it's probably good for trapping ctrl-c and fp exceptions and not much more -- but what else do you need?). Note that sigsetjmp(3) / siglongmp(3) don't seem to be part of ansi c, though... I'm not sure atm why we use that --- possibly only makes sense on unix and those can be changed to the no-sig counterparts on windows) In terms of syntax, I am not sure that the decorator approach would work. The reason the that you probably don't want to enable this for entire functions. Because it is such an invasive things, you want it on as little as possible. Thus, I almost think the with syntax would work better: with c_signals: I wouldn't call this invasive. Rather, it's expensive to set up (because of the setjmp). Thus, if a codepath uses this, it's better if it get's called only once, rather than having several (unnested) pairs during the execution. In fact, the key about supporting nesting is that we only setjmp at the outer level. So, for instance, if you have a function f which loops over a function g, and you know g traps the signals, then you may be better off (performancewise) to trap signals in f itself, so g doesn't have to repeatedly call setjmp. IOW, the hard part of trapping the signals is not trapping them, but recovering. Python recovers using the exception handling mechanism, but for C code that won't work, which is the reason python can't do anything with the signals when it's running c code. To recover, you need to call setjmp() beforehand, at a place where you know how to recover so you can use longjmp() to actually recover to a sane state. [setjmp saves the stack context, so longjmp restores, this is effectively the same as unwinding the stack, except you don't need support from the intermediate functions as you do in python or c++ exceptions] Thoughts? Cheers, Brian Best, Gonzalo PS: I'll still try to look at the code and write something more detailed about it. I feel that would help to decide on what's the sane syntax/name, since there is a bit of confusion on what _sig_on / _sig_off actually do. PPS: this seems to be very ingrained with the sage inners for library interfaces, and it's already in there, so it's hard to make a list of reasons we want to use (e.g. issues we would have otherwise, features we want it to support, etc). Since you are coming from a different camp, maybe you can try to list your reasons -- what problems do you think this would fix for you, and what enhancements would this bring up. [ok, I know some reasons for sage, but I'm not listing any to avoid biasing you... ] -- 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] testing on t2
On Fri, Mar 12, 2010 at 10:03 PM, Minh Nguyen nguyenmi...@gmail.com wrote: ... if [ $UNAME = Darwin ]; then OPT=Rp else OPT=ra fi I'm referring to the option a, which is passed to cp later on in that script. With sage-bdist as is, I can't wrap up my build. But if I remove the option a, then there is some progress. A better approach is to systematically go through the script sage-bdist and purge it of GNUism. That way, the script would happily run on t2.math, and indeed on Cygwin, Linux, Mac OS X, Solaris. This has already been discussed. Please check out http://groups.google.com/group/sage-devel/browse_thread/thread/9a45c5417e3d57a0/fd1c6c873df2d6d1?#fd1c6c873df2d6d1 before changing cp -a to something else. Long story short: using cp -Rp wouldn't preserve symlinks, leading to bloat on the bdist. You would need to use cp -PRp which is the closest to cp -a posix allows. There's also the issue of hard links which are handled by -a but not by the posix counterpart... according to the post I referred to above, there was exactly one hardlink in the sage bdist, namely the python binary (hard linked to python2.6 in the local/bin directory) which should be replaced by a symlink anyway. In the thread referred above I posted a few suggestions of how to fix these issues -- the python hard link issue, how to test the diferent behaviours of cp in different systems, etc. Gonzalo -- 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
syntax support for _sig_on / _sig_off in cython (Re: [sage-devel] Re: Memory leak)
On Sat, Mar 13, 2010 at 2:30 PM, Robert Bradshaw rober...@math.washington.edu wrote: On Mar 13, 2010, at 5:29 AM, Nicolas M. Thiery wrote: def bla(...): with sig_on: if ... raise ... elif ... return ... This is exactly the required semantics. I didn't know cython supported with-guards. Are they lightweight enough? We really only want to add a call to _sig_on macro at start and a call to _sig_off macro at end, and no other bloat. the whole process should have very tiny overhead, except for the first call to _sig_on (when signal trapping is enabled: there must be a call to sigsetjmp(3) which is somehow costly). While nesting is not supported atm, it should, and nested calls to _sig_on should be almost overhead free as well. Yes, for sure--I've been thinking about borrowing the with syntax as well. Perhaps there could also be syntax/a decorator for marking an entire function as getting and releasing the signal handler too (just as we have with the GIL). As part of incorporating this into Cython, some syntactic improvements should be considered. Any other ideas? What's the syntax for supporting the GIL? Something like that could work, I guess. Something along this lines: @with_sig_on def bla(...): if ... raise ... elif ... return ... Would be great (or whatever other syntax, like an attribute for the function, etc). The key point being that one can add or remove the with_sig_on without touching the function body. In the with syntax, the whole body needs to be reindented. Moreover, when there's a docstring, the with clause goes after the docstring, while the decorator syntax clearly displays at the top the fact that the function catches signals. The with clause is more flexible, though -- sometimes one wants to compute quickly (no signal catching) for small arguments (say you know the computation will be pretty fast) but catch the signals in other cases all in the same body. What are the options for supporting this (either the decorator/function attribute or the with-clause)? Gonzalo -- 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: Memory leak
On Fri, Mar 5, 2010 at 7:47 AM, Simon King simon.k...@nuigalway.ie wrote: I created a ticket at http://trac.sagemath.org/sage_trac/ticket/8444 Thanks Simon. I posted a patch with an explanation into that ticket, which is now awaiting review (it's one line patch). I was looking around gen.pyx, and there seems to be some more unbalanced _sig_on / _sig_off pairs, and some dubious ones. But I don't want to mess too much with that --- the proper fix would be to rewrite _sig_on / _sig_off to allow nesting while checking the balance at runtime. The hard part of this plan is that if we enforce balancing these, we would need a huge amount of effort to actually fix sage in places where there's no balance We tried this with Craig back in SD5 days, and there were *a lot* of unbalances --- though I think Craig committed fixes for some my 4.3.3 sage fails pretty badly at start if I add minimal checks like the ones commented out in interrupt.h, even if I do it *only* for gen.pyx... Maybe some general framework for this, more robust, can be made directly into cython (cf. Brian Granger's efforts in another thread) and sage usage of this can slowly migrate to the cython methods. By robust I mean - reentrancy - proper nesting - threads - runtime balance check (warn/abort in case of unbalance) What may actually be nice is to have some kind of support in cython to declare we want signals enabled for a whole function (something like a decorator or attribute). Cython would then add the calls to every entry and exit point, so we avoid the common pitfall of missing some exit code-paths. Best, Gonzalo -- 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: Memory leak
On Fri, Mar 5, 2010 at 10:47 AM, Simon King simon.k...@nuigalway.ie wrote Hi! I created a ticket at http://trac.sagemath.org/sage_trac/ticket/8444 I think this is caused by a duplicate _sig_on in the bottom part of pari.__call__. I'll post details and (possible) solution later (feel free to ping me in a few days if I forget). Best, Gonzalo -- 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] non-ASCII characters in the Sage library
On Thu, Jan 21, 2010 at 3:22 AM, Pat LeSmithe qed...@gmail.com wrote: Should we put # -*- coding: utf-8 -*- at the top of all .py and .pyx(?) files in the Sage library? I think this will allow us to use Unicode literal strings in Sage code, doctests, documentation --- without raising coding errors. I had to patch sagenb b/c doctests don't display in the notebook when they have utf-8 (this was rc0, However, I just discovered that the sagenb (in local/lib/python2.6/site-packages/sagenb-0.5-py2.6.egg/sagenb) is not under hg, so I will need to dig what I actually changed... The relevant ticket is http://trac.sagemath.org/sage_trac/ticket/6682 I'll post more about this later. BTW a few questions: a. is it necessary to put the utf-8 stanza on all files, or only on those which include non-ascii characters? b. the way the line is written, I think it will be recognized by emacs, but not by vim. Do we care about that? c. is there a way to do a sanity check to the source to make sure we don't get incorrect encodings? d. should doctests with non-ascii characters be created as unicode strings, or as regular strings with utf-8 encoding? Gonzalo -- 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: sage-4.3.1.rc0 released!
On Wed, Jan 20, 2010 at 5:47 PM, Peter Jeremy peterjer...@acm.org wrote: My personal feeling is that it would be nice if some of the more generic packages (eg bzip, zlib, readline, mercurial) were moved out of sage and made explicit requirements. +1 I think Sage is mature enough now to slowly migrate toward this. Besides, there can still be spkgs for those packages, and there could be a sage-with-batteries-included tarball with dependencies included. Gonzalo -- 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: non-ASCII characters in the Sage library
On Thu, Jan 21, 2010 at 12:16 PM, kcrisman kcris...@gmail.com wrote: Not everyone can easily use a text editor which recognizes all non- ASCII character properly, so I think we should be careful about this. I don't think that's true anymore. It may have been true ten years ago, but nowadays unicode and utf-8 is pretty much standard. For the sage source code itself, it probably amounts only to be able to spell most names correctly. But it will help fully supporting unicode, which is necessary for translations, and even for the english version students want to write comments and text in their own language, so the support is quite important. Gonzalo -- 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] non-ASCII characters in the Sage library
On Fri, Jan 22, 2010 at 12:46 AM, Minh Nguyen nguyenmi...@gmail.com wrote: With or without the above Unicode preamble, a non-ASCII character in a docstring can cause the PDF version of a document to fail to build. See ticket #8036 [1] for an example of a case where a source file contains the above preamble, but the PDF version of the reference manual fails to build due to non-ASCII characters in the docstring of a method. That needs to be fixed in the latex preamble, i.e. let latex know the file is encoded with utf8. See my comments in the ticket (and attached latex example file) [1] http://trac.sagemath.org/sage_trac/ticket/8036 Gonzalo -- 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: sage-4.3.1.rc0 released!
On Thu, Jan 21, 2010 at 6:05 PM, Robert Bradshaw rober...@math.washington.edu wrote: On Jan 21, 2010, at 6:31 AM, Gonzalo Tornaria wrote: On Wed, Jan 20, 2010 at 5:47 PM, Peter Jeremy peterjer...@acm.org wrote: My personal feeling is that it would be nice if some of the more generic packages (eg bzip, zlib, readline, mercurial) were moved out of sage and made explicit requirements. +1 I think Sage is mature enough now to slowly migrate toward this. Besides, there can still be spkgs for those packages, and there could be a sage-with-batteries-included tarball with dependencies included. What would be the advantage? The easier it is for users to go from a standard distro/OS X box to a running Sage the better. Also, there's the much more important Windows port to consider. In the long run, I think it's way easier if sage actually *comes* with the standard distro / fink / etc. If it could be done with gfortran, it can be done with other dependencies. We didn't see mountains crumbling because of that (I was annoyed as others, but only because the prereq didn't warn me, and because the change was made in the last 24 hours before release). One of the reasons we ship our own of so much stuff is that we require specific versions (e.g. you can't just drop in a new version of pari, maxima, or gap, and have it Just Work). Is that an issue for any of the above packages? Also, we require the dev versions of the above packages, not just binaries (which is what many systems come with). Agreed. The OP didn't suggest to drop those out of sage. I didn't either (not at this stage, anyway). But some of the more generic packages could **slowly** migrate toward this. I don't think there are very specific version needs for bzip, zlib, readline, mercurial, etc. (possibly a newer-than version check, and readline may be icky, etc). If sage could just work with my own distro dev libraries for some of those, that would be a huge step forward, IMO. Once it's doable with a few, the rest will follow at its own pace. Plus, there can *still* be spkgs for all the dependencies. And there could be a sage-with-batteries-included tarball which works just as it does now. And another sage-reduced-for-expert-developers-and-distros tarball which doesn't include the spkgs which can be replaced by distro packages. Even the prereq script could actually *check* the dependencies, and (offer to) download the required spkg !!! (then the tarballs could be named sage-full-install vs. sage-net-install.) IMO sage is mature enough now. Best, Gonzalo -- 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: sage-4.3.1.rc0 released!
On Thu, Jan 21, 2010 at 7:11 PM, William Stein wst...@gmail.com wrote: +1 to Robert's comments. I can't tell you how many people just in the last few days have told me that they use (and work on!) Sage *only* because when they try to build it on their computer it just worked. Do people tell you when they just skip sage because of the massive download and prospect of compiling it? Download 600Mb binary? That's 20% of the monthly allowance for some common adsl plans around here (and I think we have one of the higher levels of internet penetration in latin-america, if not the highest). Getting mathematica is almost cheaper here. Note that I *love* the fact that most of the time I can type make and it just works. Thumbs up for that!!! If it hadn't, they definitely wouldn't be involved with Sage now. Removing bzip, zlib, readline, mercurial, etc. is simply going to greatly reduce the chances for such people. I see my goal with the Sage project as *not* to compete with Pari or Singular or Macaulay2 or to try to get users that would otherwise use those systems. My goal is that Sage can compete with programs such as Mathematica which are self-contained and easy to install on many platforms. I want to make Sage something that appeals to users who do not currently use systems like Pari, Singular, etc., because they find installation and usability of those systems too icky. I think apt-get install pari-gp is the trivialest thing... I haven't compiled pari for eons. Especially because when software matures, it won't affect me as much to not have the bleeding edge release. And hey, compiling pari *also* just worked most of the time. It's not only about being easy to build --- it's also about convincing people it's easy to build, despite the scary looking size of the tarball, and moreover covincing people it's easy to develop, and worth giving code back to the commons!!! Another two thumbs up for that (and metcalfe's law). http://sagenb.org (and the notebook in general) is a little first step More like a big leap, IMO. in that direction, but there are many other steps. Make building Sage from source more difficult isn't a good step though. You are jumping to conclusions. Nobody wants to make building sage from source more difficult. Move back two spaces and read again. It was really meant to be constructive. Best, Gonzalo -- 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: sage-4.3.1.rc0 released!
On Fri, Jan 22, 2010 at 3:24 AM, Dr. David Kirkby david.kir...@onetel.net wrote: But sorting out whether the version of libraries on a system are suitable, can be tricky. Even having the right versions does not guarantee they will be found in preference to some other version. Sure. We already have related issues. For example, the prereq checks perl is installed, but it doesn't check for some perl modules which are required (but not part of debian's perl-base --- not really needed for anything except building sage). As long as it builds with libraries in current debian / fedora / ubuntu, it's ok. If you are only going to shave off 20 MB or so from the source code, it might be more hassle than it is worth. If you could cut the download time by 30%, then I could see it would probably be worth the effort in doing this. But I'm not so sure you would be able to do that. Too many packages are probably too specialised. sage 3.0.5 was 188MB, but the debian package (binary) was only 42MB. The source for the debian package is 57.6MB. Gonzalo -- 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: Sage-4.3.1.rc1 released!
On Tue, Jan 19, 2010 at 7:48 AM, Dag Sverre Seljebotn da...@student.matnat.uio.no wrote: Dima Pasechnik wrote: is it possible to make patches, instead/as well as posting full source releases? It took 4+ hours here to download rc0... One thing one could try out is to play with rsync over SSH to an account on boxen.math. rsync the rc1 file with a local copy of the rc0 tarball, and have rsync deal with computing deltas etc. If that works out well (I'm not sure how much compressed data would change) then it's probably a method with lower maintenance overhead than making patches. No, that doesn't help. What does help, to a certain extent is the following: boxen$ tar xvf sage-4.3.1.rc1.tar local$ tar xvf sage-4.3.1.rc0.tar local$ mv sage-4.3.1.rc0 sage-4.3.1.rc1 local$ rsync -avP boxen:sage-4.3.1.rc1 . [ ... I had about 97M transfer here IIRC ] local$ tar cvf sage-4.3.1.rc1.tar sage-4.3.1 local$ rsync -avP boxen:sage-4.3.1.rc1.tar . [ ... about 1M transfer IIRC ] local$ md5sum sage-4.3.1.rc1.tar 32f20dbab7aeec8529085ec41bf61552 sage-4.3.1.rc1.tar This is still way non-optimal, but a big savings anyway (100M transfer vs. 267M normal download). The reason it takes so long is because the .spkg files are bzipped -- rsync is baffled about them, so a tiny change in one spkg file ends up transfering the whole spkg. It would be *really* an advantage to recursively do the same with the spkg files themselves, but you better use the same options for bzip!! (maybe rsync the tree, then tar, then rsync the tar, then bzip, then rsync the bzip). Gonzalo -- 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] Weird failure compiling 4.3.1.alpha3
Just after successfully built dsage -- which I believe is the last spkg which gets installed. The sphinx build fails quite strangely. Running ./sage fails with the same error (TypeError: unsupported operand parent(s) for '+': 'Integer Ring' and 'Integer Ring') Gonzalo Finished installing dsage-1.0.1.p1.spkg cd /scratch/tornaria/sage-4.3.1.alpha3 . local/bin/sage-env cd local/bin/ ./sage-make_relative Making script relocatable make[1]: Leaving directory `/scratch/tornaria/sage-4.3.1.alpha3/spkg' real91m6.194s user82m59.055s sys 7m59.726s sphinx-build -b html -d /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/output/doctrees/en/developer /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/en/developer /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/output/html/en/developer Traceback (most recent call last): File /scratch/tornaria/sage-4.3.1.alpha3/local/bin/sphinx-build, line 6, in module import sage.all File /scratch/tornaria/sage-4.3.1.alpha3/local/lib/python2.6/site-packages/sage/all.py, line 72, in module from sage.rings.all import * File /scratch/tornaria/sage-4.3.1.alpha3/local/lib/python2.6/site-packages/sage/rings/all.py, line 75, in module from padics.all import * File /scratch/tornaria/sage-4.3.1.alpha3/local/lib/python2.6/site-packages/sage/rings/padics/all.py, line 2, in module from factory import Zp, Zq, Zp as pAdicRing, ZpCR, ZpCA, ZpFM, ZqCR, ZqCA, ZqFM #, ZpL, ZqL File /scratch/tornaria/sage-4.3.1.alpha3/local/lib/python2.6/site-packages/sage/rings/padics/factory.py, line 27, in module from padic_extension_leaves import * File /scratch/tornaria/sage-4.3.1.alpha3/local/lib/python2.6/site-packages/sage/rings/padics/padic_extension_leaves.py, line 34, in module from padic_ZZ_pX_FM_element import pAdicZZpXFMElement File padic_ZZ_pX_FM_element.pyx, line 1, in init sage.rings.padics.padic_ZZ_pX_FM_element (sage/rings/padics/padic_ZZ_pX_FM_element.cpp:11328) File padic_ZZ_pX_element.pyx, line 34, in init sage.rings.padics.padic_ZZ_pX_element (sage/rings/padics/padic_ZZ_pX_element.cpp:8851) File element.pyx, line 808, in sage.structure.element.ModuleElement.__add__ (sage/structure/element.c:7007) File element.pyx, line 814, in sage.structure.element.ModuleElement._add_ (sage/structure/element.c:7097) TypeError: unsupported operand parent(s) for '+': 'Integer Ring' and 'Integer Ring' Build finished. The built documents can be found in /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/output/html/en/developer sphinx-build -b html -d /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/output/doctrees/en/tutorial /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/en/tutorial /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/output/html/en/tutorial Traceback (most recent call last): File /scratch/tornaria/sage-4.3.1.alpha3/local/bin/sphinx-build, line 6, in module import sage.all File /scratch/tornaria/sage-4.3.1.alpha3/local/lib/python2.6/site-packages/sage/all.py, line 72, in module from sage.rings.all import * File /scratch/tornaria/sage-4.3.1.alpha3/local/lib/python2.6/site-packages/sage/rings/all.py, line 75, in module from padics.all import * File /scratch/tornaria/sage-4.3.1.alpha3/local/lib/python2.6/site-packages/sage/rings/padics/all.py, line 2, in module from factory import Zp, Zq, Zp as pAdicRing, ZpCR, ZpCA, ZpFM, ZqCR, ZqCA, ZqFM #, ZpL, ZqL File /scratch/tornaria/sage-4.3.1.alpha3/local/lib/python2.6/site-packages/sage/rings/padics/factory.py, line 27, in module from padic_extension_leaves import * File /scratch/tornaria/sage-4.3.1.alpha3/local/lib/python2.6/site-packages/sage/rings/padics/padic_extension_leaves.py, line 34, in module from padic_ZZ_pX_FM_element import pAdicZZpXFMElement File padic_ZZ_pX_FM_element.pyx, line 1, in init sage.rings.padics.padic_ZZ_pX_FM_element (sage/rings/padics/padic_ZZ_pX_FM_element.cpp:11328) File padic_ZZ_pX_element.pyx, line 34, in init sage.rings.padics.padic_ZZ_pX_element (sage/rings/padics/padic_ZZ_pX_element.cpp:8851) File element.pyx, line 808, in sage.structure.element.ModuleElement.__add__ (sage/structure/element.c:7007) File element.pyx, line 814, in sage.structure.element.ModuleElement._add_ (sage/structure/element.c:7097) TypeError: unsupported operand parent(s) for '+': 'Integer Ring' and 'Integer Ring' Build finished. The built documents can be found in /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/output/html/en/tutorial sphinx-build -b html -d /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/output/doctrees/en/installation /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/en/installation /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/output/html/en/installation Traceback (most recent call last): File /scratch/tornaria/sage-4.3.1.alpha3/local/bin/sphinx-build, line 6, in module import sage.all File
Re: [sage-devel] Weird failure compiling 4.3.1.alpha3
On Fri, Jan 15, 2010 at 4:45 PM, Dr. David Kirkby david.kir...@onetel.net wrote: Gonzalo Tornaria wrote: sys 7m59.726s sphinx-build -b html -d /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/output/doctrees/en/developer /scratch/tornaria/sage-4.3.1.alpha3/devel/sage/doc/en/developer I thought you had made a mistake, but see your path contains 4.3.1.alpha3. Is there a link to that? http://boxen.math.washington.edu/home/wstein/farm/src/ Gonzalo -- 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: mpir.1.2.2 fails to build on Open Solaris 06/2009 in VirtualBox
On Wed, Jan 13, 2010 at 9:18 AM, Bill Hart goodwillh...@googlemail.com wrote: Ah, I see in a later trac update you have the same problem in Fedora. But surely there you have cat /proc/cpuinfo. What information does it give you? We might be able to tackle the problem from there. This is in VirtualBox, so virtual processors? Virtualbox is possibly misreporting the cpu type in cpuid. You need to figure out which family/model it's actually reporting, and see what can be done from there. The easiest way, as Bill suggests, is to cat /proc/cpuinfo on a linux kernel running in the virtualbox, but you could also copypaste some cpuid code and run that (try unpacking mpir and playing with config.guess and friends). See related: http://trac.sagemath.org/sage_trac/ticket/5516 http://trac.sagemath.org/sage_trac/ticket/5186 http://groups.google.com/group/mpir-devel/browse_thread/thread/aeb271247ae0eec9/a90654677f9db1d5 Gonzalo -- 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: mpir.1.2.2 fails to build on Open Solaris 06/2009 in VirtualBox
On Wed, Jan 13, 2010 at 11:43 AM, Jaap Spies j.sp...@hccnet.nl wrote: gcc version 4.4.2 20091222 (Red Hat 4.4.2-20) (GCC) checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu Still misdetected, it should be nehalem-unknown-linux-gnu for optimal results if you are running on an i7. But that is probably be a virtualbox issue. On the solaris side you get i486-pc-solaris2.11, but you should be getting at least x86_64-* (as for linux). I think that you must fix the config.guess in mpir somehow... Check out http://groups.google.com/group/mpir-devel/browse_thread/thread/aeb271247ae0eec9/a90654677f9db1d5 which is quite related to this: I had the same issue running on a kvm virtual cpu, and that fixed it at least for linux. The strategy is that for 64 bit builds on x86 hardware, you always fallback to x86_64-* even if the family/model reported by cpuid seems to be of an older 32 bit only cpu. Gonzalo -- 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: mpir.1.2.2 fails to build on Open Solaris 06/2009 in VirtualBox
On Wed, Jan 13, 2010 at 12:06 PM, Jaap Spies j.sp...@hccnet.nl wrote: Gonzalo Tornaria wrote: On Wed, Jan 13, 2010 at 11:43 AM, Jaap Spiesj.sp...@hccnet.nl wrote: gcc version 4.4.2 20091222 (Red Hat 4.4.2-20) (GCC) checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu Still misdetected, it should be nehalem-unknown-linux-gnu for optimal results if you are running on an i7. But that is probably be a virtualbox issue. Not quite. In Fedora 12 on the real machine I get: gcc version 4.4.2 20091222 (Red Hat 4.4.2-20) (GCC) checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu Then that needs to be fixed with mpir itself. Can you copy cpu family, model and flags from /proc/cpuinfo? I'm think yours is a model 30 nehalem which is currently undetected by mpir. CC to mpir-devel as this needs to be fixed in cpuid.c The processor in question is a core i7 860, namely: http://processorfinder.intel.com/details.aspx?sSpec=SLBJJ# [ afaict, the main difference of the i7 800 series wrt the i7 900/xeon 5500 series is the former has 2 memory channels vs. the latter 3 memory channels ] Gonzalo -- 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] What can I test that makes use of parallel processors?
On Wed, Jan 13, 2010 at 5:52 PM, William Stein wst...@gmail.com wrote: What matters for this benchmark is the number of cores that the computer has. Though t2 can manage 128 hardware threads, it only has 16 actual *cores*. Not quite; the following is in a box with 8 cores -- 16 threads: sage: time b = bernoulli(10^5, algorithm='bernmm', num_threads=1) CPU times: user 4.84 s, sys: 0.00 s, total: 4.84 s Wall time: 4.84 s sage: timeit(bernoulli(10^5, algorithm='bernmm', num_threads=8)) 5 loops, best of 3: 1.06 s per loop sage: timeit(bernoulli(10^5, algorithm='bernmm', num_threads=16)) 5 loops, best of 3: 914 ms per loop That's 15% speedup for the extra threads... Not bad, given that going 4 -- 8 threads on the same machine or going 8 -- 16 threads on sage.math gives about 30% speedup for the same computation. I'd guess for a really cpu-bound task, the number of cores should be it, but for memory-bound tasks, having more threads may be an advantage because of memory latencies, as long as the threads don't have to compete for cache. In the end, whatever optimizes the usage of cache size / memory bandwidth between threads is probably best. Also, HT could optimize the use of arithmetic units between threads in the same core, so unless the inner loops have perfect scheduling, there's always something to gain from this approach. Best, Gonzalo -- 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] Fwd: Manual en español
2010/1/12 William Stein wst...@gmail.com: Maybe somebody who speaks Spanish can email this person back? -- Forwarded message -- From: Kelvy Segura Cuevas k.seg...@sisalril.gov.do Date: 2010/1/12 Subject: Manual en español To: wst...@gmail.com wst...@gmail.com Estimado William Stein, Donde podría encontrar un manual completo de Sage en español para poderlo usar con mayo probecho, soy lic. En matemática pura de republica dominicana. Kelvy, En http://www.sagemath.org/help.html hay un par de manuales introductorios en español. Gonzalo -- 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] bad rendering of / in notebook
On Mon, Jan 11, 2010 at 10:55 AM, John Cremona john.crem...@gmail.com wrote: In the notebook (4.3), in either a text cell between Sage cells or in the output of (for example) show(QuadraticField(-1,'i')) I see the the symbol / wrongly rendered as =. So in that example, what I see is Q[i]=(i^2+1) (with ^2 as a superscript). That's not good. I am using firefox 3.5.5 on Suse linux enterprise. Where might the problem lie? Probably a known issue with jsmath fonts and firefox 3.5. Check out http://www.math.union.edu/~dpvc/jsMath/download/jsMath-fonts.html (cf http://trac.sagemath.org/sage_trac/ticket/6483) Gonzalo -- 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] Unsetting MAKE - a better way to do it.
On Mon, Jan 11, 2010 at 5:42 PM, William Stein wst...@gmail.com wrote:
Cool. Instead of suggesting people use bits of code like this in
their spkg-install's, why don't we make a single *sage sh library*
that gets used. It could start as a script
local/bin/sage-spkg-lib
that gets sourced before spkg-install gets sourced. It could contain
at least the following functions:
* unsetmake -- based on what you wrote above
* check_err -- based on what Gonzalo posted in another thread.
I think this would be much better than scattering coding snippets in
spkg-installs, since there is one place where we can fix/change
everything related to something like this.
Sounds good... Let me suggest
arg1 ()
{
echo $1
}
resetmake ()
{
MAKE=`arg1 $MAKE`
}
This avoids spawning awk altogether... (won't spawn anything if echo
is builtin as in bash)
Alternative (no echo):
setmake1 ()
{
MAKE=$1
}
resetmake ()
{
setmake1 $MAKE
}
Also, it might be a good idea to define:
sage-spkg-lib ()
{
return
}
The idea is to override the loading of the shell library so it's not
loaded more than once.
(not sure if dashes are allowed in function names, so that may not work).
Alternative:
alias sage-spkg-lib=true
(still no spawning if true is builtin)
Gonzalo
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[sage-devel] Problems with sage on core i7 (nehalem)
As posted before, I am getting (consistent) test failures when running sage doctests on a core i7. I've been doing some more experiments and found some more interesting things about this. I'm using two different boxes: core2: Intel(R) Core(TM)2 Quad CPU Q9550 @ 2.83GHz family=6 model=23 stepping=7 nehalem: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz family=6 model=26 stepping=5 For the sake of this experiment I'm using the released sage-4.3 (doctest still fail on sage-4.3.alpha1 as reported before). A) sage-4.3 compiled on nehalem, ran on nehalem: -- doctest failures in symbolic/expression.pyx, numerical/optimize.py, interfaces/r.py (as reported earlier) B) sage-4.3 compiled on core2, ran on core2: -- all doctest pass C) sage-4.3 compiled on core2, ran on nehalem: -- all doctest pass D) sage-4.3 compiled on nehalem, ran on core2: -- many segfaults, the doctesting aborts in the end - Some conclusions: 1. the compilation on nehalem has some subtle issue which causes the doctest failures [actually the failures look all the same and related to numpy arrays, except the r failures, which may be due to a missing dependency since the system is a very bare bones debian lenny]. 2. whatever the failures are, they are triggered at compile time, since the code compiled on core2 works ok on the i7. 3. the sage-flags.txt are identical on both systems, namely ssse3 mmx sse2 pni sse cmov. However, something seems to be using i7 features, causing segfaults when running the same binary on a core2. From /proc/cpuinfo, the flags are: nehalem: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good pni monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr dca sse4_1 sse4_2 popcnt lahf_lm ida core2: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good pni dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm sse4_1 lahf_lm tpr_shadow vnmi flexpriority Only suspicious flag I see is sse4_2, since both have sse4_1 (note that the old 65nm core2 don't have sse4_1 also). Best, Gonzalo -- 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: Problems with sage on core i7 (nehalem)
On Tue, Jan 12, 2010 at 1:29 AM, Gonzalo Tornaria torna...@math.utexas.edu wrote: Only suspicious flag I see is sse4_2, since both have sse4_1 (note that the old 65nm core2 don't have sse4_1 also). At least mpir uses popcnt on nehalem, which is available for sse4_2 only. So, the sse4_2 flag should be added to the sage-flags.txt. I don't know about sse4_1. The main test case woud be: build sage on a core2 with sse4_1 (45nm) and test it on a core2 without it (65nm). Since mpir doesn't test cpu flags, only cpu models, and doesn't differentiate between those two (although they do have different model numbers), maybe sse4_1 is not a problem. Gonzalo -- 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: doctest failures in sage-4.3.1.alpha1
On Sun, Jan 10, 2010 at 8:02 PM, Gonzalo Tornaria
torna...@math.utexas.edu wrote:
cpu = 2 x quad core xeon E5520 (nehalem/i7)
os = debian 5.0/lenny (64 bit)
...
sage -t devel/sage/sage/symbolic/expression.pyx # 6 doctests failed
sage -t devel/sage/sage/numerical/optimize.py # 6 doctests failed
Not funny look below --- this is a diff of one file in scipy,
between the sage built on core2, vs. the sage built on nehalem...
---
sage-core2-x86_64-Linux/local/lib/python2.6/site-packages/scipy/optimize/optimize.py
2010-01-10 21:18:35.0 -0200
+++
sage-nehalem-x86_64-Linux/local/lib/python2.6/site-packages/scipy/optimize/optimize.py
2009-02-11 00:56:10.0 -0200
@@ -41,12 +41,6 @@
m = asarray(m)
return numpy.minimum.reduce(m,axis)
-def is_array_scalar(x):
-Test whether `x` is either a scalar or an array scalar.
-
-
-return len(atleast_1d(x) == 1)
-
abs = absolute
import __builtin__
pymin = __builtin__.min
@@ -1183,12 +1177,13 @@
# Test bounds are of correct form
-
-if not (is_array_scalar(x1) and is_array_scalar(x2)):
-raise ValueError(Optimisation bounds must be scalars
- or array scalars.)
+x1 = atleast_1d(x1)
+x2 = atleast_1d(x2)
+if len(x1) != 1 or len(x2) != 1:
+raise ValueError, Optimisation bounds must be scalars \
+ or length 1 arrays
if x1 x2:
-raise ValueError(The lower bound exceeds the upper bound.)
+raise ValueError, The lower bound exceeds the upper bound.
flag = 0
header = ' Func-count x f(x) Procedure'
-
$ diff --exclude *.pyc --exclude *.so -ru
sage-{core2,nehalem}-x86_64-Linux/local/lib/python2.6/site-packages/scipy
| diffstat
__config__.py | 10 +-
integrate/setup.py| 26 --
interpolate/setup.py | 17 ++---
odr/setup.py | 17 -
optimize/optimize.py | 17 ++---
optimize/setup.py | 14 +-
special/setup.py | 20 +++-
stats/mstats_basic.py |2 +-
stats/setup.py| 15 +--
9 files changed, 23 insertions(+), 115 deletions(-)
Why are these files patched differently in nehalem ???
Gonzalo
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[sage-devel] Re: doctest failures in sage-4.3.1.alpha1
On Tue, Jan 12, 2010 at 2:24 AM, Gonzalo Tornaria torna...@math.utexas.edu wrote: On Sun, Jan 10, 2010 at 8:02 PM, Gonzalo Tornaria torna...@math.utexas.edu wrote: cpu = 2 x quad core xeon E5520 (nehalem/i7) os = debian 5.0/lenny (64 bit) ... sage -t devel/sage/sage/symbolic/expression.pyx # 6 doctests failed sage -t devel/sage/sage/numerical/optimize.py # 6 doctests failed Not funny look below --- this is a diff of one file in scipy, between the sage built on core2, vs. the sage built on nehalem... Ugh can we forbid perl in the install scripts? It turns out this has nothing to do with the cpu, but rather with perl modules. Check out #7902. A fix is in the works. I'm testing it right now... Wrt the failure in r.py, it's the same root cause (missing perl modules) -- the issue is already open as #5964. Gonzalo PS: Can somebody explain why rebuilding just the scipy spkg triggers rebuilding the whole damn documentation, which takes way longer than rebuilding scipy (and it's clearly unnecessary). Doesn't this discourage developers? -- 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] doctest failures in sage-4.3.1.alpha1
cpu = 2 x quad core xeon E5520 (nehalem/i7) os = debian 5.0/lenny (64 bit) The following tests failed: sage -t devel/sage/sage/symbolic/expression.pyx # 6 doctests failed sage -t devel/sage/sage/numerical/optimize.py # 6 doctests failed sage -t devel/sage/sage/interfaces/r.py # 3 doctests failed sage -t devel/sage/sage/misc/sagedoc.py # 1 doctests failed The first three are exactly the same failures I got with sage 4.3 (see below). The fourth is new: sage -t devel/sage/sage/misc/sagedoc.py ** File /scratch/tornaria/sage-4.3.1.alpha1/devel/sage-main/sage/misc/sagedoc.py, line 897: sage: browse_sage_doc(identity_matrix, 'html', False)[:59] Expected: 'div class=docstring\n\n pstrongFile:/strong /v' Got: 'div class=docstring\n\n pstrongFile:/strong /s' ** 1 items had failures: 1 of 5 in __main__.example_17 ***Test Failed*** 1 failures. For whitespace errors, see the file /home/tornaria/.sage//tmp/.doctest_sagedoc.py [12.4 s] On Mon, Jan 4, 2010 at 2:07 PM, Gonzalo Tornaria torna...@math.utexas.edu wrote: -- Forwarded message -- From: Gonzalo Tornaria torna...@math.utexas.edu Date: Thu, Dec 31, 2009 at 6:10 PM Subject: Re: [sage-release] sage-4.3 To: sage-rele...@googlegroups.com I haven't seen these reported: $ \time ./sage -tp 16 devel/sage ... The following tests failed: sage -t devel/sage/sage/symbolic/expression.pyx # 6 doctests failed sage -t devel/sage/sage/numerical/optimize.py # 6 doctests failed sage -t devel/sage/sage/interfaces/r.py # 3 doctests failed -- Total time for all tests: 458.2 seconds (detailed errors below) This is a new machine with 2 * quad core xeon (nehalem) and plenty of ram, running stable Debian 5.0 (lenny). The compiler is gcc 4.3.2 (stable debian version). I'm also getting ocasional errors (in random files) which claim: A mysterious error (perhaps a memory error?) occurred, which may have crashed doctest. Is there any other explanation of this rather than a memory error? (dammit!) Details: - sage -t devel/sage/sage/symbolic/expression.pyx ** File /scratch/tornaria/sage-4.3/devel/sage-main/sage/symbolic/expression.pyx, line 6103: sage: f.find_maximum_on_interval(0,5) Expected: (0.5610963381910451, 0.8603335890...) Got: (0.5610963381910451, array([ 0.86033359])) ** File /scratch/tornaria/sage-4.3/devel/sage-main/sage/symbolic/expression.pyx, line 6105: sage: f.find_maximum_on_interval(0,5, tol=0.1, maxfun=10) Expected: (0.561090323458081..., 0.857926501456...) Got: (0.56109032345808163, array([ 0.8579265])) ** File /scratch/tornaria/sage-4.3/devel/sage-main/sage/symbolic/expression.pyx, line 6142: sage: f.find_minimum_on_interval(1, 5) Expected: (-3.288371395590..., 3.4256184695...) Got: (-3.2883713955908962, array([ 3.42561847])) ** File /scratch/tornaria/sage-4.3/devel/sage-main/sage/symbolic/expression.pyx, line 6144: sage: f.find_minimum_on_interval(1, 5, tol=1e-3) Expected: (-3.288371361890..., 3.4257507903...) Got: (-3.288371361890984, array([ 3.42575079])) ** File /scratch/tornaria/sage-4.3/devel/sage-main/sage/symbolic/expression.pyx, line 6146: sage: f.find_minimum_on_interval(1, 5, tol=1e-2, maxfun=10) Expected: (-3.288370845983..., 3.4250840220...) Got: (-3.2883708459837844, array([ 3.42508402])) ** File /scratch/tornaria/sage-4.3/devel/sage-main/sage/symbolic/expression.pyx, line 6149: sage: f.find_minimum_on_interval(1, 15) Expected: (-9.477294259479..., 9.5293344109...) Got: (-9.4772942594797929, array([ 9.52933441])) ** 2 items had failures: 2 of 5 in __main__.example_146 4 of 8 in __main__.example_147 ***Test Failed*** 6 failures. For whitespace errors, see the file /home/tornaria/.sage//tmp/.doctest_expression.py [40.2 s] - sage -t devel/sage/sage/numerical/optimize.py ** File /scratch/tornaria/sage-4.3/devel/sage-main/sage/numerical/optimize.py, line 117: sage: find_maximum_on_interval(f, 0,5) Expected: (0.561096338191..., 0.8603335890...) Got: (array
Re: [sage-devel] server pool problem
On Sun, Jan 10, 2010 at 8:49 PM, John Cremona john.crem...@gmail.com wrote: The server log ends like this (for some reason I cannot scroll back as it is running under screen): Use C-a [ to enter copy mode which allows you to see the scroll back of screen itself (pgup, arrows, etc, esc to quit). Gonzalo -- 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] How much code to convert to IEEE 754 format ?
On Sun, Jan 3, 2010 at 3:49 AM, Alex Ghitza aghi...@gmail.com wrote: On Sun, 3 Jan 2010 05:35:37 +, David Kirkby david.kir...@onetel.net wrote: Was there a good reason for choosing the name 'sgn'? It sems a bit strange to me. That's the standard mathematical notation for this function, see http://en.wikipedia.org/wiki/Sign_function Ken Thompson was once asked what he would do differently if he were redesigning the UNIX system. His reply: I'd spell creat with an e. (http://en.wikiquote.org/wiki/Kenneth_Thompson) Best, Gonzalo -- 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] doctest failures due to rounding errors on Solaris.
On Wed, Dec 30, 2009 at 10:38 PM, Dr. David Kirkby
david.kir...@onetel.net wrote:
Em, This is very odd. exp(1) gives a different result on SPARC if you build
with gcc or Sun Studio. GCC is correct, and Sun Studio is wrong. Yet Sage on
't2' was build with gcc, not Sun Studio.
gcc is actually inlining exp(1.0) to its correct value. The exp() from
the sun library is incorrect. Try this program instead:
#include math.h
#include stdio.h
#include stdlib.h
int main(int argc, char **argv) {
double x = 1.0;
if (argc1)
x = atof(argv[1]);
printf(%.16lf\n,exp(x));
}
Best, Gonzalo
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Re: [sage-devel] Notebook changes for Ipod touch and Iphone
On Wed, Nov 25, 2009 at 11:04 PM, William Stein wst...@gmail.com wrote: Another nice addition would be to use Tachyon instead of Java by default to render 3d images on the iphone. I.e., I = icosahedron() I.show(viewer='tachyon') works fine on the iphone, but it is tedious to type viewer='tachyon'. What about a global (per-worsheet?) way of choosing viewer (maybe with a pull down at the top of the ws)? Some of us don't have neither an iphone nor java. It /is/ tedious to type viewer='tachyon'. Best, Gonzalo -- 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: A Sage NSF proposal to the Computational Mathematics Program
On Mon, Nov 23, 2009 at 7:04 PM, rjf fate...@gmail.com wrote: That's helpful. Forgive me for asking for information. I see, somewhat later, that this has to do with adding type declarations. Just the ticket. To me is suggests that Python is inappropriate for numerical work -- for which C is more appropriate. Indeed, Python is inappropriate for programming anything which is cpu-intensive. IMHO, were not for cython/pyrex, sage would be doomed. Actually, I believe pyrex is one of the main reasons William settled with python for sage. And so the veneer of Python is insufficient. Of course using (optional) declarations in Lisp helps some compilers to produce better numerical code. Some of that code generation (depending on the Lisp system) is even done with C as an intermediary. And has been done that way since, oh, 1984 or so. The goal of Python/Cython is to code with *less* parenthesis than C. Other than that, it's probably the same venerable idea. Gonzalo -- 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: Implementation of Q(t) and monomials
On Sun, Nov 15, 2009 at 3:32 AM, William Stein wst...@gmail.com wrote: model name : Dual-Core AMD Opteron(tm) Processor 8220 cpu MHz : 1000.000 Why do you say 1000 MHZ when that particular processor is a 2800Mhz (=2.8Ghz) processor? [...] model name : Intel(R) Core(TM)2 Duo CPU P8400 @ 2.26GHz cpu MHz : 800.000 That cpu MHz of 800 makes no sense, given that your CPU is 2.26GHz. I'm just curious. CPU throttling? Gonzalo --~--~-~--~~~---~--~~ 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: xdg-open and Solaris.
On Tue, Nov 10, 2009 at 4:02 PM, Dr. David Kirkby david.kir...@onetel.net wrote: /opt/kirkby/sage-4.2-Solaris-10-SPARC-sun4u-SunOS/local/bin/sage-native-execute: xdg-open: not found Is 'xdg-open' supposed to be included in Sage anywhere, or is the user expected to have it on their machine? Check out http://portland.freedesktop.org/wiki/ Gonzalo --~--~-~--~~~---~--~~ 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] openSSL import error
I've just finished compilation of sage-4.2 on a netbook (atom N280) -- 6h47m walltime. The OS is debian (testing, very minimal install). I ran notebook() from sage, iceweasel (3.0.14) launches, I tried to upload a worksheet using an url, and after hitting Upload Worksheet the notebook crashes with the following error: from OpenSSL import SSL exceptions.ImportError: No module named OpenSSL I didn't spot anything strange in the build, but I wasn't really looking at it. I don't have any libssl*-dev installed if that matters. But gnutls seems to have compiled ok. I'm downloading the prebuilt binary for atom to see if it works. Gonzalo --~--~-~--~~~---~--~~ 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: openSSL import error
On Mon, Nov 9, 2009 at 6:20 PM, William Stein wst...@gmail.com wrote: Upload from a URL can't upload from a published worksheet that is published as http or https, actually. It never occurred to me to implement that. It's meant for uploading sws files, which might be sitting on the web somewhere. Uploading from the URL of a published worksheet is an interesting idea. The published worksheet has a Download link to a .sws file. I was using that as the url. I didn't expect the url of the worksheet itself to work, although it would be great to have. Gonzalo --~--~-~--~~~---~--~~ 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] Could not get source code
This is with sage 4.2 notebook (both in the atom install mentioned above and with sagenb.org): 1. enter def f(n): // return n+1 on a cell, evaluate 2. enter f?? on the second cell, evaluate. the result is a box with could not get source code. Docstrings do work. Gonzalo. --~--~-~--~~~---~--~~ 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: Set reorders elements
On Sun, Nov 8, 2009 at 2:29 AM, Alex Ghitza aghi...@gmail.com wrote:
This is a bit disconcerting:
sage: Set(['a', 'b', 'c'])
{'a', 'c', 'b'}
I am surprised by the following:
sage: s = set(['a', 'b', 'c'])
sage: repr(s)
set(['a', 'c', 'b'])
sage: str(s)
set(['a', 'c', 'b'])
so far so good, however:
sage: s
set(['a', 'b', 'c'])
???
This behaviour happens in 4.2, but NOT in 3.4.1
This doesn't happen in sage -python, but it does happen in sage
-ipython, so I guess is ipython related. However, both versions seem
to be using ipython 9.1...
Gonzalo
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[sage-devel] Re: Do we need cp -a - or would 'cp -pR' do ?
On Sat, Nov 7, 2009 at 11:00 PM, Dr. David Kirkby david.kir...@onetel.net wrote: But how did you find out these two were hard links? I'm not aware of any way to find if A is a hard link of B, unless one finds the inodes and compares them, which would be next to impossible where there are a lot of files. I assume there is some way you do this. $ ls -l sage-4.1.1/local/bin/python* -rwxr-xr-x 2 tornaria tornaria 5528068 2009-09-04 21:45 sage-4.1.1/local/bin/python -rwxr-xr-x 2 tornaria tornaria 5528068 2009-09-04 21:45 sage-4.1.1/local/bin/python2.6 -rwxr-xr-x 1 tornaria tornaria1419 2009-09-04 23:54 sage-4.1.1/local/bin/python2.6-config lrwxrwxrwx 1 tornaria tornaria 16 2009-10-30 01:25 sage-4.1.1/local/bin/python-config - python2.6-config The 2 in the second column indicates the number of hard link references; you can guess they are the same file b/c they have the same metadata --- you can confirm by looking at the inode numbers. What I actually did, is check out the tarball: $ tar tvf sage-4.1.1-core2-jsmath_fonts-x86_64-Linux.tar.gz | grep ^h hrwxr-xr-x tornaria/tornaria0 2009-09-04 21:45 sage-4.1.1-core2-jsmath_fonts-x86_64-Linux/local/bin/python link to sage-4.1.1-core2-jsmath_fonts-x86_64-Linux/local/bin/python2.6 WRT symlinks: $ tar tvf sage-4.1.1-core2-jsmath_fonts-x86_64-Linux.tar.gz | grep ^l | wc -l 125 a. fix installation of python so that a symlink is used instead of a hard link Do you know where this bit of code is? As I say, from what I can see, the link should be created as a symbolic link, not a hard link. I suppose in the python spkg... [a. is not critical, but as long as it's not done, sage-bdist should keep using -a or -d on gnu systems, to avoid bloat in the bdist tarfile] Though the bloat will already exist on OS X, as OS X uses -pR, and no -a. Their choice ;-) not waste much time over it. Clearly the use of this non-POSIX option '-a' needs to be removed asap, as it stops a binary being created on Solaris. I'm reluctant to put tests in the script to handle Solaris differently to linux, when POSIX options should be suitable for either. If its possible to do something which works on all platforms (HP-UX etc), so much the better. But that is hardly that important. rant POSIX is not suitable. There's no posix way to copy hardlinks. The standard is just too restrictive, like a dinosaur: big, fat, and slow. We can try to adjust to posix, for the sake of portability, but that doesn't make it suitable. We can do it because we are small, lean, and fast :-) /rant Gonzalo --~--~-~--~~~---~--~~ 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: Do we need cp -a - or would 'cp -pR' do ?
On Sat, Nov 7, 2009 at 11:00 PM, Dr. David Kirkby david.kir...@onetel.net wrote: Gonzalo Tornaria wrote: Is it really necessary for sage-bdist to preserve hardlinks? [ ... checking a bdist tarball of 4.1.1 ... ] there is exactly one hardlink in this bdist tarball: local/bin/python is a hardlink to local/bin/python2.6. IOW, using -P instead of -d would produce a tarball with two copies of the python binary. Shouldn't this be handled with a symbolic link instead? I would have thought so too. But I'm puzzled, as python-2.6.2.p4/spkg-install creates a symbolic link. It has the line: ln -s python2.6 python This is actually creating a local/lib/python symlink to local/lib/python2.6. It seems to me the line at fault is in file python-2.6.2.p4/src/Makefile.pre.in, line 763: (cd $(DESTDIR)$(BINDIR); $(LN) python$(VERSION)$(EXE) $(PYTHON)) an -s option to that could make a difference, I think. (I didn't try it) My suggestion would be: a. fix installation of python so that a symlink is used instead of a hard link Do you know where this bit of code is? As I say, from what I can see, the link should be created as a symbolic link, not a hard link. b. use -PRp as options for cp (this is posix!) c. for the sage-main directory, use the trailing / trick so the -L / -H option is not necessary (double check this with whoever wrote the sage-bdist script to use -L option) Actually, use a trailing /. as this is more portable. d. for systems where -P is not supported, figure out a way to copy preserving symlinks. For the HP-UX, it turns out that cp -Rp is good. It preserves symlinks, and it turned out also hard links. Gonzalo --~--~-~--~~~---~--~~ 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: Do we need cp -a - or would 'cp -pR' do ?
On Sun, Nov 8, 2009 at 9:31 PM, David Kirkby david.kir...@onetel.net wrote: Hopefully, -pR may work for any POSIX system if the reason for the hard link is known. I can't see what creates that link myself. You clearly have a much greater understanding of the issues than me. Just to clarify, the option -pR is not enough, even disregarding the hard link issue. In fact, for solaris, using -pR means that also the symlinks are not handled properly! IOW, it's really necessary to use -pRP (both p and P) --- this should work for any posix system (except for the hard link issue). This is quite an old release of HP-UX. The more modern versions are probabably better, but they will not run on my PA-RISC machine. I believe they will only run on Itanium systems. Then I would guess a newer release of HP-UX actually supports the -P option to cp. Gonzalo --~--~-~--~~~---~--~~ 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: Why is local/bin/python a hardlink to local/bin/python2.6.??
David, On Sun, Nov 8, 2009 at 10:15 PM, David Kirkby david.kir...@onetel.net wrote: If you look on the thread Do we need cp -a - or would 'cp -pR' do ? you may have noticed that Gonzalo Tornaria has discovered that local/bin/python is a hardlink to local/bin/python2.6. From what I understand, this is the only hard link in Sage. It would be better if this could be replaced by a symbolic link. you missed my answer in the other thread: I would have thought so too. But I'm puzzled, as python-2.6.2.p4/spkg-install creates a symbolic link. It has the line: ln -s python2.6 python This is actually creating a local/lib/python symlink to local/lib/python2.6. It seems to me the line at fault is in file python-2.6.2.p4/src/Makefile.pre.in, line 763: (cd $(DESTDIR)$(BINDIR); $(LN) python$(VERSION)$(EXE) $(PYTHON)) an -s option to that could make a difference, I think. (I didn't try it) Gonzalo --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Do we need cp -a - or would 'cp -pR' do ?
On Sat, Nov 7, 2009 at 6:48 AM, Dr. David Kirkby david.kir...@onetel.net wrote: cp -L$OPT devel/sage-main $TMP/devel/sage-main Maybe this is done to handle the case where sage-main is a symlink to an actual directory. The option -L means to copy symlinks as real files. Otherwise, the symlink may be copied (when using -a, at least --- unspecified by posix when using -Rp). As a matter of fact, using cp -Lra does NOT work as claimed above, because the -a option implies -P which overrides the -L option. Using cp -raL would copy symlinks, though. The actual meaning of -a in gnu cp is really -dRp, not just -Rp. The -d option should be replaced with -P posix option (preserve symlinks), except the -d also preserves hard links. I don't think posix has an option to preserve hard links. For the line with -L, if the only motivation is to follow the symlink in case sage-main itself is a symlink, the correct option is -H rather than -L, but it may be possible to use (instead of -H or -L): cp -$OPT devel/sage-main/ $TMP/devel/sage-main the extra / at the end of the source operand makes it to expand the symlink, if any. Maybe somebody (wstein?) can comment on why the -L was added to the script? WRT -d option (preserve symlinks + hardlinks). It's clearly necessary to preserve symbolic links. For instance, dynamic libraries use symlinks. Is it really necessary for sage-bdist to preserve hardlinks? [ ... checking a bdist tarball of 4.1.1 ... ] there is exactly one hardlink in this bdist tarball: local/bin/python is a hardlink to local/bin/python2.6. IOW, using -P instead of -d would produce a tarball with two copies of the python binary. Shouldn't this be handled with a symbolic link instead? - My suggestion would be: a. fix installation of python so that a symlink is used instead of a hard link b. use -PRp as options for cp (this is posix!) c. for the sage-main directory, use the trailing / trick so the -L / -H option is not necessary (double check this with whoever wrote the sage-bdist script to use -L option) d. for systems where -P is not supported, figure out a way to copy preserving symlinks. [a. is not critical, but as long as it's not done, sage-bdist should keep using -a or -d on gnu systems, to avoid bloat in the bdist tarfile] Gonzalo PS: I've attached a shell script which exhibits the different behaviours of cp with different options. You can try something like that in HP-UX to see if there is a way to preserve symbolic links in a copy. --~--~-~--~~~---~--~~ 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 -~--~~~~--~~--~--~--- cp-test.sh Description: Bourne shell script
[sage-devel] Re: sqrt(2) is real or not
On Wed, Nov 4, 2009 at 2:43 PM, William Stein wst...@gmail.com wrote: sage: Integers(7)(3) in ZZ True I found this one funny: sage: a = Integers(7)(3) sage: a in ZZ True sage: a in QQ False In the same vein: sage: b = Integers(11)(3) sage: a in ZZ True sage: b in ZZ True sage: a + b ... TypeError: unsupported operand parent(s) for '+': 'Ring of integers modulo 7' and 'Ring of integers modulo 11' On the bright side, the error message in this last one is very clear. Gonzalo --~--~-~--~~~---~--~~ 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: sqrt(2) is real or not
On Tue, Nov 3, 2009 at 3:22 PM, Florent Hivert florent.hiv...@univ-rouen.fr wrote: +1 to no simplification... Rationale: I think indeed that it is very important that the type of the result of an operator depends only of the type of the operands and not of their actual values. If is a constructor for symbolic equation, it sounds me perfectly good that sage returns the following: sage: SR Symbolic Ring sage: SR(1) SR(2) 1 2 because it returns: sage: x 2 x 2 if x is symbolic. Should I expect sage: SR(1) + SR(2) 1 + 2 just because sage: SR(x) + SR(2) x + 2 Gonzalo --~--~-~--~~~---~--~~ 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: sqrt(2) is real or not
On Tue, Nov 3, 2009 at 3:05 PM, William Stein wst...@gmail.com wrote: This reminds me of / being a constructor for elements of QQ, no matter what, i.e., a/b for a and b both integers (with b!=0) is a rational, no matter what: sage: type(2/3) type 'sage.rings.rational.Rational' sage: type(2/1) type 'sage.rings.rational.Rational' This was an important design decision that David Kohel pushed hard for early on. Having sqrt(2) 1 *not* simplify by default is consistent with this design decision in that foo bar for either foo or bar symbolic, is a constructor for a symbolic equation. I strongly agree with this design decision. However, the no simplification policy doesn't follow from this. Rather, I think, the design leads to sage: sqrt(2) 1 True sage: parent(sqrt(2) 1) Symbolic Ring i.e. a symbolic True or False this would be consistent with, e.g. sage: (SR(x) + 1) - SR(x) 1 which is 1 in SR, not in ZZ; or even sage: 2/1 2 which is 2 in QQ, not in ZZ. Gonzalo --~--~-~--~~~---~--~~ 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: PPA for Sage in Ubuntu
On Fri, Oct 30, 2009 at 10:54 PM, Ondrej Certik ond...@certik.cz wrote: I solve this problem by using gmail, filtering all messages into the sage label (folder) and then when I want to check threads, which I am involved in, I click on the sent emails link and gmail will highlight those threads that contain new emails. So it's super easy for me to see if someone has said anything. The only disadvantage is that sometimes someone replies a week later, and thus the highlighted thread will be on some older page in the sent emails view in gmail. So some button show unread would be cool. Try label:sent label:unread in the gmail search box. Gonzalo --~--~-~--~~~---~--~~ 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: cache sizes
Laptop: Intel(R) Core(TM)2 CPU T5300 @ 1.73GHz 8 0.023 7.611 16 0.046 2.018 32 0.093 2.034 64 0.289 3.097 128 0.641 2.216 256 0.744 1.160 512 1.542 2.073 1024 3.394 2.202 2048 7.826 2.305 409652.330 6.687 8192 146.481 2.799 16384 314.824 2.149 32768 662.751 2.105 65536 1331.857 2.010 32 2048 This is correct. Server: Intel(R) Core(TM)2 Quad CPU Q9550 @ 2.83GHz 8 0.014 7.452 16 0.027 2.014 32 0.055 1.999 64 0.175 3.188 128 0.400 2.282 256 0.446 1.116 512 0.919 2.060 1024 1.867 2.030 2048 3.779 2.024 4096 8.177 2.164 819225.677 3.140 16384 164.208 6.395 32768 383.568 2.336 65536 802.709 2.093 32 8192 Not quite; this core 2 quad has two 6M L2 caches (one for each pair of cores) for a total 12M of L2 (no shared L3). The L1 is correct. Gonzalo On Tue, Oct 27, 2009 at 6:51 PM, Martin Albrecht m...@informatik.uni-bremen.de wrote: Hi there, in the thread http://is.gd/4EMT8 David and I agreed that M4RI should have a better, more robust and cross- platform mechanism to check for cache sizes. Thus I wrote a little C program to check for the cache size using timings of random-ish memory access. The program is available at: http://sage.math.washington.edu/home/malb/cache.c On my Core 2 Duo and on my Opteron (both running Linux 64-bit) it does report correct sizes. So far so good. On sage.math it reports L3 cache size instead of L2 but I guess that this is probably what we want anyway (well, L2 is 3MB which I don't check explicitly since I only check powers of two) I'd appreciate if those people on this list who have different hardware or software (OSX, Solaris, PPC, Sparc) could compile the program and report back whether the program reports correct sizes for them. To compile and run: gcc -std=c99 -O3 cache.c -o cache ./cache Cheers, Martin -- name: Martin Albrecht _pgp: http://pgp.mit.edu:11371/pks/lookup?op=getsearch=0x8EF0DC99 _otr: 47F43D1A 5D68C36F 468BAEBA 640E8856 D7951CCF _www: http://www.informatik.uni-bremen.de/~malb _jab: martinralbre...@jabber.ccc.de --~--~-~--~~~---~--~~ 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: PIL -- new python imaging library
On Sun, Oct 25, 2009 at 11:57 PM, William Stein wst...@gmail.com wrote: On Sun, Oct 25, 2009 at 10:45 AM, John Cremona john.crem...@gmail.com wrote: Beautiful, thanks. Yes, I do recognise it from Lloyd's book. Here are some other images by Tom Boothby, by the way: http://8tb.us/home/boothby/cover/samples/ Awesome! Is it possible to read some analytic or geometric information off the pictures? Should modularity imply some kind of self-similarity in the pictures? Gonzalo --~--~-~--~~~---~--~~ 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: virtualbox speed
On Fri, Oct 23, 2009 at 11:41 PM, Ondrej Certik ond...@certik.cz wrote:
On Fri, Oct 23, 2009 at 4:21 PM, Ondrej Certik ond...@certik.cz wrote:
Interesting. Do you have some notes about your KVM setup? I want to
try it as well, as the ubuntu guys seem to prefer it over virtualbox:
I'm using kvm directly (not libvirt / virt-manager). This is kvm 0.72
from debian/lenny.
The command line is long, and includes the following options --- I'll
add a comment on them:
-m 2048### 2 GB of memory for this virtual machine
-smp 2 ### 2 virtual cpus
-nographic### no virtual vga
-net nic,model=virtio ### virtio network card in the guest
-net user ### user mode network support in the host
-drive file=debian-1.raw,if=virtio,boot=on
### this is the OS image (9.4GB raw file -- using virtio disk drive)
-drive file=swap-1.raw,if=virtio,cache=off
### another one for swap (4 GB)
-monitor unix:/home/vm/debian/debian-1.monitor,server,nowait
### unix socket used for control of the VM
-cpu qemu64,model=15,+ht,+ssse3,+cx16,model_id=Intel(R) Core(TM)2
Quad CPU Q9550 @ 2.83GHz
### this makes it so the cpuid in the virtual machine reports good
flags -- important when compiling sage
-kernel /boot/vmlinuz-2.6.26-1-amd64
-initrd /boot/initrd.img-2.6.26-1-amd64
-append root=/dev/vda1 ro quiet console=ttyS0,115200
### kernel options for booting the VM. I'm using 2.6.26, this is a
kernel from debian
### it's actually booting a kernel in the /boot directory of the host
OS --- but the host itself is running 2.6.29-2.
### The console option for the kernel makes it so that guest console
goes through ttyS0 (because I don't have VGA hardware in the guest)
-redir tcp:11022::22
### I can ssh to the guest through port 11022 in the host
-redir tcp:8000::8000
### I can access to port 8000 in the guest through port 8000 in the
host --- this is where the sage notebook listens
-
The host system is debian lenny
The guest system is also debian lenny
Both are 64 bit.
The machine is a core 2 quad Q9550 with 8Gb of ram.
I also explored using huge pages for the kvm memory, and it seems to
make a bit of a difference, but I'm not using that in production.
This is a shell script I use in /etc/init.d, so the VM runs
automatically at startup, etc:
---
#! /bin/sh
# Start/stop the Sage notebook server.
#
### BEGIN INIT INFO
# Provides: kvm-sage1
# Required-Start:$kvm
# Required-Stop: $kvm
# Default-Start: 2 3 4 5
# Default-Stop: 1
# Short-Description: KVM for sage1.
# Description: KVM for sage1.
### END INIT INFO
NAME=kvm-sage1
USER=tornaria
MONFILE=/home/vm/debian/debian-1.monitor
PIDFILE=/home/vm/debian/debian-1.pid
DIR=/home/vm/debian
SCRIPT=run.sh
. /lib/lsb/init-functions
case $1 in
start) log_daemon_msg Starting KVM for sage1 ${SCRIPT}
start-stop-daemon --start --quiet --pidfile ${PIDFILE} --chuid
${USER} --chdir ${DIR} --startas /usr/bin/screen -- -dmS ${NAME}
${DIR}/${SCRIPT}
log_end_msg $?
;;
stop) log_daemon_msg Stopping KVM for sage1 ${SCRIPT}
echo system_powerdown | socat -t 30 - UNIX-CONNECT:$MONFILE
/dev/null 21 ||
start-stop-daemon --stop --quiet --pidfile ${PIDFILE}
log_end_msg $?
;;
*) log_action_msg Usage: /etc/init.d/kvm-sage1 {start|stop}
exit 2
;;
esac
exit 0
-
You can see in the stop part how to use the monitor socket to control
the KVM. In the example, we issue system_powerdown, that's the
virtual equivalent of pressing the power button; the guest OS should
get an ACPI powerdown event, and it has 30 seconds to cleanly shutdown
(-t 30 option for socat).
Gonzalo
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[sage-devel] Re: virtualbox speed
For comparision, I'm using kvm to virtualize our sage notebook server. Here's the timings for your scripts: A) the real hardware 0.196608066559 1 0.191864967346 -50 B) the kvm instance 0.219820976257 (11.8% slowdown) 1 0.213951826096 (11.5% slowdown) -50 Gonzalo On Fri, Oct 23, 2009 at 7:38 PM, Ondrej Certik ond...@certik.cz wrote: Hi, I tried the latest Sage virtualbox appliance, it works on ubuntu 9.04, 64bit. I then used this simple script (in a terminal) to get some idea how fast it is: from timeit import default_timer as clock def test1(): a = 0 t = clock() for i in range(1, 10**6): a += 1/i**2 t = clock() - t print t return a print test1() and then test it on my system: $ python2.5 t.py 0.198249101639 1 and in the virtualbox: # python a.py 2.60369110107 E.g. it's about 13x slower. For comparison, in the virtual machine at linode.com, I get: $ python t.py 0.25862288475 1 Then it occured to me that maybe just floating point stuff is slow, or maybe i**2 is too big. So I modified the script: from timeit import default_timer as clock def test1(): a = 0 t = clock() for i in range(1, 10**6): if i % 2 == 0: a += i else: a -= i t = clock() - t print t return a print test1() which runs on ubuntu: $ python2.5 t.py 0.212127923965 -50 and in the virtualbox on the same machine: # python a.py 0.267327070236 -50 Which is only about 1.2x slower. So apparently virtualbox is very fast for some things. Ondrej --~--~-~--~~~---~--~~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: webMathematica 3 -- mathematica's take on web-based manipulate
On Thu, Oct 22, 2009 at 2:52 AM, William Stein wst...@gmail.com wrote: Hi, Mathematica released their web-based *manipulate* implementation: http://wolfram.com/products/webmathematica/ Alternate HTML content should be placed here. This content requires the Adobe Flash Player. Get Flash This rules it out for me... Gonzalo --~--~-~--~~~---~--~~ 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 servers
On Fri, Oct 16, 2009 at 2:18 AM, William Stein wst...@gmail.com wrote: 1. Where? (E.g., Dept. of Mathematics, University of Maryland) Centro de Matemática, Universidad de la República (Montevideo, Uruguay) 2. Why? (E.g, for our Math 411 course on differential equations) Graduate and undergraduate math courses in general and for researchers. Gonzalo --~--~-~--~~~---~--~~ 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 in Korean
On Thu, Oct 15, 2009 at 2:06 PM, Timothy Clemans timothy.clem...@gmail.com wrote: On Thu, Oct 15, 2009 at 2:42 AM, Dan Drake dr...@kaist.edu wrote: Here's a complete translation of the Sage notebook into Korean: http://math1.skku.ac.kr/ Go ahead and log in -- username test, password test95. This is the work of a couple students and professors at Sungkyunkwan University. They also translated Rob Beezer's linear algebra quick reference and have a neat mobile phone interface -- click on the different examples (예제) and check out the results. I would really like to see their translation integrated into the notebook, so that the notebook front page has a language selector. +1 I really like the homepage they created. Could that homepage along with the language translation be added to the notebook? +1 I can try to have the spanish translation done if somebody else figures out the details needed to support i18n (say, figure out gettext for python, produce the .pot files for translation, load the .po files from the notebook, the language selector feature, etc.) Best, Gonzalo --~--~-~--~~~---~--~~ 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 releases
On Wed, Oct 14, 2009 at 6:49 AM, Burcin Erocal bur...@erocal.org wrote: The status of lieutenant is the equivalent of having commit access in other open source projects. I would prefer a different term for lieutenant, but I don't have anything better now. What about editor? Gonzalo --~--~-~--~~~---~--~~ 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 releases
On Wed, Oct 14, 2009 at 7:12 AM, Dr. David Kirkby david.kir...@onetel.net wrote: 2) When submitting a patch, they attach logs showing building on all platforms, *except* the one they normally work on, since one can assume they have probably got their patch working there. I don't think this would work at all, unless there is an *easy* automated procedure to submit a patch to a bot which (a) applies the patch to the current tree (b) compiles in all platforms (c) attaches the logs to the ticket and possibly flags the ticket depending on the result of the test. OTOH, maybe if binary distributions for t2 were readily available (as they are (?) for sage.math), that would encourage some people to actually try some patches in solaris. rant BTW, logging into T2 and getting errors in my .bashrc already discourages me to get anywhere near solaris. Just one small sample: grep: illegal option -- q Usage: grep -hblcnsviw pattern file . . . Can you please check for me whether grep -q is posix or not? /rant Gonzalo --~--~-~--~~~---~--~~ 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: How should we handle the case of no gcc or g++ in the path?
On Wed, Oct 14, 2009 at 10:06 AM, Dr. David Kirkby david.kir...@onetel.net wrote: --- 3) Exit if gcc or g++ can not be found unless SAGE_PORT is exported to some non-empty value. Currently SAGE_PORT is only needed on some operating systems, and has nothing to do with compilers, but we could extend it's usage to mean any unsupported operating systems or unsupported compiler. If SAGE_PORT is exported to some non-empty value, then the build can proceed without gcc and g++ even if gcc and g++ are not in the path. --- What compiler will be used if gcc and g++ are not in the path? Presumably, this will only work if CC and CXX are set to proper compilers, right? Doesn't it make sense to: 4) check for gcc and g++ except when CC and/or CXX are set, in which case, check for CC and CXX ?? I'm probably missing something... haven't looked at prereq in a while. Best, Gonzalo --~--~-~--~~~---~--~~ 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: spkg-install's [was Re: Using a random number generator to tell the time!]
On Mon, Oct 12, 2009 at 8:45 AM, Dr. David Kirkby david.kir...@onetel.net wrote: I really like Gonzalo's suggestion to think of specific tools and also the actual people involved, rather than abstractions and standards. [...] I can see some advantages in this too, but also some pretty significant disadvantages. * Native compilers are normally better than the GNU ones (I know you [...] I totally agree targetting different compilers is a worthwhile goal. I don't think targetting different versions of cp et al is. Especially if some of them are botched. I don't think e.g. the awk srand() hack is funny at all; the posix standard at the shell level is deficient --- for instance, computing the time in seconds since the epoch is a fairly reasonable requirement which posix fails to address in a straightforward way. Gonzalo --~--~-~--~~~---~--~~ 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: notebook help needed
On Mon, Oct 12, 2009 at 2:42 PM, William Stein wst...@gmail.com wrote: name using os.path.join, which doesn't put a trailing slash in. One should write code using os.path.join too, which means you shouldn't depend on a slash being forward -- it might be backwards (on windows it is). Note that dos and windows accept both forward and backward slashes as path separators. It's just the command line which usually overrides forward slashes to be command options. Try dir C:/WINDOWS (with the quotes) Just 2 pennies worth of trivia... using os.path.sep sounds like the right think to do anyway... Gonzalo PS: the separator for MacOS 10, though, was just : IIRC, but I don't think it's relevant anymore. --~--~-~--~~~---~--~~ 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: alpha.sagenb.org
On Mon, Oct 12, 2009 at 11:44 PM, Jason Grout jason-s...@creativetrax.com wrote: Thanks. One more question; how do I start/stop the server? No screen sessions are running, for example. Since you mention screen, and in case it's useful for somebody, here's my init.d script to start the sage notebook automatically in a screen session -- so this is fully automated, but one can still attach to the running notebook in case something goes wrong... (I have a script which ssh's to the server as nbuser and runs screen) This is running in a debian 5.0 (lenny). The sage-notebook script goes into /etc/init.d, and the notebook.py script goes into /home/nbuser. Best, Gonzalo --~--~-~--~~~---~--~~ 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-notebook Description: Binary data from sage.all import notebook notebook(directory='/home/nbuser/nbfiles', port=8000, address='', secure=True, accounts=True, ulimit='-u 200 -v 50 -t 3600', open_viewer=False, timeout=120, ##server_pool=['nbu...@localhost'] )
[sage-devel] Re: Using a random number generator to tell the time!
Would it make more sense to include something like busybox (www.busybox.net) into sage? Busybox includes a shell (ash, I think), and most shellutils and textutils one would probably want to use (this includes awk, sed, etc). Instead of trying to fix the sage shell scripts to work in any combination of shell/utils/etc, just target the busybox shell with its corresponding utils. I don't know how feasible it is to compile busybox on OSX, solaris, or other unices, though. Gonzalo BusyBox combines tiny versions of many common UNIX utilities into a single small executable. It provides replacements for most of the utilities you usually find in GNU fileutils, shellutils, etc. The utilities in BusyBox generally have fewer options than their full-featured GNU cousins; however, the options that are included provide the expected functionality and behave very much like their GNU counterparts. BusyBox provides a fairly complete environment for any small or embedded system. On Sun, Oct 11, 2009 at 8:45 AM, Dr. David Kirkby david.kir...@onetel.net wrote: I thought all you mathematicians could not resist looking at this. I know it sounds crazy, but it actually forms the basis of a portable method of getting the number of seconds since 1/1/1970 on Unix. Learn more from my ticket at http://sagetrac.org/sage_trac/ticket/7188 which needs review! 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 -~--~~~~--~~--~--~---
