[sage-devel] Re: Sage 3.0.1-alpha1 released!
Thanks for the explanations! For my own build, I recovered by doing "sage -ba" as previously reported. So I don't know whether the original problem (running sage for the first time after an apparently successful build) was caused by the SAGE_PBUILD thing or not. Before doing "sage -ba" I also did export SAGE_PBUILD= which was intended to "switch off" this feature. John 2008/5/2 mabshoff <[EMAIL PROTECTED]>: > > On May 1, 9:02 pm, "John Cremona" <[EMAIL PROTECTED]> wrote: > > Hi John, > > > > Thanks -- I mistakenly thought "pbuild" was short for "parallel build". > > Yes, it is meant to emphasize the parallel nature. Gary builds > routinely with 8 cores on his box and it cuts down the build time in a > linear fashion. > > > > If it is not about building Sage, while is it called SAGE_PBUILD? > > It is building the Sage library in parallel. I guess since I sat next > to Gary when the ideas where formulated by us it is so obvious to me > that I would never consider anything else. But I guess the problem is > that Sage is three things as William always points out in his talks. > > Gary wants to do build spkg in parallel, but I am more than skeptical > if that is worth it and doesn't open up a whole other can of worms. > That said I am sure we will have parallel spkg builds in less than six > months ;) > > > > Anyway, can someone remind me what causes this and how to fix it? > > wjp found the likely cause and Gary is posting a patch, so hopefully > it will all be sorted out in rc0. > > Cheers, > > Michael > > > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: ISSAC abstract
On May 2, 3:19 am, "David Joyner" <[EMAIL PROTECTED]> wrote: > Looks good to me. I think Python is actually in the top 5 languages > now, isn't it? just for completeness, released today: http://www.linuxjournal.com/article/10065 - Readers' Choice Awards 2008 / Favorite Scripting Language: Python (28.9%) h --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: ISSAC abstract
On May 1, 2008, at 5:49 PM, William Stein wrote: > On Thu, May 1, 2008 at 4:05 PM, Robert Bradshaw > <[EMAIL PROTECTED]> wrote: >> >> On May 1, 2008, at 2:51 PM, William Stein wrote: >> >>> Hi, >>> >>> I wrote a new version of my ISSAC talk abstract. What do you think: >>> >>> http://sage.math.washington.edu/home/was/tmp/abstract.pdf >> >> I think the previous abstract (version 2) is much better--this >> abstract seems more a reaction to the recent threads on sage-devel > > Thanks for your patience with my experiments. Please see abstract > number 3: > > http://sage.math.washington.edu/home/was/tmp/abstract3.pdf > > Let me know what you think.It will probably piss off everybody, > but > I guarantee you it is the most honest thing I've ever written about > Sage. I like it. Here's a couple more suggestions: - In the second sentence the word "stupid" seems too informal. Maybe unwise/foolish? (Neither of these are as strong though.) - I think there should be a specific rebuttal to Fateman's claims, even a simple "Fortunately, he has since been proven wrong." Also, in this paragraph about Sage's growth, it might be worth having a sentence about how it has greatly overflowed its bounds as a number- theoery only tool to cover a wide range mathematics. - Givaro isn't really "high precision arithmetic" but I can't think of where it fits better - The second-to-last paragraph feels a bit disjointed. What is meant by "instead?" It also de-emphasizes the contribution of new code and makes it unclear that Sage can do a lot without the 4 M's (whereas I think you intended to say if you have the commercial software, it integrates well). I think this is just due to lots of editing. I really like the last paragraph. - Robert --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: ISSAC abstract
Dear William, On May 2, 12:23 am, "Bill Page" <[EMAIL PROTECTED]> wrote: > The previous abstract (the second one?, definitely not the first) > seemed like a good balance to me: What is Sage? What can it do? I agree. The second abstract contains the message (among other things): 1. "If you have a standard computational problem then it is very likely that Sage provides the means to solve it" This is an important message IMO, because it may convince people to work with Sage. We know the result: If people work with it, they eventually contribute to it. The third abstract almost completely drops message 1. It has the main message: 2. "If you have a computational problem that can't be solved with existing software then Sage provides a good framework to produce a solution." This is important, too, and will attract a certain type of users. I suggest to try and combine both messages in one abstract. If you ONLY have message 2., i fear that the people could think that Sage is useless for everyday's work. On the other hand, message 2 is an important point: Sage has an active community and provides framework to develop new things in a hight level of quality. Yours Simon --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: ISSAC abstract
Dear William, I am sorry about my previous post, since it was out-dated. My comment did only refer to message number 25 in this thread and to the abstract version at http://sage.math.washington.edu/home/was/tmp/abstract.pdf Now, we have http://sage.math.washington.edu/home/was/tmp/abstract3.pdf, and i like this much more. I'd encourage you to also briefly mention an example where the Sage- framework allowed for a solution of new things (such as in "linear algebra over cyclotomic number fields"), if limited space permits. The last sentence is, of course, rather bold, but that's a matter of personal style. I think the idea to use a Live CD is a very good one. It is good when people have the opportunity to try sage right on the spot. Yours Simon --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: mercurial --> plain text --> mercurial
On Apr 29, 7:14 am, "William Stein" <[EMAIL PROTECTED]> wrote: > On Tue, Apr 22, 2008 at 12:53 AM, mabshoff > Hi, > > I've made a trac ticket for this, since it seems to have got stalled: > > http://trac.sagemath.org/sage_trac/ticket/3052 > > William Robert, I have come across a case that might cause some trouble: If you change the permissions on a file you need to make a mercurial checking since hg claims the repo has been changed, which is true. But export that changeset and it is empty. GIT handles renames and permission changes and also prints those status changes in the log. So, does hg do anything about those changes internally and is it just the log that is insufficient? In the end it will not matter much since we can just add a list of files whose permissions have to be changed and restore them if it causes trouble. In case of spkg-install & friends for example that is automatically taken care of by first making the scripts executable before they are being run by sage-$FOO. Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] #2755 related doctest failure in totallyreal_rel.py
[CC to sage-devel - this email somehow didn't make it on first try :(] Hi guys, When I apply both patches from #2755 to my 3.0.1.rc0 merge tree I get the following failure in totallyreal_rel.py: sage -t devel/sage/sage/rings/number_field/totallyreal_rel.py ** File "/scratch/mabshoff/release-cycle/sage-3.0.1.rc0/tmp/totallyreal_rel.py", line 98: sage: sage.rings.number_field.totallyreal_rel.integral_elements_in_box(K, [[0,5],[0,5]]) Expected: [0, 5, 3, -alpha + 2, -alpha + 3, 1, 2, 4, alpha + 2, alpha + 3] Got: [0, 5, -alpha + 2, -alpha + 3, 1, 2, 3, 4, alpha + 2, alpha + 3] ** It looks just like the order of the list elements has been changed, so it *seems* harmless. But being paranoid I figure I would run it by the experts before "fixing" the issue. Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: ISSAC abstract
Harald Schilly wrote: > On May 2, 3:19 am, "David Joyner" <[EMAIL PROTECTED]> wrote: > Hi, >> Looks good to me. I think Python is actually in the top 5 languages >> now, isn't it? >> > > just for completeness, released today: > http://www.linuxjournal.com/article/10065 > - Readers' Choice Awards 2008 / Favorite Scripting Language: Python > (28.9%) > > Yes, but that is a subset of the greater number of computer users and while the survey compares languages for general purpose programming this is scripting. But python has a huge impact on scientific computing and that is something that is to the advantage of the mathematical computing in general. > h > Cheers, Michael > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Can't install experimental packages
On May 1, 5:01 pm, mabshoff <[EMAIL PROTECTED] dortmund.de> wrote: > There are two problems here: > > a) somebody changed the default 404 error page [we know who did it, > but no need to name names] > b) consequently the download_package command fails since it no longer > recognizes the 404 page and the new 404 page is also larger than the > magic lower bound for a "legal" spkg. > > But we are fixing the issue, tracked at #3072. One problem with the current fix is that it will only fix the issue in Sage 3.0.1 and not previous versions. The main issue is not so much that it works if you download the spkg manually, but that the *automated* download will remain broken unless the website is fixed again. Since Harald did some changes to the default 404 page he should probably clue us in what he changed. > Cheers, > > Michael Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 3.0.1-alpha1 released!
John Cremona wrote: Hi, > Thanks for the explanations! > > For my own build, I recovered by doing "sage -ba" as previously > reported. So I don't know whether the original problem (running sage > for the first time after an apparently successful build) was caused by > the SAGE_PBUILD thing or not. Before doing "sage -ba" I also did > export SAGE_PBUILD= > which was intended to "switch off" this feature. > > Yes, that is correct. There have been several more bug fixes to pbuild, especially to make it more robust on failure, so hopefully people will try it out again for 3.0.1.rc0. Pbuild will not be the default for 3.0.1, but hopefully with some more exposure and testing we can finally make that step for 3.0.2. > John > Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: Fwd: [sage-devel] Re: sloppy mult and div in quaddouble?
I decided to go ahead and open a ticket for it with a patch for spkg- install. I noticed that the CXXFLAGS needed a bit of spring cleaning as well. The ticket is #3079. --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: Fwd: [sage-devel] Re: sloppy mult and div in quaddouble?
On Fri, May 2, 2008 at 1:54 PM, Francois <[EMAIL PROTECTED]> wrote: > > I decided to go ahead and open a ticket for it with a patch for spkg- > install. > I noticed that the CXXFLAGS needed a bit of spring cleaning as well. > The ticket is #3079. I noticed and saw the CXXFLAGS issue. That puzzles me more than a little bit, but I plan to leave the -fPIC in there since we will likely switch to dynamic libs soon enough and you never know which odd tool chain requires -fPIC. Cheers, Michael > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: ISSAC abstract
On Fri, May 2, 2008 at 5:13 AM, Simon King <[EMAIL PROTECTED]> wrote: > I think the idea to use a Live CD is a very good one. It is good when > people have the opportunity to try sage right on the spot. Is there anyone in the list that can share binaries of Sage 3.x for Fedora Core 3 (a higher FC may work, but I need to test it) ? --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: A Sage Enhancement Proposal: Lattice Modules
On Apr 29, 10:00 am, "John Cremona" <[EMAIL PROTECTED]> wrote: > Jon's vision of lattices would include the ones I mentioned before > (f.g. but not necessarily free R-modules where R is a Dedekind Domain, > with one or more embeddings into RR^n or CC^n). > > In another direction: Jon, to what extent could your quadratic form > class be extended to binary forms of higher degree? The quadratic forms code as it stands does not extend to higher degree forms. I think it is better to implement anew higher degree forms, depending on what functionality is desired. There are basic choices of whether to deal with a degree n form, or it's associated linear tensor, or some combinations of the two, which make the implementations different depending on the goal. In the quadratic case, I chose to store the form coefficients and not the symmetric bilinear form. This distinction becomes important in characteristic two, but is usually ignored for most applications. The more specialized routines (equivalence testing, densities, etc.) are too specialized to apply in the context you suggest. > This seems to be quite a common situation: we have some kind of > mathematical object (in this case, binary quadratic form) which has > its own very rich structure and set of specialised methods, but which > is also a special case of various *different* other objects: in this > case, quadratic forms in more variables, or higher degree binary > forms, and so on. > In these cases, it seems like the particular application should guide the choices of where to stop. Of course, it is a good idea to be as general as possible if it's no extra work. Computing with some of the other structures mentioned are interesting, and I hope that my students will work to develop these further. We'll definitely talk about this at the UGA SAGE Days in March! =) -Jon =) --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: ISSAC abstract
On May 2, 2:02 pm, "Alfredo Portes" <[EMAIL PROTECTED]> wrote: > On Fri, May 2, 2008 at 5:13 AM, Simon King <[EMAIL PROTECTED]> wrote: > > I think the idea to use a Live CD is a very good one. It is good when > > people have the opportunity to try sage right on the spot. > > Is there anyone in the list that can share binaries of Sage 3.x for > Fedora Core 3 (a higher FC > may work, but I need to test it) ? Hi, I don't think we build FC3 binaries at the moment, but a quick glimpse seems to indicate that it ships gcc 3.4.3, so it ought to work. If you can provide us with a slim VMWare imge [minimal install+build essentials] we can build Sage binaries with out regular binary build procedure. One thing that slightly concerns me that FC3 has had support dropped a *long* time ago, i.e. that last supported release is FC8 at the moment. Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Reddit-ed
FYI: William's ISSAC abstract is on reddit's frontpage right now. http://reddit.com/info/6hvsn/comments/ Martin -- name: Martin Albrecht _pgp: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99 _www: http://www.informatik.uni-bremen.de/~malb _jab: [EMAIL PROTECTED] --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Reddit-ed
On Fri, May 2, 2008 at 6:27 AM, Martin Albrecht <[EMAIL PROTECTED]> wrote: > > FYI: William's ISSAC abstract is on reddit's frontpage right now. > > http://reddit.com/info/6hvsn/comments/ > > Martin > Wow, it seems to have definitely touched a nerve. There are also now a number of comments on the bottom of my blog post. Maybe somebody should submit a slashdot story or something... It seems like the sort of fodder they would like to rip on. William --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: #2755 related doctest failure in totallyreal_rel.py
Yes, the ordering of the elements does not at all affect the correctness of the output--the most mathematically correct thing would be to output a set. This change can be due to any number of things, but it's probably not worth ascertaining the exact cause. JV --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: #2755 related doctest failure in totallyreal_rel.py
On Fri, May 2, 2008 at 4:22 PM, John Voight <[EMAIL PROTECTED]> wrote: > Yes, the ordering of the elements does not at all affect the > correctness of the output--the most mathematically correct thing would > be to output a set. This change can be due to any number of things, > but it's probably not worth ascertaining the exact cause. > > JV > Hi John, I will then apply the patches from #2755 and fix the doctest failure. Thanks for the quick feedback. Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: #2755 related doctest failure in totallyreal_rel.py
This looks like a dict was involved at some point - maybe just sorting the list would be enough? On May 2, 8:23 am, "Michael Abshoff" <[EMAIL PROTECTED]> wrote: > On Fri, May 2, 2008 at 4:22 PM, John Voight <[EMAIL PROTECTED]> wrote: > > Yes, the ordering of the elements does not at all affect the > > correctness of the output--the most mathematically correct thing would > > be to output a set. This change can be due to any number of things, > > but it's probably not worth ascertaining the exact cause. > > > JV > > Hi John, > > I will then apply the patches from #2755 and fix the doctest failure. Thanks > for the quick feedback. > > Cheers, > > Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Reddit-ed
On Fri, May 2, 2008 at 6:27 AM, Martin Albrecht <[EMAIL PROTECTED]> wrote: > > FYI: William's ISSAC abstract is on reddit's frontpage right now. > > http://reddit.com/info/6hvsn/comments/ > > Martin > Since it seems to spark discussion I posted it to digg: http://digg.com/software/Can_There_be_a_FOSS_Alternative_to_Mathematica_and_MATLAB William --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Debian package build failure for gfan with 3.0.1alpha1
I attempted to build the 3.0.1alpha1 packages for Debian, but it doesn't build, apparently due to some type errors. The build log is attached -- I'd appreciate any guesses as to what's going on here. -Tim Abbott --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~--- /dev/cdrom: open failed: Read-only file system Attempt to close device '/dev/cdrom' which is not open. /usr/bin/apt-get -q update Get:1 http://localhost lenny Release.gpg [189B] Get:2 http://localhost lenny/updates Release.gpg [189B] Get:3 http://localhost lenny Release.gpg [189B] Get:4 http://localhost lenny Release.gpg [189B] Get:5 http://localhost lenny Release [74.4kB] Get:6 http://localhost lenny/updates Release [40.7kB] Get:7 http://localhost lenny Release [10.3kB] Get:8 http://localhost lenny Release [2352B] Ign http://localhost lenny/main Packages/DiffIndex Ign http://localhost lenny/main Sources/DiffIndex Ign http://localhost lenny/updates/main Packages/DiffIndex Ign http://localhost lenny/updates/main Sources/DiffIndex Ign http://localhost lenny/debathena Packages/DiffIndex Ign http://localhost lenny/debathena Sources/DiffIndex Ign http://localhost lenny/main Packages/DiffIndex Ign http://localhost lenny/main Sources/DiffIndex Ign http://localhost lenny/main Packages Ign http://localhost lenny/main Sources Ign http://localhost lenny/updates/main Packages Ign http://localhost lenny/updates/main Sources Ign http://localhost lenny/debathena Packages Ign http://localhost lenny/debathena Sources Ign http://localhost lenny/main Packages Ign http://localhost lenny/main Sources Get:9 http://localhost lenny/main Packages [6680kB] Get:10 http://localhost lenny/main Sources [2151kB] Get:11 http://localhost lenny/updates/main Packages [187kB] Get:12 http://localhost lenny/updates/main Sources [21.5kB] Hit http://localhost lenny/debathena Packages Hit http://localhost lenny/debathena Sources Get:13 http://localhost lenny/main Packages [8866B] Get:14 http://localhost lenny/main Sources [2745B] Fetched 9179kB in 33s (275kB/s) Reading package lists... Automatic build of gfan_0.3-0sagep3~debian4.1 on debuild by sbuild/amd64 0.57.0 Build started at 20080502-1206 ** gfan_0.3-0sagep3.dsc exists in .; copying to chroot ** Using build dependencies supplied by package: Build-Depends: cdbs (>= 0.4.27-1), debhelper (>= 5), libcdd-dev, libgmp3-dev, patchutils (>= 0.2.25), quilt Checking for already installed source dependencies... cdbs: missing Using default version 0.4.52 debhelper: missing Using default version 6.0.11 libcdd-dev: missing libgmp3-dev: missing patchutils: missing Using default version 0.2.31-4 quilt: missing Checking for source dependency conflicts... Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils diffstat file gettext gettext-base groff-base html2text intltool-debian libgmp3c2 libgmpxx4ldbl libmagic1 man-db po-debconf Suggested packages: wamerican wordlist whois vacation devscripts doc-base dh-make cvs gettext-doc groff libgmp3-doc libmpfr-dev less www-browser procmail graphviz Recommended packages: autotools-dev curl wget lynx libcompress-zlib-perl libmail-box-perl libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libcdd-dev libgmp3-dev libgmp3c2 libgmpxx4ldbl libmagic1 man-db patchutils po-debconf quilt 0 upgraded, 19 newly installed, 0 to remove and 77 not upgraded. Need to get 8451kB of archives. After this operation, 23.8MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! bsdmainutils groff-base man-db libmagic1 file gettext-base html2text gettext intltool-debian po-debconf debhelper cdbs diffstat libgmp3c2 libgmpxx4ldbl libgmp3-dev patchutils quilt libcdd-dev Authentication warning overridden. Get:1 http://localhost lenny/main bsdmainutils 6.1.10 [172kB] Get:2 http://localhost lenny/main groff-base 1.18.1.1-20 [846kB] Get:3 http://localhost lenny/main man-db 2.5.1-3 [997kB] Get:4 http://localhost lenny/main libmagic1 4.23-2 [342kB] Get:5 http://localhost lenny/main file 4.23-2 [41.0kB] Get:6 http://localhost lenny/main gettext-base 0.17-2 [123kB] Get:7 http://localhost lenny/main html2text 1.3.2a-3 [98.9kB] Get:8 http://localhost lenny/main gettext 0.17-2 [2683kB] Get:9 http://localhost lenny/main intltool-debian 0.35.0+20060710.1 [30.8kB] Get:10 http://localhost lenny/main po-debconf 1.0.12.1 [237kB] Get:11 http://localhost lenny/main de
[sage-devel] Re: Debian package build failure for gfan with 3.0.1alpha1
On Fri, May 2, 2008 at 6:16 PM, Timothy G Abbott <[EMAIL PROTECTED]> wrote: > I attempted to build the 3.0.1alpha1 packages for Debian, but it doesn't > build, apparently due to some type errors. The build log is attached -- > I'd appreciate any guesses as to what's going on here. > >-Tim Abbott > Hi Tim, we updated gfan a while ago, so this surprises me. The failure is: lp_cdd.cpp:1186: error: cannot convert 'double*' to 'const __mpq_struct*' for argument '2' to 'vo /dev/cdrom: open failed: Read-only file system Attempt to close device '/dev/cdrom' which is not open. I have no clue what is going on there and it seems very, very odd. Any chance you could try building a vanilla gfan? Let me think about this some more, maybe I can come up with something. Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] scilab
Hi, In that reddit discussion of my blog post I mentioned that SciLab (http://www.scilab.org/) is released under a custom GPL-incompatible license when somebody asked about SciLab. Also I mentioned that SciLab violates the GPL by linking in readline. Very interestingly, somebody posted that the next major release of SciLab will be GPL-compatible. See http://www.scilab.org/download/index_download.php?page=CHANGES_5.0-beta-1 This means there is potential for collaboration between the Sage and SciLab projects. I.e., we could potentially share code with them, etc. -- William -- William Stein Associate Professor of Mathematics University of Washington http://wstein.org --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: #2755 related doctest failure in totallyreal_rel.py
Is there a canonical way to sort elements of an algebraic number field? I can think of one or two, but this is a needlessly costly thing to do, IMHO. JV --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: #2755 related doctest failure in totallyreal_rel.py
On 2-May-08, at 9:46 AM, John Voight wrote: > > Is there a canonical way to sort elements of an algebraic number > field? I can think of one or two, but this is a needlessly costly > thing to do, IMHO. You're asking for a canonical representation, which amounts to a canonical choice of a defining polynomial for the field. One can sort defining polynomials and choose the "smallest" one that gives a field isomorphic to your field; this seems to be more accepted for finite fields. I think you might just want to try set([1, 3, 2]) == set([2, 3, 1, 1]) and test for what you're really getting: a set. Nick --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Fwd: Does anyone else have this matrix problem
Michael and Sage-devel, This is happening a lot (see below): > I was trying to create a random matrix with single digit integer entries using > B = random_matrix(ZZ,100,x=0,x=9) > > I get the following error and the worksheet seems to break down after that. > /usr/local/sage/local/bin/sage-sage: line 357: 7881 Illegal instruction We really need to find a way to *immediately* report that "this Sage binary doesn't work on your processor" ASAP instead of after weeks and only when people push Sage to its limits. Or we need to build better binaries. Any ideas? -- Forwarded message -- From: William Stein <[EMAIL PROTECTED]> Date: Fri, May 2, 2008 at 8:32 AM Subject: Re: Does anyone else have this matrix problem To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] On Thu, May 1, 2008 at 10:49 PM, Anusha Sekar <[EMAIL PROTECTED]> wrote: > Hi, > > I was trying to create a random matrix with single digit integer entries using > B = random_matrix(ZZ,100,x=0,x=9) > > I get the following error and the worksheet seems to break down after that. > /usr/local/sage/local/bin/sage-sage: line 357: 7881 Illegal instruction > python "$@" > This means that you downloaded and installed a binary of Sage that was optimized for a different processor than you have in your computer. E.g., maybe you're using an older Pentium, and the binary was built for a much newer one. You might try using https://sage.math.washington.edu:8102 for that problem, or building Sage from source, or get a login account on sage.math.washington.edu (ask me) or somewhere else that has Sage preinstalled. > It breaks down in the sense that all the following cells do not evaluate at all. > > Since the worksheet from class has an example with a 500x500 matrix, I > did not expect to have any problems in finding the determinant of a > 100x100. Is it some kind of overflow? Has anyone else had a similar > problem? > > Thanks > Anusha > > -- > Make a difference! > www.ashanet.org/seattle > -- William Stein Associate Professor of Mathematics University of Washington http://wstein.org -- William Stein Associate Professor of Mathematics University of Washington http://wstein.org --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: ISSAC abstract
Alfredo, I can try to build a Sage binary on Fedora 3 if you wish but I'm not optimistic. I know that my Fedora 5 could not build Sage because the compiler was too old. Fedora 3 likely has the same issue. Tim --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: Does anyone else have this matrix problem
On May 2, 7:56 pm, "William Stein" <[EMAIL PROTECTED]> wrote: > Michael and Sage-devel, No need to single me out - I read sage-devel ;) > This is happening a lot (see below): > We really need to find a way to *immediately* report that > "this Sage binary doesn't work on your processor" ASAP instead of after weeks > and only when people push Sage to its limits. > > Or we need to build better binaries. Any ideas? We can force ATLAS via magic arch switch to build binaries that do not use SSE at all. But it would slow down some operations [obviously]. It would only matter on 32 bit x86 - everywhere else this is a non-issue. For starters I would stop calling the binaries i686 since they are SSE2 binaries. Most people will probably not know what SSE2 is, so that doesn't help. What we also could do is detect non-SSE2 capable CPUs at startup on Linux x86 via the flags in /proc/cpuinfo and just refuse to start in case the CPU's capabilities are insufficient. In that case we should point people to the non-SSE binaries. Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: ISSAC abstract
On May 2, 9:18 pm, root <[EMAIL PROTECTED]> wrote: > Alfredo, Hi Tim, > I can try to build a Sage binary on Fedora 3 if you wish > but I'm not optimistic. I know that my Fedora 5 could not > build Sage because the compiler was too old. The compiler wasn't too old, it was *borken*, i.e. "internal compiler error". IIRC it was some gcc 4.1.0 and as well all know a ".0" release is just an extended beta test. FC5's rpm repo offers some gcc 4.1.1 that will likely build Sage just fine. > Fedora 3 likely has the same issue. Nope, it ships gcc 3.4.3 which is C99 compliant. I didn't use it recently, but it is quite reliable and any issue with Sage and gcc 3.4 will likely be fixed quickly. > Tim Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: Does anyone else have this matrix problem
William Stein wrote: > Michael and Sage-devel, > > This is happening a lot (see below): > > > I was trying to create a random matrix with single digit integer > entries using > > B = random_matrix(ZZ,100,x=0,x=9) > > > > I get the following error and the worksheet seems to break down after > that. > > /usr/local/sage/local/bin/sage-sage: line 357: 7881 Illegal instruction > > We really need to find a way to *immediately* report that > "this Sage binary doesn't work on your processor" ASAP instead of after weeks > and only when people push Sage to its limits. > > Or we need to build better binaries. Any ideas? Steal the CPU detection code from ATLAS and use that to test to see if the processor we're running on is the same as the processor we compiled for? That seems like a bit much. How about compiling a generic binary (i.e., minimal optimizations)? Is that possible with ATLAS and the other programs? Jason --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: ISSAC abstract
>> I can try to build a Sage binary on Fedora 3 if you wish >> but I'm not optimistic. I know that my Fedora 5 could not >> build Sage because the compiler was too old. > >The compiler wasn't too old, it was *borken*, i.e. "internal compiler >error". IIRC it was some gcc 4.1.0 and as well all know a ".0" release >is just an extended beta test. FC5's rpm repo offers some gcc 4.1.1 >that will likely build Sage just fine. > >> Fedora 3 likely has the same issue. > >Nope, it ships gcc 3.4.3 which is C99 compliant. I didn't use it >recently, but it is quite reliable and any issue with Sage and gcc 3.4 >will likely be fixed quickly. Ok. I'll try a fedora 3 build. --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: Does anyone else have this matrix problem
On May 2, 8:06 pm, Jason Grout <[EMAIL PROTECTED]> wrote: > William Stein wrote: Hi, > Steal the CPU detection code from ATLAS and use that to test to see if > the processor we're running on is the same as the processor we compiled > for? That seems like a bit much. You really don't want to do that - believe me, I have seen and improved the ATLAS cpu detection code and it requires an assembler to work. Other than that it is overblown and we can cook up something better and simpler with a three line bash script ;) > How about compiling a generic binary (i.e., minimal optimizations)? Is > that possible with ATLAS and the other programs? Yes, but then something else will break. Depending on the compiler you use it just uses SSE2 instructions unless you specifically tell the compiler not to use it. And attempting to dix that via CFLAGS and CPPFLAGS is not a good idea. Somebody needs to find some pre-SSE2 hardware and donate it to William so we can build a "last resort" binary. Anything else will likely not work. tseug from IRC did build Sage 3.0 on some Duron laptop and it took 22 hours, so building from source is generally not a good idea for people with low end hardware, but since we cannot and will not likely provide binaries for a wide range of distributions for non-SSE2 hardware due to limited and usually slow hardware it is something we will have to deal with for a while. Could we use a bunch on non-SSE2 Athlons with decent, i.e. 1GB RAM, this would be doable. > Jason Thoughts? Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Computing large Bernoulli numbers
Oleksandr Pavlyk reports on the Wolfram Blog that he has computed the 10 millionth Bernoulli number using Mathematica: http://blog.wolfram.com/2008/04/29/today-we-broke-the-bernoulli-record-from-the-analytical-engine-to-mathematica/ How does sage's Bernoulli number implementation compare? I'd like to see bernoulli(10^7) in sage beating Mathematica's time. And then computing the 20 millionth Bernoulli number... Fredrik --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: scilab
On Fri, May 2, 2008 at 10:31 AM, William Stein <[EMAIL PROTECTED]> wrote: [...] > Very interestingly, somebody posted that the next major release of > SciLab will be > GPL-compatible. See > http://www.scilab.org/download/index_download.php?page=CHANGES_5.0-beta-1 > > This means there is potential for collaboration between the Sage and > SciLab projects. > I.e., we could potentially share code with them, etc. > > -- William This is very interesting indeed. In what language is Scilab developed? I assume it's C/C++. -- Hector --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
It takes about 30 seconds on my machine to get the 10^5 Bernoulli number. The mathematica blog says it took a "development" version of mathematica 6 days to do the 10^7 calc. So it would probably take some work, but we are not that badly off as is. -M. Hampton On May 2, 12:34 pm, Fredrik Johansson <[EMAIL PROTECTED]> wrote: > Oleksandr Pavlyk reports on the Wolfram Blog that he has computed the > 10 millionth Bernoulli number using > Mathematica:http://blog.wolfram.com/2008/04/29/today-we-broke-the-bernoulli-recor... > > How does sage's Bernoulli number implementation compare? I'd like to > see bernoulli(10^7) in sage beating Mathematica's time. And then > computing the 20 millionth Bernoulli number... > > Fredrik --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
On May 2, 2008, at 2:56 PM, mhampton wrote: > It takes about 30 seconds on my machine to get the 10^5 Bernoulli > number. The mathematica blog says it took a "development" version of > mathematica 6 days to do the 10^7 calc. So it would probably take > some work, but we are not that badly off as is. But what about the asymptotics? I tried 10^5 and 2*10^5 and 4*10^5 and it wasn't pretty. david --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
I might take a look at this, as there are some ways fo computing B nos which are very much faster tha others, and not everyone knows them. Pari has something respectable, certainly. John 2008/5/2 mhampton <[EMAIL PROTECTED]>: > > It takes about 30 seconds on my machine to get the 10^5 Bernoulli > number. The mathematica blog says it took a "development" version of > mathematica 6 days to do the 10^7 calc. So it would probably take > some work, but we are not that badly off as is. > > -M. Hampton > > On May 2, 12:34 pm, Fredrik Johansson <[EMAIL PROTECTED]> > wrote: > > > Oleksandr Pavlyk reports on the Wolfram Blog that he has computed the > > 10 millionth Bernoulli number using > Mathematica:http://blog.wolfram.com/2008/04/29/today-we-broke-the-bernoulli-recor... > > > > > > How does sage's Bernoulli number implementation compare? I'd like to > > see bernoulli(10^7) in sage beating Mathematica's time. And then > > computing the 20 millionth Bernoulli number... > > > > Fredrik > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: Does anyone else have this matrix problem
Now would I know non-SSE hardware if I met it in the wild? John 2008/5/2 mabshoff <[EMAIL PROTECTED]>: > > On May 2, 8:06 pm, Jason Grout <[EMAIL PROTECTED]> wrote: > > William Stein wrote: > > Hi, > > > > Steal the CPU detection code from ATLAS and use that to test to see if > > the processor we're running on is the same as the processor we compiled > > for? That seems like a bit much. > > You really don't want to do that - believe me, I have seen and > improved the ATLAS cpu detection code and it requires an assembler to > work. Other than that it is overblown and we can cook up something > better and simpler with a three line bash script ;) > > > > How about compiling a generic binary (i.e., minimal optimizations)? Is > > that possible with ATLAS and the other programs? > > Yes, but then something else will break. Depending on the compiler you > use it just uses SSE2 instructions unless you specifically tell the > compiler not to use it. And attempting to dix that via CFLAGS and > CPPFLAGS is not a good idea. Somebody needs to find some pre-SSE2 > hardware and donate it to William so we can build a "last resort" > binary. Anything else will likely not work. > > tseug from IRC did build Sage 3.0 on some Duron laptop and it took 22 > hours, so building from source is generally not a good idea for people > with low end hardware, but since we cannot and will not likely provide > binaries for a wide range of distributions for non-SSE2 hardware due > to limited and usually slow hardware it is something we will have to > deal with for a while. Could we use a bunch on non-SSE2 Athlons with > decent, i.e. 1GB RAM, this would be doable. > > > Jason > > Thoughts? > > Cheers, > > Michael > > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
ok, so the docstring reaveals (1) that the pari version is "by far the fastest" as I suspected, but also that for n>5 that we use a gp interface rather than the pari library " since the C-library interface to PARI is limited in memory for individual operations" -- whatever that means! That might explain David's timing observations. I tihnk the pari implementation is actually quite simple (and there is a huge amount about Berouilli nos in Henri Cohen's latest book too) which suggests that doing a cython implementation would not be hard. Maybe this is time for a repeat performance of the partitions competition with M**ca! John 2008/5/2 John Cremona <[EMAIL PROTECTED]>: > I might take a look at this, as there are some ways fo computing B nos > which are very much faster tha others, and not everyone knows them. > Pari has something respectable, certainly. > > John > > 2008/5/2 mhampton <[EMAIL PROTECTED]>: > > > > > > It takes about 30 seconds on my machine to get the 10^5 Bernoulli > > number. The mathematica blog says it took a "development" version of > > mathematica 6 days to do the 10^7 calc. So it would probably take > > some work, but we are not that badly off as is. > > > > -M. Hampton > > > > On May 2, 12:34 pm, Fredrik Johansson <[EMAIL PROTECTED]> > > wrote: > > > > > Oleksandr Pavlyk reports on the Wolfram Blog that he has computed the > > > 10 millionth Bernoulli number using > Mathematica:http://blog.wolfram.com/2008/04/29/today-we-broke-the-bernoulli-recor... > > > > > > > > > > How does sage's Bernoulli number implementation compare? I'd like to > > > see bernoulli(10^7) in sage beating Mathematica's time. And then > > > computing the 20 millionth Bernoulli number... > > > > > > Fredrik > > > > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
On Fri, May 2, 2008 at 11:34 AM, Fredrik Johansson <[EMAIL PROTECTED]> wrote: > > Oleksandr Pavlyk reports on the Wolfram Blog that he has computed the > 10 millionth Bernoulli number using Mathematica: > > http://blog.wolfram.com/2008/04/29/today-we-broke-the-bernoulli-record-from-the-analytical-engine-to-mathematica/ > > How does sage's Bernoulli number implementation compare? I'd like to > see bernoulli(10^7) in sage beating Mathematica's time. And then > computing the 20 millionth Bernoulli number... > Sage's Bernoulli number is *just* PARI/GP's bernoulli number implementation. Last time I tried timing Sage versus Mathematica's Bernoulli number command (which was 2 years ago), Sage was twice as fast. William --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: Does anyone else have this matrix problem
On May 2, 9:04 pm, "John Cremona" <[EMAIL PROTECTED]> wrote: Hi John, > Now would I know non-SSE hardware if I met it in the wild? On Linux: [EMAIL PROTECTED]:/scratch/mabshoff/release-cycle/sage-3.0.1.rc0$ cat / proc/cpuinfo | grep flags flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt lm 3dnowext 3dnow pni lahf_lm cmp_legacy So: sage.math has mmx, sse, sse2, 3dnowext, 3dnow [which are all fairly obvious] and pni [==Prescott New Instruction, nee SSE3 - brilliant move by Intel] From the above info we can create a one liner bash script that returns true for SSE2 capable hardware. All x86-64 compatible CPUs have SSE2, so it is a non-issue there. > John Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: Does anyone else have this matrix problem
Thanks. I thought I had something old, but it's not *that* old! John 2008/5/2 mabshoff <[EMAIL PROTECTED]>: > > On May 2, 9:04 pm, "John Cremona" <[EMAIL PROTECTED]> wrote: > > Hi John, > > > > Now would I know non-SSE hardware if I met it in the wild? > > On Linux: > > [EMAIL PROTECTED]:/scratch/mabshoff/release-cycle/sage-3.0.1.rc0$ cat / > proc/cpuinfo | grep flags > flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge > mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext > fxsr_opt lm 3dnowext 3dnow pni lahf_lm cmp_legacy > > So: sage.math has mmx, sse, sse2, 3dnowext, 3dnow [which are all > fairly obvious] and pni [==Prescott New Instruction, nee SSE3 - > brilliant move by Intel] > > From the above info we can create a one liner bash script that returns > true for SSE2 capable hardware. All x86-64 compatible CPUs have SSE2, > so it is a non-issue there. > > > John > > > > Cheers, > > Michael > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
On Fri, May 2, 2008 at 11:34 AM, Fredrik Johansson <[EMAIL PROTECTED]> wrote: > > Oleksandr Pavlyk reports on the Wolfram Blog that he has computed the > 10 millionth Bernoulli number using Mathematica: > > http://blog.wolfram.com/2008/04/29/today-we-broke-the-bernoulli-record-from-the-analytical-engine-to-mathematica/ > > How does sage's Bernoulli number implementation compare? I'd like to > see bernoulli(10^7) in sage beating Mathematica's time. And then > computing the 20 millionth Bernoulli number... I couldn't find any information about the hardware that guy used. 64-bit? 32-bit? 1.8Ghz or 3Ghz? Could somebody write and ask? Also, when I tried bernoulli(10^7+2) directly in Sage there were a couple of issues that arose, since that command is much more designed for smaller input. I fixed those small issues. I guess we'll see in a week .. William --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
On May 2, 2008, at 3:40 PM, William Stein wrote: > Also, when I tried > > bernoulli(10^7+2) > > directly in Sage there were a couple of issues that arose, since > that command > is much more designed for smaller input. I fixed those small issues. > I guess we'll see in a week .. I hope you did: sage: x = bernoulli(10^7 + 2) and not sage: bernoulli(10^7 + 2) david --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
On Fri, May 2, 2008 at 3:40 PM, William Stein <[EMAIL PROTECTED]> wrote: > > On Fri, May 2, 2008 at 11:34 AM, Fredrik Johansson > <[EMAIL PROTECTED]> wrote: > > > > > Oleksandr Pavlyk reports on the Wolfram Blog that he has computed the > > 10 millionth Bernoulli number using Mathematica: > > > http://blog.wolfram.com/2008/04/29/today-we-broke-the-bernoulli-record-from-the-analytical-engine-to-mathematica/ > > > > How does sage's Bernoulli number implementation compare? I'd like to > > see bernoulli(10^7) in sage beating Mathematica's time. And then > > computing the 20 millionth Bernoulli number... > > I couldn't find any information about the hardware that guy used. > 64-bit? 32-bit? > 1.8Ghz or 3Ghz? Could somebody write and ask? I did earlier, and I hope he will answer. didier > > Also, when I tried > > bernoulli(10^7+2) > > directly in Sage there were a couple of issues that arose, since that command > is much more designed for smaller input. I fixed those small issues. > I guess we'll see in a week .. > > William > > > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
I think the asymptotics aren't going to go our way if we use pari. It takes 11s for 10^5 and I've been sitting here for quite a few minutes and didn't get 10^6 yet. I think pari uses the zeta function to compute bernoulli numbers. If I'm reading the code right it first computes 1/zeta(n) using the Euler product, then computes the numerator of the bernoulli number to the required precision using this value, then divides by the required denominator, which is just a product of primes. Bill. On 2 May, 20:11, "William Stein" <[EMAIL PROTECTED]> wrote: > On Fri, May 2, 2008 at 11:34 AM, Fredrik Johansson > > <[EMAIL PROTECTED]> wrote: > > > Oleksandr Pavlyk reports on the Wolfram Blog that he has computed the > > 10 millionth Bernoulli number using Mathematica: > > http://blog.wolfram.com/2008/04/29/today-we-broke-the-bernoulli-recor... > > > How does sage's Bernoulli number implementation compare? I'd like to > > see bernoulli(10^7) in sage beating Mathematica's time. And then > > computing the 20 millionth Bernoulli number... > > Sage's Bernoulli number is *just* PARI/GP's bernoulli number implementation. > > Last time I tried timing Sage versus Mathematica's Bernoulli number command > (which was 2 years ago), Sage was twice as fast. > > William --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
On Fri, May 2, 2008 at 12:10 PM, John Cremona <[EMAIL PROTECTED]> wrote: > > ok, so the docstring reaveals (1) that the pari version is "by far the > fastest" as I suspected, but also that for n>5 that we use a gp > interface rather than the pari library " since the C-library interface > to PARI > is limited in memory for individual operations" -- whatever that > means! That's out of date now that Gonzalo T. and I fixed the pari interface so that it automatically doubles the stack if needed. The code needs to be fixed to never use gp by default. If you explicitly use algorithm='pari' it will still switch to gp; changing this was one of my fixes to my code so I could try this. Tom is trying the whole calculation directly in GP. He also did a log fit to timings and estimates it should take about a week in Sage on his machine. We'll see. > > That might explain David's timing observations. > > I tihnk the pari implementation is actually quite simple (and there is > a huge amount about Berouilli nos in Henri Cohen's latest book too) > which suggests that doing a cython implementation would not be hard. > > Maybe this is time for a repeat performance of the partitions > competition with M**ca! The complexity mostly depends on the precision one uses in computing a certain Euler product approximation to zeta and also the number of factors in the product. If you look at the PARI source code the comments do *not* inspire confidence in its correctness. I had a student give a provable bound on precision and number of factors needed and wasn't able to get anything as good as what PARI uses. Here's the funny part of the PARI code (in trans3.c): /* 1.712086 = ??? */ t = log( gtodouble(d) ) + (n + 0.5) * log(n) - n*(1+log2PI) + 1.712086; -- William --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
On May 2, 2008, at 3:43 PM, Bill Hart wrote: > I think the asymptotics aren't going to go our way if we use pari. It > takes 11s for 10^5 and I've been sitting here for quite a few minutes > and didn't get 10^6 yet. So far I have on a 2.6GHz opteron: sage: time x = bernoulli(6) Wall time: 3.79 sage: time x = bernoulli(12) Wall time: 16.97 sage: time x = bernoulli(24) Wall time: 118.24 sage: time x = bernoulli(48) Wall time: 540.25 and I'll report back with 96 hopefully within an hour. david --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
On Fri, May 2, 2008 at 12:41 PM, David Harvey <[EMAIL PROTECTED]> wrote:
>
>
> On May 2, 2008, at 3:40 PM, William Stein wrote:
>
> > Also, when I tried
> >
> > bernoulli(10^7+2)
> >
> > directly in Sage there were a couple of issues that arose, since
> > that command
> > is much more designed for smaller input. I fixed those small issues.
> > I guess we'll see in a week ..
>
> I hope you did:
>
> sage: x = bernoulli(10^7 + 2)
>
> and not
>
> sage: bernoulli(10^7 + 2)
>
> david
I did:
t=cputime(); pari.allocatemem(); pari.allocatemem();
pari.allocatemem(); pari.allocatemem(); pari.allocatemem();
pari.allocatemem(); pari.allocatemem(); pari.allocatemem(); b =
bernoulli(10^7+2, algorithm='pari'); b.save('bern.sobj');
save(t,'time.sobj')
after patching Sage to always use the PARI C library if algorithm='pari'.
-- William
--~--~-~--~~~---~--~~
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[sage-devel] Re: Computing large Bernoulli numbers
On May 2, 2008, at 3:45 PM, William Stein wrote: > The complexity mostly depends on the precision one uses in > computing a certain Euler product approximation to zeta > and also the number of factors in the product. If you look > at the PARI source code the comments do *not* inspire confidence in > its correctness. I had a student give a provable bound on precision > and number of factors needed and wasn't able to get anything > as good as what PARI uses. > > Here's the funny part of the PARI code (in trans3.c): > > /* 1.712086 = ??? */ > t = log( gtodouble(d) ) + (n + 0.5) * log(n) - n*(1+log2PI) + > 1.712086; One way to check it is to use the bernoulli_mod_p_single() function, which computes B_k mod p for a single p and k, and uses a completely independent algorithm. sage: x = bernoulli(24) sage: p = next_prime(50) sage: bernoulli_mod_p_single(p, 24) 498812 sage: x % p 498812 sage: p = next_prime(10^6) sage: bernoulli_mod_p_single(p, 24) 841174 sage: x % p 841174 So I would say the answer is correct. david --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
On Fri, May 2, 2008 at 12:55 PM, David Harvey <[EMAIL PROTECTED]> wrote: > > > On May 2, 2008, at 3:45 PM, William Stein wrote: > > > The complexity mostly depends on the precision one uses in > > computing a certain Euler product approximation to zeta > > and also the number of factors in the product. If you look > > at the PARI source code the comments do *not* inspire confidence in > > its correctness. I had a student give a provable bound on precision > > and number of factors needed and wasn't able to get anything > > as good as what PARI uses. > > > > Here's the funny part of the PARI code (in trans3.c): > > > > /* 1.712086 = ??? */ > > t = log( gtodouble(d) ) + (n + 0.5) * log(n) - n*(1+log2PI) + > > 1.712086; > > One way to check it is to use the bernoulli_mod_p_single() function, > which computes B_k mod p for a single p and k, and uses a completely > independent algorithm. > > sage: x = bernoulli(24) > > sage: p = next_prime(50) > sage: bernoulli_mod_p_single(p, 24) > 498812 > sage: x % p > 498812 > > sage: p = next_prime(10^6) > sage: bernoulli_mod_p_single(p, 24) > 841174 > sage: x % p > 841174 > > So I would say the answer is correct. > > david I've done numerous similar tests, and I definitely don't think PARI is giving wrong answers. The issue is just that I've written a paper to generalize the algorithm to generalized Bernoulli numbers, and was very annoyed that I couldn't prove that even the algorithm used by PARI worked. -- William --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
Funny this should come up. William just gave a take-home midterm in which we had to predict the runtime for various computations, so I wrote some generic code to help. According to my code, and some liberal assumptions, it should take 5.1 days. I've attached the plots that show the curves I fit to some runtime data (x-axis is log(n,1.5) y-axis is seconds). However, this same code predicted that computing the determinant of a 1x1 matrix with single-digit entries would take 20 hours, but it really took 30 hours. So my estimates are not to be trusted too much as the numbers grow... On Fri, 2 May 2008, David Harvey wrote: > > > On May 2, 2008, at 3:43 PM, Bill Hart wrote: > >> I think the asymptotics aren't going to go our way if we use pari. It >> takes 11s for 10^5 and I've been sitting here for quite a few minutes >> and didn't get 10^6 yet. > > So far I have on a 2.6GHz opteron: > > sage: time x = bernoulli(6) > Wall time: 3.79 > > sage: time x = bernoulli(12) > Wall time: 16.97 > > sage: time x = bernoulli(24) > Wall time: 118.24 > > sage: time x = bernoulli(48) > Wall time: 540.25 > > and I'll report back with 96 hopefully within an hour. > > david > > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~--- <>
[sage-devel] Re: Computing large Bernoulli numbers
On May 2, 2008, at 4:08 PM, [EMAIL PROTECTED] wrote: > Funny this should come up. William just gave a take-home midterm > in which we had to predict the runtime for various computations, so > I wrote some generic code to help. According to my code, and some > liberal assumptions, it should take 5.1 days. I've attached the > plots that show the curves I fit to some runtime data (x-axis is log > (n,1.5) y-axis is seconds). Sorry, could you please say more precisely what the two axes are? I'm seeing negative time the way I interpret your statement. david --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
Sorry, the y-axis in the lower plot is log(time in seconds). On Fri, 2 May 2008, David Harvey wrote: > > > On May 2, 2008, at 4:08 PM, [EMAIL PROTECTED] wrote: > >> Funny this should come up. William just gave a take-home midterm >> in which we had to predict the runtime for various computations, so >> I wrote some generic code to help. According to my code, and some >> liberal assumptions, it should take 5.1 days. I've attached the >> plots that show the curves I fit to some runtime data (x-axis is log >> (n,1.5) y-axis is seconds). > > Sorry, could you please say more precisely what the two axes are? I'm > seeing negative time the way I interpret your statement. > > david > > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] RFC: article for OpenWetWare
I am more or less done my draft of a Sage/Cython article for OpenWetWare. I think this is a good minor opportunity to expose a different community to Sage. The bioinformatics community is already fairly pro-open-source, and OpenWetWare readers are self-selected to be more so. Before it is made "live" and linked to, I would be interested in comments: http://openwetware.org/wiki/User:Marshall_Hampton/Sage -M. Hampton On May 1, 9:21 am, mhampton <[EMAIL PROTECTED]> wrote: > Recently I read a nice article on > OpenWetWare:http://openwetware.org/wiki/Julius_B._Lucks/Projects/Python_All_A_Sci... > and after writing to the author about Sage he encouraged me to write > something on O.W.W. about Sage. I mentioned this in the sage-devel > IRC room a couple of weeks ago and asked if anyone would like to > help. This is a more formal advertisement for involvement. > > If you are in William Stein's 480 class, contributing to this may > satisfy some sort of requirement for that, but you should clarify that > with him directly. > > OpenWetWare's audience is mainly scientists in biology and > bioinformatics. The article linked to above already does a good job > of explaining the biopython; I will write something about the added > value of using biopython in Sage, with some of our other visualization > tools like JMol. > > There are two main areas where I could use a little help: 1) Cython > and 2) R/scipy.stats. If I have to, I can come up with some examples > myself. If anyone out there has a biological background and can think > of a short example with Cython or statistics in sage, that would be > great. Even better would be an interact example; I might use my > coalescent example > athttp://wiki.sagemath.org/interact#head-62b94dd3fb456a549958ee2978cd3b... > but it would be nice to have something simpler. > > I am also open to other ideas for highlighting advantages of Sage, > particularly if they are relevant to this audience. > > I would like to get this done pretty quickly, ideally within a week. > > Cheers, > > Marshall Hampton > University of Minnesota, Duluth > Department of Mathematics and Statistics and the Integrated > Biosciences Program --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
One more data point (2.6GHz opteron): sage: time x = bernoulli(6) Wall time: 3.79 sage: time x = bernoulli(12) Wall time: 16.97 sage: time x = bernoulli(24) Wall time: 118.24 sage: time x = bernoulli(48) Wall time: 540.25 sage: time x = bernoulli(96) Wall time: 2436.06 The ratios between successive times are: 4.47757255936675 6.96758986446671 4.56909675236806 4.50913465987969 If we guess that it's "really" 4.5, then the complexity is N^(log (4.5) / log(2)) = N^2.17. This is puzzling; I thought the algorithm was supposed to be better than quadratic. Does anyone know what the theoretical complexity is supposed to be? Anyway, extrapolating gives about 4.5 days, pretty much the same as what Tom estimates. I'm going to start it running now. david --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: Does anyone else have this matrix problem
On May 2, 2008, at 11:25 AM, mabshoff wrote: > On May 2, 8:06 pm, Jason Grout <[EMAIL PROTECTED]> wrote: >> William Stein wrote: > > Hi, > >> Steal the CPU detection code from ATLAS and use that to test to >> see if >> the processor we're running on is the same as the processor we >> compiled >> for? That seems like a bit much. > > You really don't want to do that - believe me, I have seen and > improved the ATLAS cpu detection code and it requires an assembler to > work. Other than that it is overblown and we can cook up something > better and simpler with a three line bash script ;) > >> How about compiling a generic binary (i.e., minimal >> optimizations)? Is >> that possible with ATLAS and the other programs? > > Yes, but then something else will break. Depending on the compiler you > use it just uses SSE2 instructions unless you specifically tell the > compiler not to use it. And attempting to dix that via CFLAGS and > CPPFLAGS is not a good idea. Somebody needs to find some pre-SSE2 > hardware and donate it to William so we can build a "last resort" > binary. Anything else will likely not work. > > tseug from IRC did build Sage 3.0 on some Duron laptop and it took 22 > hours, so building from source is generally not a good idea for people > with low end hardware, but since we cannot and will not likely provide > binaries for a wide range of distributions for non-SSE2 hardware due > to limited and usually slow hardware it is something we will have to > deal with for a while. Could we use a bunch on non-SSE2 Athlons with > decent, i.e. 1GB RAM, this would be doable. I'm sure the UW Math department has machines that old which we could get for free when the swap out hardware. (One would probably want to add some RAM though, the box I used to have in my office only had 256 MB). - Robert --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
Here is some more information about the machine used to compute this: -- Forwarded message -- From: Oleksandr Pavlyk <[EMAIL PROTECTED]> Date: Fri, May 2, 2008 at 4:29 PM Subject: Re: Today We Broke the Bernoulli Record: From the Analytical Engine to Mathematica To: didier deshommes <[EMAIL PROTECTED]> Hi Didier, I used Linux, with 64 bit AMD processor: AMD Opteron(tm) Processor 250 cpu MHz : 1000.000 cache size : 1024 KB and 8GB of memory, but as I say in the blog, I did not use that much. The calculations were done using development build of Mathematica, but calculations will go through in any flavor of Mathematica version 6 as well, to the best of my knowledge. Just run Timing[ result = BernoulliB[10^7]; ] It will take about twice longer on 32-bit processors, thus about 2 weeks. Please do not hesitate to ask further questions. Sincerely, Oleksandr Pavlyk On Fri, May 2, 2008 at 2:12 PM, didier deshommes <[EMAIL PROTECTED]> wrote: > Hi Dr. Pavlyk, > My question is in referrence to your blog post: > > http://blog.wolfram.com/2008/04/29/today-we-broke-the-bernoulli-record-from-the-analytical-engine-to-mathematica/ > > - Do you have the specs of the machine you ran this off? CPU, memory, etc. > - I assume this function is in the development version of mathematica? > > Thanks for your informative post! > > didier > On Fri, May 2, 2008 at 3:43 PM, didier deshommes <[EMAIL PROTECTED]> wrote: > On Fri, May 2, 2008 at 3:40 PM, William Stein <[EMAIL PROTECTED]> wrote: > > > > On Fri, May 2, 2008 at 11:34 AM, Fredrik Johansson > > <[EMAIL PROTECTED]> wrote: > > > > > > > > Oleksandr Pavlyk reports on the Wolfram Blog that he has computed the > > > 10 millionth Bernoulli number using Mathematica: > > > > http://blog.wolfram.com/2008/04/29/today-we-broke-the-bernoulli-record-from-the-analytical-engine-to-mathematica/ > > > > > > How does sage's Bernoulli number implementation compare? I'd like to > > > see bernoulli(10^7) in sage beating Mathematica's time. And then > > > computing the 20 millionth Bernoulli number... > > > > I couldn't find any information about the hardware that guy used. > > 64-bit? 32-bit? > > 1.8Ghz or 3Ghz? Could somebody write and ask? > > I did earlier, and I hope he will answer. > > didier > > > > > > > Also, when I tried > > > > bernoulli(10^7+2) > > > > directly in Sage there were a couple of issues that arose, since that > command > > is much more designed for smaller input. I fixed those small issues. > > I guess we'll see in a week .. > > > > William > > > > > > > > > > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
On May 2, 10:34 pm, "didier deshommes" <[EMAIL PROTECTED]> wrote: > Here is some more information about the machine used to compute this: Hi, > Hi Didier, > > I used Linux, with 64 bit AMD processor: > > AMD Opteron(tm) Processor 250 > cpu MHz : 1000.000 > cache size : 1024 KB FYI: That CPU runs at 2.4GHz when not throttled, like in this case. I assume that it would run at full speed during the computation :) > and 8GB of memory, but as I say in the blog, I did > not use that much. Yep. Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: Does anyone else have this matrix problem
On May 2, 10:28 pm, Robert Bradshaw <[EMAIL PROTECTED]> wrote: > On May 2, 2008, at 11:25 AM, mabshoff wrote: > > Could we use a bunch on non-SSE2 Athlons with > > decent, i.e. 1GB RAM, this would be doable. > > I'm sure the UW Math department has machines that old which we could > get for free when the swap out hardware. (One would probably want to > add some RAM though, the box I used to have in my office only had 256 > MB). That would be nice. RAM is cheap, so I would guess it is mostly about finding a physical place for the boxen to stash. > - Robert Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: mercurial --> plain text --> mercurial
On May 2, 2008, at 2:39 AM, mabshoff wrote: > On Apr 29, 7:14 am, "William Stein" <[EMAIL PROTECTED]> wrote: >> On Tue, Apr 22, 2008 at 12:53 AM, mabshoff > > >> Hi, >> >> I've made a trac ticket for this, since it seems to have got stalled: >> >>http://trac.sagemath.org/sage_trac/ticket/3052 >> >> William > > Robert, > > I have come across a case that might cause some trouble: If you change > the permissions on a file you need to make a mercurial checking since > hg claims the repo has been changed, which is true. But export that > changeset and it is empty. GIT handles renames and permission changes > and also prints those status changes in the log. So, does hg do > anything about those changes internally and is it just the log that is > insufficient? In the end it will not matter much since we can just add > a list of files whose permissions have to be changed and restore them > if it causes trouble. In case of spkg-install & friends for example > that is automatically taken care of by first making the scripts > executable before they are being run by sage-$FOO. Yep, that is one of the things I've noticed. The patch comment is insufficient in this case. - Robert --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
I did some computations using von Staudt's theorem and up to 40 no errors. Of course that doesn't prove anything for much larger n. Bill. On 2 May, 21:04, "William Stein" <[EMAIL PROTECTED]> wrote: > On Fri, May 2, 2008 at 12:55 PM, David Harvey <[EMAIL PROTECTED]> wrote: > > > On May 2, 2008, at 3:45 PM, William Stein wrote: > > > > The complexity mostly depends on the precision one uses in > > > computing a certain Euler product approximation to zeta > > > and also the number of factors in the product. If you look > > > at the PARI source code the comments do *not* inspire confidence in > > > its correctness. I had a student give a provable bound on precision > > > and number of factors needed and wasn't able to get anything > > > as good as what PARI uses. > > > > Here's the funny part of the PARI code (in trans3.c): > > > > /* 1.712086 = ??? */ > > > t = log( gtodouble(d) ) + (n + 0.5) * log(n) - n*(1+log2PI) + > > > 1.712086; > > > One way to check it is to use the bernoulli_mod_p_single() function, > > which computes B_k mod p for a single p and k, and uses a completely > > independent algorithm. > > > sage: x = bernoulli(24) > > > sage: p = next_prime(50) > > sage: bernoulli_mod_p_single(p, 24) > > 498812 > > sage: x % p > > 498812 > > > sage: p = next_prime(10^6) > > sage: bernoulli_mod_p_single(p, 24) > > 841174 > > sage: x % p > > 841174 > > > So I would say the answer is correct. > > > david > > I've done numerous similar tests, and > I definitely don't think PARI is giving wrong answers. > The issue is just that I've written a paper to generalize > the algorithm to generalized Bernoulli numbers, and was > very annoyed that I couldn't prove that even the algorithm > used by PARI worked. > > -- William --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: mercurial --> plain text --> mercurial
Robert Bradshaw wrote: > On May 2, 2008, at 2:39 AM, mabshoff wrote: > >> On Apr 29, 7:14 am, "William Stein" <[EMAIL PROTECTED]> wrote: >>> On Tue, Apr 22, 2008 at 12:53 AM, mabshoff >> >> >>> Hi, >>> >>> I've made a trac ticket for this, since it seems to have got stalled: >>> >>>http://trac.sagemath.org/sage_trac/ticket/3052 >>> >>> William >> Robert, >> >> I have come across a case that might cause some trouble: If you change >> the permissions on a file you need to make a mercurial checking since >> hg claims the repo has been changed, which is true. But export that >> changeset and it is empty. GIT handles renames and permission changes >> and also prints those status changes in the log. So, does hg do >> anything about those changes internally and is it just the log that is >> insufficient? In the end it will not matter much since we can just add >> a list of files whose permissions have to be changed and restore them >> if it causes trouble. In case of spkg-install & friends for example >> that is automatically taken care of by first making the scripts >> executable before they are being run by sage-$FOO. > > Yep, that is one of the things I've noticed. The patch comment is > insufficient in this case. Can the git-style diffs somehow help? hg diff --git Jason --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Fwd: Does anyone else have this matrix problem
The Sage lab on UW campus has a lot of shelf space :-) On Fri, May 2, 2008 at 1:43 PM, mabshoff <[EMAIL PROTECTED]> wrote: > > > > On May 2, 10:28 pm, Robert Bradshaw <[EMAIL PROTECTED]> > wrote: > > > On May 2, 2008, at 11:25 AM, mabshoff wrote: > > > > > > > Could we use a bunch on non-SSE2 Athlons with > > > decent, i.e. 1GB RAM, this would be doable. > > > > I'm sure the UW Math department has machines that old which we could > > get for free when the swap out hardware. (One would probably want to > > add some RAM though, the box I used to have in my office only had 256 > > MB). > > That would be nice. RAM is cheap, so I would guess it is mostly about > finding a physical place for the boxen to stash. > > > - Robert > > Cheers, > > Michael > > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: RFC: article for OpenWetWare
Hi! On May 2, 10:17 pm, mhampton <[EMAIL PROTECTED]> wrote: > I am more or less done my draft of a Sage/Cython article for > OpenWetWare. I think this is a good minor opportunity to expose a > different community to Sage. The bioinformatics community is already > fairly pro-open-source, and OpenWetWare readers are self-selected to > be more so. Before it is made "live" and linked to, I would be > interested in comments: > > http://openwetware.org/wiki/User:Marshall_Hampton/Sage I like this article! Obviously you took into account what audience you'll have. This is a wise thing to do. In the reddit-blog on William's ISSAC-abstract, some commentors seem to have the impression that Sage mainly is algebra, hence, not a good tool for engineers. Perhaps one may point them to your article. Yours Simon --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
The theoretical complexity of all the algorithms that rely on recurrences is supposed to be n^2. But this doesn't take into account the size of the numbers themselves. When you do this they are all about n^3 as far as I can see. You can use Ramanujan identities, the Akiyama-Tanigawa algorithm, the identity used by Lovelace, but all are n^3 or so. The theoretical complexity of the version using the zeta function looks something like n log n steps at precision n log n, i.e. time n^2 (log n)^2. Bill. On 2 May, 21:24, David Harvey <[EMAIL PROTECTED]> wrote: > One more data point (2.6GHz opteron): > > sage: time x = bernoulli(6) > Wall time: 3.79 > > sage: time x = bernoulli(12) > Wall time: 16.97 > > sage: time x = bernoulli(24) > Wall time: 118.24 > > sage: time x = bernoulli(48) > Wall time: 540.25 > > sage: time x = bernoulli(96) > Wall time: 2436.06 > > The ratios between successive times are: > > 4.47757255936675 > 6.96758986446671 > 4.56909675236806 > 4.50913465987969 > > If we guess that it's "really" 4.5, then the complexity is N^(log > (4.5) / log(2)) = N^2.17. This is puzzling; I thought the algorithm > was supposed to be better than quadratic. Does anyone know what the > theoretical complexity is supposed to be? > > Anyway, extrapolating gives about 4.5 days, pretty much the same as > what Tom estimates. I'm going to start it running now. > > david --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Debian package build failure for gfan with 3.0.1alpha1
On May 3, 4:25 am, "Michael Abshoff" <[EMAIL PROTECTED]> wrote: > On Fri, May 2, 2008 at 6:16 PM, Timothy G Abbott <[EMAIL PROTECTED]> wrote: > > > I attempted to build the 3.0.1alpha1 packages for Debian, but it doesn't > > build, apparently due to some type errors. The build log is attached -- > > I'd appreciate any guesses as to what's going on here. > > >-Tim Abbott > > Hi Tim, > > we updated gfan a while ago, so this surprises me. > > > > The failure is: > > lp_cdd.cpp:1186: error: cannot convert 'double*' to 'const __mpq_struct*' > for argument '2' to 'vo /dev/cdrom: open failed: Read-only file system > Attempt to close device '/dev/cdrom' which is not open. > > I have no clue what is going on there and it seems very, very odd. Any > chance you could try building a vanilla gfan? > > Let me think about this some more, maybe I can come up with something. > I got it! -IGMPRATIONAL should be -DGMPRATIONAL Do not know where that came from in your package. Francois --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: scilab
I think this is interesting too but was unable to compile it nor get the binary to work. On Fri, May 2, 2008 at 2:52 PM, Hector Villafuerte <[EMAIL PROTECTED]> wrote: > > On Fri, May 2, 2008 at 10:31 AM, William Stein <[EMAIL PROTECTED]> wrote: > [...] > > > Very interestingly, somebody posted that the next major release of > > SciLab will be > > GPL-compatible. See > > http://www.scilab.org/download/index_download.php?page=CHANGES_5.0-beta-1 > > > > This means there is potential for collaboration between the Sage and > > SciLab projects. > > I.e., we could potentially share code with them, etc. > > > > -- William > > > This is very interesting indeed. In what language is Scilab developed? > I assume it's C/C++. > > -- > Hector > > > > > > --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 3.0.1-alpha1 released!
Hi, built fine of Arch linux 32 bit without any change, didn't run tests yet but will soon... anyway small off-topic - I was making spkg for R 2.7 and RPy 1.0.2 to see if it would work (2.7 have some nice Cairo graphics driver in addition to X11 and others, examples from wiki already works), but --- I noticed that RPy 1.0.1 included in r-2.6.1.p15 contains whole Mercurial repo (.hg and .hgignore), is this normal practice to include repo for small packages for history or it got to spkg by mistake? cheers, Andrzej --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Computing large Bernoulli numbers
Actually, it might be n/log(n) steps, so the time might be something like n^2 though there are other terms involved. Bill. On 3 May, 00:30, Bill Hart <[EMAIL PROTECTED]> wrote: > The theoretical complexity of all the algorithms that rely on > recurrences is supposed to be n^2. But this doesn't take into account > the size of the numbers themselves. When you do this they are all > about n^3 as far as I can see. You can use Ramanujan identities, the > Akiyama-Tanigawa algorithm, the identity used by Lovelace, but all are > n^3 or so. > > The theoretical complexity of the version using the zeta function > looks something like n log n steps at precision n log n, i.e. time n^2 > (log n)^2. > > Bill. > > On 2 May, 21:24, David Harvey <[EMAIL PROTECTED]> wrote: > > > One more data point (2.6GHz opteron): > > > sage: time x = bernoulli(6) > > Wall time: 3.79 > > > sage: time x = bernoulli(12) > > Wall time: 16.97 > > > sage: time x = bernoulli(24) > > Wall time: 118.24 > > > sage: time x = bernoulli(48) > > Wall time: 540.25 > > > sage: time x = bernoulli(96) > > Wall time: 2436.06 > > > The ratios between successive times are: > > > 4.47757255936675 > > 6.96758986446671 > > 4.56909675236806 > > 4.50913465987969 > > > If we guess that it's "really" 4.5, then the complexity is N^(log > > (4.5) / log(2)) = N^2.17. This is puzzling; I thought the algorithm > > was supposed to be better than quadratic. Does anyone know what the > > theoretical complexity is supposed to be? > > > Anyway, extrapolating gives about 4.5 days, pretty much the same as > > what Tom estimates. I'm going to start it running now. > > > david --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Sage 3.0.1-alpha1 released!
On May 3, 1:50 am, Andrzej Giniewicz <[EMAIL PROTECTED]> wrote: > Hi, > > built fine of Arch linux 32 bit without any change, didn't run tests > yet but will soon... > > anyway small off-topic - I was making spkg for R 2.7 and RPy 1.0.2 to > see if it would work (2.7 have some nice Cairo graphics driver in > addition to X11 and others, examples from wiki already works), but --- > I noticed that RPy 1.0.1 included in r-2.6.1.p15 contains whole > Mercurial repo (.hg and .hgignore), is this normal practice to include > repo for small packages for history or it got to spkg by mistake? Yes, that is normal and the hg repo should not have the sources under revision control. There are exceptions to that rule, but rpy isn't one of those. Now that R 2.7 is out we should upgrade and also move rpy into its own top level spkg. This is now #3086 > cheers, > Andrzej Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Debian package build failure for gfan with 3.0.1alpha1
On May 2, 7:31 pm, Francois <[EMAIL PROTECTED]> wrote: > I got it! -IGMPRATIONAL should be -DGMPRATIONAL > Do not know where that came from in your package. > > Francois Indeed; that was a typo in my package introduced when I fixed a different bug. It would have probably taken me a long time to notice that. Thanks! -Tim Abbott --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: Debian package build failure for gfan with 3.0.1alpha1
On May 3, 6:41 am, tabbott <[EMAIL PROTECTED]> wrote: > On May 2, 7:31 pm, Francois <[EMAIL PROTECTED]> wrote: > > > I got it! -IGMPRATIONAL should be -DGMPRATIONAL > > Do not know where that came from in your package. > > > Francois > > Indeed; that was a typo in my package introduced when I fixed a > different bug. It would have probably taken me a long time to notice > that. Thanks! > > -Tim Abbott Hi Tim, I am currently starting to put together 3.0.1.final - so if you have a last minute fix ready I can merge it and the palp ticket you just opened into 3.0.1. Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: scilab
On Fri, May 2, 2008 at 5:41 PM, David Joyner <[EMAIL PROTECTED]> wrote: > > I think this is interesting too but was unable to compile it nor get > the binary to work. > So I downloaded these two packages for scilab-5.0-beta-1: http://www.scilab.org/download/5.0-beta-1/prerequirements-scilab-5.0-beta-1-src.tar.gz http://www.scilab.org/download/5.0-beta-1/scilab-5.0-beta-1-src.tar.gz Doing ./configure kept failing until I got everything it needed, except matio (http://sourceforge.net/projects/matio) since I couldn't find it in Ubuntu 8.04. Summarizing, here's what needs to be done: $ sudo apt-get install gfortran sun-java6-jdk ant libncurses5-dev ocaml-native-compilers libxml2-dev lapack3-dev atlas3-base-dev libpcre3-dev tcl-dev tk-dev These are the dependencies... talking about multiple languages: fortran, java, ocaml, tcl/tk... I found this link after all that experimentation: http://wiki.scilab.org/Dependencies_of_Scilab_5.X Package: gfortran -- Description: The GNU Fortran 95 compiler Package: sun-java6-jdk -- Description: Sun Java(TM) Development Kit (JDK) 6 Package: ant -- Description: Java based build tool like make Package: libncurses5-dev -- Description: Developer's libraries and docs for ncurses Package: ocaml-native-compilers -- Description: Native code compilers of the ocaml suite (the .opt ones) Package: libxml2-dev -- Description: Development files for the GNOME XML library Package: lapack3-dev -- Description: library of linear algebra routines 3 - static version Package: atlas3-base-dev -- Description: Automatically Tuned Linear Algebra Software,generic static Package: libpcre3-dev -- Description: Perl 5 Compatible Regular Expression Library - development files Package: tcl-dev -- Description: The Tool Command Language (default version) - development files Package: tk-dev -- Description: The Tk toolkit for Tcl and X11 (default version) - development files $ ./configure --without-matio $ make all It build successfully, but then... $ ./scilab-bin /home/hector/scilab/scilab-5.0-beta-1/.libs/lt-scilab-bin: error while loading shared libraries: libjava.so: cannot open shared object file: No such file or directory This is all running within VMware with Mac OS X as host system: $ uname -a Linux ah-kan 2.6.24-16-server #1 SMP Thu Apr 10 13:58:00 UTC 2008 i686 GNU/Linux $ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description:Ubuntu 8.04 Release:8.04 Codename: hardy -- Hector --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Sage 3.0.1.rc0 released!
Hello, This is the end of the 3.0.1 release cycle. The build was announced in IRC about eight hours ago, but since I took a long nap in the meantime I never posted to sage-devel ;) Gary's pbuild has been improved and three bugs have been fixed. Please try it out again for feedback. To use pbuild export SAGE_PBUILD=yes before building Sage. The number of threads used during the build of the Sage library is set via SAGE_BUILD_THREADS, i.e. export SAGE_BUILD_THREADS=8 for eight threads. Switching between pbuild and normal build is not possible in all cases, so in case of problems nuke the build directory on devel/sage. Things should "just work" in this release [famous last words], but there are some reported oddities with pexpect behaving badly. We have so far been unable to reproduce and of those issue on a local system [Gary claims testdoc.py hangs for him on sage.math - but it doesn't for me], so if you see anything please let us know. Sources and binaries are in the usual place: http://sage.math.washington.edu/home/mabshoff/release-cycles-3.0.1/sage-3.0.1.rc0.tar http://sage.math.washington.edu/home/mabshoff/release-cycles-3.0.1/sage-3.0.1.rc0-sage.math-only-x86_64-Linux.tar.gz This is the end of the release cycle. A handful more patches are planned for 3.0.1.final. Anything non-blocker will be considered for 3.0.2. Cheers, Michael Merged in rc0: #2755: Andrey Novoseltsev: lattice_polytope.py update #3060: Marshall Hampton, Michael Abshoff: update optional biopython package to 1.45 release #3062: Timothy Clemans: implement __oct__ special method for the integers #3070: Robert Miller: bug in SymmetricGroup(1).cayley_graph() #3071: Gary Furnish: Using pbuild does not create site-packages sage symlink #3072: Willem Jan Palenstijn: sage -i numeric-24.2 (and all other experimental packages) fails #3074: Robert Bradshaw: update Cyton to the 0.9.6.14 release #3076: Michael Abshoff: spkg-debian in extcode spkg not executable #3077: Gary Furnish: pbuild does not return properly on failure #3078: Willem Jan Palenstijn: sage's spkg-install doesn't return failure if build failed #3082: William Stein: sage-3.0.1.alpha1: a twist.py doctest failure --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
