Re: [sage-combinat-devel] Re: combinat.sagemath.org
On Wed, Mar 22, 2017 at 11:20 AM, Anne Schilling wrote: > Hi! > > The website http://combinat.sagemath.org/ seems to be down right now. I > agree with Nicolas, that it would be good to keep this website. For example, > we had > a list of all publications citing sage-combinat etc. there. This should be > kept! What is your plan for hosting this content and website? I'm not going to do it. I am willing to point combinat.sagemath.org at an ip adddress... > The Wiki page looks very different from before! It used to start with a list > of upcoming/recent events. Now it just has some links to disconnected > websites. What is "the wiki page"? https://wiki.sagemath.org/ still starts with a list of upcoming/recent events... > > Best, > > Anne > > > On Wednesday, March 22, 2017 at 6:14:47 AM UTC-7, Matthew Rennekamp wrote: >> >> Hey, all. >> It's been awhile since this discussion. Are there any more Combinat people >> that want these files open, or possibly the subdomain pointing to the >> SageWiki page? >> I've changed my mind to support whoever administers the GitHub account to >> move files on there, as long as there are more clear reasons for eg. forked >> repos like MathJax, which seem to be there just because they can. So, if >> there won't be a combinat.sagemath.org website, what does everyone on this >> mailing list think of putting it all on GitHub? > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at https://groups.google.com/group/sage-combinat-devel. > For more options, visit https://groups.google.com/d/optout. -- William (http://wstein.org) -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-combinat-devel] Re: combinat.sagemath.org
On Sat, Jan 14, 2017 at 12:03 PM, Nicolas M. Thiery wrote: > Nevertheless, Sage-Combinat and http://combinat.sagemath.org/ are > cited in many places, including 100+ publications. So we want this URL > to keep working, for historical reasons and future work. > > Hence my advocacy for keeping the wiki pages > http://wiki.sagemath.org/Combinat/* where they are, and making sure > the URL http://combinat.sagemath.org/ redirects there. Harald Schilly and I can both instantly point the DNS for combinat.sagemath.org anywhere you want -- just tell us. Regarding physical hardware, a lot is just turned off due to the UPS breaking, and other issues (lack of manpower)... William -- William (http://wstein.org) -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-combinat-devel] combinat.sagemath.org
On Thu, Jan 12, 2017 at 7:38 PM, Matthew Rennekamp wrote: > I'm working on the www.sagemath.org & SageWiki. What happened to > combinat.sagemath.org? Are there other places those files are stored? The machine exists, and I have a backup copy of all files. As with sage.math.washington.edu, let me know if you're interested in going through and collating and cleaning things up, and I can get you access... William > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at https://groups.google.com/group/sage-combinat-devel. > For more options, visit https://groups.google.com/d/optout. -- William (http://wstein.org) -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: [sage-combinat-devel] Multiple versions of SageMath's documentation online
Hi, I just checked and searching for sage help online in Google now frequently returns results at doc.sagemath.org. Yeah! William On Mon, Aug 22, 2016 at 11:25 PM, Nicolas M. Thiery wrote: > On Mon, Aug 22, 2016 at 09:10:55AM -0700, Samuel Lelievre wrote: >>I guess once the Google indexing of doc.sagemath.org is solved, >>we should probably remove this redirection. > > No rush, but that would be nice indeed. It should be easy to add a > banner on the old combinat doc to warn that it's outdated. > >>It would be worth to open a Sage trac ticket dedicated >>to moving the sage-combinat tutorials into Sage proper. > > That's: > > http://trac.sagemath.org/ticket/16810 > > with this chunk completed recently: > > https://trac.sagemath.org/ticket/20618 > > Cheers, > Nicolas > -- > Nicolas M. Thiéry "Isil" > http://Nicolas.Thiery.name/ > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-de...@googlegroups.com. > Visit this group at https://groups.google.com/group/sage-devel. > For more options, visit https://groups.google.com/d/optout. -- William (http://wstein.org) -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-combinat-devel] Re: Copying installations on SMC
On Sat, Jun 13, 2015 at 9:04 AM, Darij Grinberg wrote: > Hi Anne, > > ah, this got updated while I wasn't looking :) Thanks for the reminder! > It got updated because you were looking :-) > > Best regards, > Darij > > On Sat, Jun 13, 2015 at 5:58 PM, Anne Schilling > wrote: > > Hi Darij, > > > >> Step 3: maybe explain how to tell when the copying is complete? I > >> think it took more than 3min for me (I used "du -s" to check on it). > >> > >> Step 4: > >> IOError: [Errno 122] Disk quota exceeded > >> > >> What should I do? > > > > Perhaps you skipped Step 1?? > > > > 1. Open the SMC project that you intend to use for development, or > create a new project. Send an email with THE LINK TO YOUR PROJECT (under > Settings) to h...@sagemath.com and say that you are using > > this project for legit Sage development. Wait for the reply before > continuing. You MUST DO THIS SINCE DEFAULT PROJECTS DO NOT HAVE SUFFICIENT > DISK SPACE. > > > > Best, > > > > Anne > > > > -- > > You received this message because you are subscribed to the Google > Groups "sage-combinat-devel" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to sage-combinat-devel+unsubscr...@googlegroups.com. > > To post to this group, send email to > sage-combinat-devel@googlegroups.com. > > Visit this group at http://groups.google.com/group/sage-combinat-devel. > > For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-combinat-devel. > For more options, visit https://groups.google.com/d/optout. > -- William (http://wstein.org) -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-combinat-devel] Sage Days 65 mini report
On Friday, June 12, 2015, Anne Schilling wrote: > Actually, Peter Tingley's Sage was not working due to some git problems > (committing on top of the develop branch)! That has been fixed. So it was > not really an install problem. > > The SageMathCloud was great for those who had trouble installing Sage on > their own computer. Sometimes we had connection issues to the SMC (the > wheel was just spinning). Franco gave a nice talk on how A fixed a bug that causes this today. Email me if you see it > to copy the latest version onto one's own Sage developer project. That > saves to actually run the install (so Darij, your "complaints" are not > really valid since copying only takes a few minutes). > > Best, > > Anne > > > > > On Jun 12, 2015, at 18:26, William Stein > wrote: > > > >> On Fri, Jun 12, 2015 at 1:28 PM, Franco Saliola > wrote: > >> > >> Here is a mini report on Sage Day 65. I'm not an organizer so this is > not > >> official. > >> Thanks to Anne Schilling for helping to prepare this. > >> > >> - 24 tickets on trac are tagged with `sagedays65` or `sd65`. Some of > these > >> have > >> been positively reviewed and marked as fixed. Some are waiting for > review > >> (hint, hint). Several of these tickets include contributions from new > >> users. > >> > >> - Installation troubles: > >> > >>- several people had a hard difficult time installing Sage on their > >> machines (8-10 people) > >> > >>- there were people who did not have a working development version on > >> their > >> machines by the end of the week (4-5 people); two of these people > were > >> the organizers of the Sage Days > > > > This is a bummer. It gives me even more motivation to make > > SageMathCloud Sage-developer friendly.I'm also curious if anybody > > has any -- possibly *radical* -- suggestions about how to address this > > problem using new ideas. > > > > > >> > >>- number of participants: 40 > >> > >>- some thing that really helped was the Sage Development Images > project > >> > >> - A possible warning to future organizers of Sage Days: We had good > internet > >> access, but the university network blocked all ssh connections! This > was > >> mainly resolved on the first day, but there were still some issues with > >> pulling/pushing through the `git trac` command. > >> > >> Franco > >> > >> -- > >> You received this message because you are subscribed to the Google > Groups > >> "sage-combinat-devel" group. > >> To unsubscribe from this group and stop receiving emails from it, send > an > >> email to sage-combinat-devel+unsubscr...@googlegroups.com > . > >> To post to this group, send email to > sage-combinat-devel@googlegroups.com . > >> Visit this group at http://groups.google.com/group/sage-combinat-devel. > >> For more options, visit https://groups.google.com/d/optout. > > > > > > > > -- > > William (http://wstein.org) > > > > -- > > You received this message because you are subscribed to the Google > Groups "sage-combinat-devel" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to sage-combinat-devel+unsubscr...@googlegroups.com > . > > To post to this group, send email to > sage-combinat-devel@googlegroups.com . > > Visit this group at http://groups.google.com/group/sage-combinat-devel. > > For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com . > To post to this group, send email to sage-de...@googlegroups.com > . > Visit this group at http://groups.google.com/group/sage-devel. > For more options, visit https://groups.google.com/d/optout. > -- Sent from my massive iPhone 6 plus. -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-combinat-devel] Sage Days 65 mini report
On Fri, Jun 12, 2015 at 1:28 PM, Franco Saliola wrote: > > Here is a mini report on Sage Day 65. I'm not an organizer so this is not > official. > Thanks to Anne Schilling for helping to prepare this. > > - 24 tickets on trac are tagged with `sagedays65` or `sd65`. Some of these > have > been positively reviewed and marked as fixed. Some are waiting for review > (hint, hint). Several of these tickets include contributions from new > users. > > - Installation troubles: > > - several people had a hard difficult time installing Sage on their > machines (8-10 people) > > - there were people who did not have a working development version on > their > machines by the end of the week (4-5 people); two of these people were > the organizers of the Sage Days This is a bummer. It gives me even more motivation to make SageMathCloud Sage-developer friendly.I'm also curious if anybody has any -- possibly *radical* -- suggestions about how to address this problem using new ideas. > > - number of participants: 40 > > - some thing that really helped was the Sage Development Images project > > - A possible warning to future organizers of Sage Days: We had good internet > access, but the university network blocked all ssh connections! This was > mainly resolved on the first day, but there were still some issues with > pulling/pushing through the `git trac` command. > > Franco > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-combinat-devel. > For more options, visit https://groups.google.com/d/optout. -- William (http://wstein.org) -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
[sage-combinat-devel] Re: [sage-devel] sequences in SageMath
On Mon, Jun 1, 2015 at 2:49 AM, Daniel Krenn wrote: > Dear all, > > similar to > graphs.some_graph > or to > codes.some_code > (and similar), I propose to introduce > sequences.some_sequence > which should provide a unified access point to all possible sequences in > SageMath. For example, there is fibonacci_sequence in > sage.combinat.combinat, binary_recurring_sequence (somewhere in > combinat) and various other code. Also there is sloane.[tab] with sloane sequences > > One motivation for creating this, is to include here many sequences, > which can be calculated term-by-term (from the previously calculated > ones, i.e., recursively) or where the first N terms can be calculated at > once efficiently. > Nevertheless, it can also provide an interface to sequences, where each > term can be calculated explicitly (without dealing with the previous ones). > > This posting is to discuss this new feature at this early stage (see > trac ticket #18565 [1] for a draft). > > - In this draft, all sequences are iterator/generator expressions > (finite or maybe infinite). This is to keep it simple. [*] > What do you think about this? > > - At the moment this module is in sage.combinat. Another option would be > to create sage.sequences and put it there. Any opinions on this? > > - In the trac ticket, the function fibonacci_sequence will be > deprecated, since this is then sequence.fibonacci(...). I am also happy > not to deprecate it and keep it as it is (only changing the code to > avoid code duplication) > > - I found a function fibonacci_xrange. It is completly unclear (to me) > from the name, what this function does (in particular, why "xrange" (and > not a simple "range"). For this reason, I propose to deprecate this > function (an alternative with the new sequences-interface is provided). > > - Should the oeis-functionality be included in some way (at some point)? > At the moment > iter(oeis(...).first_terms()) > comes closest. > > Best wishes > > Daniel > > [1] http://trac.sagemath.org/ticket/18565 > > [*] An alternative would be to create a class and do it in a similar way > as sage.combinat.words.Word (of course in this case much more has to be > done than now; (common base-class for words/sequences?!? ...not sure > what to think about this...)). > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-de...@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-devel. > For more options, visit https://groups.google.com/d/optout. -- William (http://wstein.org) -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
[sage-combinat-devel] bug report: "interval graph recognition"
This is a bug report from a Sage user...
===
Hi,
I would like to report a bug in an interval graph recognition
procedure. I am using Sage online (cloud.sagemath.com).
Here is the code:
d='GvGNp?'
G = Graph(d)
i = G.is_interval(certificate = True)
g2 = graphs.IntervalGraph(i.values())
g2.is_isomorphic(G)
Problem:
g2.is_isomorphic(G) gives "False"
print i gives "{0: (0, 6), 1: (1, 4), 2: (5, 12), 3: (2, 7), 4: (14,
16), 5: (15, 17), 6: (3, 10), 7: (11, 13)}"
Alternative software reports that the graph is not interval, while
sage reports that it is, but reported certificate does not match to
the tested graph.
Best regards,
Damian Bogdanowicz, PhD
Gdansk University of Technology, Gdansk, Poland
--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
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[sage-combinat-devel] Re: combinat.math.washington.edu
On Tue, Jan 6, 2015 at 1:40 PM, William Stein wrote: > On Sat, Jan 3, 2015 at 8:23 PM, William Stein wrote: >> Hi, >> >> The computer combinat.math.washington.edu is down... again. Sort of. >> It responds to ping requests, but I can't ssh in. > > A minor update: there are notifications about physical hardware > failures on the front of the machine, so it may be longer than > expected until combinat is running again. Hi, combinat.math.washington.edu is working again now as before. One local scratch disk seems to have failed. However, everything else seems to be working fine. I won't be messing with it for the next week or two, but plan to SMC-ify it at some point (I'll post in advance). In the meantime, I hope people will log in and use it! 64 cores. 192GB RAM. William -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
[sage-combinat-devel] Re: combinat.math.washington.edu
On Sat, Jan 3, 2015 at 8:23 PM, William Stein wrote: > Hi, > > The computer combinat.math.washington.edu is down... again. Sort of. > It responds to ping requests, but I can't ssh in. A minor update: there are notifications about physical hardware failures on the front of the machine, so it may be longer than expected until combinat is running again. william -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-combinat-devel] Re: combinat.math.washington.edu
On Sun, Jan 4, 2015 at 2:06 PM, Andrew wrote: > Hi William, > > Is it possible to access beta code and git branches from SMC? Yes -- one can do 100% full sage development on your own personal copy of Sage using SMC. And it's all snapshotted and backed up offsite. William > > Last Year I was running calculations on the combinat server using some > private git branches. Once I have brushed up the code a little I'd like to > start these again. I can certainly push this code to trac but it will be a > while before it is ready for review as I'll have a busy year. > > Andrew > > > On Sunday, 4 January 2015 15:23:56 UTC+11, William Stein wrote: >> >> Hi, >> >> The computer combinat.math.washington.edu is down... again. Sort of. >> It responds to ping requests, but I can't ssh in. >> >> I suspect that not a lot of people are actively using it lately, since >> this is the second time it has gone down for over a week in the last 3 >> months, and nobody (except my student Hao Chen), seems to have >> noticed. >> >> I'm considering doing the following. I'll shutdown combinat >> completely, reformat the disk, and set it up as a node of the >> cloud.sagemath.com (SMC). It'll still have the amazing 64 cores and >> huge (192GB) RAM. However, instead of login in directly to it, people >> can email me to request that I move a particular SMC project to >> combinat. It will then have access to expanded compute resources. >> The advantage of this, is that it is much easier for me to maintain. >> In particular, SMC has automated scripts to take care of using cgroups >> to explicitly limit usage of compute resources by a given project, I >> have extensive monitoring code in place so I know when things go down, >> and I everything runs in virtual machines, so when there are problems >> I can easily fix them in a few minutes remotely. Also, it's much >> easier to grant fair usage to projects.As it is now with default >> linux on combinat, basically any user can just bring down the computer >> by using too much memory/disk/whatever, which is probably what >> happened in this case (I don't know). >> >> Thoughts? >> >> Obviously, this may be a bit slower and the max memory will be less >> (as things are in a VM) for specific research-level computations. >> However, a working computer is way better than a regularly-crashing >> computer, in my opinion.Also, given the weeks of downtime that >> nobody (except Hao) notices, maybe people aren't using combinat at all >> anyways, due to it being only a remote linux box. Personally, I >> think SMC makes using remote Linux boxes much easier. >> >> -- William >> >> -- >> William Stein >> Professor of Mathematics >> University of Washington >> http://wstein.org > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-combinat-devel. > For more options, visit https://groups.google.com/d/optout. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-combinat-devel] combinat.math.washington.edu
On Sat, Jan 3, 2015 at 8:53 PM, Anne Schilling wrote: > Hi William, > > I have used combinat in the past for big research computations, but > not very recently (and I think I might have brought down the machine > at some point due to too much memory use). So as long as we can still > use the machine when we have large computations, I am ok with your plan. > > > Could you please be very specific what we need to do to get access > when running large computations? We would need to log onto SMC and then > e-mail you to move the process over? That's precisely what I was thinking... except instead of "process" it's a "project", which is basically the same thing as a Linux account. For combinatorics researchers I would set the timeout of the project to infinite, and raise other quotas.Also, once you have a project you can directly ssh into "it" (using any ssh program) if you want, which in this could would literally just mean ssh'ing into an account running on a big virtual machine on combinat. One plus of this whole approach is that it's really easy to add your students/collaborators without my intervention. Once you have a "sage-combinat" project, if you want to have some students work on something there, just have them make SMC accounts then go to the project's settings and add them under collaborators (or just add them by email and they get an invite). I don't even have to be involved at all. A big problem probably with combinat.math.washington.edu, is that in practice people often want their grad students to do the real work :-), and it's a pain to get them accounts on combinat.math. In fact, I haven't made any accounts on combinat.math for anybody in months, and I'm not even sure currently if I can easily do so. Amusingly, in a typical day, the number of new accounts on SMC is almost the same as the total number of accounts I've ever given on that *.math.washington.edu compute cluster. Another SMC benefit is snapshots every few minutes, so if you accidentally delete a bunch of files, you can easily recover them... > I might still have some data/programs on the machine that I have not backed > up. I'll reboot combinat.math on Monday. Any files you have in /home/username are actually stored via NSF in a separate location, not on combinat.math, so they won't be impacted. William > Best, > > Anne > > On 1/3/15 8:23 PM, William Stein wrote: >> Hi, >> >> The computer combinat.math.washington.edu is down... again. Sort of. >> It responds to ping requests, but I can't ssh in. >> >> I suspect that not a lot of people are actively using it lately, since >> this is the second time it has gone down for over a week in the last 3 >> months, and nobody (except my student Hao Chen), seems to have >> noticed. >> >> I'm considering doing the following. I'll shutdown combinat >> completely, reformat the disk, and set it up as a node of the >> cloud.sagemath.com (SMC). It'll still have the amazing 64 cores and >> huge (192GB) RAM. However, instead of login in directly to it, people >> can email me to request that I move a particular SMC project to >> combinat. It will then have access to expanded compute resources. >> The advantage of this, is that it is much easier for me to maintain. >> In particular, SMC has automated scripts to take care of using cgroups >> to explicitly limit usage of compute resources by a given project, I >> have extensive monitoring code in place so I know when things go down, >> and I everything runs in virtual machines, so when there are problems >> I can easily fix them in a few minutes remotely. Also, it's much >> easier to grant fair usage to projects.As it is now with default >> linux on combinat, basically any user can just bring down the computer >> by using too much memory/disk/whatever, which is probably what >> happened in this case (I don't know). >> >> Thoughts? >> >> Obviously, this may be a bit slower and the max memory will be less >> (as things are in a VM) for specific research-level computations. >> However, a working computer is way better than a regularly-crashing >> computer, in my opinion.Also, given the weeks of downtime that >> nobody (except Hao) notices, maybe people aren't using combinat at all >> anyways, due to it being only a remote linux box. Personally, I >> think SMC makes using remote Linux boxes much easier. >> >> -- William > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving ema
[sage-combinat-devel] combinat.math.washington.edu
Hi, The computer combinat.math.washington.edu is down... again. Sort of. It responds to ping requests, but I can't ssh in. I suspect that not a lot of people are actively using it lately, since this is the second time it has gone down for over a week in the last 3 months, and nobody (except my student Hao Chen), seems to have noticed. I'm considering doing the following. I'll shutdown combinat completely, reformat the disk, and set it up as a node of the cloud.sagemath.com (SMC). It'll still have the amazing 64 cores and huge (192GB) RAM. However, instead of login in directly to it, people can email me to request that I move a particular SMC project to combinat. It will then have access to expanded compute resources. The advantage of this, is that it is much easier for me to maintain. In particular, SMC has automated scripts to take care of using cgroups to explicitly limit usage of compute resources by a given project, I have extensive monitoring code in place so I know when things go down, and I everything runs in virtual machines, so when there are problems I can easily fix them in a few minutes remotely. Also, it's much easier to grant fair usage to projects.As it is now with default linux on combinat, basically any user can just bring down the computer by using too much memory/disk/whatever, which is probably what happened in this case (I don't know). Thoughts? Obviously, this may be a bit slower and the max memory will be less (as things are in a VM) for specific research-level computations. However, a working computer is way better than a regularly-crashing computer, in my opinion.Also, given the weeks of downtime that nobody (except Hao) notices, maybe people aren't using combinat at all anyways, due to it being only a remote linux box. Personally, I think SMC makes using remote Linux boxes much easier. -- William -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
[sage-combinat-devel] ClassicalCrystalOfAlcovePaths?
Hi, Somebody (mateon1) reported this bug in Sage on gitter [1]: There is a mystery thing in the global namespace of Sage on startup called ClassicalCrystalOfAlcovePaths. As far as I can tell, doing *anything* with this global object just bombs. ClassicalCrystalOfAlcovePaths? ClassicalCrystalOfAlcovePaths(inputs), etc. Of course using ClassicalCrystalOfAlcovePaths functionality as documented here works: https://github.com/sagemath/sage/blob/master/src/sage/combinat/crystals/alcove_path.py [1] https://gitter.im/sagemath/cloud -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-combinat-devel] Diversity to foster sage development
On Wed, May 28, 2014 at 3:56 PM, Paul-Olivier Dehaye wrote: > Out of my confused state after a long day: > I think I still want sage to be a " free open source alternative ", and its > primary audience to be typical users of the Ma's. But the Ma's have indeed > evolved since 2005. Maybe it might be worth, as a start, listing how they > have changed? The goal of the exercise would not be to copycat what they do, > but maybe to understand how the Ma's pipelines work now. Some Ma-related "events" since 2005 that I noticed: * Maplesoft was bought by a Japanese company around 2008... I don't know anything about what ended up happening as a result. * Mathworks bought MuPAD, so now they own computer algebra capabilities (instead of just reselling Maple). iPad app. They also sponsor a radio program on NPR that I here every day :-). * Wolfram Inc. introduced Wolfram|Alpha and Manipulate. iPad app. They are developing a web-based notebook interface, which I think just looks exactly like desktop Mathematica. I don't know if a plugin is required. * Magma made a deal with the Simons Foundation to make Magma available for free to North American academic institutions. John Cannon is still guiding Magma development, which is moving along at a stable rate. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-combinat-devel] Project: add hundreds of contributors to sage
On Wed, May 28, 2014 at 3:30 PM, Paul-Olivier Dehaye wrote: > Again, in the big wave of emails, this one also got misdirected: > > Hi everyone, > > I am looking for people who want to help me, in one way or another, bring > hundreds of new first time contributors to sage. If I do not find enough > partners, I will look for other more suitable python-based projects. > > The idea would be quite simple: teach python programming around some > mathematics (such as combinatorics) and simultaneously produce code that > would be useful for research and worth including in sage. Two catches: > students are given individual problems to work on, and the course is taught > on Coursera. Motivation for the students would come in various ways: > internships, for instance. Quality of the code would be ensured by > peer-testing the programs. > > If you do not know what Coursera or MOOCs are, you are welcome to take my > upcoming course > https://class.coursera.org/massiveteaching-001 > > If you are interested to play with a MOOC platform yourself, you might want > first to watch the videostream of the 2pm-3pm slot of this conference I am > co-organising on Tuesday: > tinyurl.com/openedx-zurich > as it will help you assess the technical challenges. > > I am looking at a start date for the course of around October-November, and > to bring the discussion off the mailing list (to private) so as to keep an > element of surprise for the students. An obstruction to getting code contributions from "hundreds of new developers" into Sage is the Sage development process via trac, as documented in the Sage Developers guide. I have 40 students in my class this quarter, and have encouraged them all to make contributions to Sage via the standard trac process. Maybe 2 have succeeded, and when I point them out the documentation and look at it myself, I wince.This is not to say that the process is bad -- in fact, for people making major contributions over time, our current system is pretty reasonable overall, and in some ways quite good. But for somebody new to software development who wants to make a few small contributions, e.g., add an example to a docstring, it is not definitely optimal. One possible approach for your course would be to do everything through pull requests on github, which are ridiculously easy to make. Then we (i.e., some expert sage developers) would aggregate some of those contributions into a smaller number of trac tickets, which would get included in Sage in the traditional way. This approach would be nice since it wouldn't require changing anything about Sage development or infrastructure, but would allow us to try out new approaches, which might later influence the Sage development process. It would be interesting to think about "low hanging fruit" sage development projects. There's a *ton* of obvious things one might want to implement for Sage... which are now already done well. E.g., I had students in my class tell me what they wanted to do their final projects on, and in the majority of cases I had to point out that what they wanted to do was already done in Sage well (or at least done many times over well in Python). They often still did the projects, but making it clear that it was for-fun toy code. However, one example is applying transforms to a 2d plot in Sage -- that seems not done, though we have 3d transforms in Sage. I know trac is supposed to have "beginning tickets", but when I send beginners to trac, they invariably claim to find nothing to do. So a big list of low hanging fruit that would make sense to implement in Sage would be useful. Again, an example is: - implement functions like rotate, translate, etc., for 2d graphics objects, like the corresponding 3d functions. That said, Sage is getting mature enough at the easy things that I wouldn't be surprised if somebody responds to this email and says -- oh, that's easy, via converting the plot to matplotlib, or something... Of course when I think about more advanced mathematics, Sage has a million obvious gaps to fill, and is extremely immature with a huge amount of low hanging fruit. But this is all grad student level stuff. -- William > > Let me know! > > Paul > > Paul-Olivier Dehaye > SNF Professor of Mathematics > University of Zurich > skype: lokami_lokami (preferred) > phone: +41 76 407 57 96 > chat: pauloliv...@gmail.com > twitter: podehaye > freenode irc: pdehaye > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. >
Re: [sage-combinat-devel] Diversity to foster sage development
t is only to the credit of the PSF to take this > stance. This is very different from other languages apparently. > > Maybe my perspective of the python community was skewed by the fact that > pycon is a US-centric conference. I would be curious to see how it compares > to EuroPython for those aspects, but will be unable to attend. > > All this is especially true I would think for software like sage, which > aims to be a replacement to the large CAS software companies. Look at all > the outreach efforts that have "Wolfram" in their name. I am not saying > that the sage core community should develop a copy of the whole Wolfram > ecosystem. What I am advocating is to understand that beyond sage there is > a wider ecosystem of people who are devoted to goals around sage (LMFDB, > sage-combinat, findstat, sagemathcloud, the failed sage-explorer,...), > possibly different from yours but that active mutual cooperation would be > beneficial. While 90% of the code of these projects will not belong to > sage, it is important that their extension points do sit in the code and > are thought through, because these extension points welcome creativity and > other innovators to build cool stuff on top of sage, and make it easier for > the core contributors to help them too, with epsilon additional effort. > > Finally, for the specific context of how successful mathematical > communities work together, I would advise anyone to read papers by Ursula > Martin and her coauthors. In light of all that, what do you think of the Sage mission statement? "Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab." It's meant to be technically very inclusive, and was something I made up back in 2005. It might be worth revisiting it, especially in light of your remarks about Wolfram outreach above, my own recent push to create something (SageMathCloud), which is certainly different than just "an alternative to Ma's", etc. I'm also very +1 to diversity, reaching out to industry, etc. -- William -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-combinat-devel] Re: Russian
On Fri, Jan 31, 2014 at 2:43 PM, Anna Clawson wrote: > Thanks, fixed! > > >> >> span() must be "Линейная оболочка" rather than "Подпространство" >> >> (the latter means "subspace") > > > In the original English document: > Subspace: span(vectors, field) > which is why I translated it as "подпространство". I understand that both > "linear span" and "subspace" make sense in this context. How about > translating it as "линейное подпространство"? > > time vs. timeit: I think it would be best to translate the descriptions of > these commands in a way that succinctly highlights the difference between > them. So what's really the difference between time and timeit? time runs a command once and displays the time. One usually uses this for a potentially long computation. timeit runs a command a bunch of times (possibly thousands), then provides some data about the time it takes to run, which hopefully averages out errors. You use this typically when benchmarking some small section of code. > > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-combinat-devel. > For more options, visit https://groups.google.com/groups/opt_out. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-combinat-devel] Re: Russian
On Fri, Jan 31, 2014 at 1:45 PM, Andrey Novoseltsev wrote: > On Friday, 31 January 2014 14:39:00 UTC-7, Dima Pasechnik wrote: >> >> On 2014-01-19, Christian Stump wrote: >> > Below my office mate's term for lattice polytope: >> > >> > >> > lattice polytope is >> > целочисленный многогранник >> > (by the way, both polytope and polyhedron are translated in Russian by >> > this >> > single word). >> no. "polyhedron" == "полиэдр" >> > > Никогда не слышал! Although I'm not sure where I could have. Wow, you Russians use explanation points a lot more when you're talking (about) Russian :-). William > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-combinat-devel. > For more options, visit https://groups.google.com/groups/opt_out. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-combinat-devel] Re: Russian
2014-01-31 Dima Pasechnik :
> On 2014-01-22, Andrey Novoseltsev wrote:
>> On Monday, 20 January 2014 22:20:10 UTC-7, Anna Clawson wrote:
>>>
>>> Here is the translation of the document. Anyone who knows Russian is
>>> welcome to proofread it!
>>>
>>>
>>> https://drive.google.com/file/d/0B87aVe10sJDAUU8wUjg5Vmo3UDg/edit?usp=sharing
>>>
>>> Cheers,
>>> Anna
>>>
>>
>> Awesome! Although I would translate Calculus as "Анализ" or "Математический
>> анализ" = (Mathematical) Analysis.
> +1
>> At least that was the way to go 10 years
>> ago, when people also could understand "журналирование" instead of
>> "логгирование" for logging.
> some further nitpicking, and not only - in few places it's plain wrong:
Thanks!!
>
> "Арифметический интервал" should be "Интервальная арифметика"
>
> "Установить размер/пропорции" -> "Задать размер/пропорции"
>
> "полярный график" -> "график в полярных координатах"
>
> "Сочетание графических элементов" -> "Наложение графических элементов"
>
> "Остаток n при делениии..." -> "Остаток n от деления..."
>
> "Орграф" -> "Ориентированный граф"
>
> "Ребра" -> "Кратчайший путь"
> (i.e. shortest path. "ребра" mean "edges"!)
>
> "Таблицы" -> "Табло"
>
> "Матрица Хессенберга" -> "Хессенбергова форма матрицы"
>
> "Ограничить матрицу в подпространство" -> "Ограничить матрицу на
> подпространство"
>
> "Задать точное время выполнения..." -> "Замерить точное время
> выполнения..."
> ("задать" means "set"!)
>
> -
> at some point there should be put in a ticket to review, please cc me.
I don't think (?) that the quickrefs are part of Sage itself. They
are just latex and pdf files that are attached to the wiki. So
there's no referee process.
Any thoughts about including them in sage?
> Cheers,
> Dima
>
>
> --
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--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
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Re: [sage-combinat-devel] Russian
On Sat, Jan 18, 2014 at 7:55 PM, Volker Braun wrote: > On Saturday, January 18, 2014 6:52:29 AM UTC-5, darijgrinberg wrote: >> >> > - Combinatorics: "crystals" - I'm assuming this literally means >> > 'crystals' and is related to physical structures. >> No idea about this > > > As a physicist by training, I'm always amused how mathematicians never seem > to remember the original meaning of physics terms ;-) Thanks for your physicist help. Also, a minor note -- the person who wrote the original question is a linguist (not a mathematician). -- William > >> >> BTW I am not very convinced about physical meaning (in this subject, >> not even the word "quantum" tends to come from physics) > > > It does have its origin in quantum integrable models and solutions of the > quantum Yang Baxter equation, so at least that name is somewhat justified. > But as far as I know "crystals" has no physical/chemical meaning... > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-combinat-devel. > For more options, visit https://groups.google.com/groups/opt_out. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/groups/opt_out.
[sage-combinat-devel] Russian
Hi Sage-Combinat devs, Anna Clawson is translating the Sage quick reference to Russian. She has some questions about how to translate several *algebraic combinatorics* terms. If anybody reading this knows combinatorics in Russian, or has a Russian colleague, could you clear up the below? - Combinatorics: "tableau" - I'm wondering if I should translate it generically as 'table' (which is a term in Russian combinatorics) or is it something more specific - maybe if you gave more of a description I could figure it out. - Combinatorics: "word" - is that a special term or does it literally mean 'word'? - Combinatorics: "root system" - IDK. Which area of combinatorics is it related to? - Combinatorics: "crystals" - I'm assuming this literally means 'crystals' and is related to physical structures. - Lattice polytope - IDK. Tried to google different things in Russian but didn't get anything meaningful. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-combinat-devel] Sage-Combinat Days 2014
On Tue, Dec 3, 2013 at 5:49 AM, Adrien Boussicault wrote: > Dear Sage-Combinat lovers, > > We are thinking about organizing new Sage-Combinat days in > February-May. > > The tradition is to reserve a Guest house at Cernay-la-ville, during one week, > from Saturday to Saturday. I've added this as Sage Days 57 here: http://wiki.sagemath.org/Workshops > > We want to choose a date for that event. > > For this purpose, we have created a doodle. > To each week, you can choose two different days : Monday or/and Thursday > to tell us if you can be present during the beginning of the week or/and > during > the end of the week. > > The doodle is here : > http://framadate.org/studs.php?sondage=zil1twp4pz5tmq5l > > Cheers, > > Adrien Boussicault > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-combinat-devel. > For more options, visit https://groups.google.com/groups/opt_out. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-combinat-devel] Terminated jobs on combinat server?
We could repartition the new /scratch disk to provide a bigger swap...? On Jun 18, 2013 2:00 AM, "Anne Schilling" wrote: > Hi Andrew, > > I also had a large job running on combinat. I just checked and it also > seems to have > disappeared. Too bad! So it might be good to find out what happened!? > > Best, > > Anne > > On 6/17/13 11:29 PM, Florent Hivert wrote: > > Hi Andrew, > > > >>> I definitely didn't kill them, and the machine hasn't been rebooted in > >>> 2 months. Your jobs might have used too much memory and been killed > >>> by the Linux kernel. > >>> > >>> Thanks William, that's probably what happened. I'll try and improve my > >> memory management! > > > > I'm sorry your computation where stopped. > > > > I have some extremely CPU intensive computations running on combinat. I > > designed it to run on the CPU cache so that it needs very few memory: It > > actually runs on 32 core but take less than a MB of memory. I'm watching > it on > > a regular basis and I remember seeing one of your code which had > allocated > > mode than 30 GB. If there were only one it shouldn't pose any problem on > > combinat. However, there are some virtual machine running and several > other > > memory eating processes. > > > > Cheers, > > > > Florent > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-combinat-devel. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-combinat-devel] Terminated jobs on combinat server?
On Mon, Jun 17, 2013 at 4:25 PM, Andrew Mathas wrote: > Hi All, > > I had some (very long and quite intensive but niced) jobs running on the > combinat server but they have all been terminated. I'm not sure whether this > was done accidentally or because they were hogging resources or for some > other reason (although I was monitoring them and they seemed OK). This > calculation has been all that I have had time for sagewise for the past few > months:( Unfortunately I have lost some of the calculation but luckily I can > restart them within a few days of when they died. > > Before restarting them I thought that I should check to see if I was > breaking the usage guidelines or etiquette. Please advise! I definitely didn't kill them, and the machine hasn't been rebooted in 2 months. Your jobs might have used too much memory and been killed by the Linux kernel. > > Cheers, > Andrew > > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-combinat-devel. > For more options, visit https://groups.google.com/groups/opt_out. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel. For more options, visit https://groups.google.com/groups/opt_out.
[sage-combinat-devel] Re: [sage-algebra] Paper publication of the book "Calcul Mathematique avec Sage"
On Tue, Jun 11, 2013 at 8:01 AM, Nicolas M. Thiery wrote: > Dear Sage(-Combinat) developpers, > > We are happy to announce the paper publication of our french book > "Calcul Mathématique avec Sage". It's available from your favorite > online book store for a dozen dollars. Of course the electronic > version remains and will remain free! I just bought it from amazon... and you should too! -- William > > http://sagebook.gforge.inria.fr/ > > "Calcul Mathématique avec Sage" is the first generalist book about > Sage. Written jointly by teachers and researchers it emphasizes the > underlying mathematics for a good understanding and usage of the > system. The first part is targeted at undergraduate students, while > the others cover a spectrum of entry level graduate classes. > > A. Casamayou, N. Cohen, G. Connan, T. Dumont, L. Fousse, F. Maltey, > M. Meulien, M. Mezzarobba, C. Pernet, N. M. Thiéry, P. Zimmermann > > PS: some of the chapters have already been translated in English. > Volunteers to translate more chapters are very welcome and should get > in touch with us. > > -- > Nicolas M. Thiéry "Isil" > http://Nicolas.Thiery.name/ > > -- > You received this message because you are subscribed to the Google Groups > "sage-algebra" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-algebra+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-combinat-devel] Re: [sage-devel] Re: use Sage!
On Tue, Jun 4, 2013 at 10:36 PM, Minh Nguyen wrote: > Hi William, > > On Tue, Jun 4, 2013 at 2:41 AM, William Stein wrote: >> Would somebody like Minh Nguyen be willing to do technical copyediting >> in exchange for a percentage of sales? > > I might be crazy for saying this, but I would rather donate my time > for copy editing than risk a conflict of interest. That's not crazy at all. It's exactly the spirit that makes Sage great! -- William > > -- > Regards, > Minh Van Nguyen > http://bit.ly/mvngu -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-combinat-devel] Re: [sage-devel] Re: use Sage!
On Sun, May 5, 2013 at 6:00 PM, rjf wrote: [...] > but if you have already written it and Springer would like to publish it, > and it doesn't interfere with your ownership, it seems like you have > nothing to lose. But make sure you don't give away something > unintentionally, whether it is right or your valuable time and energy. > > RJF > You make some excellent points. I think a review process, editorial board, and useful reviews/rankings on Amazon.com are starting to matter more to people than "it's published by Springer (or O'Reilly)". These are things we can accomplish together, and it will be exactly the same amount of work as it would be to put together a series through Springer. For example, we can encourage many people on sage-devel to fill out amazon.com reviews of the books, so people will get a sense that the book has been looked at by experts. Also, Springer would charge about $40/copy, and give us about $5 royalties per book. I think we could charge $20/copy and make twice as much per book sold (not that making money is a motivation for this sort of thing!), while charging readers half as much. See http://www.amazon.com/Calcul-math%C3%A9matique-avec-Sage-Zimmerman/dp/1481191047/ for an example. What do people think? Do you think we can create our own series, of just as high of quality as Springer, but more inexpensive for readers, and with a creative commons license? Would somebody like Minh Nguyen be willing to do technical copyediting in exchange for a percentage of sales? -- William -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-combinat-devel] Re: poll for making dot2tex a standard spkg
On Wed, May 22, 2013 at 3:36 PM, Volker Braun wrote: > Isn't graphviz under the EPL? Thats not so bad. And we don't even want to > link to it, so its perfectly fine for us to distribute it. Yes, but EPL is GPL incompatible, so it can't be a standard package. I shouldn't have used the word "nasty" to describe it in my previous email. > How about a new category of "extra" spkgs that are nice to have but not > really required. We could even install them by default, if wanted. Perhaps > only if you have internet access during installation. The license > requirements could be relaxed, since by this definition we don't link to it. Just to be clear -- are you making any proposal about what's in the binaries that are distributed from sagemath.org, or just what gets built when one downloads the source? I'm not comfortable including any GPL-incompatible packages in the Sage binaries from sagemath.org, but something like you describe at build time seems like it would be very useful. > And I would propose that the failure of build/check of an "extra" spkg on a > platform would not prevent Sage from installing successfully. > > There is quite a list of TeX packages that the pdf docs use but the average > TeX installation does't have. > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-combinat-devel] Re: [sage-devel] poll for making dot2tex a standard spkg
On May 22, 2013 11:45 AM, "Nicolas M. Thiery" wrote: > > On Wed, May 22, 2013 at 10:39:36AM -0700, William Stein wrote: > > I installed the dot2tex package on https://cloud.sagemath.com, but > > when I try to actually use it with this example: > > > > g = sage.categories.category.category_graph() > > g.set_latex_options(format="dot2tex") > > view(g, pdflatex=True, tightpage = True) > > > > I just get this error: > > > > RuntimeError: > > dot2tex not available. > > > > graphviz is installed systemwide via "sudo apt-get install graphviz". > > Thanks for the report. Which version of Sage? which version of the > dot2tex spkg? > > Sage 5.10 beta requires a new dot2tex package (due to the upgrade of > matplotlib); this is being resolved in #14594 (and actually the source > of this discussion). > It's sage 5.10 beta. I guess that's the problem > > > There is plenty of code in the Sage library that only works in the > > > presence of optional packages. But we ship it standard. Or shall we > > > extract, e.g. the interface to Maple/Magma/... as optional packages? :-) > > > > Maple/Magma/etc. are not optional packages. > > Yup. Like graphviz they are external programs that can, or not, be > provided by the user's system. > > > A network service that only binds to localhost doesn't need ssl. > > Also, one can easily (one line) make an *ssh tunnel* to run the > > notebook securely on a remote machine without installing pyopenssl. > > Granted, my example is not 100% bullet proof :-) I am just saying > that, most of the time when you use the notebook code, you do need > other stuff which is not necessarily there by default. > > > > An answer is that graphviz is often already installed on the system. > > > In which case nothing needs to be done. > > > > I think graphviz has compiled code, whereas dot2tex is python code, so > > graphviz could be hard to install. > > Yes, though it's provided precompiled on most OS, so it's not so bad. > > > Also relevant is that graphviz has a nasty GPL-incompatible license, > > so we can never ever include it with Sage, whereas dot2tex has a very, > > very standard open license: > > > > https://code.google.com/p/dot2tex/source/browse/LICENSE > > +1 > > Cheers, > Nicolas > -- > Nicolas M. Thiéry "Isil" > http://Nicolas.Thiery.name/ > > -- > You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-combinat-devel] Re: [sage-devel] poll for making dot2tex a standard spkg
On Wed, May 22, 2013 at 9:58 AM, Nicolas M. Thiery wrote: > On Wed, May 22, 2013 at 09:13:09AM -0700, kcrisman wrote: >> A standard package which is only useful in the presence of an optional >> package doesn't make sense to me. > > It simplifies our users's life, and that is useful! Also it simplifies > *my* life: I am tired, e.g. during Sage Days, of having to explain > about Sage packages to our complete beginners for something that is > often one of the very first feature that they want to play with. I installed the dot2tex package on https://cloud.sagemath.com, but when I try to actually use it with this example: g = sage.categories.category.category_graph() g.set_latex_options(format="dot2tex") view(g, pdflatex=True, tightpage = True) I just get this error: RuntimeError: dot2tex not available. graphviz is installed systemwide via "sudo apt-get install graphviz". Anyway, I'm surprised that I'm thwarted at using dot2tex to do anything with Sage on an Ubuntu 12.04 LTS system, which is pretty standard. > > There is plenty of code in the Sage library that only works in the > presence of optional packages. But we ship it standard. Or shall we > extract, e.g. the interface to Maple/Magma/... as optional packages? :-) Maple/Magma/etc. are not optional packages. > A partial answer for Dima: for the notebook spkg to be useful, you > need either a local browser or you want to be running it securely, > which requires the optional pyopenssl spkg. A network service that only binds to localhost doesn't need ssl. Also, one can easily (one line) make an *ssh tunnel* to run the notebook securely on a remote machine without installing pyopenssl. > So there already exists a > standard spkg that depends on an optional spkg or an optional system > package. > >> And I fail to see why installing both graphviz and dot2tex is >> more difficult than just installing dot2tex (either as optional >> Sage package or system-wide). > > (I assume you meant graphviz in this last sentence) > > An answer is that graphviz is often already installed on the system. > In which case nothing needs to be done. I think graphviz has compiled code, whereas dot2tex is python code, so graphviz could be hard to install. Also relevant is that graphviz has a nasty GPL-incompatible license, so we can never ever include it with Sage, whereas dot2tex has a very, very standard open license: https://code.google.com/p/dot2tex/source/browse/LICENSE > > Cheers, > Nicolas > > PS: one technical question: can a pure python spkg be installed > without any development tools (e.g. without having X-code installed on > MacOS X)? > > -- > Nicolas M. Thiéry "Isil" > http://Nicolas.Thiery.name/ > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-combinat-devel] Re: [sage-cloud] 4ti2
On Fri, May 17, 2013 at 10:33 AM, davidp wrote: > There will be a workshop on chip-firing and critical groups at AIM in the > second week of July: > > http://www.aimath.org/ARCC/workshops/chipfiring.html > > I am just starting to think about how sagecloud might be utilized there. > One > package that would be great to have access to for those of us interested in > the > Riemann-Roch theory on graphs and in tropical geometry would be 4ti2, which > seems to be somewhat broken at the moment. Would it be possible to use 4ti2 > somehow with sagecloud? Working 4ti2 will be in the next update to cloud (i.e., today or tomorrow). However, when it runs it's somewhat annoyingly verbose. - P.S. For the record, here's my saga of getting 4ti2 to work for cloud.sagemath.com: I install the 4ti2 optional sage spkg into the system-wide Sage install. However, it evidently doesn't work at all since when I do ./sage -t --optional=all devel/sage/sage/interfaces/four_ti_2.py all tests fail with a message about "Error: Unable to find 4ti2 executable `4ti2gmp' ". There is a trac ticket about the 4ti2 build being broken... (http://trac.sagemath.org/sage_trac/ticket/13498). 4ti2gmp It's not in Ubuntu, so I can't install it system-wide: root@compute2a:/usr/local/sage/sage-5.10.beta3# apt-cache search 4ti2 This page suggests the last release of 4ti2 was in 2008?http://www.4ti2.de/ This looks promising to install system-wide: http://www.latte-4ti2.de/ However, it fails instantly when trying to build on a stock Ubuntu 12.04LTS 64-bit Linux install with "configure: error: could not find a working compiler, see config.log for details make: *** [gmp-4.2.4/config.status] Error 1"... which is pretty odd. Somebody has revived the project at github: https://github.com/tom111/4ti2 However, this has no ./configure file, so when I do "automake", then "./configure", I get: salvus@compute2a:/usr/local/sage/sage-5.10.beta3/tmp/4ti2$ ./configure ./configure: line 1818: syntax error near unexpected token `foreign' ./configure: line 1818: `AM_INIT_AUTOMAKE(foreign)' The trac ticket mentioned above has a link to "latte-integrale", which contains a 4ti2: http://www.math.ucdavis.edu/~latte/software/latte-integrale-1.5.3.tar.gz but this fails as above to build: configure: error: could not find a working compiler, see config.log for details make: *** [gmp-4.2.4/config.status] Error 1 However, when I tried extracting the 4ti2 tarball *inside* of the latte-integrale package and directly building that... it works! The test suite in Sage runs, and the output matches (except loading a test data file), but is much more verbose now. -- William > > Thanks, > Dave > > -- > You received this message because you are subscribed to the Google Groups > "sage-cloud" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-cloud+unsubscr...@googlegroups.com. > To post to this group, send email to sage-cl...@googlegroups.com. > Visit this group at http://groups.google.com/group/sage-cloud?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-combinat-devel] use Sage!
Hi Sage-Developers, There is a big series of small books about R that Springer publishes: http://www.springer.com/series/6991?detailsPage=titles The editorial director of that series at Springer just talked with me on the phone for a while, and he says these are among "Springers best selling books"; moreover, he believes they have a major impact on making R a really viable platform for computational statistics. He wants to know if we want to create a series like this for Sage. The timing would be good, giving how the level of maturity and comprehensive functionality of Sage, at least compared to a few years ago.For *this* series, Springer appears amenable to authors keeping copyright, and for there being a free (but slightly different) web-version of a given book. As a concrete example, the thematic tutorial on combinatorics at http://sagemath.org/doc/reference/combinat/sage/combinat/tutorial.html# could be expanded into a short book (maybe 100 pages), published by Springer, and still have the shorter similar version included with Sage. In other words, they are more amenable to flexible copyright and distribution with *this* series of books than with many of their other more traditional offerings. If you have something that you could see being polished into a book for inclusion in a series called "Use Sage!" for Springer, let me know. If there is sufficient interest, then this could help substantially with our mission statement: "Create a free open source viable alternative to Magma, Maple, Mathematica, and Matlab."(In fact, Springer believes their book series plays a big role in R's extreme popularity.) I've also talked with both the AMS and with O'Reilly about similar projects, but it doesn't seem to work out. Also, both publishers (especially O'Reilly) seemed much more "allergic" to material in the books being partly duplicated online. -- William -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-combinat-devel] Re: sage.math down?
Now sage.math = boxen.math. On Mar 22, 2013 6:36 PM, "Keshav Kini" wrote: > Dima Pasechnik writes: > >> On Wed, 20 Mar 2013 at 08:28AM -0400, Anne Schilling wrote: > >>> Is http://sage.math.washington.edu/ down? For the past couple of days > >>> I tried to download from there and have not been able to connect. > > I'd say http://boxen.math.washington.edu/ > > is your best bet now (it shares most things with sage.math, IMHO) > > Even shorter, you can use http://wstein.org/home/ to replace > http://boxen.math.washington.edu/home/ :) > > -Keshav > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-combinat-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > Visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-combinat-devel] Re: combinat.sagemath.org down?
HI, We were messing with some config stuff on combinat -- sorry for the inconvenience! combinat.sagemath.org will be back very soon. On Tue, Feb 26, 2013 at 9:55 PM, Anne Schilling wrote: > Hi William, > > Is it possible that > > combinat.sagemath.org > > is down? It does not seem possible to connect to the sage-combinat queue. > > Thank you, > > Anne -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-combinat-devel] Fwd: [lmdb] switching to Git
Hi Sage-Combinat, Harald Schilly wrote a nice talk (see below) about Git to help with moving the LMFDB.org project to git... -- Forwarded message -- From: Harald Schilly Date: Fri, Dec 14, 2012 at 8:34 AM Subject: Re: [lmdb] switching to Git To: lmdb On Fri, Dec 14, 2012 at 4:52 PM, John Cremona wrote: > I have been reading up on it any way ... Good to have you on board :-) And btw, I've made a talk about Git some time ago, hence it's no issue at all to do some introduction to Git again. code: https://github.com/haraldschilly/yagt slides online: http://haraldschilly.github.com/yagt (space key, or down arrow, and ESC for the daring) It's a "bottom up" explanation, probably not what you expect for an introduction, but trust me, it helps in the long run ... H -- You received this message because you are subscribed to the Google Groups "lmdb" group. To post to this group, send email to l...@googlegroups.com. To unsubscribe from this group, send email to lmdb+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/lmdb?hl=en. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: combinat out again?
On Thu, Dec 13, 2012 at 11:55 AM, William Stein wrote: > On Wed, Dec 12, 2012 at 11:30 PM, William Stein wrote: >> On Wed, Dec 12, 2012 at 7:00 PM, Anne Schilling >> wrote: >>> Hi William, >>> >>> Is combinat.math.washington.edu out once again? The machine does not >>> seem to respond. >> >> It's not crashed due to a memory error, since it responds to ping >> requests. However, I can't ssh into it, which can happen when too >> many people run jobs at once (and the vm.overcommit ratio is too big, >> and there isn't enough swap). I'll get the sysadmins to reboot the >> machine tomorrow morning, then tighten up the vm.overcommit, and add >> more swap. > > The machine is back up. > The vm.overcommit stuff looks fine -- it's the same settings as on > sage.math, etc. > > Later today, I'm going to add an extra 96GB of swap to the little 32GB > of swap currently there; this should help with stability a lot. I changed the vm.overcommit settings to: vm.overcommit_memory=2 vm.overcommit_ratio=60 and I've added the swap, so now there's 134GB of swap: root@combinat:/etc# free total used free sharedbuffers cached Mem: 198068436 20060256 178008180 0 5854844144288 -/+ buffers/cache: 15330484 182737952 Swap:134537208 0 134537208 Let me know if there's any trouble. I can buy and install another disk so we have more swap, if people feel that is a good idea (there is definitely plenty of room in the grant for this.) -- William > > William > >> >> -- William >> >>> I saw that several people were running heavy computations on it for the >>> last week and until yesterday, everything seemed fine. >> >> >> >>> >>> Thanks, >>> >>> Anne >>> >>> On 12/6/12 10:36 AM, William Stein wrote: >>>> Hi, >>>> >>>> After moving memory around, memtest86 (and the BIOS memtest) detected >>>> no errors. If people can try to stress test >>>> combinat.math.washington.edu for the next 24 hours (especially with >>>> large-memory computations), that would be very useful! >>>> >>>> William >>>> >>>> On Wed, Dec 5, 2012 at 3:25 PM, William Stein wrote: >>>>> Hi, >>>>> >>>>> Andrew Ohana and I swapped two chips around and are currently running >>>>> memtest86 on >>>>> combinat.math. I'll check on the results tomorrow at about noon. >>>>> >>>>> -- William >>>>> >>>>> On Tue, Dec 4, 2012 at 10:49 PM, Andrew Mathas >>>>> wrote: >>>>>> Yes, thank you for taking care of this William. I am sure you have better >>>>>> things to do! >>>>>> >>>>>> Andrew >>>>>> >> >> >> >> -- >> William Stein >> Professor of Mathematics >> University of Washington >> http://wstein.org > > > > -- > William Stein > Professor of Mathematics > University of Washington > http://wstein.org -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: combinat out again?
On Wed, Dec 12, 2012 at 11:30 PM, William Stein wrote: > On Wed, Dec 12, 2012 at 7:00 PM, Anne Schilling wrote: >> Hi William, >> >> Is combinat.math.washington.edu out once again? The machine does not >> seem to respond. > > It's not crashed due to a memory error, since it responds to ping > requests. However, I can't ssh into it, which can happen when too > many people run jobs at once (and the vm.overcommit ratio is too big, > and there isn't enough swap). I'll get the sysadmins to reboot the > machine tomorrow morning, then tighten up the vm.overcommit, and add > more swap. The machine is back up. The vm.overcommit stuff looks fine -- it's the same settings as on sage.math, etc. Later today, I'm going to add an extra 96GB of swap to the little 32GB of swap currently there; this should help with stability a lot. William > > -- William > >> I saw that several people were running heavy computations on it for the >> last week and until yesterday, everything seemed fine. > > > >> >> Thanks, >> >> Anne >> >> On 12/6/12 10:36 AM, William Stein wrote: >>> Hi, >>> >>> After moving memory around, memtest86 (and the BIOS memtest) detected >>> no errors. If people can try to stress test >>> combinat.math.washington.edu for the next 24 hours (especially with >>> large-memory computations), that would be very useful! >>> >>> William >>> >>> On Wed, Dec 5, 2012 at 3:25 PM, William Stein wrote: >>>> Hi, >>>> >>>> Andrew Ohana and I swapped two chips around and are currently running >>>> memtest86 on >>>> combinat.math. I'll check on the results tomorrow at about noon. >>>> >>>> -- William >>>> >>>> On Tue, Dec 4, 2012 at 10:49 PM, Andrew Mathas >>>> wrote: >>>>> Yes, thank you for taking care of this William. I am sure you have better >>>>> things to do! >>>>> >>>>> Andrew >>>>> > > > > -- > William Stein > Professor of Mathematics > University of Washington > http://wstein.org -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: combinat out again?
On Wed, Dec 12, 2012 at 7:00 PM, Anne Schilling wrote: > Hi William, > > Is combinat.math.washington.edu out once again? The machine does not > seem to respond. It's not crashed due to a memory error, since it responds to ping requests. However, I can't ssh into it, which can happen when too many people run jobs at once (and the vm.overcommit ratio is too big, and there isn't enough swap). I'll get the sysadmins to reboot the machine tomorrow morning, then tighten up the vm.overcommit, and add more swap. -- William > I saw that several people were running heavy computations on it for the > last week and until yesterday, everything seemed fine. > > Thanks, > > Anne > > On 12/6/12 10:36 AM, William Stein wrote: >> Hi, >> >> After moving memory around, memtest86 (and the BIOS memtest) detected >> no errors. If people can try to stress test >> combinat.math.washington.edu for the next 24 hours (especially with >> large-memory computations), that would be very useful! >> >> William >> >> On Wed, Dec 5, 2012 at 3:25 PM, William Stein wrote: >>> Hi, >>> >>> Andrew Ohana and I swapped two chips around and are currently running >>> memtest86 on >>> combinat.math. I'll check on the results tomorrow at about noon. >>> >>> -- William >>> >>> On Tue, Dec 4, 2012 at 10:49 PM, Andrew Mathas >>> wrote: >>>> Yes, thank you for taking care of this William. I am sure you have better >>>> things to do! >>>> >>>> Andrew >>>> -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: combinat out again?
On Thu, Dec 6, 2012 at 4:27 PM, Andrew Mathas wrote: > >> Are they related to Sage combinatorics research? > > > Of course, otherwise I wouldn't ask. (I'm computing the graded dimensions of > simple modules and the graded dimensions of hom-spaces (for some reducible > modules).) Send me an offlist email with your desired login name. > > Andrew > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/sage-combinat-devel/-/YgHntXOrxdYJ. > > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: combinat out again?
On Thu, Dec 6, 2012 at 3:48 PM, Andrew Mathas wrote: > Is anyone able to get an account on combinat.math.washington.edu? I could > certainly run some memory intensive jobs if required. Are they related to Sage combinatorics research? William > > > Andrew > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/sage-combinat-devel/-/9RLf_AKvIyEJ. > > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: combinat out again?
Hi, After moving memory around, memtest86 (and the BIOS memtest) detected no errors. If people can try to stress test combinat.math.washington.edu for the next 24 hours (especially with large-memory computations), that would be very useful! William On Wed, Dec 5, 2012 at 3:25 PM, William Stein wrote: > Hi, > > Andrew Ohana and I swapped two chips around and are currently running > memtest86 on > combinat.math. I'll check on the results tomorrow at about noon. > > -- William > > On Tue, Dec 4, 2012 at 10:49 PM, Andrew Mathas > wrote: >> Yes, thank you for taking care of this William. I am sure you have better >> things to do! >> >> Andrew >> >> -- >> You received this message because you are subscribed to the Google Groups >> "sage-combinat-devel" group. >> To view this discussion on the web visit >> https://groups.google.com/d/msg/sage-combinat-devel/-/K5CWg3EqOQ0J. >> >> To post to this group, send email to sage-combinat-devel@googlegroups.com. >> To unsubscribe from this group, send email to >> sage-combinat-devel+unsubscr...@googlegroups.com. >> For more options, visit this group at >> http://groups.google.com/group/sage-combinat-devel?hl=en. > > > > -- > William Stein > Professor of Mathematics > University of Washington > http://wstein.org -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: combinat out again?
On Tue, Dec 4, 2012 at 8:39 PM, Keshav Kini wrote: > Anne Schilling writes: >> Hi William, >> >> Since the machine has been down quite a bit and we bought it from the >> NSF grant, do you think it would be a good idea to ask for an exchange? > > William sent a mail to the sagemath-users list saying that Dell will be > replacing a faulty (?) memory module in the combinat.math.washington.edu > machine, after which "this will stop happening":: Yes. However, they want me to do some more testing first -- they will either (1) replace a memory chip, or (2) replace the entire motherboard. This will be completely covered under the warranty, and should be done pretty quickly (and certainly within the next 10 days at worst). > >> It turns out that indeed combinat.math.washington.edu was down with a >> memory error again. I've rebooted it.Dell will also be fixing it >> (by replacing the DIMM) this week, so this will stop happening. This >> means some downtime (for combinat only) later this week (not yet >> scheduled). > > -Keshav > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] combinat out again?
Yes, it crashed again. The hardware is thus likely faulty - I'll find out more tomorrow. On Dec 2, 2012 2:43 PM, "Anne Schilling" wrote: > Dear William, > > Is combinat.sagemath.org down again? The machine does not respond > to my requests. > > Best, > > Anne > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Sage-combinat repo down
Hi, On Monday, Andrew Ohana and I re-seated DIMM C3 in combinat.math.washington.edu. So far (2 days later) the machine is up and working fine. -- William On Fri, Nov 16, 2012 at 1:02 PM, Travis Scrimshaw wrote: > Thank you for taking care of this. > > Thanks, > Travis > > > On Thursday, November 15, 2012 2:09:46 PM UTC-8, William Stein wrote: >> >> Hi, >> >> I power cycled the machine. It stated clearly on the display that a >> memory cheap *must* be re-seated. I hope I can do this tomorrow >> morning, which will of course mean downtime. >> >> I don't know how hard it will be to figure out which chip "DIMM C3" >> actually is. The machine has a *lot* of memory chips in it. >> >> In the meantime, I suggest moving the combinat repo to another machine. >> >> -- William >> >> >> On Thu, Nov 15, 2012 at 12:27 PM, William Stein wrote: >> > There may be a memory issue. I'm going to the server room to >> > physically reboot it again right now. >> > >> > On Thu, Nov 15, 2012 at 9:27 AM, Travis Scrimshaw >> > wrote: >> >> Hey, >> >>Sorry to sound like a broken record, but I believe the sage-combinat >> >> server is down again. What's the status on getting it back up? >> >> >> >> Thanks, >> >> Travis >> >> >> >> -- >> >> You received this message because you are subscribed to the Google >> >> Groups >> >> "sage-combinat-devel" group. >> >> To view this discussion on the web visit >> >> https://groups.google.com/d/msg/sage-combinat-devel/-/-oTs4VAzqAwJ. >> >> To post to this group, send email to sage-comb...@googlegroups.com. >> >> To unsubscribe from this group, send email to >> >> sage-combinat-devel+unsubscr...@googlegroups.com. >> >> For more options, visit this group at >> >> http://groups.google.com/group/sage-combinat-devel?hl=en. >> > >> > >> > >> > -- >> > William Stein >> > Professor of Mathematics >> > University of Washington >> > http://wstein.org >> >> >> >> -- >> William Stein >> Professor of Mathematics >> University of Washington >> http://wstein.org > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/sage-combinat-devel/-/L6qOF5ygxdYJ. > > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Sage-combinat repo down
Hi, I power cycled the machine. It stated clearly on the display that a memory cheap *must* be re-seated. I hope I can do this tomorrow morning, which will of course mean downtime. I don't know how hard it will be to figure out which chip "DIMM C3" actually is. The machine has a *lot* of memory chips in it. In the meantime, I suggest moving the combinat repo to another machine. -- William On Thu, Nov 15, 2012 at 12:27 PM, William Stein wrote: > There may be a memory issue. I'm going to the server room to > physically reboot it again right now. > > On Thu, Nov 15, 2012 at 9:27 AM, Travis Scrimshaw wrote: >> Hey, >>Sorry to sound like a broken record, but I believe the sage-combinat >> server is down again. What's the status on getting it back up? >> >> Thanks, >> Travis >> >> -- >> You received this message because you are subscribed to the Google Groups >> "sage-combinat-devel" group. >> To view this discussion on the web visit >> https://groups.google.com/d/msg/sage-combinat-devel/-/-oTs4VAzqAwJ. >> To post to this group, send email to sage-combinat-devel@googlegroups.com. >> To unsubscribe from this group, send email to >> sage-combinat-devel+unsubscr...@googlegroups.com. >> For more options, visit this group at >> http://groups.google.com/group/sage-combinat-devel?hl=en. > > > > -- > William Stein > Professor of Mathematics > University of Washington > http://wstein.org -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Sage-combinat repo down
There may be a memory issue. I'm going to the server room to physically reboot it again right now. On Thu, Nov 15, 2012 at 9:27 AM, Travis Scrimshaw wrote: > Hey, >Sorry to sound like a broken record, but I believe the sage-combinat > server is down again. What's the status on getting it back up? > > Thanks, > Travis > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/sage-combinat-devel/-/-oTs4VAzqAwJ. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: sage-combinat repo is still down
Hi, A sysadmin rebooted combinat.math. He reports that "Fyi, the status indicator on the front was displaying a multibit error on DIMM C7. After power cycling, the display came up blue (no errors). It may be nothing, it may be the problem. Just sharing in case it helps." This computer has a huge amount of RAM in it, which I guess increases the chances of failure... -- William On Tue, Nov 13, 2012 at 7:55 AM, William Stein wrote: > On Mon, Nov 12, 2012 at 8:52 PM, Travis Scrimshaw wrote: >> Hey everyone, >>I believe the repo is down again. Any estimated time on a revival? > > The computer combinat.math.washington.edu is completely not responding > at all. This hasn't happened before ever -- it's not a firewall or > other issue. Also, I can't reboot the computer remotely. However, > I'll reboot it when I'm in the department next, which will be within > 26 hours of right now. > > -- William > >> >> Thanks, >> Travis >> >> >> On Monday, November 5, 2012 7:18:28 AM UTC-8, Christian Stump wrote: >>> >>> Hi all, >>> >>> any idea what the problem with the sage-combinat repository is, or >>> when it will be alive again? >>> >>> Thanks, Christian >> >> -- >> You received this message because you are subscribed to the Google Groups >> "sage-combinat-devel" group. >> To view this discussion on the web visit >> https://groups.google.com/d/msg/sage-combinat-devel/-/Ug9Pl1sD7HsJ. >> >> To post to this group, send email to sage-combinat-devel@googlegroups.com. >> To unsubscribe from this group, send email to >> sage-combinat-devel+unsubscr...@googlegroups.com. >> For more options, visit this group at >> http://groups.google.com/group/sage-combinat-devel?hl=en. > > > > -- > William Stein > Professor of Mathematics > University of Washington > http://wstein.org -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: sage-combinat repo is still down
On Mon, Nov 12, 2012 at 8:52 PM, Travis Scrimshaw wrote: > Hey everyone, >I believe the repo is down again. Any estimated time on a revival? The computer combinat.math.washington.edu is completely not responding at all. This hasn't happened before ever -- it's not a firewall or other issue. Also, I can't reboot the computer remotely. However, I'll reboot it when I'm in the department next, which will be within 26 hours of right now. -- William > > Thanks, > Travis > > > On Monday, November 5, 2012 7:18:28 AM UTC-8, Christian Stump wrote: >> >> Hi all, >> >> any idea what the problem with the sage-combinat repository is, or >> when it will be alive again? >> >> Thanks, Christian > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/sage-combinat-devel/-/Ug9Pl1sD7HsJ. > > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] sage-combinat repo is still down
Hi, I fixed combinat. It had not crashed, but something was amis with the networking. I restarted the network interface, and most things worked, but I couldn't get /home to properly remount over NFS. So I applied a bunch of OS updates, many involving networking, rebooted (for the first time in 2 months), and now everything seems fine. This may have been a networking-related bug in Ubuntu 12.04.1LTS. With luck it is fixed by this new upgrade. There were no processes running on combinat at the time, so the reboot should have been minimally invasive. William On Mon, Nov 5, 2012 at 7:37 AM, William Stein wrote: > > > On Mon, Nov 5, 2012 at 7:18 AM, Christian Stump > wrote: > >> Hi all, >> >> any idea what the problem with the sage-combinat repository is, or >> when it will be alive again? >> > > It looks like the machine is firewall'ing itself, yet again, for no > apparent reason, or ssh got killed: > > wstein@sage:~$ ping combinat > PING combinat (128.208.160.193) 56(84) bytes of data. > 64 bytes from combinat (128.208.160.193): icmp_seq=1 ttl=64 time=0.194 ms > 64 bytes from combinat (128.208.160.193): icmp_seq=2 ttl=64 time=0.356 ms > ... > wstein@sage:~$ ssh combinat > ssh_exchange_identification: Connection closed by remote host > > I will hook a console up to it today, within the next few hours, and see > what happened. > I uninstalled the firewall, fail2ban, and ubuntu automatic upgrades, so > I'm surprised by this. > > -- William > > >> >> Thanks, Christian >> >> -- >> You received this message because you are subscribed to the Google Groups >> "sage-combinat-devel" group. >> To post to this group, send email to sage-combinat-devel@googlegroups.com >> . >> To unsubscribe from this group, send email to >> sage-combinat-devel+unsubscr...@googlegroups.com. >> For more options, visit this group at >> http://groups.google.com/group/sage-combinat-devel?hl=en. >> >> > > > -- > William Stein > Professor of Mathematics > University of Washington > http://wstein.org > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] sage-combinat repo is still down
On Mon, Nov 5, 2012 at 7:18 AM, Christian Stump wrote: > Hi all, > > any idea what the problem with the sage-combinat repository is, or > when it will be alive again? > It looks like the machine is firewall'ing itself, yet again, for no apparent reason, or ssh got killed: wstein@sage:~$ ping combinat PING combinat (128.208.160.193) 56(84) bytes of data. 64 bytes from combinat (128.208.160.193): icmp_seq=1 ttl=64 time=0.194 ms 64 bytes from combinat (128.208.160.193): icmp_seq=2 ttl=64 time=0.356 ms ... wstein@sage:~$ ssh combinat ssh_exchange_identification: Connection closed by remote host I will hook a console up to it today, within the next few hours, and see what happened. I uninstalled the firewall, fail2ban, and ubuntu automatic upgrades, so I'm surprised by this. -- William > > Thanks, Christian > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] new computer on the sage cluster
Hi Sagemath-Users, The sage-combinat group and I obtained some support from the NSF, and used it to buy this new powerful computer, which is now on the sage.math.washington.edu cluster: combinat -- mainly for combinatorics research (192GB RAM, 64 cores, Opteron) -- William -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] Re: [sage-devel] PyCox: Computing with (finite) Coxeter groups and Iwahori-Hecke algebras
On Fri, Jan 27, 2012 at 1:21 AM, davidp wrote:
> I just noticed this post to the arXiv. Is Meinholf Geck in touch with
> Sage?
>
> --Dave
I'm not sure, but he mentions Sage numerous times on page 1, and
suggests Sage was the inspiration for him writing the code in Python.
Also, he explains how to use his package within Sage.
>
> Title: PyCox: Computing with (finite) Coxeter groups and Iwahori-Hecke
> algebras
> Authors: Meinolf Geck
> Categories: math.RT
> Comments: 31 pages
> MSC-class: 20C40, 20C08
> \\
> We introduce the computer algebra package {\sf PyCox}, written
> entirely in
> the {\sf Python} language. It implements a set of algorithms - in a
> spirit
> similar to the older {\sf CHEVIE} system - for working with Coxeter
> groups and
> Hecke algebras. This includes a new variation of the traditional
> algorithm for
> computing Kazhdan-Lusztig cells and $W$-graphs, which works
> efficiently for all
> groups of rank $\leq 8$ (except $E_8$). Our experiments suggest a re-
> definition
> of Lusztig's "special" representations which, conjecturally, should
> also apply
> to the unequal parameter case.
> \\ ( http://arxiv.org/abs/1201.5566 , 39kb)
>
> --
> To post to this group, send an email to sage-de...@googlegroups.com
> To unsubscribe from this group, send an email to
> sage-devel+unsubscr...@googlegroups.com
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> http://groups.google.com/group/sage-devel
> URL: http://www.sagemath.org
--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
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Re: [sage-combinat-devel] Combinatorica-like commands in Sage
On Mon, Nov 21, 2011 at 2:54 PM, Raymond N. Greenwell wrote: > When I try to import a csv file into Sage, Sage can't locate the file, > indicating that it's > not looking in the folder where I put the file. How do I find where Sage is > looking, so > I can put the file there? Note that this is on a Mac... You could use Terminal (and the cd command) to navigate to where the file is and type "pwd", which means "print working directory". You'll get something that looks a little like /Users/greenwell/math/stuff Use that path. -- William > > Thanks! > > On Nov 11, 2011, at 4:42 PM, William Stein wrote: > >> On Wed, Nov 9, 2011 at 5:52 PM, Raymond N. Greenwell >> wrote: >>> I've been having some problems with Combinatorica, and someone >>> suggested I try Sage. Can Sage import a csv file and then turn it into >>> a graph, such as with the Combinatorica commands: >>> m = Import["medalcomparison3.csv"] >>> g = FromAdjacencyMatrix[m, Type -> Directed] >> >> Python (hence Sage) can import csv files as explained here: >> >> http://docs.python.org/library/csv.html >> >> Sage can make a graph out of an adjacency matrix A using the Graph(A) >> command. >> Type "Graph?" for more on making graphs from matrices etc. >> >> In Sage you can make matrices in many ways. Type "matrix?" for more on how. >> >>> Also, can it give a minimum chain partition, such as with the >>> Combinatorica command: >>> MinimumChainPartition[g] >> >> As far as I can tell, this is not implemented in Sage. >> >>> I have found that this Combinatorica command does not always give what >>> one would expect; the results seem to violate the Dilworth Theorem. >>> >>> Thanks! >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "sage-combinat-devel" group. >>> To post to this group, send email to sage-combinat-devel@googlegroups.com. >>> To unsubscribe from this group, send email to >>> sage-combinat-devel+unsubscr...@googlegroups.com. >>> For more options, visit this group at >>> http://groups.google.com/group/sage-combinat-devel?hl=en. >>> >>> >> >> >> >> -- >> William Stein >> Professor of Mathematics >> University of Washington >> http://wstein.org >> > > * > Raymond N. Greenwell mat...@hofstra.edu > Professor of Mathematics (516) 463-5573 > 103 Hofstra University > Hempstead, NY 11549-1030 > http://people.hofstra.edu/rgreenwell > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: dot2tex, combinat
On Mon, Nov 21, 2011 at 7:01 PM, Anne Schilling wrote:
> On 11/21/11 8:24 AM, William Stein wrote:
>> On Mon, Nov 21, 2011 at 8:08 AM, Dima Pasechnik wrote:
>>> This means you have graphviz spkg installed under macosx...
>>> I cannot seem to be able to accomplish this:
>>> http://trac.sagemath.org/sage_trac/ticket/7438
>>
>> I installed graphviz under OS X by installing it from the Graphviz
>> website, instead of using the spkg.
>
> After installing dot2tex using
>
> sage -i dot2tex
>
> does the command
>
> sage: CrystalOfTableaux(['A',2], shape=[1]).latex()
> '\n\\begin{tikzpicture}[>=latex,line join=bevel,]\n%%\n\\node (1) at
> (8bp,162bp) [draw,draw=none]
> {${\\def\\lr#1{\\multicolumn{1}{|@{\\hspace{.6ex}}c@{\\hspace{.6ex}}|}{\\raisebox{-.3ex}{$#1$}}}\\raisebox{-.6ex}{$\\begin{array}[b]{c}\\cline{1-1}\\lr{1}\\cline{1-1}\\end{array}$}}$};\n
> \\node
> (3) at (8bp,10bp) [draw,draw=none]
> {${\\def\\lr#1{\\multicolumn{1}{|@{\\hspace{.6ex}}c@{\\hspace{.6ex}}|}{\\raisebox{-.3ex}{$#1$}}}\\raisebox{-.6ex}{$\\begin{array}[b]{c}\\cline{1-1}\\lr{3}\\cline{1-1}\\end{array}$}}$};\n
> \\node
> (2) at (8bp,86bp) [draw,draw=none]
> {${\\def\\lr#1{\\multicolumn{1}{|@{\\hspace{.6ex}}c@{\\hspace{.6ex}}|}{\\raisebox{-.3ex}{$#1$}}}\\raisebox{-.6ex}{$\\begin{array}[b]{c}\\cline{1-1}\\lr{2}\\cline{1-1}\\end{array}$}}$};\n
> \\draw
> [blue,->] (1) ..controls (8bp,140.79bp) and (8bp,121.03bp) .. (2);\n
> \\definecolor{strokecol}{rgb}{0.0,0.0,0.0};\n
> \\pgfsetstrokecolor{strokecol}\n \\draw (17bp,124bp) node {$1$};\n \\draw
> [red,->] (2) ..controls (8bp,64.789bp) and (8bp,45.027bp) .. (3);\n \\draw
> (17bp,48bp) node {$2$};\n%\n\\end{tikzpicture}\n'
>
> work?
Yes.
When I was preparing my talk, I was evidently using sage-4.7.1. I
upgraded to a newer version of Sage, and the issue is totally
resolved. Sorry for the noise and thanks for the further debugging questions.
Just to confirm, doing
sage: CrystalOfTableaux(['A',2], shape=[1]).latex_file('/tmp/a.tex')
sage:
no longer gives an error for me, and it *does* create the file
/tmp/a.tex and if I go to the /tmp directory, pdflatex it, and view
the
resulting pdf, then I get the diagram.
The traceback from before (with sage-4.7.1) was this, but who cares,
since it's fixed now:
sage: C = CrystalOfTableaux(['A',2], shape=[1])
sage: C.latex_file('/tmp/a.tex')
dot2tex not available. Install after running 'sage -sh'
---
TypeError Traceback (most recent call last)
/Users/wstein/sage/install/sage-4.7.1.rc0/ in ()
/Users/wstein/sage/install/sage-4.7.1.rc0/local/lib/python2.6/site-packages/sage/categories/crystals.pyc
in latex_file(self, filename)
379
380 f = open(filename, 'w')
--> 381 f.write(header + self.latex() + footer)
382 f.close()
TypeError: cannot concatenate 'str' and 'NoneType' objects
>
> I do have
>
> from sage.misc.latex import latex
> latex.add_to_preamble('\\usepackage{tikz}')
> latex.add_to_jsmath_avoid_list('\\begin{tikzpicture}')
>
> in my init.sage file. I am not sure whether this makes a difference.
>
> Best,
>
> Anne
>
> --
> You received this message because you are subscribed to the Google Groups
> "sage-combinat-devel" group.
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> For more options, visit this group at
> http://groups.google.com/group/sage-combinat-devel?hl=en.
>
>
--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
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Re: [sage-combinat-devel] Re: dot2tex, combinat
On Mon, Nov 21, 2011 at 8:08 AM, Dima Pasechnik wrote: > This means you have graphviz spkg installed under macosx... > I cannot seem to be able to accomplish this: > http://trac.sagemath.org/sage_trac/ticket/7438 I installed graphviz under OS X by installing it from the Graphviz website, instead of using the spkg. William > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/sage-combinat-devel/-/e3UHcC27lokJ. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] dot2tex, combinat
On Sat, Nov 19, 2011 at 12:52 PM, Anne Schilling wrote:
> Hi William!
>
>
>> On Sat, Nov 19, 2011 at 09:47:51AM -0800, William Stein wrote:
>>> I tried this example from [1]:
>>>
>>> CrystalOfTableaux("A2", shape=[2,1]).latex_file("/tmp/a2rho.tex")
>>>
>>> After installing dot2tex, I get the error "sh: latex: command not
>>> found; ERROR Failed to process input". I'm using OS X, and of
>>> course I do have the latest latex fully installed and the command
>>> "latex" works fine from the command line.
>>
>> Just to make sure: does latex work from sage -sh?
Yes,
(sage subshell) deep:~ wstein$ latex
This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
restricted \write18 enabled.
**
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[sage-combinat-devel] dot2tex, combinat
Hi Sage-Combinat,
I tried this example from [1]:
CrystalOfTableaux("A2", shape=[2,1]).latex_file("/tmp/a2rho.tex")
After installing dot2tex, I get the error "sh: latex: command not
found; ERRORFailed to process input".I'm using OS X, and of
course I do have the latest latex fully installed and the command
"latex" works fine from the command line.
Incidentally, I was trying to get a quick executive summary or tour of
"algebraic combinatorics" in Sage, since I'm giving a talk on Sage at
a combinatorics conference about an hour from now, but I couldn't find
anything like [2] say. Is there something?I was hoping the guided
tour in the Sage tutorial [3] would have something about combinatorics
(or even graphs), but no.
I'm curious if I'm missing something obvious. The solution for my
talk will be to show the table of contents from the Combinatorics
chapter of the reference manual... which I guess (?) totally excludes
anything in the famous combinat patch queue.
[1]
http://combinat.sagemath.org/doc/thematic_tutorials/lie/crystals.html#tableaux-and-representations-of
[2] http://sagemath.org/doc/bordeaux_2008/
[3] http://sagemath.org/doc/tutorial/index.html
--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
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Re: [sage-combinat-devel] Combinatorica-like commands in Sage
On Wed, Nov 9, 2011 at 5:52 PM, Raymond N. Greenwell wrote: > I've been having some problems with Combinatorica, and someone > suggested I try Sage. Can Sage import a csv file and then turn it into > a graph, such as with the Combinatorica commands: > m = Import["medalcomparison3.csv"] > g = FromAdjacencyMatrix[m, Type -> Directed] Python (hence Sage) can import csv files as explained here: http://docs.python.org/library/csv.html Sage can make a graph out of an adjacency matrix A using the Graph(A) command. Type "Graph?" for more on making graphs from matrices etc. In Sage you can make matrices in many ways. Type "matrix?" for more on how. > Also, can it give a minimum chain partition, such as with the > Combinatorica command: > MinimumChainPartition[g] As far as I can tell, this is not implemented in Sage. > I have found that this Combinatorica command does not always give what > one would expect; the results seem to violate the Dilworth Theorem. > > Thanks! > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: AIM workshop proposal: opinion
On Tue, Nov 1, 2011 at 11:27 AM, Paul-Olivier Dehaye wrote: >> "(with quality ranging from poor to excellent: wikipedia, PlanetMath >> [3], WolframjAlpha [5])." >> I get the sense you might be saying that Wikipedia is poor quality and >> Wolphram|Alpha is excellent. > Certainly not! Corrected. > >> * "Interaction with the data then tends to be very limited:" One >> thing about OEIS is that a lot of the "interaction" is via people >> contributing new information, and a *lot* of that happens with OEIS, >> right? This was a big argument for why it should be truly free >> (rather than their initial "5% only" rule). > Not familiar with this story. When OEIS was released by the OEIS foundation a year or so ago, they put strong restrictions on how much of the content other people could redistribute. I found this very disturbing and worrisome, since we violate that contents with the sloane spkg. I started a bit of a campaign about this to get them to change the license... and after much internal discussion they did. > As far as I know, if you can't do "custom searches" with OEIS. You > have to download the whole thing and program your own for that. > For instance, if you know the value of your sequence at primes only, > you don't want to fill the sequence with 0s at non-primes and hope > superseeker (by email) will identify that submission as > A010051*something. If you messed up your submission, wait another > hour... > >> * "At some point, the associated algorithms have been reimplemented in >> Mathematica, into the package KnotTheory`" Just curious -- was that >> funded, or done by Wolfram, or? > I don't know who funded it, but judging from > http://katlas.org/wiki/Setup > Dror Bar-Natan had significant influence if he didn't do it himself. > >> * Regarding the human genome being "relatively small", just say how >> big it is (in megabytes). I think it's pretty tiny, if I remember >> right. And it has a "good" copyright (I think). Just saying it is >> possible for one person to "hold it", still allows for the possibility >> that it is 20 terabytes (say). I wonder how many terabytes I can >> hold... I have some 6TB backup disks for sage.math, and I could hold a >> few at once :-) > For everyone's information, the FASTA file looks like it is 1.5Gb. > It's also as heavy as a bookcase > http://en.wikipedia.org/wiki/File:Wellcome_genome_bookcase.png > Maybe I can barely hold one copy. > >> * Top of page 3, describing what you propose to do: this is perhaps >> the most important part of the proposal feels a bit unclear and murky >> to me, so could be made a bit clearer (maybe structure it into 3 >> paragraphs). Also, you might say that this is a plan, but you are >> flexible about changing anything if there are sufficiently compelling >> arguments for design at the workshop. Also, it would be really good >> if you could get feedback on this proposal from Jon Bober and Harald >> Schilly, since your proposal could potentially be read as: "we looked >> at what they did, and it wasn't very good, so we are going to rewrite >> it from scratch using Object Oriented Programming!" (I know I'm >> exaggerating here...) > Yes, ok. > >> I really, really hope this gets funded. > Thanks > >> >> William >> >> >>> Paul >>> >> >> >> >> -- >> William Stein >> Professor of Mathematics >> University of Washington >> http://wstein.org >> >> -- >> You received this message because you are subscribed to the Google Groups >> "sage-combinat-devel" group. >> To post to this group, send email to sage-combinat-devel@googlegroups.com. >> To unsubscribe from this group, send email to >> sage-combinat-devel+unsubscr...@googlegroups.com. >> For more options, visit this group at >> http://groups.google.com/group/sage-combinat-devel?hl=en. >> >> > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] Re: AIM workshop proposal: opinion
On Tue, Nov 1, 2011 at 3:03 AM, Paul-Olivier Dehaye wrote: > Dear all, > I am about to submit a workshop proposal to the American Institute of > Mathematics. The deadline is today, Nov. 1st (fortunately, US time). > The current title of the proposal is "Sage and databases: L-functions > and combinatorial objects". > You can see the pdf at > http://combinat.sagemath.org/misc/raw-file/eae7d2865a9e/grants/2011-11-01-AIM-workshop/aim.pdf > (and can access the source via the sage-combinat repo -> misc -> grants ). > Comments more than welcome! * When you write: "(with quality ranging from poor to excellent: wikipedia, PlanetMath [3], WolframjAlpha [5])." I get the sense you might be saying that Wikipedia is poor quality and Wolphram|Alpha is excellent. * "Interaction with the data then tends to be very limited:" One thing about OEIS is that a lot of the "interaction" is via people contributing new information, and a *lot* of that happens with OEIS, right? This was a big argument for why it should be truly free (rather than their initial "5% only" rule). * "At some point, the associated algorithms have been reimplemented in Mathematica, into the package KnotTheory`"Just curious -- was that funded, or done by Wolfram, or? * Regarding the human genome being "relatively small", just say how big it is (in megabytes). I think it's pretty tiny, if I remember right. And it has a "good" copyright (I think). Just saying it is possible for one person to "hold it", still allows for the possibility that it is 20 terabytes (say). I wonder how many terabytes I can hold... I have some 6TB backup disks for sage.math, and I could hold a few at once :-) * Top of page 3, describing what you propose to do: this is perhaps the most important part of the proposal feels a bit unclear and murky to me, so could be made a bit clearer (maybe structure it into 3 paragraphs). Also, you might say that this is a plan, but you are flexible about changing anything if there are sufficiently compelling arguments for design at the workshop.Also, it would be really good if you could get feedback on this proposal from Jon Bober and Harald Schilly, since your proposal could potentially be read as: "we looked at what they did, and it wasn't very good, so we are going to rewrite it from scratch using Object Oriented Programming!" (I know I'm exaggerating here...) I really, really hope this gets funded. William > Paul > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Multiple databases and sage
On Wed, Oct 19, 2011 at 11:50 AM, Vincent Delecroix <20100.delecr...@gmail.com> wrote: > Hello, > >> I am currently participating in a sage-based project that aims to >> integrate a lot of number theory databases >> [...] > > I am very interested in the project since I have the problem of > interfacing databases in Sage from various sources (in particular, one > sounds number theoretical: the database of congruence subgroups of > Cummins and Pauli). > >> I expect these to be very common problems when trying to integrate >> mathematical data from various sources into sage, regardless of the >> area of mathematics. >> >> Some participants of the sage-combinat project are pushing for the >> concept of "Categories" [...] >> >> I think that similarly the problems I have described in the first >> paragraph could be partly solved from a new concept of >> "MathematicalDatabases" >> [...] > > I am not one of the master of the categorical stuff in Sage, but as > far as I know there are yet some Python library that intends to > interact with databases in an object oriented manner. They are > designed in such way that (after the configuration step) you can > manipulate the data regardless of the implementation of the database. > It separates three concepts "communication with database" (and you > never take care of this), "representation in database" and "the Python > object that you manipulate" (and which is built from an entry in the > database). > > I know sqlalchemy, but after few research I found the Zope Object Database. > I do not recommend using ZODB (=Zope Object Database). If nothing else, there was a recent proposal to remove it from Sage, and nobody was against it. I wrote this for my own use of SQLite from Sage: http://code.google.com/p/nosqlite/ -- William > I do not know if this of any help. > > Is there a page to see yhe advancement/questions/problems of your project ? > > Best, > Vincent > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: conflict in trac_9128-sphinx_links_all-fh.patch
On Thu, Aug 25, 2011 at 12:52 AM, Nicolas M. Thiery wrote: > On Wed, Aug 24, 2011 at 02:57:48PM -0700, William Stein wrote: >> On Sat, Aug 20, 2011 at 12:21 AM, Nicolas M. Thiery >> > Ah shoot, I forgot to check the push permissions. On >> > combinat.sagemath.org, the directories /home/combinat/hg/patches and >> > /home/combinat/hg/misc belonged (recursively) to www-data, so that the >> > web server could have write access on those. Could you change the >> > permissions similarly on boxen? I guess using combinat as user, and >> > www-data (or whatever the analogue is for apache2 on boxen) as group >> > would be good to give write access to both combinat by ssh and the web >> > server. I guess just doing this permission change on >> > /home/combinat/hg/.hg/store (and same for misc) is both sufficient and >> > safer. >> >> Done. Now what? Can we do the switch? > > I am still getting: > > abandon : HTTP Error 500: Permission denied: .hg/store/lock > > I guess that's because the group is still missing write permissions > (recursively): > > drwxr-xr-x 3 combinat www-data 4096 2011-08-18 00:38 store Fixed... hopefully. William -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: conflict in trac_9128-sphinx_links_all-fh.patch
On Sat, Aug 20, 2011 at 12:21 AM, Nicolas M. Thiery wrote: > On Fri, Aug 19, 2011 at 02:42:16PM -0700, William Stein wrote: >> I've made the changes to the apache config you mentioned below. Can >> you double check them below? Once you write back to confirm, I'll >> change apache so it is combinat.sagemath.or instead of >> wintrac.sagemath.org pointing at boxen, then shutdown the virtual >> machine. > > Ah shoot, I forgot to check the push permissions. On > combinat.sagemath.org, the directories /home/combinat/hg/patches and > /home/combinat/hg/misc belonged (recursively) to www-data, so that the > web server could have write access on those. Could you change the > permissions similarly on boxen? I guess using combinat as user, and > www-data (or whatever the analogue is for apache2 on boxen) as group > would be good to give write access to both combinat by ssh and the web > server. I guess just doing this permission change on > /home/combinat/hg/.hg/store (and same for misc) is both sufficient and > safer. Done. Now what? Can we do the switch? -- William -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: conflict in trac_9128-sphinx_links_all-fh.patch
Hi Nicolas, I've made the changes to the apache config you mentioned below. Can you double check them below? Once you write back to confirm, I'll change apache so it is combinat.sagemath.or instead of wintrac.sagemath.org pointing at boxen, then shutdown the virtual machine. -- William On Thu, Aug 18, 2011 at 1:08 AM, Nicolas M. Thiery wrote: > Hi William, Mike, > > On Tue, Aug 16, 2011 at 11:04:56AM -0700, William Stein wrote: >> The htaccess was somewhat wrong -- I had to move all that content to >> /etc/apache2/httpd.conf, > > Ah right, ScriptAliasMatch can't be in the .htaccess. Too bad, I was > hoping to put as much as possible there so that we would not need to > bother the sysadmin whenever some configuration tweaking was needed > for combinat.sagemath.org. > >> and change some broken links (combinat/www/hg --> combinat/hg). > > Oops. Thanks. > >> But I did that, and setup the new server as >> >> http://wintrac.sagemath.org >> >> for *testing*, since we evidently aren't using wintrac.sagemath.org right >> now. >> >> So try http://wintrac.sagemath.org, >> http://wintrac.sagemath.org/patches, and >> http://wintrac.sagemath.org/misc >> and let me know if it works or not. > > It seems to work fine! Thanks! > > Remaining minor issue: currently http://wintrac.sagemath.org/patches/ > works, but not http://wintrac.sagemath.org/patches due to some > extraneous / I had put in the config. Also, the authentication seems > to be ignored indeed; but that's not urgent, so I'll leave that to > Mike to double check since he had set it up. > > So we can go on with the migration, with this final config section for > combinat.sagemath.org: > > ## > > RewriteEngine On > ServerName combinat.sagemath.org > DocumentRoot /home/combinat/www/ > > > AuthType Digest > AuthName "sage.math.washington.edu" > AuthDigestProvider file > AuthUserFile /var/trac/sage_trac/conf/passwd > > Require valid-user > > # TODO: /code should be completely in read only > > > # Let mercurial's hgwebdir handle the patches/, code/, and misc/ hg > repository > ScriptAliasMatch ^(/patches.*) /home/combinat/hg/hgwebdir.cgi/$1 > ScriptAliasMatch ^(/misc.*) /home/combinat/hg/hgwebdir.cgi/$1 > ScriptAliasMatch ^(/code.*) /home/combinat/hg/hgwebdir.cgi/$1 > > > ## > > Then, after double checking, the virtual machine can be turned off. > > Thanks again! > > Best, > Nicolas > > PS: I am back home and will be more or less online 9am-11pm (Paris) in > the coming weeks. > > -- > Nicolas M. Thiéry "Isil" > http://Nicolas.Thiery.name/ > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: conflict in trac_9128-sphinx_links_all-fh.patch
On Mon, Aug 15, 2011 at 2:00 AM, Nicolas M. Thiery wrote: > Hi William, Mike, > > Thanks for creating the combinat account on boxen! I have setup > /home/combinat on boxen to prepare the migration of > combinat.sagemath.org from the current virtual machine. It might now > be enough to replace the current combinat.sagemath.org section in > /etc/apache2/httpd.conf on boxen by: > > # > # combinat.sagemath.org homepage > # > > ServerName combinat.sagemath.org > DocumentRoot /home/combinat/www/ > > > And maybe do some DNS reconfiguration. > > That being said, I could not test the configuration and it's been a > while I haven't played with an apache server; so no guarantees > whatsoever! > > Could you please review on boxen: > > - /home/combinat/README > - /home/combinat/www/.htaccess The htaccess was somewhat wrong -- I had to move all that content to /etc/apache2/httpd.conf, and change some broken links (combinat/www/hg --> combinat/hg). But I did that, and setup the new server as http://wintrac.sagemath.org for *testing*, since we evidently aren't using wintrac.sagemath.org right now. So try http://wintrac.sagemath.org, http://wintrac.sagemath.org/patches, and http://wintrac.sagemath.org/misc and let me know if it works or not. I don't know if the authentication is setup correctly. William > - /home/combinat/hg/hgweb.config > > If there is some issue and you would like me to debug it, could you > setup a combinat-test.sagemath.org virtual web server (in the DNS and > in httpd.conf) for me to play around, before we do the final > migratation of combinat.sagemath.org? > > Cheers, > Nicolas > -- > Nicolas M. Thiéry "Isil" > http://Nicolas.Thiery.name/ > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: Problems installing combinat
On Tue, Aug 9, 2011 at 10:48 AM, Christian Stump wrote: > Hi William, > >>> I've started the virtual machine again, so it should be back in a few >>> minutes. > > the status went from no response to Service Temporarily Unavailable, > or are the few minutes not yet over? The virtual machine failed to start because the virtual DHCP server had disappeared. I tried recreating it which worked. Now the virtual machine won't start with an error "VBoxHeadless: ERROR: failed to create the VirtualBox object! ERROR: code NS_BASE_STREAM_WOULD_BLOCK (0x80470007) - Stream operation would block (extended info not available) Most likely, the VirtualBox COM server is not running or failed to start." So I restarted everything related with virtual box (kernel modules, etc.), and now the virtual machine is booting up fine. As a result, the combinat server is up. -- William > > Best, Christian > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] Re: conflict in trac_9128-sphinx_links_all-fh.patch
On Aug 8, 4:29 am, "Nicolas M. Thiery" wrote: > Hi William! > > On Tue, Aug 02, 2011 at 05:50:58PM -0700, William Stein wrote: > > I initiated a reboot of the virtual machine. > > > By the way, I would be thrilled if somebody could move > > combinat.sagemath.org from the virtual machine to boxen, since then I > > wouldn't have to run that virtual machine anymore. > > I could possibly give it a shot in the coming days. Do you have > pointers to the install/setup files of other similar servers on boxen > that I could start from? Great! I made a combinat user on boxen.math.washington.edu. Can you send me an ssh public key, so I can make it so you can login to combi...@boxen.math.washington.edu? William -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: Problems installing combinat
On Tue, Aug 9, 2011 at 9:57 AM, Christian Stump wrote: > Salut, > >> And back down?http://combinat.sagemath.org/patches/gives >> me again ``Service Temporarily Unavailable''. > > Is there any chance of getting back the server today? We would like to > have some things available for the next sage demo at the msri summer > school on cluster algebras tomorrow... I've started the virtual machine again, so it should be back in a few minutes. I very, very, very strongly encourage somebody to please, please, volunteer to move this patch repository to boxen.math.washington.edu, so I can turn off the virtual machine.Then this problem with the virtual machine crashing, not being up, etc., will disappear. -- William > > Thanks, Christian > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] conflict in trac_9128-sphinx_links_all-fh.patch
On Tue, Aug 2, 2011 at 5:31 PM, Christian Stump wrote: >> As usual, could you be more specific (sage-version... etc, did you correctly >> update your guard with sage -conbinat qselect or sage -update). It is ok on >> my >> computer with a sage-combinat install one week old. I'm on a extremely sloppy >> network and sage-combinat server is down. So there is nothing I can do >> now. Sorry... > > Salut Florent, > > the server is still down... I use version 4.7, and I think the guards > should all be correct. But I will redo it once the server runs again. I initiated a reboot of the virtual machine. By the way, I would be thrilled if somebody could move combinat.sagemath.org from the virtual machine to boxen, since then I wouldn't have to run that virtual machine anymore. > > Best, Christian > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] temporary combinat.sagemath.org downtime
Hi, I rebooted the sagemath virtual machine (on which combinat.sagemath.org and nothing else currently sits), and it's taking a long time (hour?) due to a forced ext3 filesystem check. -- William -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: How to install (parts of) the combinat queue on many machines?
Hi, I'm just curious. What are the *drawbacks* of installing the combinat queue? What if I installed it into http://sagenb.org, just viewing it as another optional package (I install dozens of optional packages). -- William On Fri, Jul 15, 2011 at 12:22 PM, Christian Stump wrote: > Hi all! > > we now have a public sage notebook with the combinat queue applied > running on sage.lacim.uqam.ca. Everything seems to run smoothly, but > we are still in the TEST PHASE, so please NO SERIOUS RESEARCH so far, > accounts and worksheets MIGHT GET DELETED. > > As we want to have 20 students using it at the same time at a summer > school on cluster algebras in 2 weeks, we would like to make some > real-world tests, so we need some VOLUNTEERS to test. > > So far, I logged in this morning with 12 accounts doing heavy > computations, and the cpu and memory was able to handle that: around > 80% or the resources were used, so the limit was not too far. > > Maybe some people could start creating accounts and play to get some > feedback! If possible, we would like to have multiple accounts running > various things and get a usage peak on > > MONDAY 11am EDT. > > In the long-run, this (or such a) notebook might be also an idea to be > used on sage-combinat days during sage introductions in order to save > all the time used installing sage on everyone's computer. What do you > think? > > Best, Christian > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] combinat.sagemath.org
Hi, I've been migrating services off of the sagemath virtual machine back to run natively on boxen.math.washington.edu. The *only* thing that is left that is being served off of the sagemath virtual machine is combinat.sagemath.org, which is I think: (1) top level page redirects to the standard sagemath wiki (2) an hg repo http://combinat.sagemath.org/patches Who can help me to migrate this stuff back to boxen, so I can finally turn of the sagemath virtual machine? I want to point out that right now this virtual machine is not backed up. I don't have a good way to back it up, since it consists of one massive 148GB file: -rw--- 1 wstein wstein 148G 2009-12-20 01:24 sagemath.vdi It would make a lot of sense to me for me to create an account "combinat" on boxen.math.washington.edu, move the hg files there, then serve them via apache on boxen.So, I've made such an account just now, and put a copy of /home/combinat/hg in there, so at least there is a recent backup of that. -- William -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] change base ring of free module
On Wed, Jul 13, 2011 at 12:22 PM, Martin Rubey wrote: > Martin Rubey writes: > >> Dear combinat gurus! >> >> I have a basis and two CombinatorialFreeModules over this basis, say one >> over QQ and the other over QQ[q]. I'd like to convert elements from the >> first into the second. Is there a built-in way to do this, or do I have >> to iterate over the coefficients? > > Sorry, I mis-asked: should have been tensor products of > CombinatorialFreeModules. It would be helpful if you posted a complete example. William > > >> >> (I'm not sure whether this should go to sage-support. feel free to >> redirect, I'm reading both) >> >> Thanks a lot, >> >> Martin > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-devel@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-devel@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Grant applications
On Fri, Nov 5, 2010 at 3:15 AM, Nicolas M. Thiery wrote: > Dear Sage-Combinat developers, > > It is the time of the year for grant applications! > > Anne, Jason, Dan, ... are planning to apply for an NSF "Computational > Mathematics" grant. See the wiki (link below) for details, and let us > know if you would like to participate. John Palmieri and I applied for an NSF "Computational Math" grant for Sage one year ago, and got it. Here's the complete application: http://wstein.org/grants/compmath09/ I also applied for an NSF Computational Math grant for Sage back in 2006, and also got it -- though they reduced the budget to "one postdoc": http://wstein.org/grants/sage-06/ In the second one, I think "Algebra and Number Theory" paid for part of the budget. So you might give the combinatorics-relevant program director at NSF a heads up about your COMPMATH proposal. > > We (French) should think about applying to ANR grants. > > Franco, François, Mike, ... maybe there is some analogues that should > be investigated in Canada? > > To help coordinate the various projects, I have setup: > > - A page on our wiki listing the current and former grant > applications that involved *-Combinat: > > http://wiki.sagemath.org/combinat/Grants > > Please expand on it! > > In particular: > - Florent: please expand the section on ANR "Moules" grant > - Anne, Mike, ...: please double check the FRG grant > > - A private google group sage-combinat-grants for coordinating grant > applications. Let me know if you would like to use it for a > specific grant application. We can also create new groups as > needed. > > - A directory in our misc mercurial server for working on grant > application material and keeping track of old material (if you do > not mind it being public; otherwise you could use instead > e.g. bitbucket): > > http://combinat.sagemath.org/misc/file/tip/grants > > Cheers, > Nicolas > -- > Nicolas M. Thiéry "Isil" > http://Nicolas.Thiery.name/ > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-de...@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] Re: [sage-support] Changing the path of an edge in a graph
On Sat, Aug 14, 2010 at 9:22 PM, Nathann Cohen wrote: >> Clarification: Sage's plot code does not "interact" with the GPL >> incompatible graphviz library in any way. > > ?.. So we have a graphviz spkg and absolutely no interface between the two ? > O_o I'm sorry, that's not what I meant.You can do sage: g = graphs.PetersenGraph() sage: g.plot(layout='graphviz') and graphviz would then evidently somehow get used, I guess. I just meant that by default Sage's plotting code doesn't use it at all. I could test the above though, since (not surprisingly) the optional graphviz spkg fails to install for me (on bog standard OS X 10.6), and installing graphviz from the web isn't enough because the above requres dot2tex. `../../lib/gvc/no_demand_loading.c make[3]: *** No rule to make target `../../plugin/pango/libgvplugin_pango.la', needed by `dot_builtins'. Stop. make[3]: *** Waiting for unfinished jobs mv -f .deps/no_demand_loading.Tpo .deps/no_demand_loading.Po mv -f .deps/dot.Tpo .deps/dot.Po make[2]: *** [all-recursive] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 Error building Graphviz --- I tried on sage.math.washington.edu (linux) and the build succeeds, but sage: g = graphs.PetersenGraph() sage: g.plot(layout='graphviz') still fails with a "dot2tex" error: /mnt/usb1/scratch/wstein/build/sage-4.5.2.rc0/local/lib/python2.6/site-packages/sage/graphs/dot2tex_utils.pyc in assert_have_dot2tex() 60 raise RuntimeError(check_error_string) 61 except ImportError: ---> 62 raise RuntimeError(missing_error_string) 63 64 def quoted_latex(x): RuntimeError: dot2tex not available. Please see :meth:`sage.graphs.generic_graph.GenericGraph.layout_graphviz` for installation instructions. I tried installing dot2tex on sage.math.washington.edu (via apt-get), but the above error stays. So I have absolutely no clue how to get g.plot(layout='graphviz') to actually do anything useful. On the other hand, one can use the command g.graphviz_to_file_named(...) to save a description of g in graphviz format to a file, which one can then open with Graphviz directly. That works (and is what I illustrated in my graph talk, which is here: http://sagemath.org/help-video.html). -- William -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] Re: Sage Development video/screencast
Hi, I also made a 25-minute screencast/video introduction to graph theory in Sage: * Stream Video: http://vimeo.com/14046039 (this will work about 30 minutes from now) * Complete video (180MB): http://sage.math.washington.edu/home/wstein/video/sagedays25/Graph%20Theory%20in%20Sage.m4v * Sage Worksheet: http://sagenb.org/home/pub/2352/ -- William On Tue, Aug 10, 2010 at 3:52 PM, William Stein wrote: > Hi, > > I created a screencast (with picture-in-picture video of me) on how to > contribute to Sage: > > * Streaming video: http://vimeo.com/14044496 > > * Download the whole video: > http://sage.math.washington.edu/home/wstein/video/sagedays25/Contributing%20to%20Sage.m4v > > * PDF of the slides: > http://wiki.sagemath.org/daysindia25/schedule?action=AttachFile&do=view&target=stein-contrib.pdf > > The video is about 40 minutes long. > > -- William > > -- > William Stein > Professor of Mathematics > University of Washington > http://wstein.org > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Python, Sage, categories
On Tue, Jul 27, 2010 at 11:20 AM, Nicolas M. Thiery wrote: > On Tue, Jul 27, 2010 at 02:05:21AM -0700, Robert Bradshaw wrote: >> > Option 4 is to fix this defect in Cython. I played around with this >> > the other night and the problem is this: the Python C API has only one >> > slot for both __getattr__ and __getattribute__. If you only overload >> > the former, CPython can't tell, and assumes you overrode the latter. >> > It then creates a pure Python stub in your Python classes which call >> > the __getattribute__ wrapper via Python semantics. I'm thinking if we >> > can surpress or delete that wrapper if only __getattr__ is implemented >> > then it will just inherit the slot. I haven't had a chance to try this >> > out though. >> >> And, catching up on my Cython email, Carl Witty may have essentially >> done this! http://trac.cython.org/cython_trac/ticket/561 > > Carl, Robert, thanks so much for investigating this! Yes, indeed. This is absolutely fantastic work you guys did! > > Wow a general speed improvement over all non cdef classes will be good :-) > I am looking forward timing results and trying it out! Yes, indeed. And by the way my Cython benchmark was for a non-cdef'd but still Cython class. So everything is consistent. Thanks again Carl, etc.! William > > Cheers, > Nicolas > -- > Nicolas M. Thiéry "Isil" > http://Nicolas.Thiery.name/ > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-de...@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Python, Sage, categories
On Mon, Jul 26, 2010 at 3:36 PM, Nicolas M. Thiery wrote: > William, > > > There is a strong technical issue that needs to be resolved, and for > which I explicitly take the blame. And I understand your frustration > when fighting with zillions of technical points. However I perceived > your e-mail as unfairly bashing the sage-combinat community, which > is just putting me off. Now, I should just step back and answer in a > couple hours, but on the other hand this discussion needs to get > going on the technical side. > > Deep breath. > I'm very sorry to have unfairly bashed the sage-combinat community, and I'm glad you've jumped to their defense to clarify matters. I was exhausted after a very long, sleepless coding sprint (days and days) trying to speed things up, and very surprised to discover this source of a speed issue. My email was certainly very unfairly rewritten. I hope you'll accept my apology. > > On Mon, Jul 26, 2010 at 11:53:59AM -0700, William Stein wrote: >> I'm talking about the __getattr__ that you added. Simply commenting >> out the __getattr__ function leads to a significant speedup. This >> has been replicated by several other people, and this thread >> contains a deep investigation into why this is happening (though >> things still aren't clear). > > Then, do you have an explanation for why this does not show up above? > Can you reproduce my timings? > >> >> A few months ago some code was added to Sage by the combinat folks >> >> called "categories". I recently learned ObjectiveC, and found out >> >> that this idea of "categories" goes back to smalltalk at least, and >> >> was fully implemented in ObjectiveC in the mid 1980s. It has little >> >> to do with category theory in the sense of mathematics, though is >> >> related. Basically, it is a way to attach a bunch of generic >> >> methods to a class without using inheritance. >> > >> > That's a very reductive view. And actually quite inaccurate: most of >> > Sage's parents and elements *do* get their generic methods from the >> > categories, through class inheritance. There is indeed one exception: >> > extension types (i.e. Cython classes), which currently use the getattr >> > hack (because Cython does not support yet any form of multiple >> > inheritance). >> >> Do you know anything about Objective C or smalltalk or "categories" in >> those languages? > > I haven't played with them directly. But from looking around this very > much looks like what "extends" do in other languages I played with > (Aldor, ...). And which I would love to have in Python as well (I am > actually planning to make a crude implementation of it, for plain > Python classes, for use with my external experimental code; it should > just be a couple lines of code). > > So yes, the getattr hack is some sort of dynamic implementation of > categories (in smalltalk sense), which is a building block for the > implementation of "real" categories (in the Sage sense) for extension > types. > >> I don't really care about blame; I just want to find a way to >> resolve this problem. I've slowed down/messed up etc., so many >> things in Sage over the years, it isn't even funny. > > > I am glad to hear that, because that did not show up in your e-mail. > > >> I think the impact depends a lot on how many python def'd methods the >> class has. E.g., I was testing with the huge number field classes, >> and the slowdown is much greater than with testing with a naked class >> that just derives from Element. I did not notice any real difference >> between otherwise identical Cython and Python classes. > > I just had a look at the Python sources (in Object/typeobject.c), and > it's all about the difference between slot_tp_getattro and > slot_tp_getattr_hook, the later being a bit more complicated than the > former. I did not see obvious reasons for having it slower for large > classes, except for the lookup of the __getattr__ method. That makes a lot of sense. > From > glancing at it, it sounds like this could be optimized, and in > particular that the getattr lookup could be delayed until it is really > used (if at all). This does not tell anything about Cython I guess. > > Also it sounds like __getattr__ could be set to None if it is not > really needed, and then on the next call getattro_hook would switch > tp_getattro to the fast simple implementation slot_tp_getattroback. At > least this could solve the issue for Python clas
Re: [sage-combinat-devel] Python, Sage, categories
On Mon, Jul 26, 2010 at 11:31 AM, Nicolas M. Thiery
wrote:
> On Fri, Jul 23, 2010 at 01:05:00PM -0700, William Stein wrote:
>> During the last few weeks I've spent time optimizing code, among
>> other things.
>
> Great!
>
>> A surprising number of random things I look at in Sage are too slow
>> by a factor of 10-100, usually due to programming style. One way to
>> help to remedy that would be to write a book or article about how to
>> program Cython + Python *efficiently*, and avoid the numerous traps.
>> Basically, one false move in Python when implementing mathematics
>> algorithms can knock you down by a factor of 10-100 in speed.
>
> Definitely.
>
>> As an example of this, try multiplying polynomials in ZZ['x'] in
>> Sage right now:
>>
>> sage: R. = ZZ[]
>> sage: timeit('x*x',number=10^6)
>> 100 loops, best of 3: 1.96 µs per loop
>>
>> FLINT could do that multiply in a few hundred nanoseconds, so why does
>> it take 2 microseconds (2000 nanoseconds)? Because the code is
>> complicated and general, but was written without any thought about
>> efficiency. By making a few changes (really making the code less
>> clever), I get:
>>
>> sage: timeit('x*x', number=10^6)
>> 100 loops, best of 3: 687 ns per loop
>>
>> The categories implementation as it is in Sage must be changed or
>> removed. There, I got your attention.
>
> Let's see about this.
>
> That's before any category code:
>
> zephyr> /opt/sage-4.2.1/sage
> sage: R. = ZZ[]
> sage: timeit('x*x',number=10^6)
> 100 loops, best of 3: 1.14 µs per loop
>
> That's after the integration of the main category patches:
>
> zephyr-~monoid>/opt/sage-4.3/sage -br main
>
> sage: R. = ZZ[]
> sage: timeit('x*x',number=10^6)
> 100 loops, best of 3: 1.12 µs per loop
>
> That's after #7921: Categories for extension types via __getattr___:
>
> zephyr-~monoid>/opt/sage-4.3.2/sage -br main
> sage: R. = ZZ[]
> sage: timeit('x*x',number=10^6)
> 100 loops, best of 3: 1.13 µs per loop
>
> That's now:
>
> zephyr-~monoid>/opt/sage-4.4.4/sage -br main
> sage: R. = ZZ[]
> sage: timeit('x*x',number=10^6)
> 100 loops, best of 3: 1.19 µs per loop
>
> Please don't blame this one on categories. The overhead is in the
> coercion code which was written by our favorite Cython expert.
I'm talking about the __getattr__ that you added. Simply commenting
out the __getattr__ function
leads to a significant speedup. This has been replicated by several
other people, and this
thread contains a deep investigation into why this is happening
(though things still aren't clear).
(But you realized all this below.)
> Now, should the coercion code be changed or removed because it is too
> generic and horribly slow? First note that we are speaking about a
> speed factor of 2 or 3, not 10 or 100. And this is for very low level
> arithmetic; the overhead would be negligible on anything more
> complicated (if not just larger polynomials). So the right thing to do
> is simply to override the generic code by optimized code for those
> element classes which have very cheap arithmetic. That's what has
> been done for ZZ, ... and as far as I know everybody is happy about
> this approach.
The point -- which you miss -- is that the way the category idea is
implemented in Sage surprisingly causes *all* attribute
lookups to slowdown substantially. It can easily be the case that a
whole program is just a sequence of attribute lookups,
so the performance penalty of slowing this down is significant.
> speed factor of 2 or 3, not 10 or 100
A factor of 2 or 3 is very significant when it happens uniformly
across the board.
>> A few months ago some code was added to Sage by the combinat folks
>> called "categories". I recently learned ObjectiveC, and found out
>> that this idea of "categories" goes back to smalltalk at least, and
>> was fully implemented in ObjectiveC in the mid 1980s. It has little
>> to do with category theory in the sense of mathematics, though is
>> related. Basically, it is a way to attach a bunch of generic
>> methods to a class without using inheritance.
>
> That's a very reductive view. And actually quite inaccurate: most of
> Sage's parents and elements *do* get their generic methods from the
> categories, through class inheritance. There is indeed one exception:
> extension types (i.e. Cython classes), which currently use the getattr
> hack (because Cython does not support yet any form o
[sage-combinat-devel] Python, Sage, categories
Hi,
During the last few weeks I've spent time optimizing code, among other
things. A surprising number of random things I look at in Sage are
too slow by a factor of 10-100,
usually due to programming style.One way to help to remedy that
would be to write a book or article about how to program Cython +
Python *efficiently*, and avoid the numerous traps. Basically, one
false move in Python when implementing mathematics algorithms can
knock you down by a factor of 10-100 in speed. As an example of
this, try multiplying polynomials in ZZ['x'] in Sage right now:
sage: R. = ZZ[]
sage: timeit('x*x',number=10^6)
100 loops, best of 3: 1.96 µs per loop
FLINT could do that multiply in a few hundred nanoseconds, so why does
it take 2 microseconds (2000 nanoseconds)? Because the code is
complicated and general, but was written without any thought about
efficiency. By making a few changes (really making the code less
clever), I get:
sage: timeit('x*x', number=10^6)
100 loops, best of 3: 687 ns per loop
The categories implementation as it is in Sage must be changed or
removed. There, I got your attention.
A few months ago some code was added to Sage by the combinat folks
called "categories". I recently learned ObjectiveC, and found out
that this idea of "categories" goes back to smalltalk at least, and
was fully implemented in ObjectiveC in the mid 1980s. It has little
to do with category theory in the sense of mathematics, though is
related. Basically, it is a way to attach a bunch of generic methods
to a class without using inheritance. So far so good.
The combinat folks implemented this programming idea in Sage not by
changing the Python languge, but by defining a custom __getattr__
method at sticking it in the base classes for Sage parents and
elements. The problem: this means that every single method lookup on
every single Sage object seem to now have about 1500nanoseconds added
to it in completely unnecessary overhead. Most of what Sage does is
call functions, so this is a huge, huge problem. Try it out for
yourself:
(1) Start up Sage and try this:
flat:~ wstein$ sage-4.4.4
--
| Sage Version 4.4.4, Release Date: 2010-06-23 |
| Type notebook() for the GUI, and license() for information.|
--
sage: QQ.testit = 'foobar'
sage: timeit('QQ.testit',number=10^6)
100 loops, best of 3: 2.43 µs per loop
sage: timeit('QQ.testit',number=10^6)
100 loops, best of 3: 2.53 µs per loop
This is on my OS X laptop, so your timings may be different.
(2) Now go into SAGE_ROOT/devel/sage/sage/structure/parent.pyx
and change the line
def __getattr__(self, name):
to
def x__getattr__(self, name):
then restart sage with "sage -br"
--
| Sage Version 4.4.4, Release Date: 2010-06-23 |
| Type notebook() for the GUI, and license() for information.|
--
sage: QQ.testit = 'foobar'
sage: timeit('QQ.testit',number=10^6)
100 loops, best of 3: 1.53 µs per loop
sage: timeit('QQ.testit',number=10^6)
100 loops, best of 3: 1.54 µs per loop
This is a major problem. The best solution I can think of at present
is to remove these methods from the top level of Sage, then add
objects like Parent_cat and Element_cat, and put them there. Then
change all the combinat objects to derive from those classes. I'm not
sure this would work though.
Anyway, a slowdown of more than 1 microsecond on everything throughout
sage is absolutely unacceptable.
So, big question -- am I just confused? It seems impossible that
nobody noticed this before, or that people made a conscious decision
to let this code in if it slows down Sage this much. (I.e., my guess
is that nobody even bothered to benchmark the code when refereeing
it.)
Robert B: since you were the one who decided to let this into Sage,
and since I know you know Python insanely well, am I just missing
something here? It seems to me like this one patch is a huge drain on
Sage's performance... So much so that I'm personally tempted to
just remove it for my own work. But maybe I'm just missing something
obvious.
--William
--
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org
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[sage-combinat-devel] sage-4.4.4
Hi, Sage-4.4.4 is out http://sage.math.washington.edu/home/release/sage-4.4.4/sage-4.4.4.tar I'm emailing you guys on combinat, since this release has a lot of combinat in it... Binaries will appear soon enough... -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Pickling issue with words
On Sun, Jun 13, 2010 at 3:24 PM, Sébastien Labbé wrote: >>Hi word people! > > Hi cristal people! > > _class__sage_combinat_crystals_tensor_product_TensorProductOfClassicalCrystalsWithGenerators__.sobj >> doctest:1: DeprecationWarning: Your word object is saved in an old file >> format since FiniteWord_over_OrderedAlphabet is deprecated and will be >> deleted in a future version of Sage (you can use FiniteWord_list instead). >> You can re-save your word by typing "word.save(filename)" to ensure that it >> will load in future versions of Sage. >> doctest:1: DeprecationWarning: Your word object is saved in an old file >> format since AbstractWord is deprecated and will be deleted in a future >> version of Sage (you can use FiniteWord_list instead). You can re-save your >> word by typing "word.save(filename)" to ensure that it will load in future >> versions of Sage. >> doctest:1: DeprecationWarning: Your word object is saved in an old file >> format since Word_over_Alphabet is deprecated and will be deleted in a >> future version of Sage (you can use FiniteWord_list instead). You can >> re-save your word by typing "word.save(filename)" to ensure that it will >> load in future versions of Sage. >> doctest:1: DeprecationWarning: Your word object is saved in an old file >> format since Word_over_OrderedAlphabet is deprecated and will be deleted in >> a future version of Sage (you can use FiniteWord_list instead). You can >> re-save your word by typing "word.save(filename)" to ensure that it will >> load in future versions of Sage. >> doctest:1: DeprecationWarning: ChristoffelWord_Lower is deprecated, use >> LowerChristoffelWord instead >> Failed: >> >> _class__sage_combinat_crystals_tensor_product_FullTensorProductOfClassicalCrystals__.sobj >> >> _class__sage_combinat_crystals_tensor_product_TensorProductOfClassicalCrystalsWithGenerators__.sobj >> Successfully unpickled 569 objects. >> Failed to unpickle 2 objects. > > Indeed, there are maybe 6 word objects being pickled in the pickle jar > but they all date from a long time ago and all of them have been > deprecated since one year. I would like to remove those 6 pickled > object from the pickle jar and replace them with the new generation of > words that got in Sage during summer 2009. This way, it would really > make sure that we do not break the pickle of objects that are really > used. Also, this will allow us to then clean up the code a lot, > because some kind of arabesques are being done to support the old > stuff... > > I know William prefer to keep old objects in the pickle jar, but in > this case, I would like to remove them Will put time on this when > I have time... I do prefer keeping old pickles (that's the point of the pickle jar), but I definitely don't want to get in the way of the sage-combinatorics group, and understand that your code is under very active development. Thanks for the work you're doing on cleanup! William > > Cheers, > > Sébastien > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-de...@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Sage 4.4.3
On Wed, Jun 2, 2010 at 3:02 PM, William Stein wrote: > On Wed, Jun 2, 2010 at 1:31 PM, Nicolas M. Thiery > wrote: >> Dear release managers! >> >> What's the current time line for Sage 4.4.3? >> >> We have been working hard those last days on flushing the >> Sage-Combinat queue, and have more than 25 patches with positive >> review ready for inclusion. Well, there is still some work ahead, with >> 15 patches under review and about 125 others still under development :-) >> >> We have a developers meeting on June 14-th - 18-th, and it would be of >> great help if those patches could be merged in 4.4.3 by then, or even >> better if 4.4.3 was released. Any luck? >> >> Thanks! > > Basically nobody has been working on Sage releases lately. I did some > work on 4.4.3 during > the first day of Sage days last week, and it has lingered, because I > simply don't have the time. > There are 94 tickets with positive review: > http://trac.sagemath.org/sage_trac/report/32 > > There is also an alpha1 of sage-4.4.3 here, and two tiny doctests failures > > > http://sage.math.washington.edu/home/wstein/build/release/4.4.3/sage-4.4.3.alpha1.tar > > Failures on sage.math: > > sage -t -long "devel/sage/sage/graphs/generic_graph.py" > sage -t -long "devel/sage/sage/sets/set.py" > Total time for all tests: 8037.9 seconds > > This fails to build on OS X, due to some changes we made to get it to > build on Cygwin. > > The alpha above makes almost no changes to the core Sage library. > > Of the "25 patches with positive review ready for inclusion" that you > mentioned above, > are they all changes to the core Sage library? Or do the patch spkg's, etc.? > > One possibility would be to test/stabilize the current 4.4.3.alpha* > (i.e., fix the fallout from the cygwin > related tickets), include those 25 patches (all to the sage library), > and release 4.4.3 on Saturday. > If you like that, then make a clean sage-4.4.2, apply all 25 patches, > test it, and I can just pull those > changes in, and that will be 4.4.3. Hi, I didn't get any feedback on this proposal, and now I've decided to just do a feature freeze on 4.4.3, since I applied all the critical/blocker fixes listed on trac, fixed the bugs mentioned before (with sets and pynac), and just want to release something after going through the build checklist. It would make great sense to have another Sage release before June 14. I don't want to be the one to make it. If you really want one that definitely has the combinat stuff correctly merged in, perhaps you could be that release manager, taking the 4.4.3 release as a start? William -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] Re: [sage-release] Re: Sage 4.4.3
(sorry for the crossposting) On Wed, Jun 2, 2010 at 3:58 PM, leif wrote: >> There is also an alpha1 of sage-4.4.3 here, and two tiny doctests failures >> >> http://sage.math.washington.edu/home/wstein/build/release/4.4.3/sage-... >> >> Failures on sage.math: >> >> sage -t -long "devel/sage/sage/graphs/generic_graph.py" > > *Tiny* doctest failure?! This might break lots of documentation/texts > prepared with Sage (and I guess breaks the notebook output as well). > I've qualified this "critical", though I'd rather consider this a > blocker. (See ticket #9086.) Nobody proposed releasing Sage without fixing this. >> sage -t -long "devel/sage/sage/sets/set.py" >> Total time for all tests: 8037.9 seconds >> >> This fails to build on OS X, due to some changes we made to get it to >> build on Cygwin. >> >> The alpha above makes almost no changes to the core Sage library. >> >> Of the "25 patches with positive review ready for inclusion" that you >> mentioned above, >> are they all changes to the core Sage library? Or do the patch spkg's, etc.? >> >> One possibility would be to test/stabilize the current 4.4.3.alpha* >> (i.e., fix the fallout from the cygwin >> related tickets), include those 25 patches (all to the sage library), >> and release 4.4.3 on Saturday. > > Burcin said he won't be able to fix #9086 until next week... Burcin isn't the only person that knows how to work on Pynac. >> If you like that, then make a clean sage-4.4.2, apply all 25 patches, >> test it, and I can just pull those >> changes in, and that will be 4.4.3. > > If module_list.py isn't affected by those patches... It depends on how module_list.py is effected. -- William -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Sage 4.4.3
On Wed, Jun 2, 2010 at 1:31 PM, Nicolas M. Thiery wrote: > Dear release managers! > > What's the current time line for Sage 4.4.3? > > We have been working hard those last days on flushing the > Sage-Combinat queue, and have more than 25 patches with positive > review ready for inclusion. Well, there is still some work ahead, with > 15 patches under review and about 125 others still under development :-) > > We have a developers meeting on June 14-th - 18-th, and it would be of > great help if those patches could be merged in 4.4.3 by then, or even > better if 4.4.3 was released. Any luck? > > Thanks! Basically nobody has been working on Sage releases lately. I did some work on 4.4.3 during the first day of Sage days last week, and it has lingered, because I simply don't have the time. There are 94 tickets with positive review: http://trac.sagemath.org/sage_trac/report/32 There is also an alpha1 of sage-4.4.3 here, and two tiny doctests failures http://sage.math.washington.edu/home/wstein/build/release/4.4.3/sage-4.4.3.alpha1.tar Failures on sage.math: sage -t -long "devel/sage/sage/graphs/generic_graph.py" sage -t -long "devel/sage/sage/sets/set.py" Total time for all tests: 8037.9 seconds This fails to build on OS X, due to some changes we made to get it to build on Cygwin. The alpha above makes almost no changes to the core Sage library. Of the "25 patches with positive review ready for inclusion" that you mentioned above, are they all changes to the core Sage library? Or do the patch spkg's, etc.? One possibility would be to test/stabilize the current 4.4.3.alpha* (i.e., fix the fallout from the cygwin related tickets), include those 25 patches (all to the sage library), and release 4.4.3 on Saturday. If you like that, then make a clean sage-4.4.2, apply all 25 patches, test it, and I can just pull those changes in, and that will be 4.4.3. -- William -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: Fwd: [sage-devel] Re: [sage-combinat-devel] factorization in polynomial rings
On Fri, May 21, 2010 at 5:03 PM, Anne Schilling wrote: > Hi Simon! > > Thank you very much for your answer. > >> On May 18, 7:47 am, Anne Schilling wrote: >>> >>> sage: LD.=LaurentPolynomialRing(QQ) >>> sage: P=PolynomialRing(LD,'z',2) >> >> Sage tries to use Singular to factor your polynomial. Hence, it needs >> to convert both your polynomial and its ring to Singular. >> >> The problem is that your coefficients are Laurent Polynomials, but >> Singular can only do the fraction field of the Laurent polynomial >> ring. >> >> So, you can do: >> >> sage: LD.=LaurentPolynomialRing(QQ) >> sage: P=PolynomialRing(Frac(LD),'z',2) >> sage: z = P.gens() >> sage: f = z[0]**2-d**2*z[1]**2 >> sage: f.factor() >> (-z0 + (-d)*z1) * (-z0 + d*z1) > > There still seems to be a problem though, since Sage does not > recognize that the answer is in P. See: > > -- > | Sage Version 4.4.1, Release Date: 2010-05-02 | > | Type notebook() for the GUI, and license() for information. | > -- > Loading Sage library. Current Mercurial branch is: combinat > sage: LD.=LaurentPolynomialRing(QQ) > sage: P=PolynomialRing(Frac(LD),'z',2) > sage: z=P.gens() > sage: f=z[0]**2-d**2*z[1]**2 > sage: f in P > True > sage: g=f.factor() > sage: g > (-z0 + (-d)*z1) * (-z0 + d*z1) > sage: g in P > False This is for the same reason that: sage: factor(6) in ZZ False sage: factor(6) 2 * 3 sage: type(factor(6)) A factorization is not an element, but a formal product -- it is its own class. You can use .prod(), though: sage: F = factor(6) sage: F.prod() 6 sage: F.prod() in ZZ True -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Request for Comments (graph genus)
On Thu, Apr 29, 2010 at 8:01 PM, Tom Boothby wrote: > I've been working on a new implementation of an algorithm to compute > the genus of graphs. Throughout the process, I've been bound by the > chains of backwards compatibility. As I've attempted to finish off > the patch, I've found some deeply unsettling details in the current > implementation. I'd like to hear from somebody (anybody) who computes > the genus of graphs with Sage, or cares about this sort of thing in > general. > > Currently, the following features exist within Sage: > > * computing the minimal/maximal genus for connected graphs > * computing the minimal/maximal genus for connected graphs > respecting a boundary (ordered or unordered) > * computing the genus of graph with a combinatorial embedding > supplied by the user > > where we define the maximal genus as the maximum obtained by a > combinatorial embedding. > > The following are completely broken, or **built on hypotheses that are > almost certainly false**: > > * computing anything about combinatorial embeddings of graphs with > more than one parallel edge or loop (we can accept up to 1 extra edge > due to a rounding error) > * computing the maximal genus for graphs respecting a boundary (this > includes a conspicuously incorrect doctest) > * computing anything about combinatorial embeddings of directed graphs > * computing the genus of an empty graph (har har) > > Also, what does work (simple connected graphs) is so slow, it makes my > eyes bleed. > > I'd like to remove anything referring to the "maximal" genus of a > graph. It seems to have been implemented purely because it was easy > to do so. I could also be convinced that we should keep this feature, > and raise a NotImplementedError where the implementation is senseless. > > Also, I might like to make it possible to compute the genus of > multigraphs and looped graphs. Part of the difficulty in this is that > embeddings are represented with the assumption that graphs are simple, > so this would result in a change that appears backwards incompatible > -- however, I believe that the only thing lost would be non-simple > graphs, where an incorrect answer was given anyway. Alternately, I'd > be happy to never compute anything about these graphs -- the only > reason *not* to think about embeddings of simple graphs is that the > max genus goes up with extra parallel edges. More reason not to > support the max genus. > > Issues to vote on: > > 1) Max Genus: > a [ ] Remove every reference to maximal genus > b [ ] Raise NotImplementedError for max genus computations that are > not supported > c [ ] Delay everything indefinitely until somebody cares enough to > make max genus work while respecting embeddings (I probably won't do > this) > > 2) Looped Multigraphs: > a [ ] Break backwards compatibility in some cases > b [ ] Raise NotImplementedError on anything involving embeddings of > multigraphs (note, we could still compute the minimal genus with this > option) > > For your consideration, my currently-existing code is about ten > thousand times faster for simple graphs, and is working very well. My > votes are: > > 1) a > 2) b > After discussing this at length with Tom in person, I vote for 1) b 2) b Why: 1) googling for "maximal genus" does turn up many papers that appear to use the term, and leaving support in doesn't sound too difficult for Tom. Also, option b) leaves open the possibility of other people doing further work later. 2) Tom said -- either choose b) or this code isn't going in. Again, option b) leaves open the possibility of other people doing further work later. -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: [sage-release] Sage 4.4.rc0 released
On Mon, Apr 26, 2010 at 12:46 AM, Florent Hivert wrote: > Hi There, > > On Fri, Apr 23, 2010 at 08:30:38PM -0700, John Palmieri wrote: >> This release candidate for Sage 4.4 closed 19 tickets (on top of >> 4.4.alpha1). On trac, these tickets were labeled as "merged into >> 4.4.alpha2", but then I decided that alpha2 should be the same as rc0. > > Cool ! So there is a good chance that we'll have 4.4 for sage 20.5 next week > at Toronto ! This is perfect... > > I'm however embarrassed to have the following question/request: > - how do we decide to make some ticket blocker for a release. Is it possible > at this stage to make #8746 blocker for 4.4. Here is the rationale: Given the testing that has happened, I personally view 4.4 as already done. I probably should have officially released it yesterday. John P. -- are you OK with your 4.4.rc being released? Make 8746 high priority for 4.4.1. I've made a new 4.4.1 milestone just now by the way. William > > The Posets library (by Franco Saliola) allows to deals with small Partially > Ordered SETS. This kind of structure is extremely useful an common in > combinatorics. Usually we play with one poset at a time, seeking for > particular property of one of them. For my research I had to play with many of > them and I discovered that the equality was (very fast) but completely broken, > preventing them to be used eg. as key in dict. This was fixed in #7438. We > solved this together with Nicolas Borie (which is a student of Nicolas Thiéry) > and this was merged in alpha0. However we didn't realize that doing this we > slowed of the most common usage that is comparing element in a single poset by > several order of magnitude. I take the full blame for this mistake which I > consider as an important regression. #8746 solve this common use issue. > > So is there still possible to merge #8746 while having 4.4 out before sage > days 20.5 ? I realize that I should have marked this ticket as critical or > blocker at its creation but I don't know how this is decided so that I never > change this field... Many Apologies for this late request. > > Cheers, > > Florent > > -- > You received this message because you are subscribed to the Google Groups > "sage-combinat-devel" group. > To post to this group, send email to sage-combinat-de...@googlegroups.com. > To unsubscribe from this group, send email to > sage-combinat-devel+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-combinat-devel?hl=en. > > -- William Stein Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] Re: [sage-devel] How to doc-test tab completion, revisited
Hi,
I'm cc'ing this to sage-combinat, since I recall that somewhere there
recently broke tab completion, so might be responsible for this (?).
On Fri, Apr 2, 2010 at 7:20 AM, Simon King wrote:
> Hi!
>
> A while ago, I asked how to doc test tab completion, in the case of a
> class with a custom __getattr__ method. See
> http://groups.google.com/group/sage-devel/browse_thread/thread/1bf6652891c4e45/232b75c9fe2d8c6c?lnk=gst&q=tab+completion+doc+test#232b75c9fe2d8c6c
>
> Eventually, I used to successfully doctest it such as here:
> sage: H =
> sage: import sagenb.misc.support as s
> sage: s.completions('H.f',globals(),system='python')
> ['H.factorise', ...
>
> But this doesn't work anymore (sage 4.3.4). What has changed?
>
> IIRC, in order to have tab completion, it suffices if
> H.__members__
> returns all attributes of H that H.__getattr__ knows about.
>
> And indeed, tab completion works fine, manually. But s.completions
> does not find all completions. What else can I do in the doc tests?
Does "tab completion work fine, manually" in the notebook?
William
>
> Best regards,
> Simon
>
> --
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> http://groups.google.com/group/sage-devel
> URL: http://www.sagemath.org
>
> To unsubscribe, reply using "remove me" as the subject.
>
--
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org
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[sage-combinat-devel] Categories fallout? -- Mysterious attributes
Hi, Somebody reported an odd bug, which may be caused by the category rewrite that Nicolas T. did. http://trac.sagemath.org/sage_trac/ticket/8613 sage: R = QQ['t'] sage: R.su R.sum R.summation R.summation_from_element_class_add sage: R.sum --- AttributeErrorTraceback (most recent call last) /home/marc/co/sage-4.3.4/ in () /home/marc/co/sage-4.3.4/local/lib/python2.6/site-packages/sage/structure/parent.so in sage.structure.parent.Parent.__getattr__ (sage/structure/parent.c:5120)() /home/marc/co/sage-4.3.4/local/lib/python2.6/site-packages/sage/structure/parent.so in sage.structure.parent.raise_attribute_error (sage/structure/parent.c:2638)() AttributeError: 'PolynomialRing_field' object has no attribute 'sum' sage: 'sum' in R.__dir__() True -- William Stein Associate Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Re: Sage Days 20 Status Report
On Mon, Mar 1, 2010 at 12:00 PM, Nicolas Borie wrote: > Chevie is a very huge package... > > --> from http://www.math.rwth-aachen.de/~CHEVIE/how-get.html: > It is now very easy to get the GAP part of CHEVIE - you only need to > install GAP, version 3.4.4, released in April 97 (see GAP for > details). > --- > Yes, Chevie work only with GAP3... > > --> from http://www.gap-system.org/Gap3/status3.html > Changing from GAP 3 to GAP 4 > If you still have private programs written in GAP 3 the functionality > of which you would like to have in GAP 4 it may be the best idea to > rewrite them from scratch. > > > Some people who used to contribute to Chevie are very interresting by > Sage. They are still working with GAP3. They are ok to contribute to > sage but an interface can make sweater their migration. It's true an > interface is not an easy job (Many thanks to Franco) and everybody > mind a lot before the decision... Huge +1. I've not used Chevie but I've ported a lot of code to Sage, and having an interface allowing one to run the original code is incredibly helpful.It makes it much easier to work incrementally (falling back to existing code to do parts of the computation not yet ported), test the new code versus the old code for correctness and speed, etc. It's ironic that it will be possible to fully use Chevie from within Sage, but *not* from within GAP4. That might very well make porting to Sage easier than porting to GAP4 would be. Evidently, porting Chevie to GAP4 must be really, really hard if nobody has done it after 13 years... I was just reading about Chevie on their website. One part says "Here is brief summary of what's new compared to the latest released version, CHEVIE 3.1 distributed with GAP 3.4.4." So Chevie evidently used to actually be a *part* of GAP 3 (at least included with it). I hope somebody can explain to me what happened socially/politically with the GAP3 --> GAP4 transition; it seems pretty intense to just leave behind a whole major component like that; I hope we never have to do something similar with Sage, though I could see how it could happen do to bad planning. I couldn't find the GAP part of Chevie at http://www.math.rwth-aachen.de/~CHEVIE/how-get.htmlIt says: "it's easy, just get GAP 3" :-) -- William -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] Re: Sage Days 20 Videos
On Sat, Feb 27, 2010 at 6:10 PM, Sébastien Labbé wrote: >> the Videos of Sage Days 20 [1] will be available here > > The initial format of the videos are MP4 (huge files). I converted > them to mpeg before uploading them. In the hope this format will make > you happy. Suggestions are welcome. > Thanks. Regarding the corresponding slides, they seem to be here http://www.lirmm.fr/arith/wiki/MathInfo2010/SageDays#toc8 However, I find them completely *impossible* to download. The site seems to be secure, e.g., and I simply can't get the worksheets. Maybe you could also upload them to http://sage.math.washington.edu/home/slabbe/days20/ since as is it seems impossible to get any worksheets, due to self-signed certificates and stuff. William -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] Re: [sage-release] a Sage 4.3.3.alpha2 release to incorporate changes from Sage Days 20
On Sunday, February 21, 2010, Minh Nguyen wrote: > On Mon, Feb 22, 2010 at 7:55 AM, Minh Nguyen wrote: > > > >> It's mostly due to the new Moin Moin spkg at ticket #3693: >> >> [mv...@sage sage-src]$ du -hs sage-4.3.2/spkg/standard/moin-1.5.7.p3.spkg >> 3.7M sage-4.3.2/spkg/standard/moin-1.5.7.p3.spkg >> [mv...@sage sage-src]$ du -hs >> sage-4.3.3.alpha1/spkg/standard/moin-1.9.1.p1.spkg >> 29M sage-4.3.3.alpha1/spkg/standard/moin-1.9.1.p1.spkg > > I forgot to say that it could take some time to work out which part of > moin-1.9.1.p1.spkg could be removed from the src/ directory. It might > even be the case that everything in moin-1.9.1.p1.spkg is required for > that package to work correctly. I think it is fine to leave the spkg as is for now. I just wanted to make sure there was some good reason for the increase in size, and it looksike there is. Thanks for figuring this out. > > -- > Regards > Minh Van Nguyen > > -- > You received this message because you are subscribed to the Google Groups > "sage-release" group. > To post to this group, send email to sage-rele...@googlegroups.com. > To unsubscribe from this group, send email to > sage-release+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-release?hl=en. > > -- William Stein Associate Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] Re: [sage-release] a Sage 4.3.3.alpha2 release to incorporate changes from Sage Days 20
On Sun, Feb 21, 2010 at 4:27 AM, Minh Nguyen wrote: > Hi William, > > On Sun, Feb 21, 2010 at 3:09 AM, William Stein wrote: > > > >> I hope 4.3.3 can be out... tomorrow. > > This is not an official announcement. The Sage 4.3.3 source tarball is > done and available under > > http://sage.math.washington.edu/home/release/sage-4.3.3/ > > It is essentially the same as Sage 4.3.3.alpha1, with no changes at > all since that release. Oh, I should have checked the builds on the build farm. There are the following remaining issues in alpha1: (1) On 32-bit Ubuntu, there is numerical noise in misc/functional.py: wst...@ubuntu32:/tmp/wstein/farm/sage-4.3.3.alpha1$ ./sage -t devel/sage/sage/misc/functional.py sage -t "devel/sage/sage/misc/functional.py" sh: kpsewhich: not found sh: kpsewhich: not found ** File "/tmp/wstein/farm/sage-4.3.3.alpha1/devel/sage/sage/misc/functional.py", line 705: sage: h.n() Expected: 0.33944794097891573 Got: 0.33944794097891567 ** 1 items had failures: 1 of 14 in __main__.example_28 ***Test Failed*** 1 failures. I realized the above got discussed to death in another thread. However, you said 4.3.3 = 4.3.3.alpha1, and if so, we can't release with the above failure. Anyway, http://trac.sagemath.org/sage_trac/ticket/8314 has to get merged in before we can release 4.3.3, since we can't release with test failures on Ubuntu 32. (2) This bug #8231 makes the notebook completely insanely frustrating and painful to use for everybody. I just looked, and evidently it stalled out and the fix didn't get in. John had tested it, but didn't sign off, so I just refereed it. I can't release another sage with this broken. So can you swap out sagenb-0.7.5 for sagenb-0.7.5.1, which I just posted here: http://sage.math.washington.edu/home/wstein/patches/sagenb/sagenb-0.7.5.1.spkg and which does nothing but add this one bugfix. This of course won't impact doctesting, since it's in the notebook. (3) There is a jump in size between 4.3.2 and 4.3.3: wst...@sage:~/build$ ls -lh *.tar -rw-r--r-- 1 wstein wstein 263M 2010-02-06 01:18 sage-4.3.2.tar -rw-r--r-- 1 wstein wstein 293M 2010-02-21 04:15 sage-4.3.3.tar Any idea why? So could you fix the above 3 issues and roll a new 4.3.3? William -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
[sage-combinat-devel] Re: [sage-release] a Sage 4.3.3.alpha2 release to incorporate changes from Sage Days 20
On Sat, Feb 20, 2010 at 5:20 AM, Minh Nguyen wrote: > Hi folks, > > On Sat, Feb 20, 2010 at 11:58 PM, slabbe wrote: >>> This is the final alpha release of Sage 4.3.3. The next release would >>> be an rc0. The development version of Sage is now in feature freeze. >> >> Does that mean only ticket solving a defect will be merged into sage >> until sage-4.4.1? >> >> The Sage days 20 are beginning on Monday. I think there will be a big >> loads of tickets being created/reviewed/solved in the next 10 days. >> Moreover, I will explain how to contribute to sage to at least three >> persons. It would be nice if their first ticket could be reviewed and >> merged in sage-4.3.3especially since sage-4.4 is planned to be a >> stabiliser release. If it is fine with release managers, I would >> propose a sage-4.3.3.alpha2 version that would contain the first quick >> results of Sage Days 20. > > I would like to put forward a proposal for creating a Sage > 4.3.3.alpha2 release that would incorporate positively reviewed > tickets resulting from Sage Days 20. I think it would be much, much better to release 4.3.3 ASAP (say tomorrow!). You, Mitesh, and countless build testers have already put a huge amount of work into stabilizing that release, and it contains many critical bugfixes (e.g., for the notebook) that I wish we had released a week ago. Waiting for patches to be written and refereed, etc., from another Sage Days will simply push the release back at least two weeks. I think we should release 4.3.3 as soon as possible. If there are suddenly a bunch of positively reviewed tickets in http://trac.sagemath.org/sage_trac/report/11, then make a 4.3.4 release in a week. Regarding the stabilization 4.4 release, I see the point of that release to: (1) deal with a bunch of really annoying critical bugs (2) not rush. So I don't see it as absolutely having to be right after 4.3.3. William > There was a recent vote to create > a Sage 4.4 "stabilization release" [1,2]. If implemented, this > stabilization release is to fix (long-standing) annoying bugs, among > other stabilization fixes. I think the Sage-Combinat team also > anticipates that there would be new features and bug fixes resulting > from Sage Days 20, and it would be good to get those merged as soon as > possible. If a Sage 4.3.3.alpha2 is to be created, I expect Sage 4.3.3 > to be out early March. I hope 4.3.3 can be out... tomorrow. > > Thoughts? > > >> Cordially, >> >> Sébastien > > [1] > http://groups.google.com/group/sage-release/browse_thread/thread/185cc40eaff38e1c > > [2] > http://groups.google.com/group/sage-devel/browse_thread/thread/185cc40eaff38e1c > > -- > Regards > Minh Van Nguyen > > -- > You received this message because you are subscribed to the Google Groups > "sage-release" group. > To post to this group, send email to sage-rele...@googlegroups.com. > To unsubscribe from this group, send email to > sage-release+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/sage-release?hl=en. > > -- William Stein Associate Professor of Mathematics University of Washington http://wstein.org -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Symmetric functions / importing standard shorthands in the interpreter namespace
On Sun, Jan 3, 2010 at 6:59 AM, Nicolas M. Thiery wrote: > On Mon, Dec 28, 2009 at 02:49:15PM -0500, Mike Hansen wrote: >> On Sun, Dec 27, 2009 at 7:45 PM, William Stein wrote: >> > What precisely is a "shorthand"? It seems like a bad name. >> > >> > Maybe >> > >> > sage: S.inject_elements() >> > >> > or >> > >> > sage: S.inject_special_elements() >> > >> > or something? Or maybe I misunderstand? >> >> Typically, when one works with symmetric functions, you want/need to >> define (at least) 5 different parents named p, m, s, e, and h. So, >> the inject_shorthands defines all of these parents and puts them in >> the namespace. > > Yup. Also, we will soon generalize this to other contexts, like root > systems, Hecke algebras, etc: > > > sage: R = RootSystem(["A",4]).weight_lattice() > sage: R.inject_shorthands() > > which would typically define: > > alpha: the simple roots (elements of R) > alphacheck: the simple coroots (elements of the dual space) > s: the simple reflections (functions from R to R) > W: the Weyl group (a group of functions from R to R) > ... > > The goal being to provide the standard short notations used by > researchers in the root system / ... community. > > Suggestions for a better name are still welcome! > Now that you explain what it really does, I think your choice of name is sensible. I also think supporting this capability is *excellent* -- users really love this sort of thing. -- William -- You received this message because you are subscribed to the Google Groups "sage-combinat-devel" group. To post to this group, send email to sage-combinat-de...@googlegroups.com. To unsubscribe from this group, send email to sage-combinat-devel+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en.
Re: [sage-combinat-devel] Symmetric functions / importing standard shorthands in the interpreter namespace
On Sun, Dec 27, 2009 at 2:59 PM, Nicolas M. Thiery
wrote:
> Dear William, dear symmetric function fans,
>
> On Wed, Dec 23, 2009 at 02:59:18PM -0800, William Stein wrote:
>> > sage: sage.misc.misc.inject_variables(dict('a':1, 'b':3))
>> > sage: a
>> > 1
>> > sage: b
>> > 3
>>
>> That sounds very good.
>
> Up to little changes, patch up on #7776
>
>> Since we already have
>>
>> sage: R. = QQ[]
>> sage: R.inj
>> R.inject_variables R.injvar
>> sage: R.inject_variables()
>> Defining x, y, z
>>
>> I think inject_variables would be good... or better might be to
>> deprecate inject_variables and change it to
>>
>> inject_generators()
>>
>> since that is what it really does. Thoughts?
>
> Not much myself. For symmetric functions I sticked so far to:
>
> sage: S = SymmetricFunctions(QQ)
> sage: S.inject_shorthands()
>
> Since those shorthands are not really generators.
What precisely is a "shorthand"? It seems like a bad name.
Maybe
sage: S.inject_elements()
or
sage: S.inject_special_elements()
or something? Or maybe I misunderstand?
William
>
> Patch up at #. Who wants to review this cool number?
>
> Cheers,
> Nicolas
> --
> Nicolas M. Thiéry "Isil"
> http://Nicolas.Thiery.name/
>
> --
>
> You received this message because you are subscribed to the Google Groups
> "sage-combinat-devel" group.
> To post to this group, send email to sage-combinat-de...@googlegroups.com.
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> For more options, visit this group at
> http://groups.google.com/group/sage-combinat-devel?hl=en.
>
>
>
--
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org
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Re: [sage-combinat-devel] Symmetric functions / importing standard shorthands in the interpreter namespace
On Wed, Dec 23, 2009 at 2:48 PM, Nicolas M. Thiery
wrote:
> On Wed, Dec 23, 2009 at 02:37:22PM -0800, William Stein wrote:
>> On Wed, Dec 23, 2009 at 2:31 PM, Nicolas M. Thiery
>> wrote:
>> > On Wed, Dec 23, 2009 at 02:01:22PM -0800, William Stein wrote:
>> >> > I stumbled recently into a nifty feature of the IPython interpreter
>> >> > allowing for easy manipulations of the global namespace of the
>> >> > interpreter, at the python level. Thanks to it, one can now do:
>> >> >
>> >> > sage: S = SymmetricFunctions(ZZ)
>> >> > sage: S.import_shorthands()
>> >> > sage: s[1] + e[2] * p[1,1] + 2*h[3] + m[2,1]
>> >> > s[1] - 2*s[1, 1, 1] + s[1, 1, 1, 1] + s[2, 1] + 2*s[2, 1, 1] + s[2,
>> >> > 2] + 2*s[3] + s[3, 1]
>> >> > sage: s
>> >> > Symmetric Function Algebra over Integer Ring, Schur symmetric
>> >> > functions as basis
>> >> > sage: e
>> >> > Symmetric Function Algebra over Integer Ring, Elementary symmetric
>> >> > functions as basis
>> >> > ...
>> >>
>> >> What happens in the notebook (which in no way uses IPython)? Does it
>> >> at least fail gracefully?
>> >
>> > Good point. I am using that seldom the notebook that I did not even
>> > think about it :-) Let me try ... Ok, as I expected, it's not that
>> > graceful:
>> >
>> > Traceback (click to the left for traceback)
>> > ...
>> > AttributeError: 'NoneType' object has no attribute 'to_user_ns'
>> >
>> > Is there an easy way to manipulate the global namespace for the
>> > notebook? For IPython, I am using:
>>
>> No, not exactly. The notebook is just pure Python (right now).
>>
>> That said, from *Cython* you can get at the true global namespace by
>> using the command globals(). See
>>
>> sage/sage/ext/interactive_constructors_c.pyx
>>
>> for code that does this sort of thing, which works uniformly in both
>> IPython, pure python, and the notebook.
>
> Yeah, I had seen this. I was specifically happy to have found a
> non-cython way to do it. But uniformity has its value. I guess I'll
> make a very small Python wrapper around the Cython globals call, and
> then have import_shorthands use it.
>
> sage: sage.misc.misc.inject_variables(dict('a':1, 'b':3))
> sage: a
> 1
> sage: b
> 3
That sounds very good.
> Any better suggestion for the location/name of this function?
> import_variables? Or should we use S.inject_shorthands() above?
>
Since we already have
sage: R. = QQ[]
sage: R.inj
R.inject_variables R.injvar
sage: R.inject_variables()
Defining x, y, z
I think inject_variables would be good... or better might be to
deprecate inject_variables and change it to
inject_generators()
since that is what it really does. Thoughts?
-- William
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