Re: [sage-devel] Re: Have you considered having a Sage Journal?

[Ursula Whitcher]

It might also be worth looking at the Journal of Software in Algebra and 
Geometry:



https://msp.org/jsag/about/journal/about.html


Their current focus is Macaulay2, but as I recall, some of the editors 
have previously expressed interest in including Sage-based articles as well.



UAW


On 5/25/2020 9:11 AM, kcrisman wrote:



On Sunday, May 24, 2020 at 2:44:12 AM UTC-4, Diego Sejas wrote:

Hello, Sage Community!

I am not completely sure that this is the correct place to propose
an idea like this, but I think that here it can be upvoted or
downvoted, and commented.

I have been thinking for a long time that the Sage Community
should have a Journal for everyone of us being able to read what
is going on with Sage; how it is being used in research,
education, etc.; what improvements have been made; etc., etc.,
etc. Perhaps an annual publication, so it is not so much of a
burden for the editors (?).

Since the *Global Virtual SageDays 109* is approaching (yay!!!),
it could be a good moment to discuss this idea with the community.
Actually, I can see that somebody already asked about how people
is using Sage in research, education, etc.

(https://ask.sagemath.org/question/51524/how-do-you-use-sagemath-in-research-education/)


That could evolve into a small journal with a few articles about
the use of Sage, if enough people collaborate.


There was actually a proposal like this quite a long time ago:

https://web.archive.org/web/20100615075428/https://www.sagemath.org/jsage/ref.html

The idea was to have a place where people could publish code in a 
refereed sense.  To my recollection, at that time there wasn't enough 
interest from academic departments (and perhaps still isn't) in 
awarding promotion based on such code.


Other groups do have such publications, e.g. the TuGboat 
(https://tug.org/tugboat/) for TeX or the R Journal 
(https://journal.r-project.org).  I think those that do may have an 
order of magnitude higher number of "power users", though.  But it 
would be great to have something like this for Sage.  An annual 
edition would seem reasonable, and certainly would be great for 
visibility/publicity (see the moribund 
https://groups.google.com/forum/#!forum/sage-marketing for one of many 
attempts at this).

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Re: [sage-devel] Making the transition from user to developer

[Ursula Whitcher]

On 7/11/2018 3:19 PM, profgr...@gmail.com wrote:
What would be a good way for a Sage user with a basic programming 
background to learn about Sage development and how codebases are built?  
Projects ultimately of interest so far are (1) a "show-my-steps" feature 
for differentiation in Sage or (2) a feature for generating proofs by 
induction for some class of problems.  Are there any relevant 
tutorial-like things?


A very good way is to attend a Sage Days.

There are some tutorials in the Developers' Guide:

https://doc.sagemath.org/html/en/developer/

A good first project is nearly always finding something unclear in the 
Developers' Guide and fixing it.


Does "a basic programming background" include some knowledge of Python? 
If not, picking up a little bit of Python is a good place to start.


--Ursula Whitcher.

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Re: [sage-devel] Sage developer co-authors article on women's representation in subfields

[Ursula Whitcher]

On 5/25/2018 11:26 AM, William Stein wrote:

I can't / wont read it because of the paywall.  Can you copy/paste the
paragraph that mentions Sage?  (or screenshot it).  Fair use of small
excerpts...


Math Intelligencer changed the biographies to third-person; my draft was:

***

I earned a mathematics Ph.D. from the University of Washington, where I 
wrote my dissertation on algebraic geometry problems inspired by 
questions in string theory. I spent two years as a Teaching and Research 
Postdoctoral Fellow at Harvey Mudd College, and five years as an 
assistant and then associate professor at the University of 
Wisconsin-Eau Claire, where I met Abra. I'm now an Associate Editor at 
Mathematical Reviews, a service of the American Mathematical Society. 
I'm interested in experimental and computational approaches to both pure 
and applied mathematical problems, and am active in the SageMath 
open-source community.


When I'm not doing math, I enjoy rock climbing, knitting, writing 
poetry, and using my academic library card for unmathematical purposes. 
Right now I'm reading up on the Aztecs, Merovingian archaeology, and 
irregular tactics in modern warfare.


***

--Ursula Whitcher.

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Re: [sage-devel] Sage developer co-authors article on women's representation in subfields

[Ursula Whitcher]

On 5/25/2018 11:02 AM, kcrisman wrote:
Unfortunately a paywall, but very interesting data and analysis relevant 
to mathematical software communities too - plus, Sage developer and 
co-author Ursula Whitcher of Math Reviews gives a shout-out to SageMath 
in the author bio :)

https://link.springer.com/article/10.1007%2Fs00283-017-9761-7


Thank you!

There's a preprint version on the arXiv, naturally:

https://arxiv.org/abs/1509.07824

(And I did a bunch of the data analysis in python, using skills I 
learned from Sage development!)


UAW

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Re: [sage-devel] Non-negative integer vectors

[Ursula Whitcher]

Here's a ticket:

https://trac.sagemath.org/ticket/23939

Should be a nice beginner task, if anyone's looking for one!

--Ursula.

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Re: [sage-devel] Non-negative integer vectors

[Ursula Whitcher]

Yes, that looks like exactly the functionality I wanted!

Why doesn't the documentation at 

http://doc.sagemath.org/html/en/reference/combinat/sage/combinat/integer_vector.html

link to the documentation for integer lists?

--Ursula.

On Thursday, September 28, 2017 at 10:27:14 AM UTC-4, vdelecroix wrote:
>
> Do you mean 
>
> sage: IntegerListsLex(length=2, min_sum=0, max_sum=5).list() 
> [[5, 0], 
>   [4, 1], 
>   [4, 0], 
>   [3, 2], 
>   [3, 1], 
>   [3, 0], 
>   [2, 3], 
>   [2, 2], 
>   [2, 1], 
>   [2, 0], 
>   [1, 4], 
>   [1, 3], 
>   [1, 2], 
>   [1, 1], 
>   [1, 0], 
>   [0, 5], 
>   [0, 4], 
>   [0, 3], 
>   [0, 2], 
>   [0, 1], 
>   [0, 0]] 
>
> On 28/09/2017 15:55, u...@umich.edu  wrote: 
> > In preparation for Sage Days 91, I'm looking at the thesis of Malcolm 
> Kotok 
> > (as in https://trac.sagemath.org/ticket/19865 ). That thesis 
> incorporates a 
> > class to list all non-negative integer vectors of a fixed length with 
> sum 
> > less than n. 
> > 
> > I see that we already have an IntegerVectors class for non-negative 
> integer 
> > vectors with sum exactly n: 
> > 
> > 
> http://doc.sagemath.org/html/en/reference/combinat/sage/combinat/integer_vector.html
>  
> > 
> > Would it be useful to expand that class to list vectors with sum at most 
> n? 
> > If so, what should the input parameters look like? 
> > 
> > --Ursula Whitcher. 
> > 
>

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[sage-devel] bug report: error when computing cardinality of point sets

[Ursula Whitcher]

Asking Sage to compute the cardinality of point sets of projective 
varieties over finite fields produces an infinite recursion error.  This is 
weird, since the count_points() function works just fine (albeit slowly) in 
this situation.

Here's an example.

Entering:

F = FiniteField(37)
P3.<x,y,z,w> = ProjectiveSpace(3,F)
P3.point_set().cardinality()

yields an error that begins:

Error in lines 3-3 Traceback (most recent call last): File 
"/projects/sage/sage-7.3/local/lib/python2.7/site-packages/smc_sagews/sage_server.py",
 
line 976, in execute exec compile(block+'\n', '', 'single') in namespace, 
locals File "", line 1, in  File 
"/projects/sage/sage-7.3/local/lib/python2.7/site-packages/sage/schemes/generic/homset.py",
 
line 584, in cardinality return sum(ZZ.one() for point in self) File 
"/projects/sage/sage-7.3/local/lib/python2.7/site-packages/sage/schemes/generic/homset.py",
 
line 584, in  return sum(ZZ.one() for point in self) File 
"sage/structure/parent.pyx", line 1596, in 
sage.structure.parent.Parent.__getitem__ 
(/projects/sage/sage-7.3/src/build/cythonized/sage/structure/parent.c:12913) 
return self.list()[n] File 
"/projects/sage/sage-7.3/local/lib/python2.7/site-packages/sage/schemes/generic/homset.py",
 
line 602, in list return tuple(self) File 
"/projects/sage/sage-7.3/local/lib/python2.7/site-packages/sage/schemes/generic/homset.py",
 
line 584, in cardinality return sum(ZZ.one() for point in self) File 
"/projects/sage/sage-7.3/local/lib/python2.7/site-packages/sage/schemes/generic/homset.py",
 
line 584, in  return sum(ZZ.one() for point in self) File 
"sage/structure/parent.pyx", line 1596, in 
sage.structure.parent.Parent.__getitem__ 
(/projects/sage/sage-7.3/src/build/cythonized/sage/structure/parent.c:12913) 
return self.list()[n]

continues looping for a while, and ends:

File "sage/structure/parent.pyx", line 1596, in 
sage.structure.parent.Parent.__getitem__ 
(/projects/sage/sage-7.3/src/build/cythonized/sage/structure/parent.c:12913) 
return self.list()[n] File 
"/projects/sage/sage-7.3/local/lib/python2.7/site-packages/sage/schemes/generic/homset.py",
 
line 602, in list return tuple(self) File 
"/projects/sage/sage-7.3/local/lib/python2.7/site-packages/sage/schemes/generic/homset.py",
 
line 584, in cardinality return sum(ZZ.one() for point in self) File 
"/projects/sage/sage-7.3/local/lib/python2.7/site-packages/sage/schemes/generic/homset.py",
 
line 584, in  return sum(ZZ.one() for point in self) File 
"sage/structure/parent.pyx", line 1590, in 
sage.structure.parent.Parent.__getitem__ 
(/projects/sage/sage-7.3/src/build/cythonized/sage/structure/parent.c:12742) 
meth = getattr_from_other_class(self, self._category.parent_class, 
'__getitem__') File "sage/structure/misc.pyx", line 250, in 
sage.structure.misc.getattr_from_other_class 
(/projects/sage/sage-7.3/src/build/cythonized/sage/structure/misc.c:1731) 
if isinstance(self, cls): RuntimeError: maximum recursion depth exceeded 
while calling a Python object

On the other hand, 

P3.count_points(1)

returns [52060].

--Ursula.

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[sage-devel] Fw: Request for Information on Future Needs for Advanced Cyberinfrastructure to Support Science and Engineering Research (NSF CI 2030)

[Whitcher, Ursula A.]

I want to draw the Sage community's attention to this NSF call for comment on 
"advanced cyberinfrastructure".  Specifically, the NSF is asking what sorts of 
computing resources it should prioritize.  We should tell them to support 
open-source software in mathematics!


Is anyone interested in a coordinated Sage response?


--Ursula.



From: dmsnews <dmsn...@listserv.nsf.gov> on behalf of Henry Warchall 
<hwarc...@nsf.gov>
Sent: Tuesday, January 10, 2017 5:07 PM
To: dmsn...@listserv.nsf.gov
Subject: Request for Information on Future Needs for Advanced 
Cyberinfrastructure to Support Science and Engineering Research (NSF CI 2030)

Dear Colleagues:

In the past two decades, advanced cyberinfrastructure has become a critical 
element of science and engineering research – a result of the increasing scope 
and accuracy of simulations of natural and engineered systems as well as the 
growing volume of data generated by instruments, simulations, experiments, and 
observations. The National Science Foundation (NSF) embraces an expansive, 
ecosystem view of research cyberinfrastructure – spanning advanced computing 
resources, data and software infrastructure, workflow systems and approaches, 
networking, cybersecurity, and associated workforce development – elements 
whose design and deployment are motivated by evolving research priorities as 
well as the dynamics of the scientific process. The critical role of this broad 
spectrum of shared cyberinfrastructure resources, capabilities, and services – 
and their integration – in enabling science and engineering research has been 
reaffirmed by the National Strategic Computing Initiative [3], which was 
announced in July 2015, and in the National Academies' 2016 report [4] on 
Future Directions for NSF Advanced Computing Infrastructure to Support U.S. 
Science and Engineering in 2017-2020. While these efforts are 
computing-centric, they expose the inherent inseparability of computing from 
the larger cyber ecosystem. With this message, NSF seeks input that provides a 
holistic view of the future needs for advanced cyberinfrastructure for 
advancing the Nation's research enterprise.

In 2009, NSF undertook a community-informed analysis of cyberinfrastructure 
needs that led to the formulation of a vision, a strategy, and a set of 
programmatic initiatives together comprising the current NSF-wide effort 
entitled Cyberinfrastructure for 21st Century Science and Engineering (CIF21) 
[5]. Since that analysis, many changes have taken place in terms of scientific 
challenges and opportunities as well as technological progress. To continue to 
take full advantage of the potential provided by cyberinfrastructure to advance 
science and engineering research, NSF is beginning to formulate an updated 
strategy as well as concrete plans for future investments in this area. In this 
endeavor, NSF will focus on complementing and supporting forward-looking 
cyberinfrastructure for research that institutions and universities are 
unlikely to be able to deploy on their own. In addition, NSF seeks to stimulate 
innovative use of cyberinfrastructure for research to spur advances not 
otherwise possible, particularly in emerging areas of science and engineering 
research. Finally, NSF supports the exploration of approaches to sustainability 
that address the unique needs of research cyberinfrastructure, including the 
scientific, technical, and human aspects of cyberinfrastructure.

In this Request for Information (RFI), NSF encourages community input to inform 
the Foundation's strategy and plans for an advanced cyberinfrastructure that 
will enable the frontiers of science and engineering to continue to advance 
over the next decade and beyond (NSF CI 2030). This whole-of-NSF activity 
recognizes that researchers in different disciplines may need different 
resources; may have differing priorities for access, interoperability, and 
continuity; and may require external expertise to address the most critical 
problems in their discipline. We therefore strongly encourage researchers in 
all fields of science, engineering, and education to respond to this Request 
for Information.

HOW TO RESPOND TO THIS RFI

NSF invites both individuals and groups of individuals to provide input on the 
specific scientific and engineering research challenges that require advanced 
cyberinfrastructure for their solutions, via the following submission website: 
http://www.nsfci2030.org .

The online submission form requires the following information [1]:

* Author names(s) and affiliation(s).
* Valid contact email address.
* Research domain(s), discipline(s)/sub-discipline(s) of the author(s).
* Title of the response, and an abstract (200 words) summarizing the response.
* Question 1 (maximum 1200 words) – Research Challenge(s). Describe current or 
emerging science or engineering research challenge(s), providing context in 
terms of rece

[sage-devel] broken FAQ link in Sage documentation

[Ursula Whitcher]

The FAQ entry at

http://doc.sagemath.org/html/en/faq/faq-contribute.html#can-i-contribute-to-sage-using-sagemathcloud

has a link to 

https://github.com/sagemath/cloud/wiki/FAQ

This forwards to

https://github.com/sagemathinc/smc/wiki/FAQ

which lands at "General and Miscellaneous Questions".

It should instead point to 

https://github.com/sagemathinc/smc/wiki/SageMath-Development-on-SageMathCloud

if that link is stable.

--Ursula.

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[sage-devel] notices article

[Ursula Whitcher]

Jeroen, William, and I have an article about SageMath in the September 
edition of the Notices of the AMS, which is appearing in mailboxes now:

http://www.ams.org/publications/journals/notices/201608/rnoti-p928.pdf

--Ursula.

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Re: [sage-devel] citing Sage: the SageMath version

[Whitcher, Ursula A.]

On 4/1/2016 1:34 AM, Daniel Krenn wrote:

> I suggest something like:
>
> @Manual{SageMath:2016:7.1,
>key =  {SageMath},
>author =   {The SageMath Developers},
>title ={{SageMath} {M}athematics {S}oftware ({V}ersion 7.1)},
>note = {\url{http://www.sagemath.org}},
>year = 2016,
> }

Would SageMath Software be better?  Isn't SageMath Mathematics Software 
a little redundant?

--Ursula.

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[sage-devel] citing Sage: the SageMath version

[Ursula Whitcher]

I noticed that the Wiki entry on citing Sage

https://wiki.sagemath.org/Publications_using_SAGE

does not reflect the rebranding of Sage as SageMath.  How should the 
citation change?

--Ursula.

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[sage-devel] invisible contour lines in contour plots

[Ursula Whitcher]

In Sage's contour plots, the default colors shade from black to white.  
This applies to both the shades used to fill and the actual color of the 
contour lines.  If you turn off the fill color, the highest contour will be 
white-on-white, and thus invisible.  Here's an example (notice the label 
floating apparently in the middle of nowhere):

x,y = var('x,y')
pl = contour_plot(-10*(x^2+y^2), (x,-1,1), (y,-1,1), fill = False, labels = 
True, label_fontsize = 13).show()

You can fix this by making all the contour lines black.  The keyword 
cmap=[(0,0,0)] worked for me.

Can we change the defaults so that fill=False does not default to 
white-on-white?  Or add a keyword that will make all contour lines the same 
color?  Or at least add an example about this to the documentation?

--Ursula.

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Re: [sage-devel] invisible contour lines in contour plots

[Whitcher, Ursula A.]

On 12/8/2015 4:04 PM, William Stein wrote:
>> Can we change the defaults so that fill=False does not default to
>> white-on-white?  Or add a keyword that will make all contour lines the same
>> color?  Or at least add an example about this to the documentation?
>>
>
> What does Mathematica do?
>
>https://reference.wolfram.com/language/ref/ContourPlot.html

Mathematica defaults to making all of the contour lines the same shade 
of gray, rather than coloring them to match the adjacent fill color.  So 
does Wolfram Alpha:

http://www.wolframalpha.com/input/?i=contour+plot+-10%28x^2%2By^2%29

UAW

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[sage-devel] checkpointing enumeration of points on hypersurfaces in toric varieties

[Ursula Whitcher]

While discussing Ticket 16953, which improves functionality for enumerating 
points in toric varieties over finite fields, I said:

The actual functionality works fine, albeit slowly. I would find it 
helpful if there were a way to save partial progress when computing a point 
set: I'm interested in examples that are large enough that the Sage cloud 
may kill the process before I'm done.

Volker responded:

I hear you, and I agree that checkpointing is an important feature. But 
its not really clear how that should be implemented or how the interface 
would look like. I guess the iterator is (or can be made) pickleable, but 
really checkpointing needs to be added on the @parallel level. In the short 
run its probably easier to email William to request a longer timeout on 
your project...

Since checkpointing ideas are beyond the scope of Ticket 16953, I'm moving 
this discussion here.  Some thoughts:

* I'm particularly interested in examples involving hypersurfaces in smooth 
toric varieties over finite fields.  For smooth toric varieties, one can 
stratify the points according to which torus they lie in, which in turn is 
tracked combinatorially by elements of the fan.  Could one report which 
toruses have been checked?  Or make it possible to check only in a certain 
torus?  Presumably most of the time will be spent checking points in the 
big torus, but on the other hand I can imagine somebody might only *care* 
about points in the big torus, so this might be useful functionality to 
separate.

* More naively, should there be an option to report *which* points lie on a 
hypersurface?  For toy examples, seeing some points might be enough to 
guess the rest.  More generally, I can imagine applications where somebody 
might be happy to find *any* points on a hypersurface over a finite field, 
and not care about whether all of them have been identified.  

--Ursula.

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[sage-devel] documentation bug: git-trac instructions don't mention git commit

[Ursula Whitcher]

I found a documentation bug: literally following the instructions for 
ticket creation and updates at 
http://doc.sagemath.org/html/en/developer/git_trac.html results in the 
publication of empty tickets, because there's no mention of *committing* 
changes.  This is now ticket 18504:

http://trac.sagemath.org/ticket/18504

If I were to fix these instructions, I would add something along the lines 
of, Now, edit some files.  You can save the changes you have made by 
typing 'git commit -a' and recording a commit message.  Your commit message 
should be a short summary of what you have done, featuring an evocative 
verb.  However, I am by no means a git expert.  Are there other important 
commands we should recommend here?

--Ursula.

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[sage-devel] Should the Sage FAQ link to the SageMathCloud FAQ?

[Ursula Whitcher]

The Sage FAQ at:

http://doc.sagemath.org/html/en/faq/index.html

does not mention the SageMathCloud FAQ at:

https://github.com/sagemath/cloud/wiki/FAQ .

Should we add a question to the Sage FAQ along the lines of How can I find 
more information about the SageMathCloud (TM)? that sends readers to the 
SageMathCloud FAQ?  Or should we port some of the SageMathCloud FAQ to the 
main Sage FAQ?

--Ursula.

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[sage-devel] Re: VOTE: code of conduct - ends Monday at midnight, PST.

[Ursula Whitcher]

[x ] Yes -- adopt the code of conduct stated below (*)

UAW

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[sage-devel] Re: Code of Conduct

[Ursula Whitcher]

On Friday, November 14, 2014 6:05:02 AM UTC-6, mmarco wrote:


 So, about the code of conduct, it sounds like a nice set of guidelines. 
 But, do we really need it? I mean, has it been some hard conflict that i 
 have not been aware of? I know that we have some trolling and flaming going 
 on every once in a while, but it doesn't seem to have been harmful so far. 
 In general, the discussion here is very respectfull (I haven't seen any 
 RTFM answer to people asling for help, for instance). My impression is that 
 the Sage community is nice for newcommers. We have done quite well so far 
 without a code of conduct.


Frames of reference vary.  When I am interacting with Sage developers, I 
routinely edit my draft posts to make them more assertive and less nice. 

--Ursula.

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Re: [sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

[Whitcher, Ursula A.]

On 11/14/2014 3:05 AM, rjf wrote:

 If the  AMS Notices is publishing papers that should instead be
 submitted to computer science publications
 (Software Practice and Experience comes to mind),  should computer
 science journals publish
 papers on pure mathematics?

Bear in mind that the Notices isn't a research journal.  It publishes 
expository articles, opinion pieces, and news-magazine style writing. 
The submissions guidelines specifically state that discussion should be 
geared toward non-experts.

--Ursula.

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Re: [sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

[Ursula Whitcher]

On 11/13/2014 3:05 AM, Jeroen Demeyer wrote:

On 2014-11-12 21:33, Ursula Whitcher wrote:

On 11/11/2014 4:46 AM, Jeroen Demeyer wrote:


* The sentence A recent tweak of another part of Sage’s matrix code had
changed the definition of “small n” to n = 63. is wrong:
what had changed is the bound on p to compute the determinant over GF(p)
using LinBox (for larger p, we compute determinants over GF(p) by
lifting to ZZ): it used to be the case that the bound in LinBox depended
on n, this was changed to a fixed bound for p which was less than the
old value for n = 63.


What's the fixed bound?


2^23, so the largest prime number is 8388593.


This is fixed as in the old, bad constant, rather than an improved 
bound which fixed the problem, right?


UAW

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Re: [sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

[Ursula Whitcher]

On 11/11/2014 3:41 AM, Dr. David Kirkby (Kirkby Microwave Ltd) wrote:


If I am honest,  I am not that convinced it is a good follow up comment,


OK, I won't put your name on it ;)


but ignoring that, if this was to be the basis of an article, I can
think of some improvements.


Thanks for the comments!


1) Add a time line. How long it took from the reporting of the bug,  to
the bug fixed, peer reviewed, then to release of a new
alpha/beta/release candidate and finally to the release of a stable
version with the bug fixed.

I suspect it was faster than the year or so the bug has remained in
Mathematica.


All I can see from trac is that everything happened 22 months ago.  How 
do I find how long it took to go from positive review to stable release?



2) Take out the early reference to Sage getting the determinate correct
that Mathematica gets right. Apart from boasting rights,  I am not
convinced it adds anything useful.


It gives us an excuse to show off the public worksheet.  I could 
relegate this to a footnote, though.



3) The initial priority is stated to be major,  but the priority can be
changed by others, and most obviously by the release manager. So not
every blocker bug gets fixed by the next release of Sage.


But the ones that aren't fixed are no longer blockers, right?

UAW

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Re: [sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

[Ursula Whitcher]

On 11/11/2014 4:46 AM, Jeroen Demeyer wrote:


* The sentence A recent tweak of another part of Sage’s matrix code had
changed the definition of “small n” to n = 63. is wrong:
what had changed is the bound on p to compute the determinant over GF(p)
using LinBox (for larger p, we compute determinants over GF(p) by
lifting to ZZ): it used to be the case that the bound in LinBox depended
on n, this was changed to a fixed bound for p which was less than the
old value for n = 63.


What's the fixed bound?

UAW

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Re: [sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

[Ursula Whitcher]

On Mon, Nov 10, 2014 at 3:08 PM, Ursula Whitcher whitc...@uwec.edu wrote:

On 11/5/2014 8:24 AM, William Stein wrote:


* By we write up above, I mean you write up something very, very
rough, post it here, and get feedback.



Done!

http://people.uwec.edu/whitchua/notes/sagebugprocess.pdf


Article at

http://people.uwec.edu/whitchua/notes/sagebugprocess.pdf

has been updated based on feedback.

UAW

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Re: [sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

[Ursula Whitcher]

On 11/5/2014 8:24 AM, William Stein wrote:


* By we write up above, I mean you write up something very, very
rough, post it here, and get feedback.


Done!

http://people.uwec.edu/whitchua/notes/sagebugprocess.pdf

I stuck with Ticket 14032 as my example; I think the tradeoff of 
interesting algorithm vs. boring bug is OK for a general math audience.


Questions:

* Who found the bug corresponding to ticket 14032?  Was the computation 
in service of an interesting research question?


* Originally, William said working modulo a few additional primes. 
Does this mean doing p-adic lifting again, or just black-box computing 
det A (mod p), as I have implied?


* How fast is the p-adic algorithm?  William said it was faster than 
Mathematica; does someone have some graphs?


* Is Jeroen Demeyer still a postdoc?  Where was Volker at the time of 
our story?


--Ursula.

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Re: [sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

[Ursula Whitcher]

On 11/3/2014 4:05 PM, William Stein wrote:

I'm sure the
AMS would be very interesting in publishing more pieces that involve
computational mathematics/software, and likely only don't because they
don't have quality submissions enough to choose from.   I published
one there several years ago about open source [1].

  -- William


Did you write the full article and then submit it to the Notices, or did 
you query the editors with a proposal first?  They officially accept 
both types of submissions; do you know whether one method has better 
chances in practice?


UAW

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Re: [sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

[Ursula Whitcher]

On 11/4/2014 6:04 AM, Volker Braun wrote:


Agree. A reasonable article should

[...]

b) talk about bug tracking and prioritization, stopgaps


How DOES bug prioritization work in Sage?  You can pick 
blocker/critical/major/minor/trivial when you're creating a ticket. 
Does someone double-check those choices, or is prioritization 
essentially up to the folks working on a given ticket?  Is the rule that 
blocker-level bugs must be fixed before releasing a new version of Sage?


UAW

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Re: [sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

[Ursula Whitcher]

At some point, William wrote:


I wrote that det code in Sage (though in Sage-6.4 it'll likely be
replaced by a call to FLINT...). It computes det(A) in a very
interesting way, which is asymptotically massively faster than
Mathematica. To compute det(A), choose a random vector v and solve
Ax = v using a p-adic lifting algorithm (the one
inhttps://cs.uwaterloo.ca/~astorjoh/iml.html). One can prove --using
Cramer's rule--that the lcm of the denominators of the entries of x
will then be a divisor d of det(A), and with high probability one
expects that det(A)/d is a tiny integer. One can then provably
(using the Hadamard bound) find det(A) by working modulo a few
additional primes and using the Chinese Remainder theorem.


At some other point, Volker wrote:


There have been subtle bugs in determinants of integer matrices in
Sage before, e.g. http://trac.sagemath.org/ticket/14032
determinant() of integer matrices of size in [51,63] broken. Open
source doesn't make Sage magically bug-free.


The note on ticket 14032 about the bug's solution is:

The problem was an infinite recursion where we compute a determinant 
over ZZ by working mod p and we compute a determinant over GF(p) by 
lifting to ZZ...


Was the algorithm that should have been used here for finding a 
determinant over GF(p) the same as the one that William is describing? 
Or did it rely on a different way to compute a determinant over ZZ by 
working mod p?


UAW

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[sage-devel] Re: The Misfortunes of a Trio of Mathematicians Using Computer Algebra Systems

[Ursula Whitcher]

On Friday, October 24, 2014 7:55:39 PM UTC-5, jason wrote:



 P.S. It would be interesting to see if Sage can do the calculation they 
 identified as buggy in mathematica.  That would make for a cool 
 follow-up editorial. 


So is somebody actively working on a followup editorial/ letter to the 
editor?

--Ursula. 

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Re: orthogonal sums of root lattices was Re: [sage-devel] Lattices?

[Ursula Whitcher]

On 4/3/2014 4:45 AM, Martin Albrecht wrote:

Hi Ursula,

just to mention: there isn't much framework in that ticket, it merely creates
an IntegerLattice class and adds a few useful methods.

In particular, at the moment lattices over QQ (or RR) are not implemented, but
I guess this could be added relatively quickly.


Yes, lattices over QQ would be nice.  Right now I think the biggest 
conceptual tool I want is the ability to construct a lattice by 
specifying its Gram matrix, rather than by specifying an embedding in R^n.


Would it be useful to you to know my wishlist?  And if so, should I put 
it over here or on the ticket?


--Ursula.

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Re: [sage-devel] Lattice, RealLattice, ComplexLattice, VectorSpaceLattice: a bikeshed question

[Ursula Whitcher]

On Thursday, April 3, 2014 9:28:41 AM UTC-5, John Cremona wrote:


 Or one could give the Gram matrix G (A^t * A (in the real case), which 
 is real and positive definite.  You definitely need to be able to 
 define a lattice just by its Gram matrix;  theoretically one can go 
 from such a G via a factorization G=A^t * A to a basis representation 
 (not unique). 


There are situations where it is very useful to allow Gram matrices which 
are *not* positive definite.  In particular, both the negative definite and 
indefinite cases arise when doing computations in algebraic geometry 
involving K3 surfaces. There are some nice results of Nikulin on existence 
and uniqueness of lattice embeddings that only apply to the indefinite case.

Anyone want to team up with me and spend a week in July (the first month I 
realistically have time, sigh) implementing some of this?

--Ursula.

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orthogonal sums of root lattices was Re: [sage-devel] Lattices?

[Ursula]

On Friday, March 21, 2014 7:40:09 AM UTC-5, Martin Albrecht wrote:

 Simon gave me some hints how to integrate the new class into the category 
 framework, so the ticket now *needs review* hint hint: 

 http://trac.sagemath.org/ticket/15976 
  


Hi, all!

I would like to be able to construct and manipulate elements of orthogonal 
sums of root lattices (e.g., A_5 + E_8).  Is Martin's ticket (above) the 
best framework for doing this?  Or is it possible to construct such an 
object using the code for root systems that already exists in Sage?

--Ursula.

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[sage-devel] change_ring and affine patches for toric varieties

[Ursula]

When you change the ring for a toric variety, that ring change does not 
propagate to the affine patches on the toric variety.

Here's an example:

o = lattice_polytope.octahedron(3)
cube = o.polar()
VRes = CPRFanoToricVariety(Delta_polar=cube, coordinate_points=all)
q =5^2
field = GF(q, 'a')
VRes.change_ring(field)
patch = VRes.affine_patch(0)
em = patch.embedding_morphism()
emDomain = em.domain()
emDomain.base_ring()

This returns

Rational Field.

VRes is a 3-dimensional toric variety, so emDomain should be field^3.  If 
you try to map an element of field^3 into VRes using the patch embedding 
morphism, you get a type error due to a failed coercion.

For example,

em(emDomain(field(1), field(1), field(1)))

returns

TypeError: Unable to coerce 1 (type 
'sage.rings.finite_rings.element_givaro.FiniteField_givaroElement') to 
Rational

--Ursula.

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[sage-devel] Re: change_ring and affine patches for toric varieties

[Ursula]

On Monday, July 15, 2013 3:09:29 PM UTC-7, Volker Braun wrote:

 That is correct. The change_ring() methods in Sage return a new object and 
 do _not_ modify the original object:


Fair enough.  I think we have found a true coercion problem involving 
finite fields  toric varieties, though.  This one arises when constructing 
anticanonical hypersurfaces in a Fano toric variety with coefficients in a 
finite field.

Let's make a smooth Fano toric variety over a finite field of non-prime 
order:

o = lattice_polytope.octahedron(3)
cube = o.polar()
VRes = CPRFanoToricVariety(Delta_polar=cube, coordinate_points=all)
field = GF(5^2, 'a')
X=VRes.change_ring(field)

Then let's define a hypersurface with coefficients specified by a list of 
elements in our field:

hyp = X.anticanonical_hypersurface(monomial_points=vertices+origin, 
coefficients=[field(1),field(1),field(1),field(1),field(1),field(1),field(3)])

This raises a type error:

Error in lines 6-6 Traceback (most recent call last): File 
/mnt/home/7tQIE6sJ/.sagemathcloud/sage_server.py, line 494, in execute 
exec compile(block+'\n', '', 'single') in namespace, locals File , line 
1, in module File 
/mnt/home/7tQIE6sJ/sage-5.10-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/local/lib/python2.7/site-packages/sage/schemes/toric/fano_variety.py,
 
line 905, in anticanonical_hypersurface return 
AnticanonicalHypersurface(self, **kwds) File 
/mnt/home/7tQIE6sJ/sage-5.10-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/local/lib/python2.7/site-packages/sage/schemes/toric/fano_variety.py,
 
line 1438, in __init__ for m, coef in zip(monomial_points, coefficients)) 
File 
/mnt/home/7tQIE6sJ/sage-5.10-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/local/lib/python2.7/site-packages/sage/schemes/toric/fano_variety.py,
 
line 1432, in genexpr coefficients = (F(SR(coef)) for coef in 
coefficients) File parent.pyx, line 961, in 
sage.structure.parent.Parent.__call__ (sage/structure/parent.c:8136) File 
coerce_maps.pyx, line 82, in 
sage.structure.coerce_maps.DefaultConvertMap_unique._call_ 
(sage/structure/coerce_maps.c:3856) File coerce_maps.pyx, line 77, in 
sage.structure.coerce_maps.DefaultConvertMap_unique._call_ 
(sage/structure/coerce_maps.c:3757) File 
/mnt/home/7tQIE6sJ/sage-5.10-linux-64bit-ubuntu_12.04.2_lts-x86_64-Linux/local/lib/python2.7/site-packages/sage/rings/finite_rings/finite_field_givaro.py,
 
line 362, in _element_constructor_ return self._cache.element_from_data(e) 
File element_givaro.pyx, line 377, in 
sage.rings.finite_rings.element_givaro.Cache_givaro.element_from_data 
(sage/rings/finite_rings/element_givaro.cpp:6428) File 
element_givaro.pyx, line 490, in 
sage.rings.finite_rings.element_givaro.Cache_givaro.element_from_data 
(sage/rings/finite_rings/element_givaro.cpp:6126) TypeError: unable to 
coerce

We suspect the problematic coercion comes from this line in the 
AnticanonicalHypersurface class:

# Direct conversion a/b to F does not work in Sage-4.6.alpha3,
# so we go through SR, even though it is quite slow.
coefficients = (F(SR(coef)) for coef in coefficients)

--Ursula.

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Re: [sage-devel] Re: problems installing TOPCOM for triangulations?

[Ursula Whitcher]

On 7/2/2013 1:51 PM, Volker Braun wrote:

I agree that this is a usability wart... though really I think the whole
idea of installing further components while Sage is running is a bad
design choice. For example, if you end up modifying shared libraries
that are currently mmaped then bad things will happen.


So why doesn't TOPCOM install with Sage by default?

UAW

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Re: [sage-devel] Re: problems installing TOPCOM for triangulations?

[Ursula Whitcher]

On 7/1/2013 8:42 PM, Volker Braun wrote:

You need to restart the notebook since the test output is cached...


Yes, that seems to have solved the problem.   You might want to add a 
note to this effect in the documentation for Triangulations of a point 
configuration.


--Ursula.

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[sage-devel] problems installing TOPCOM for triangulations?

[Ursula]

I'm running sage-5.10.rc0.

When I evaluate the following code:

p = ReflexivePolytope(3,2)
points = p.points().columns()
pointConfig = PointConfiguration(points)
regular = pointConfig.restrict_to_regular_triangulations(True)
regular

I get the error:

You must install TOPCOM to test for regularity.

But I have installed TOPCOM, using the command install_package('TOPCOM') in the 
notebook!

Any ideas what is going on?  The full traceback on my error message is:

Traceback (most recent call last):
  File stdin, line 1, in module
  File _sage_input_12.py, line 10, in module
exec compile(u'open(___code___.py,w).write(# -*- coding: utf-8 -*-\\n 
+ 
_support_.preparse_worksheet_cell(base64.b64decode(cCA9IFJlZmxleGl2ZVBvbHl0b3BlKDMsMikKcG9pbnRzID0gcC5wb2ludHMoKS5jb2x1bW5zKCkKcG9pbnRDb25maWcgPSBQb2ludENvbmZpZ3VyYXRpb24ocG9pbnRzKQpyZWd1bGFyID0gcG9pbnRDb25maWcucmVzdHJpY3RfdG9fcmVndWxhcl90cmlhbmd1bGF0aW9ucyhUcnVlKQpyZWd1bGFy),globals())+\\n);
 execfile(os.path.abspath(___code___.py))
  File , line 1, in module

  File /tmp/tmpVZpwc_/___code___.py, line 6, in module
regular = pointConfig.restrict_to_regular_triangulations(True)
  File 
/home/whitchua/sage-5.10.rc0/local/lib/python2.7/site-packages/sage/geometry/triangulation/point_configuration.py,
 line 790, in restrict_to_regular_triangulations
star=self._star)
  File classcall_metaclass.pyx, line 330, in 
sage.misc.classcall_metaclass.ClasscallMetaclass.__call__ 
(build/cythonized/sage/misc/classcall_metaclass.c:1224)
  File 
/home/whitchua/sage-5.10.rc0/local/lib/python2.7/site-packages/sage/geometry/triangulation/point_configuration.py,
 line 311, in __classcall__
.__classcall__(cls, points, connected, fine, regular, star, defined_affine)
  File cachefunc.pyx, line 992, in 
sage.misc.cachefunc.WeakCachedFunction.__call__ 
(build/cythonized/sage/misc/cachefunc.c:5394)
  File 
/home/whitchua/sage-5.10.rc0/local/lib/python2.7/site-packages/sage/structure/unique_representation.py,
 line 447, in __classcall__
instance = typecall(cls, *args, **options)
  File classcall_metaclass.pyx, line 518, in 
sage.misc.classcall_metaclass.typecall 
(build/cythonized/sage/misc/classcall_metaclass.c:1586)
  File 
/home/whitchua/sage-5.10.rc0/local/lib/python2.7/site-packages/sage/geometry/triangulation/point_configuration.py,
 line 342, in __init__
raise ValueError, 'You must install TOPCOM to test for regularity.'
ValueError: You must install TOPCOM to test for regularity.

--Ursula Whitcher.


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Re: [sage-devel] Re: problems installing TOPCOM for triangulations?

[Ursula Whitcher]

On 7/1/2013 8:26 PM, Volker Braun wrote:

The interface checks whether the utility program points2placingtriang
from TOPCOM is available, and didn't find it in your install. Do you
have Sage's current spkg of TOPCOM installed or some other version?


I ran

install_package('TOPCOM')

from the notebook command line, so I have whatever version installed 
automatically.



Just for the record, you almost certainly want

regular.restrict_to_star_triangulations([0,0,0])

as well.


Not actually, I'm not trying to construct a fan for a toric variety :)

UAW

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Re: [sage-devel] Re: R build error in 5.10 was Re: ATLAS build error on CentOS

[Ursula Whitcher]

On 6/5/2013 8:50 PM, leif wrote:


This appears to be an upstream bug; despite that we configure with
'--with-readline=$SAGE_LOCAL', the corresponding '-L...' is missing in
the linker command such that your system's libreadline gets picked up.

You can try:

$ env LDFLAGS=-L/home/whitchua/sage-5.10.rc0/local/lib ./sage -i
spkg/standard/r-2.15.2.p2.spkg

and if that worked, resume the normal build with

$ make


This worked!  Thank you so much for your help.

UAW

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Re: [sage-devel] Re: R build error in 5.10 was Re: ATLAS build error on CentOS

[Ursula Whitcher]

On 6/5/2013 10:13 PM, leif wrote:


Ursula, can you confirm that `LIBRARY_PATH` is set in your shell?

E.g., what does the following give?

$ ./sage --sh -c 'echo $LIBRARY_PATH'



/home/whitchua/sage-5.10.rc0/local/lib

--Ursula.

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Re: [sage-devel] Using ssh for port-forwarding

[Ursula]

I made a FAQ entry on the wiki incorporating these instructions for SSH 
tunneling and Windows:

http://wiki.sagemath.org/faq#I_installed_Sage_on_a_Unix_or_Linux_server_where_I_have_an_account.2C_but_my_personal_computer_runs_Windows.__How_do_I_access_the_Sage_notebook.3F

--Ursula.

On Wednesday, February 7, 2007 1:44:44 AM UTC-6, boo...@u.washington.edu 
wrote:

 Instructions for PuTTY:

 In the host configuration, go to the Connection-SSH-Tunnels category.

 Enter the following settings towards the bottom:

 Source port: 8100
 Destination: localhost:8000

 Click the Local radio button, and press the Add button.

 Once logged in, run

 user@A sage -notebook

 and point your browser to
 http://localhost:8100

 On Tue, 6 Feb 2007, Nils Bruin wrote:

 
  The following is easily found on the man page of ssh, but William
  pointed out to me that many users may not be aware of the possibility
  to use ssh to forward ports. In particular, if you want to run sage -
  notebook on computer A, but only want to let it listen to a local
  port out of security considerations and yet want to run a web browser
  on computer B to connect to the server, you can do the following
 
  user@B firefox 
  user@B ssh -L 8000:localhost:8000 user@A
  user@A sage -notebook
  []
  ---
  now, in firefox on B, you can visit http://localhost:8000, which will
  get tunneled by ssh to port 8000 on A and hence will give you a
  connection to the sage notebook on A.
 
  I am sure one can use ssh on windows to do port forwarding as well.
  Perhaps someone who knows can reply with a small note explaining how?
 
  Enjoy.
 
 
  
 




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[sage-devel] ATLAS build error on CentOS

[Ursula]

I'm trying to install Sage in my personal directory on a system running 
CentOS.  (The system is a small research cluster belonging to one of the 
professors in the chemistry department at my institution; I don't know a 
lot about its configuration, and I certainly don't have root access, so 
please bear with me.)

When I ran make, I received the following error message, along with 
instructions to post to sage-devel:

---

***
Error building Sage.

The following package(s) may have failed to build:

package: atlas-3.8.4.p1
log file: /home/whitchua/sage-5.9/logs/pkgs/atlas-3.8.4.p1.log
build directory: /home/whitchua/sage-5.9/spkg/build/atlas-3.8.4.p1

---

The full log file for atlas is a bit long for a single email, but you can 
find it at:

https://www.dropbox.com/s/brnvxh48mu36g05/atlas-3.8.4.p1.log

--Ursula.



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Re: [sage-devel] ATLAS build error on CentOS

[Ursula Whitcher]

On 6/5/2013 11:01 AM, Jeroen Demeyer wrote:

On 06/05/2013 05:57 PM, Ursula wrote:

https://www.dropbox.com/s/brnvxh48mu36g05/atlas-3.8.4.p1.log


The log file seems to be truncated, the last part is missing.



I re-downloaded it.  Try again?

UAW

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Re: [sage-devel] Re: ATLAS build error on CentOS

[Ursula Whitcher]

On 6/5/2013 11:06 AM, Volker Braun wrote:

Can you try the new ATLAS (for example in sage-5.10.rc0)


Sorry, I don't know how I would do that.  Can you expand a little?

UAW

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Re: [sage-devel] ATLAS build error on CentOS

[Ursula Whitcher]

On 6/5/2013 11:16 AM, Jeroen Demeyer wrote:


https://www.dropbox.com/s/brnvxh48mu36g05/atlas-3.8.4.p1.log


The log file seems to be truncated, the last part is missing.



I re-downloaded it.  Try again?


The file is longer than before, but still truncated :-(


Can you tell me what the end of the file ought to look like?  I'm not 
sure whether the truncation is due to my SFTP client, Dropbox, or the 
failed build.


UAW

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Re: [sage-devel] Re: ATLAS build error on CentOS

[Ursula Whitcher]

On 6/5/2013 5:11 PM, Volker Braun wrote:

On Wednesday, June 5, 2013 8:42:03 PM UTC+1, Snark wrote:

  takes about 25 minutes, because SAGE_ATLAS_LIB is set in the global
  environment by default.
Well, not everyone has a big  recent server.


My laptop builds Sage in 25 minutes...


I followed William's instructions precisely just after he posted them 
(which means no attempts at optimization), and the build is still in 
progress, six hours later.


On the bright side, I haven't had any ATLAS errors yet!

UAW

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Re: [sage-devel] Re: ATLAS build error on CentOS

[Ursula Whitcher]

On 6/5/2013 6:01 PM, leif wrote:

Ursula Whitcher wrote:

I followed William's instructions precisely just after he posted them
(which means no attempts at optimization), and the build is still in
progress, six hours later.


I'm not sure what you mean by no attempts to optimization.

(And you're apparently not building in parallel, which requires
exporting MAKE='make -jN', N the max. number of jobs.)


What I meant by no attempts at optimization was if I had tried to use 
the fact that this is a cluster, the installation would probably have 
gone faster.  I think that includes not building in parallel!



Out of curiosity:  What does 'cat /proc/cpuinfo' give?


vendor_id   : AuthenticAMD
cpu family  : 16
model   : 8
model name  : Six-Core AMD Opteron(tm) Processor 2427
stepping: 0
cpu MHz : 800.000
cache size  : 512 KB
physical id : 0
siblings: 6
core id : 4
cpu cores   : 6
apicid  : 4
fpu : yes
fpu_exception   : yes
cpuid level : 5
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext 
fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc nonstop_tsc pni 
cx16 popcnt lahf_lm cmp_legacy svm extapic cr8_legacy altmovcr8 abm 
sse4a misalignsse 3dnowprefetch osvw

bogomips: 4422.17
TLB size: 1024 4K pages
clflush size: 64
cache_alignment : 64
address sizes   : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

processor   : 5
vendor_id   : AuthenticAMD
cpu family  : 16
model   : 8
model name  : Six-Core AMD Opteron(tm) Processor 2427
stepping: 0
cpu MHz : 800.000
cache size  : 512 KB
physical id : 0
siblings: 6
core id : 5
cpu cores   : 6
apicid  : 5
fpu : yes
fpu_exception   : yes
cpuid level : 5
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext 
fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc nonstop_tsc pni 
cx16 popcnt lahf_lm cmp_legacy svm extapic cr8_legacy altmovcr8 abm 
sse4a misalignsse 3dnowprefetch osvw

bogomips: 4422.03
TLB size: 1024 4K pages
clflush size: 64
cache_alignment : 64
address sizes   : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

processor   : 6
vendor_id   : AuthenticAMD
cpu family  : 16
model   : 8
model name  : Six-Core AMD Opteron(tm) Processor 2427
stepping: 0
cpu MHz : 800.000
cache size  : 512 KB
physical id : 1
siblings: 6
core id : 0
cpu cores   : 6
apicid  : 8
fpu : yes
fpu_exception   : yes
cpuid level : 5
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext 
fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc nonstop_tsc pni 
cx16 popcnt lahf_lm cmp_legacy svm extapic cr8_legacy altmovcr8 abm 
sse4a misalignsse 3dnowprefetch osvw

bogomips: 4421.84
TLB size: 1024 4K pages
clflush size: 64
cache_alignment : 64
address sizes   : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

processor   : 7
vendor_id   : AuthenticAMD
cpu family  : 16
model   : 8
model name  : Six-Core AMD Opteron(tm) Processor 2427
stepping: 0
cpu MHz : 800.000
cache size  : 512 KB
physical id : 1
siblings: 6
core id : 1
cpu cores   : 6
apicid  : 9
fpu : yes
fpu_exception   : yes
cpuid level : 5
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext 
fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc nonstop_tsc pni 
cx16 popcnt lahf_lm cmp_legacy svm extapic cr8_legacy altmovcr8 abm 
sse4a misalignsse 3dnowprefetch osvw

bogomips: 4422.10
TLB size: 1024 4K pages
clflush size: 64
cache_alignment : 64
address sizes   : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

processor   : 8
vendor_id   : AuthenticAMD
cpu family  : 16
model   : 8
model name  : Six-Core AMD Opteron(tm) Processor 2427
stepping: 0
cpu MHz : 800.000
cache size  : 512 KB
physical id : 1
siblings: 6
core id : 2
cpu cores   : 6
apicid  : 10
fpu : yes
fpu_exception   : yes
cpuid level : 5
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext 
fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc

[sage-devel] optional packages without root access?

[Ursula]

I am using the copy of Sage installed on sage.math.washington.edu from
the command line.  I do not have root access.

I would like to use some commands which require the optional package
gap_packages-4.4.10_4 .  Because I don't have root access to this
system, running:

sage -i gap_packages-4.4.10_4

does not work.

Would it be possible to install gap_packages-4.4.10_4 to a directory
within my home directory, and then instruct Sage to check this
directory when looking for packages?  It seems like this would be a
fairly simple scripting change.

(I am also wondering if there is a way to use commands requiring
gap_packages-4.4.10_4 from a notebook at sagenb.org?)

UAW

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[sage-devel] Re: optional packages without root access?

[Ursula]

On Jul 15, 2:30 pm, Mike Hansen [EMAIL PROTECTED] wrote:
  Would it be possible to install gap_packages-4.4.10_4 to a directory
  within my home directory, and then instruct Sage to check this
  directory when looking for packages?  It seems like this would be a
  fairly simple scripting change.

 You'd have to tell GAP to use this special directory, and it would
 only work for this particular optional package.

It's actually really easy to tell GAP how to use a subdirectory of
your home directory for additional packages: you create a directory
called pkg , and then you start GAP using the command

gap -l 'path/homedir;'

where path/homedir is, of course, the path to your home directory.

However, I don't know how to tell commands in Sage that use GAP that
they ought to use GAP packages from the pkg directory in my home
directory.  If this is obvious given the above command, please
enlighten me.

 I don't see a good
 way to do what you want in general for optional packages.

 If you want to customize a Sage install, then you should just install
 your own copy of Sage in your home directory.

 --Mike

I could do this.  I could also use HAP directly, or in conjunction
with reading all of David Joyner's source code for group cohomology,
which would surely teach me quite a lot about both Sage and GAP, to
say nothing of group cohomology.

I'm resisting because I believe that Sage ought to be designed in such
a way that it is *possible* to interact with Sage as a user, not a
developer.  If I were a system administrator at a math department
other than the University of Washington, I would be very interested in
installing Sage for my users, because it combines lots of other freely
available packages into one easy-to-install-and-maintain big chunk.
However, I would *not* want to force all of my users to maintain
separate copies of Sage, because they would invariably forget to
update it.  Nor would I wish to spend all of my time installing
optional packages for other people.

UAW

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