Re: [sage-support] cypari fails to build on Ubuntu 18.04

[Jeroen Demeyer]

On 2019-06-18 15:16, Kevin Horton wrote:

2. It is quite possible low memory is the issue, as I'm trying to
install it on a Linode virtual server with 1 GB RAM.


Yes, that's probably not enough for a big compilation. I would recommend 
at least 4GB of RAM, but you may get away with 2GB... at least if you 
don't build the documentation: use "make build" to build all of Sage 
without the documentation.


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Re: [sage-support] cypari fails to build on Ubuntu 18.04

[Jeroen Demeyer]

Internal compiler error typically means one of the following:
- Running out of memory during compilation
- Buggy compiler
- Hardware problem

So the following questions need to be answered:

1. Is the problem reproducible? What happens when you try again?

2. Is this a machine with little memory or were you doing many things at 
the same time (possibly compiling in parallel) such that you could have 
run out memory?


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Re: [sage-support] Re: Computing a Groebner Basis (singular algorithm) raises an error

[Jeroen Demeyer]

On 2019-05-27 16:11, Tracy Hall wrote:

in particular it seems to have undefined
behavior in subsequent calls after it has been interrupted by alarm().


This is simply a fact of life and not really considered to be a bug. You 
should not rely on the fact that interruptions (using either CTRL-C or 
alarm) work perfectly. Don't use alarm() for serious computations.


If you need proper timeouts, one thing you can do is spawn multiple Sage 
processes or fork one Sage process. Then you can kill the whole process 
after a certain amount of time.


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Re: [sage-support] I absolutely dont know why but i am getting an error.

[Jeroen Demeyer]

On 2019-04-17 09:32, Oliver Thiel wrote:

Hello,

I absolutely dont know why but i am getting an error.


What did you do? What happened *exactly*?

See also https://www.chiark.greenend.org.uk/~sgtatham/bugs.html

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Re: [sage-support] Interface to 4ti2

[Jeroen Demeyer]

On 2019-03-20 05:21, 'benyamin alizade' via sage-support wrote:

When I run |sage -i 4ti2, it returns that -i is an unknown option for sage.


What happens *exactly*?

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Re: [sage-support] A case of immaculate conception...

[Jeroen Demeyer]

On 2019-03-19 12:52, Emmanuel Charpentier wrote:

Defining a symbolic function seems to declare its arguments.


I tend to think that everything on the left of the '=' sign in an 
assignment is stuff that is assigned to. So


  (a, b, c) = range(3)

assigns to a, b and c.

  R. = ZZ[]

assigns to R and x.

  func(x) = x

assigns to func and x.

So in this sense, it's expected.

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Re: [sage-support] much memory is used...

[Jeroen Demeyer]

On 2018-10-09 12:00, Dima Pasechnik wrote:

Well, primitive,  as opposed to added by Sage. E.g. I suppose one cannot use it
for RDF.


If you really want to get elements of RDF, you could use a Sage vector 
instead.


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Re: [sage-support] much memory is used...

[Jeroen Demeyer]

On 2018-10-08 14:28, Dima Pasechnik wrote:

Can you use array.array on anything that's not a primitive Python type?


I don't know what you mean with "primitive Python type". Anyway, it 
supports various kinds of basic C types (like double for example). Docs 
here:


https://docs.python.org/2/library/array.html

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Re: [sage-support] much memory is used...

[Jeroen Demeyer]

On 2018-10-08 13:19, Thierry Dumont wrote:

So my list should use less than 1gb, if it phi was a C array.


But it's not a C array. There is overhead for Python garbage collection, 
the Sage parent, the Cython virtual method table...


If you really want a C array, use array.array or numpy.

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Re: [sage-support] Sage crashes on start

[Jeroen Demeyer]

On 2018-07-18 05:58, 'Naturelover' via sage-support wrote:

I just installed SageMath 7.6


Why such an old version?

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Re: [sage-support] Re: building documentation: says I should use a sage shell, but i am

[Jeroen Demeyer]

On 2018-06-18 04:22, Matthew Lancellotti wrote:

I am able to get around the first error by commenting out the try catch
loop in conf.py:


Which conf.py file are you talking about?

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Re: [sage-support] Re: building documentation: says I should use a sage shell, but i am

[Jeroen Demeyer]

On 2018-06-18 05:54, Matthew Lancellotti wrote:

sage-7.6-Ubuntu_14.04-x86_64.tar.bz2


Do you have a good reason to use an outdated version of Sage? Version 
8.2 has been released.


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Re: [sage-support] PARI/GP error in wrapping custom-defined PARI functions in Sage using the command gp.set()

[Jeroen Demeyer]

On 2018-06-18 09:50, am...@ma.iitr.ac.in wrote:

I have a library in PARI/GP and since Sage also supports the GP
calculator I have been trying to shift my library using gp.set() and
gp.get() commands. So far all functions are working but I got a PARI/GP
error while implementing this function in Sage using gp.set(). Here is
the code of that function:

compareSides(printedgesonscreen=0) =
{
   local( edge, edgesCheckList1:list, edgesCheckList2:list,
cancelCriterion);

   edgesCheckList1 = listcreate(2*numberOfLines);
   edgesCheckList2 = listcreate(2*numberOfLines);

   for (j = 1, numberOfSpheres,
if( deleteFlag[j] == 0,

  if( printedgesonscreen == 1,
  print("Cell ",j," lies on the hemisphere with center at ",
   divideInNumberField(K,Lambda[j],Mu[j]) );
  print(" with radius square ", radiusSquare[j],
 " and has the following edges:");
   );

   for( s = 1, length( pointsOfLine[j]),

  edge = setintersect(Set(pointsOfLine[j][s]),
 Set(pointsOfSphere[j]:list));

  if(length(edge) == 2,

 if(printedgesonscreen == 1, print(edge); );

 if( setsearch(Set(edgesCheckList1),edge),

 if(setsearch(Set(edgesCheckList2),edge),

 if (printedgesonscreen == 1,
   print("***Error in function
compareSides: triple edge in cell diagram");
 );
,
 listput(edgesCheckList2,edge);
 );
, /* else not yet entered in edgesCheckList1 */
 listput(edgesCheckList1,edge);
 );

  );
  if(length(edge) > 2,
 print("***Error in function compareSides: edge with
three corners");
  );
   );
);
   );

   if(Set(edgesCheckList1) == Set(edgesCheckList2),

 print("All ", length(edgesCheckList1), " = ",
 length(edgesCheckList2)," edges appear twice.");
 if( length(edgesCheckList1) > 3,
 cancelCriterion = 1
 ,
 cancelCriterion = 0
 );
 , /* else some edges do not appear twice. */
 print("Some edges do not appear twice:");

print(setminus(Set(edgesCheckList1),Set(edgesCheckList2)));
   );
   listkill(edgesCheckList1); listkill(edgesCheckList2);
   /* Return */ cancelCriterion
};


I have run this function in the GP calculator of Sage using the
gp.console() command and it works fine but I don't understand why it is
not working using gp.set(). Here is the implementation I did:

gp.set('compareSides(printedgesonscreen=0)','{  local( edge,
edgesCheckList1:list, edgesCheckList2:list, cancelCriterion);
edgesCheckList1 = listcreate(2*numberOfLines);  edgesCheckList2 =
listcreate(2*numberOfLines);  for (j = 1, numberOfSpheres,   if(
deleteFlag[j] == 0, if( printedgesonscreen == 1,
print("Cell ",j," lies on the hemisphere with center at
",  divideInNumberField(K,Lambda[j],Mu[j])
); print(" with radius square ",
radiusSquare[j]," and has the following edges:");
);   for( s = 1, length( pointsOfLine[j]), edge =
setintersect(Set(pointsOfLine[j][s]),
Set(pointsOfSphere[j]:list)); if(length(edge) ==
2, if(printedgesonscreen == 1, print(edge);
);if(
setsearch(Set(edgesCheckList1),edge),
if(setsearch(Set(edgesCheckList2),edge),
if (printedgesonscreen == 1, print("***Error in function compareSides:
triple edge in cell diagram");
);   ,
listput(edgesCheckList2,edge);
);   , /* else not yet entered in edgesCheckList1
*/listput(edgesCheckList1,edge);
); ); if(length(edge) >
2,print("***Error in function compareSides: edge with
three corners"); );  );   ); );  if(Set(edgesCheckList1) ==
Set(edgesCheckList2), print("All ", length(edgesCheckList1),
" = ",length(edgesCheckList2)," edges appear
twice.");if( length(edgesCheckList1) > 3,
cancelCriterion = 1;,cancelCriterion =
0;);, /* else some edges do not appear twice.
*/print("Some edges do not appear
twice:");
print(setminus(Set(edgesCheckList1),Set(edgesCheckList2)));  );
listkill(edgesCheckList1); listkill(edgesCheckList2);  /* Return */
cancelCriterion}')

When I run this in Sage it shows a PARI/GP error and outputs the whole
code. I have been trying to find the bug since the last 3 days. Please
help me regarding this. Thank you.

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Re: [sage-support] Re: PariError: bug in LLL_cmbf [no factor], please report

[Jeroen Demeyer]

Thanks for checking. In the mean time, I guess the problem might be 
related to the fact that I'm using a non-default value for primelimit in 
GP (100 instead of 50).


But if you say that the problem is fixed by the PARI upgrade, I consider 
this issue closed.


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Re: [sage-support] Re: PariError: bug in LLL_cmbf [no factor], please report

[Jeroen Demeyer]

On 2018-06-13 10:25, John Cremona wrote:

THanks for looking into this Jeroen (I hoped you would).  The file
bug.gp  you attached causes an error in the latest gp
(version 2.10.0), after increasing parisizemax I get the same error
message.


What are the *exact steps* for reproducing it? I still haven't managed 
so far.


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Re: [sage-support] Re: PariError: bug in LLL_cmbf [no factor], please report

[Jeroen Demeyer]

I haven't managed to reproduce it in GP, I have no idea why. Typically, 
it's not so hard to translate a Sage bug like this to a PARI/GP bug. It 
must be something rather subtle. I'll try again tomorrow.


I did manage to reproduce it with the PARI-in-Sage by running the 
attached GP script in Sage:


sage: pari('read("/tmp/bug.gp")')
---
PariError Traceback (most recent call last)
 in ()
> 1 pari('read("/tmp/bug.gp")')

cypari2/pari_instance.pyx in cypari2.pari_instance.Pari.__call__()

cypari2/gen.pyx in cypari2.gen.objtogen()

cypari2/handle_error.pyx in cypari2.handle_error._pari_err_handle()

PariError: nffactor: bug in LLL_cmbf [no factor], please report

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bug.gp
Description: application/gnuplot

Re: [sage-support] Upgrade to 8.2 hangs at ncurses

[Jeroen Demeyer]

On 2018-05-10 19:38, Robert Gross wrote:

I have aliased cp to "cp -i" and "mv" to "mv -i".


What do you mean this *exactly*?

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Re: [sage-support] Cython in jupyter notebook

[Jeroen Demeyer]

On 2018-04-15 16:08, Simon King wrote:

Hi!

The following cython code compiles fine in SageMath command line version
and it *used* to compile fine in the jupyter notebook one year ago:


Fix at https://trac.sagemath.org/ticket/25177

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Re: [sage-support] ipywidgets and sage

[Jeroen Demeyer]

On 2018-03-21 11:49, Marcin Kostur wrote:

btw, will it be sufficient when major version number will match?


Probably, but I cannot say for sure.

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Re: [sage-support] ipywidgets and sage

[Jeroen Demeyer]

On 2018-03-21 10:05, Marcin Kostur wrote:

Hi,

How to get working ipywidgets *or @interact" when using sagemath kernel
in external jupyter/jupyterlab?


The problem is the version of ipywidgets in Sage must match with the 
version in the external jupyter. If you are using Sage 8.1, this is 
ipywidgets 6. With a recent beta version of Sage, this is ipywidgets 7.


And don't forget to clear your browser cache after changing versions.

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Re: [sage-support] Issue compiling Cython code that uses Sage

[Jeroen Demeyer]

On 2018-03-15 13:22, Marc Mezzarobba wrote:

but the variant below doesn't?


That's certainly a bug: https://trac.sagemath.org/ticket/24987

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Re: [sage-support] Has Big-Endian support been deprecated yet?

[Jeroen Demeyer]

On 2018-03-13 20:33, Kim Walisch wrote:

primecount currently only supports little-endian CPUs.


That sounds very fishy to me. What are you doing in your code that it 
supports only little-endian?


If your code only works for a particular endianness, it probably means 
that you are nasty stuff which is going to break anyway on some 
architectures or with some compilers.


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Re: [sage-support] Sage Crash Report

[Jeroen Demeyer]

On 2018-03-10 12:29, Alasdair McAndrew wrote:

As created just now.  Enjoy!


How did you get that SageMath installation on your computer? Was it a 
binary install, a source install, an upgrade from an earlier version?


In any case, I would suggest to simply reinstall Sage.

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Re: [sage-support] avoiding startup time cost with multiple invocations

[Jeroen Demeyer]

On 2018-01-10 19:27, Vincent Delecroix wrote:

Have a look at

https://docs.python.org/2/extending/embedding.html


Even simpler would be to use Cython to interface between C++ and 
Python/Sage.


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Re: [sage-support] LattE failed to build

[Jeroen Demeyer]

There seems to be a problem with your networking setup. Does this help:

https://superuser.com/questions/879731/osx-ssh-could-not-resolve-hostname-nodename-nor-servname-provided-or-not-kno

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Re: [sage-support] LattE failed to build

[Jeroen Demeyer]

Logs please

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Re: [sage-support] Re: Map from S.base() to S?

[Jeroen Demeyer]

Thanks!

On 2017-11-27 10:14, Simon King wrote:

Hi Jeroen,

On 2017-11-27, Jeroen Demeyer <jdeme...@cage.ugent.be> wrote:

I might be missing something, but is there a generic recipe in Sage to
get a map from S.base() to S? I want something which works in as much
generality as possible for any structure S. I feel like that should
exist but I couldn't find it.


   sage: R.<a,b>=QQ[]
   sage: R.from_base_ring?

Not sure if this answers your question, as this isn't a map but a
conversion method.

Other than that, if you really want the result as a map, just exploit
the coercion/conversion framework:

   sage: R.convert_map_from(R.base())
   Polynomial base injection morphism:
 From: Rational Field
 To:   Multivariate Polynomial Ring in a, b over Rational Field

I suppose you know the difference between a coercion and a conversion
map, and you know that in a non-unital algebra (which I think aren't
implemented in Sage) a conversion from the base ring doesn't really
make sense.


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[sage-support] Map from S.base() to S?

[Jeroen Demeyer]

I might be missing something, but is there a generic recipe in Sage to 
get a map from S.base() to S? I want something which works in as much 
generality as possible for any structure S. I feel like that should 
exist but I couldn't find it.


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Re: [sage-support] Sage Crash Report

[Jeroen Demeyer]

On 2017-10-26 10:50, Dima Pasechnik wrote:

from your log:

ImportError: libgfortran.so.3: cannot open shared object file: No such file or 
directory

installing libfortran3  will fix the problem.



Or waiting for Sage 8.1 since that problem has been fixed in the mean time.

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Re: [sage-support] Sage Crash Report

[Jeroen Demeyer]

This is a known problem which will be fixed for Sage 8.1

For now, you have to install gfortran from your Fedora distribution.

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Re: [sage-support] Sage Crash Support

[Jeroen Demeyer]

On 2017-10-22 21:14, Alvaro Ezequiel wrote:

I installed Sage correctly. When I'm going to execute it this happens
and crash...


What happens?

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Re: [sage-support] Sage Crash Report

[Jeroen Demeyer]

On 2017-10-22 21:01, Jan Groenewald wrote:

If you can email this file to the developers
...provided with information on how you installed Sage, what OS you are 
using, which version of Sage you are running, what command you ran when 
you got this error.


Too many people think that a "Crash Report" is sufficient information.

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Re: [sage-support] Sage crash on first run - can't find the fortran compiler

[Jeroen Demeyer]

This should be fixed in the next version of Sage:

https://github.com/sagemath/binary-pkg/pull/12

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Re: [sage-support] Troubleshooting standalone scripting issues (seeking knowledge about interpreter and preparser)

[Jeroen Demeyer]

Confirmed, this is a bug in the tutorial.

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Re: [sage-support] Sage 8.0.beta12 Crash Report

[Jeroen Demeyer]

This is a customized version of Sage. For example, the file 
src/sage/dynamics/complex_dynamics/mandel_julia.py (which is causing the 
problems) does not exist in the official SageMath.


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Re: [sage-support] Trouble building development version

[Jeroen Demeyer]

On 2017-06-15 17:48, David Loeffler wrote:

I just downloaded the sage-8.0.beta10 tarball, unpacked it, and typed
'make'. After a short interval, I got the error message below. What am I
doing wrong?


Do you have any unusual environment variables set?

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Re: [sage-support] How to use Sphinx to create documentation for a project that uses Sage?

[Jeroen Demeyer]

On 2017-05-31 12:42, Paul Leopardi wrote:



On Wednesday, 31 May 2017 19:39:32 UTC+10, Jeroen Demeyer wrote:

I think you need to import sage.all first, before importing anything
else from sage.


Thanks, in which file do you mean, every Python file that uses Sage, or
some specific file?


Well, you just have to make sure that the statement "import sage.all" is 
executed at least once before importing anything from Sage. Now, in 
practice, the easiest way to achieve that is to put "import sage.all" in 
the top-level __init__.py file of your package. Note that this will 
cause Sage imported when importing anything from your package (this may 
or may not be what you want).


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Re: [sage-support] How to use Sphinx to create documentation for a project that uses Sage?

[Jeroen Demeyer]

On 2017-05-31 12:55, Paul Leopardi wrote:

Thanks, I think I figured out what you mean. I updated conf.py to
contain the following:


That's not what I meant since I said that the issues you are having are 
unrelated to Sphinx. So by "fixing" it in Sphinx you are working around 
the problem, not actually fixing the problem.


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Re: [sage-support] How to use Sphinx to create documentation for a project that uses Sage?

[Jeroen Demeyer]

I think you need to import sage.all first, before importing anything 
else from sage.


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Re: [sage-support] How to use Sphinx to create documentation for a project that uses Sage?

[Jeroen Demeyer]

On 2017-05-30 15:24, Paul Leopardi wrote:

Do you understand the problem yet, or do I need to explain it again in
greater detail?


I understand the problem, but you are focusing too much on the detail of 
Sphinx. The problem is unrelated to Sphinx; it has to do with your 
Sage/Python installation in general.


Sphinx needs to be able to import your modules to document them. There 
is nothing Sphinx-specific about this, it's just usual Python imports. I 
am assuming that your package works within Sage but not outside of Sage. 
That means that you need to run Sphinx also within the Sage environment.


The easiest way to do this is running a Sage shell:

$ sage --sh

And now do everything again within this environment.

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Re: [sage-support] How to use Sphinx to create documentation for a project that uses Sage?

[Jeroen Demeyer]

On 2017-05-28 14:33, Paul Leopardi wrote:

Hello,
I am trying to create HTML documentation for my Boolean-Cayley-graphs
project ( https://github.com/penguian/Boolean-Cayley-graphs ) that uses
Sage.
If I try to just use Sphinx, following the instructions at
https://codeandchaos.wordpress.com/2012/07/30/sphinx-autodoc-tutorial-for-dummies/


Good! Since you are sending this email, I assume that something is not 
working for you. What is the problem?


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Re: [sage-support] Problem compiling Sage 7.6 from source

[Jeroen Demeyer]

Is the problem reproducible, i.e. does it happen again if you rebuild Sage?

Which compiler are you using?

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Re: [sage-support] complex numbers printing real part + imaginary part

[Jeroen Demeyer]

On 2017-04-11 18:25, Pedro Cruz wrote:

Hello,

sage is printing b*I + a and we want to see a + b * I


Do you have a complete example?

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Re: [sage-support] sage-7.6 build fails on Fedora-21

[Jeroen Demeyer]

On 2017-03-28 06:34, Jose Gaetan Pierre wrote:

sage-7.6 fails on fedora-21 (7.4 built ok). error occurred during
dochtml build of graphs.


Complete log file please.

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Re: [sage-support] Sage Crash Report

[Jeroen Demeyer]

On 2017-03-19 14:08, Kam wrote:

Attached is a report about a crash that happened here in Chicago...
enjoy the read!  :)


Don't press CTRL-C when Sage is starting up and all should be fine.

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Re: [sage-support] Doubt related to commits in trac

[Jeroen Demeyer]

On 2017-03-10 09:39, Ashutosh Ahelleya wrote:

Heyy,

Thanks and yes I am using git trac.


Maybe you forgot to run

$ git trac checkout 22312

when changing tickets.

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Re: [sage-support] Running sage scripts noninteractively (possible bug)

[Jeroen Demeyer]

On 2017-03-07 10:19, Jeroen Demeyer wrote:

On 2017-03-06 23:58, Watson Ladd wrote:

Or should I just change to load instead of attach?


The problem is limited to load(), so that would work.


Sorry: I meant to say: the problem is limited to attach(), so load() 
should work.


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Re: [sage-support] Running sage scripts noninteractively (possible bug)

[Jeroen Demeyer]

On 2017-03-06 23:58, Watson Ladd wrote:

Or should I just change to load instead of attach?


The problem is limited to load(), so that would work.

Thinking about it, actually attach() only makes sense in interactive 
sessions. So I see no reason to use it in scripts.


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Re: [sage-support] Running sage scripts noninteractively (possible bug)

[Jeroen Demeyer]

Confirmed: https://trac.sagemath.org/ticket/22527

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Re: [sage-support] Running sage scripts noninteractively (possible bug)

[Jeroen Demeyer]

We need more details. In particular it would be useful to attach a 
minimal testcase with the problematic .sage files.


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Re: [sage-support] Silly Cython question

[Jeroen Demeyer]

On 2017-02-21 22:02, Watson Ladd wrote:

I am having trouble figuring out which imports I need to get the
right names to appear


Use the import_statements() function to determine which import 
statements you need. There shouldn't be a difference between Python and 
Cython regarding import statements.


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[sage-support] Example GAP computation

[Jeroen Demeyer]

Can somebody please provide some example "hello-world" GAP computation? 
Just something which can be used to showcase the abilities of GAP but 
which takes at most a few seconds to run.


I need this to make a "Demo" GAP notebook for OpenDreamKit.

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Re: [sage-support] Compilation of 7.6.beta1 on Ubuntu 16-10

[Jeroen Demeyer]

On 2017-01-31 12:24, Thierry Dumont wrote:

I just git clone sage, then checkout origin/develop and make.
Then after some time, Python 3 is installed and compiled.


Are you really sure about that? Did you set the SAGE_PYTHON3 environment 
variable?


Could you please send your logs/install.log for a single serial build 
such that we can see what might be wrong?


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Re: [sage-support] Compilation of 7.6.beta1 on Ubuntu 16-10

[Jeroen Demeyer]

On 2017-01-31 09:42, Thierry Dumont wrote:

When trying to compile 7.6.beta1, which installed Python3, I got a
cython problem (cmp...):


That's not news... Nobody ever said that Sage works with Python 3.

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Re: [sage-support] Cython problem

[Jeroen Demeyer]

On 2017-01-25 17:07, jordan.h.e...@gmail.com wrote:

Hello,

I've been trying to use cython in Jupyter and it fails to compile.
My version of Sage is 7.3. It was installe from the ppa.
I run Linux Mint.


I guess that you are missing a compiler toolchain. In your case, the 
system header files like /usr/include/limits.h are missing.


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Re: [sage-support] Sage needing write access to itself

[Jeroen Demeyer]

Also: please describe *exactly* what goes wrong ("this doesn't work" is 
not precise enough to understand the problem).


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Re: [sage-support] Sage needing write access to itself

[Jeroen Demeyer]

Exactly how did you build/install Sage?

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Re: [sage-support] "Precision too low for generators, not given"

[Jeroen Demeyer]

On 2017-01-05 13:17, Erick Knight wrote:

Thanks for both of your replies.  Just to double check so that I don't
have any misunderstanding, PARI is correctly determining whether my
ideal is principal, and if it is, it is attempting to produce a
generator.  It may fail at that, but, since I never ask it for a
generator, this produces no incorrect outputs.  Is that where this
warning comes from and what I should make of it?


Yes, I think that's right.

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Re: [sage-support] "Precision too low for generators, not given"

[Jeroen Demeyer]

Sorry, I was wrong. I actually looked at the PARI source code this time 
and the warning comes from the bnfisprincipal() function to determine 
the class of a given ideal in the class group (so, in particular, it can 
be used to check whether an ideal is principal). This function can also 
compute a generator of the ideal, but it might fail doing that, giving 
the warning message. I believe this does not affect the correctness.


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Re: [sage-support] "Precision too low for generators, not given"

[Jeroen Demeyer]

I think it means that PARI didn't compute the unit group for certain 
number fields. Since you don't need the unit group, I see no issue.


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Re: [sage-support] Re: Something like Mathematica's `Interact`?

[Jeroen Demeyer]

On 2016-12-07 04:45, William Stein wrote:

You can also track progress
on porting interact to Jupyter at [3], though it looks like nobody has
touched that in several months.


For the record, the main obstacle here is the release of ipywidgets 6 
(currently in beta!). I don't want to rely on git master versions of 
packages anymore.


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Re: [sage-support] Re: How to limit heavy computations

[Jeroen Demeyer]

On 2016-11-27 14:10, Jori Mäntysalo wrote:

In general it is not easy to limit resource usage in Linux.


It's not easy, that's true. But that's independent of the fact that 
ulimit within SageNB simply doesn't work due to some SageNB bug. I have 
known about this bug for years but never bothered to fix it (mainly 
because there are a lot of hoops to jump through to develop anything for 
SageNB).


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Re: [sage-support] Sage Crash Report

[Jeroen Demeyer]

Details please... How did you install Sage?

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Re: [sage-support] Re: Unable to launch SageMath 7.4 on macOS Sierra (10.12.1)

[Jeroen Demeyer]

On 2016-11-08 23:01, quark67000 wrote:

It seems that on 7.4, SageMath has a bad signals.sofile on the Mac version.


No, this problem almost certainly has nothing to do with signals.so

As Volker said, it is https://trac.sagemath.org/ticket/21772

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Re: [sage-support] How could I import igraph or python-igraph in the python bundled with sage?

[Jeroen Demeyer]

On 2016-11-07 13:52, Eden Harder wrote:

I installed sagemath with hombrew on MacOS. And later I use `sage -i
python_igraph` to install python_igraph. After that, I found that

1. I cannot import python_igraph in sage


The correct command is:

import igraph

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Re: [sage-support] Re: @interact command not working in Sage 7.3 & 7.4

[Jeroen Demeyer]

On 2016-10-27 00:02, kcrisman wrote:

That said, there are still some incompatibilities in interact syntax,
the last I heard (Jason Grout said the jupyter people were working
actively no that, though).


In interact *syntax* or interact *functionality*? Of course, the 
interact functionality is quite different, but that is fixed by 
https://trac.sagemath.org/ticket/21267


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Re: [sage-support] QQbar coercion question

[Jeroen Demeyer]

On 2016-10-24 17:54, Nils Bruin wrote:

Pow is not *that* special.


It is more special than you think. Currently, powering does not go 
through the coercion framework at all. So actions won't get looked up...


Of course, this could be changed. However, the *default* implementation 
of all arithmetic operations (coercing both arguments to a common 
parent) is probably not the right thing to do for __pow__.


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Re: [sage-support] @interact command not working in Sage 7.3 & 7.4

[Jeroen Demeyer]

On 2016-10-23 19:03, ahauskne...@umassd.edu wrote:

Hi the @interact command no longer seems to be working in Sage 7.3 and
Sage 7.4 on an Mac Book Pro running El Capitan:


Works for me on Sage 7.5.beta0. In fact I did some @interact developed 
recently and I never had a problem like that.


Interestingly, the error that you get is exactly the error when running 
that code in the command-line (where interacts obviously don't work).


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Re: [sage-support] QQbar coercion question

[Jeroen Demeyer]

On 2016-10-23 10:33, Vincent Delecroix wrote:

In general, pow(a, b) should only depend on parent(a) and parent(b)
and not the actual values of a and b. This is how behave all
arithmetic operations.


+1

I don't see it as a problem that 2^QQbar(1) fails.

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Re: [sage-support] How to return an RDF (or CDF) value from a Cython function ?

[Jeroen Demeyer]

On 2016-10-17 15:10, Emmanuel Charpentier wrote:

Thank you Vincent. this is much clearer.

It seems that I have some things left to understand about the Sage class
and types hierarchies.


There is a difference between a type and a parent.

A parent is a mathematical object. It is the mathematical set that your 
object belongs to.


A type is a computer-science object. It defines the implementation of 
your object and the methods that it has.


Now, for CDF it turns out that there is a 1-to-1 correspondence between 
type and parent. But in most cases, this is not true. For example, 
elements of GF(2^2) and GF(17^3) have the same type but not the same parent.


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Re: [sage-support] How to catch exceptional values (+ in plot3d, one exceptional point ruins the whole plot).

[Jeroen Demeyer]

On 2016-10-11 22:07, William Stein wrote:

 try: return abs(gamma(x+I*y))
 except: return 0


That is almost never what you want, since this will also catch things 
like KeyboardInterrupt. Better use


try:
...
except Exception:
...

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Re: [sage-support] Re: Element vs UniqueRepresentation

[Jeroen Demeyer]

On 2016-10-10 17:31, Simon King wrote:

I just tested that in the current Sage development version my
proof-of-concept would still work.


But still Python 2, right?


And looking at
_PyType_CalculateMetaclass, I don't see why it wouldn't work in Python3.


Maybe I'm misunderstanding you, but what I wanted to say is: Python 3 
doesn't have any place to hook a custom metaclass. In Python 3, with


class X(B1, ..., Bn)

the metaclass of X must be one of the metaclasses of the Bi, there is no 
way to override it (except of course when you explicitly specify the 
metaclass). Of course, I can always be wrong...


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Re: [sage-support] Element vs UniqueRepresentation

[Jeroen Demeyer]

Try this:

sage: from sage.misc.inherit_comparison import 
InheritComparisonClasscallMetaclass

sage: class A(Element, UniqueRepresentation):
: __metaclass__ = InheritComparisonClasscallMetaclass

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Re: [sage-support] huge virtual memory size when launching 7.3

[Jeroen Demeyer]

On 2016-09-21 16:19, Jonathan Bober wrote:

I moved discussion to sage-devel, but wanted to add for anyone who comes
across this and has problems: my simple temporary workaround is to
change the line

paristack_setsize(size, mem.virtual_memory_limit() // 4)

to

paristack_setsize(size, min(mem.virtual_memory_limit() // 4, 10))

in the file src/sage/libs/pari/pari_instance.pyx. (And then run sage -b.)


As I already mentioned earlier in this thread, even more easy is to 
change the memory at runtime, when starting up Sage:


pari.allocatemem(10^7, 10^7)

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Re: [sage-support] FYI : ipywidgets allows (sort of) interactive Sage graphs in Jupyter notebook.

[Jeroen Demeyer]

On 2016-09-20 22:09, Emmanuel Charpentier wrote:

May I ask why ? (Just curious, no hostility whatsoever implied...).


Because those packages are installed and the nbextension is enabled in 
Sage by default: https://trac.sagemath.org/ticket/21256


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Re: [sage-support] FYI : ipywidgets allows (sort of) interactive Sage graphs in Jupyter notebook.

[Jeroen Demeyer]

On 2016-09-20 16:12, Emmanuel Charpentier wrote:

sage -pip install ipywidgets

echo "jupyter nbextension enable --py --sys-prefix widgetsnbextension" |
sage -sh


In recent Sage betas, the above should not be needed.

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Re: [sage-support] huge virtual memory size when launching 7.3

[Jeroen Demeyer]

On 2016-09-20 12:54, Jonathan Bober wrote:

 From reading what you've sent, I guess that what you have in mind is
calling mmap with PROT_NONE and then calling mprotect() to change that
to read/write whenever growing the stack? That seems like it might be a
reasonable thing to do (though I'm only basing that on spending a few
minutes reading what you sent, not from any actual knowledge that I had
before).


Yes, that is my idea.


I'm willing to devote some time (not today) to figuring out what the
right thing to do is (maybe the above is already the right thing) /
implementing this / reviewing this.


I don't mind implementing it. What I *do* mind is that I implement it 
and that the patch rots away on Sage Trac in needs_review state (highly 
specialized patches like these have a higher chance of that). That's why 
I asked for a commitment to review.


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Re: [sage-support] huge virtual memory size when launching 7.3

[Jeroen Demeyer]

After spending some time reading on the subject, I think I might have a 
solution to this "problem". It involves calling mmap() with PROT_NONE, 
which will require a patch to upstream PARI.


However, before implementing this, I would like a *strong commitment* 
from somebody to review my patch when I'm finished. Otherwise I'm just 
wasting my time.


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Re: [sage-support] Re: huge virtual memory size when launching 7.3

[Jeroen Demeyer]

On 2016-09-19 19:58, Jeroen Demeyer wrote:

* https://lwn.net/Articles/627557/


This last page indicates that one should use PROT_NONE to work around 
the issue you are having.


Note this nice quote:

> Sadly, the commit charge implications of MAP_NORESERVE are documented 
but silently broken, but the commit charge implications of PROT_NONE are 
undocumented and in theory mutable in future releases.


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Re: [sage-support] Re: huge virtual memory size when launching 7.3

[Jeroen Demeyer]

On 2016-09-19 14:04, Jonathan Bober wrote:

With overcommit_memory set to 2, I'm not sure that there is a right
thing to do. If I'm the only person in the world with this problem, then
I should keep my mouth shut and get with the times, but I don't think
this setup is so unreasonable.


Some pointers indicating that the Linux implementation of 
overcommit_memory=2 has issues:

* https://lkml.org/lkml/2005/8/8/46
* https://lwn.net/Articles/627557/

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Re: [sage-support] Re: huge virtual memory size when launching 7.3

[Jeroen Demeyer]

On 2016-09-19 19:01, William Stein wrote:

We should revert whatever trac ticket did this


The first version of this is from
https://trac.sagemath.org/ticket/19883


or at least make it an option to not allocate such a large address space.


That's easy to do. How would you see the user interface for this?


This huge vm
allocation is clearly an even worse hack dealing with PARI's very
hackish "memory management".


It is really not so bad as it looks. Let me recall that this is only 
about *virtual memory*. Normally, there are no consequences to 
allocating a huge amount of virtual memory. Apparently, there are 
unusual Linux settings in which it does cause problems. Unfortunately, I 
don't see an easy solution for this.



Making it the default is surprising.


I am open for suggestions, what would you make the default then?

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Re: [sage-support] Re: huge virtual memory size when launching 7.3

[Jeroen Demeyer]

On 2016-09-19 14:04, Jonathan Bober wrote:

That doesn't really solve the problem, which I phrased poorly. The
machine has an (antiquated) setup where, when a process requests X bytes
of memory, the kernel reserves X bytes of physical memory for it.


Well, in that case you would indeed "lose" 1/4 of your physical memory 
using the defaults that Sage uses for the PARI virtual stack. If you are 
unwilling to change your OS settings, then you can still manually change 
the PARi stack size with


from sage.libs.pari.all import pari
pari.allocatemem(4*10^6, 4*10^6)


Anyway, where exactly is this allocation coming from? Is it a default
PARI setting, or does it come from the way that Sage uses PARI?


It is because of the way how Sage uses PARI.


I mean, to whom should I address my "hate mail"? :)


That would be me...

Jeroen.


PS: The Sage <-> GAP interface has exactly the same problem, but with a 
smaller default memory allocation.


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Re: [sage-support] Re: huge virtual memory size when launching 7.3

[Jeroen Demeyer]

On 2016-09-19 13:02, Jonathan Bober wrote:

If I ulimit -v 8 GB, say, (which is 512/64), and the PARI allocater
immediately grabs 2 GB of the virtual address space for itself, then
that seems like it leaves only 6 GB for malloc/sage_malloc/whatever
else, which would be effectively limiting the physical memory available
in some situations.


Then use a larger value for "ulimit -v" or add some swap space.


This is not the default, and you probably wouldn't want to
run your laptop this way


But it is an advanced setting. Given that, I assume that you are clever 
enough to do the right thing.


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Re: [sage-support] Re: huge virtual memory size when launching 7.3

[Jeroen Demeyer]

On 2016-09-19 11:54, Jonathan Bober wrote:

But in that case the memory does effectively get "used", if it is the
case that a quarter of the machine's memory is only available from the
PARI memory allocater. If I'm not using the PARI parts of Sage, is that
memory completely wasted?


There should not be any consequences apart from the artificially high 
value of virtual memory used. It certainly does not affect the physical 
memory or swap space which is effectively available.


So the question becomes: what uses the "virtual memory used" value? 
Apparently, the Linux overcommit thing does use that value (which is 
surprising to me, I never really understood how this overcommit stuff 
works).



Jeroen.

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Re: [sage-support] Re: huge virtual memory size when launching 7.3

[Jeroen Demeyer]

Why don't you use ulimit -v to limit the per-process available memory? 
That would make sense when starting lots of processes even without the 
PARI non-issue.


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Re: [sage-support] Interface to lie broken in sage 7.3?

[Jeroen Demeyer]

The *real* underlying problem is of course that LiE doesn't come with a 
build/install system, which makes such strange steps necessary. This is 
also the (only?) reason why this is an experimental (instead of 
optional) package.


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Re: [sage-support] Re: huge virtual memory size when launching 7.3

[Jeroen Demeyer]

On 2016-08-31 08:57, Thierry Dumont wrote:

On machine 2, sage stating process (as mesured with top) uses about 39GB
(no more...) out of 153.79 available.


It doesn't actually "use" that memory. It is reserved virtual memory but 
it does not take up physical memory or swap space.


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Re: [sage-support] Re: huge virtual memory size when launching 7.3

[Jeroen Demeyer]

On 2016-08-30 20:26, leif wrote:

this makes the usage of 'ulimit -v' nearly impossible


I don't see why. You can still use 'ulimit -v'.

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Re: [sage-support] Dividing a matrix by integer one returns a matrix over rational field

[Jeroen Demeyer]

There is a general philosophy in Sage that the *parent* of the output of 
an operation should only depend on the *parent* of the inputs.


So, because 5/2 is a Rational, also 5/1 should be a Rational.

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Re: [sage-support] Re: Building Sage 7.2 from source: Error installing package gcc-4.9.3.p1

[Jeroen Demeyer]

On 2016-05-28 04:41, paulmasson wrote:

Yes, I did git clone of sage.git on github.

Do you think I should just delete it all and start again fresh? Is that the 
usual way to address such seemingly random errors?


No idea. There is clearly something wrong with your setup but I cannot 
tell what...


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Re: [sage-support] Re: Building Sage 7.2 from source: Error installing package gcc-4.9.3.p1

[Jeroen Demeyer]

On 2016-05-27 04:30, paulmasson wrote:

File is indeed not in the indicated directory.


It should be there.

Please try "make sagelib-clean" and then run "make" again and see if the 
problem remains...


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Re: [sage-support] Re: How to get all solutions of a MILP?

[Jeroen Demeyer]

On 2016-05-18 13:44, Dima Pasechnik wrote:

Do you mean that you want a cleaner
interface for p.polyhedron() in the
case when p has more than 1 variable?

Yes. Example:

sage: P = MixedIntegerLinearProgram(solver="PPL")
sage: x = P.new_variable(nonnegative=True)
sage: y = P.new_variable(nonnegative=True)
sage: P.add_constraint(x[3] + y[1] <= 1)
sage: P.add_constraint(x[0] + x[1] + x[2] + x[3] <= y[1] - y[0])
sage: P.polyhedron().integral_points()
((0, 0, 0, 0, 0, 0),
 (0, 1, 0, 0, 0, 0),
 (0, 1, 0, 0, 0, 1),
 (0, 1, 0, 0, 1, 0),
 (0, 1, 0, 1, 0, 0),
 (0, 1, 1, 0, 0, 0))

Question: how to map the above list of points to the variables of the MILP?

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Re: [sage-support] Re: How to get all solutions of a MILP?

[Jeroen Demeyer]

On 2016-04-19 15:00, Dima Pasechnik wrote:

here is an example:

sage: P=3*polytopes.cube()
sage: (p,x)=P.to_linear_program(solver='ppl',return_variable=True)
sage: p.set_objective(x[0]) # maximizing x[0] over 3 times inflated unit
cube
sage: p.solve()
3
sage: p.add_constraint(x[0]==3) # restrict to the optimal face
sage: Q=p.polyhedron() # get the polytope
sage: len(Q.integral_points()) # find its points (not printing...)
49


I agree that this sort-of works, but it's not at all clear how to get 
the mapping between MILP variables and polyhedron dimensions. The next 
step would be to get x[0] from those 49 points. In this case, it is easy 
since there is only 1 variable, but in general?


Jeroen.

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Re: [sage-support] Re: Issue build sagemath 7.2 from source.

[Jeroen Demeyer]

Please send the complete log

/home/pietrol/Sage/sage-7.2/logs/pkgs/gcc-4.9.3.p1.log

together with

/home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/gcc-4.9.3.p1/build/config.log

or any other config.log located inside 
/home/pietrol/Sage/sage-7.2/local/var/tmp/sage/build/gcc-4.9.3.p1


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Re: [sage-support] Issue build sagemath 7.2 from source.

[Jeroen Demeyer]

On 2016-05-17 13:33, Pietro Liguori wrote:

Hi all,
I try to build sagemath 7.2 from source. My computer is Red Hat
Enterprise Linux Server release 5.11 (Tikanga) x86_64.


I suggest you run "make distclean" and "make" again. If that also fails, 
send the logfile of the package which failed.


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[sage-support] How to get all solutions of a MILP?

[Jeroen Demeyer]

Hello,

I have a MixedIntegerLinearProgram where all variables are integers. I 
want to minimize one of the variables, but I need *all* solutions, i.e. 
all assignments to the variables which minimize the goal function (I 
know that this list is finite). Is there a simple way to do this?


Thanks,
Jeroen.

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Re: [sage-support] Need handholding about Sage Git good practices.

[Jeroen Demeyer]

On 2016-04-01 21:31, Emmanuel Charpentier wrote:

Fine, but now, my
patch contains about 890 (IIRC) commits already in 7.2beta2.


What's your definition of "contains" here? Your branch (I guess that's 
what you meant with "patch") "contains" all commits made in the past in 
Sage. I don't see what's so special about the 890 most recent ones.


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Re: [sage-support] Re: Re: Multivariate division with remainder of polynomials

[Jeroen Demeyer]

On 2016-03-31 11:06, Marc Mezzarobba wrote:

Jeroen Demeyer wrote:

Is there any reason that quo_rem is not consistent with .mod()? That
is no longer arbitrary and would also extend the Euclidean division of
univariate polynomials.


Not quite: you'd have to return a tuple of quotients.


I don't get what you mean. What I am saying is that the following two 
should return the same answer:


p.mod([q])
p.quo_rem(q)[1]

I see no reason why this is currently not the case.

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Re: [sage-support] Re: Multivariate division with remainder of polynomials

[Jeroen Demeyer]

On 2016-03-30 16:08, Marc Mezzarobba wrote:

I think it is just a more or less arbitrary function that satisfies
quo*q + rem == p and extends the Euclidean division of univariate
polynomials. (But // can still be useful for exact divisions or
divisions by monomials...)


Is there any reason that quo_rem is not consistent with .mod()? That is 
no longer arbitrary and would also extend the Euclidean division of 
univariate polynomials.



Is multivariate division in the sense of
https://en.wikipedia.org/wiki/Gr%C3%B6bner_basis#Reduction implemented
somewhere in Sage?


Yes: p.mod(ideal) or ideal.reduce(p).


Thanks for the help. Note that p.mod(list of generators) also works.

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Re: [sage-support] Moore–Penrose pseudoinverse?

[Jeroen Demeyer]

This is now implemented and ready for review at

http://trac.sagemath.org/ticket/20287

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