Re: [sage-support] about the speed of tha Magma interface

[Pierre Guillot]

>Can Sage do this determinant on its own? 

Sage tries to convert the matrix to a dense one before computing the 
determinant (the documentation for sparse matrices says so). And as a 
result, you never see the end of it, no.

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Re: [sage-support] about the speed of tha Magma interface

[Dima Pasechnik]

On Tue, Feb 26, 2019 at 5:42 PM Pierre Guillot  wrote:
>
> Hi again,
>
> Mostly, this does the job :
>
> def sparse_magma_matrix(mat):
> s= "SparseMatrix(" + str(mat.nrows()) + ", " + str(mat.ncols()) + ", ["
> entries= ", ".join([ "<"+str(i+1)+", " + str(j+1)+", "+str(mat[i,j])+">" 
> for i,j in mat.dict() ])
> return s + entries + "])"
>
> One should probably worry about the coefficient ring -- as such, it only 
> works if Magma can guess what it is by itself.
>
> For anyone reading this, concretely, i have then tried:
>
> f= open("foo.m", "w")
> f.write("M:= " + sparse_magma_matrix(mat) + ";")
> f.close()
>
> Then within Magma, I have created the polynomial ring -- which, it turned 
> out, had to be the appropriate fraction field, otherwise the determinant 
> function does not work -- so in my case :
>
> R:= FunctionField(GF(5), 6) ;
>
> and then:
>
> load "foo.m";
>
> (don't forget the ; at the end!!!)
>
> Then i tried
>
> Determinant(M);
>
> and, amazingly, Magma gives an answer instantly. Absolutely incredible :-)

Can Sage do this determinant on its own?

Just wondering (yes, Sage is lacking in sparse matrices over
multivariate polynomial rings support).

>
>
>
>
>
>
>
>
>
>
> On Tuesday, February 26, 2019 at 6:21:44 PM UTC+1, John Cremona wrote:
>>
>>
>>
>> On Tue, 26 Feb 2019 at 17:01, Vincent Delecroix <20100.d...@gmail.com> wrote:
>>>
>>> I don't think this has ever been implemented in Sage. You
>>> have to figure out how to create a sparse matrix in magma
>>> and write Sage code to produce it. You can get inspiration
>>> from the current code of _magma_init_
>>>
>>>  def _magma_init_(self):
>>>  P = magma(self.parent())
>>>  v = [x._magma_init_(magma) for x in self.list()]
>>>  return '%s![%s]'%(P.name(), ','.join(v))
>>>
>>> Vincent
>>
>>
>> This would be a very useful addition (for some people).  Magma constructs 
>> sparse matrices using SparseMatrix() with several interfaces including
>>
>> (m::RngIntElt, n::RngIntElt, Q::SeqEnum[Tup]) -> MtrxSprs
>>
>> The m by n sparse matrix, whose entries are given by the tuples in Q 
>> of the form  (specifying that x is at entry (i, j)).
>>
>> Example:
>>
>> > M:=SparseMatrix(3,3,[<1,1,1>,<2,2,1>,<3,3,1>]);
>> > IdentitySparseMatrix(Integers(), 3) eq M;
>> true
>>
>>
>>
>>>
>>>
>>> Le 26/02/2019 à 17:55, Pierre Guillot a écrit :
>>> > Thanks! I think to know where the issue is :
>>> >
>>> > M= random_matrix(ZZ, 10, sparse= True, density= 0.1)
>>> > M._magma_init_(magma)
>>> >
>>> > '_sage_[11]![0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-14,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,8,0,0,0,0]'
>>> >
>>> >
>>> > This does not look like a sparse matrix to me : it's been converted to a
>>> > "dense" matrix before magma code was produced...
>>> >
>>> > no wonder if my 50,000 x 50,000 matrix takes forever to load...
>>> >
>>> > If anyone has an easy fix, it would be great. Otherwise, i'll have to 
>>> > learn
>>> > the syntax for sparse matrices in magma, and figure out how magma reads
>>> > from a file...
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>>
>>> --
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>>> "sage-support" group.
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>>> email to sage-support...@googlegroups.com.
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>
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Re: [sage-support] about the speed of tha Magma interface

[Pierre Guillot]

Hi again,

Mostly, this does the job :

def sparse_magma_matrix(mat):
s= "SparseMatrix(" + str(mat.nrows()) + ", " + str(mat.ncols()) + ", ["
entries= ", ".join([ "<"+str(i+1)+", " + str(j+1)+", 
"+str(mat[i,j])+">" for i,j in mat.dict() ])
return s + entries + "])"

One should probably worry about the coefficient ring -- as such, it only 
works if Magma can guess what it is by itself.

For anyone reading this, concretely, i have then tried:

f= open("foo.m", "w")
f.write("M:= " + sparse_magma_matrix(mat) + ";")
f.close()

Then within Magma, I have created the polynomial ring -- which, it turned 
out, had to be the appropriate fraction field, otherwise the determinant 
function does not work -- so in my case :

R:= FunctionField(GF(5), 6) ;

and then:

load "foo.m";

(don't forget the ; at the end!!!)

Then i tried 

Determinant(M);

and, amazingly, Magma gives an answer instantly. Absolutely incredible :-)










On Tuesday, February 26, 2019 at 6:21:44 PM UTC+1, John Cremona wrote:
>
>
>
> On Tue, 26 Feb 2019 at 17:01, Vincent Delecroix <20100.d...@gmail.com 
> > wrote:
>
>> I don't think this has ever been implemented in Sage. You
>> have to figure out how to create a sparse matrix in magma
>> and write Sage code to produce it. You can get inspiration
>> from the current code of _magma_init_
>>
>>  def _magma_init_(self):
>>  P = magma(self.parent())
>>  v = [x._magma_init_(magma) for x in self.list()]
>>  return '%s![%s]'%(P.name(), ','.join(v))
>>
>> Vincent
>>
>
> This would be a very useful addition (for some people).  Magma constructs 
> sparse matrices using SparseMatrix() with several interfaces including
>
> (m::RngIntElt, n::RngIntElt, Q::SeqEnum[Tup]) -> MtrxSprs
>
> The m by n sparse matrix, whose entries are given by the tuples in 
> Q of the form  (specifying that x is at entry (i, j)).
>
> Example:
>
> > M:=SparseMatrix(3,3,[<1,1,1>,<2,2,1>,<3,3,1>]);
> > IdentitySparseMatrix(Integers(), 3) eq M;  
> true
>
>
>  
>
>>
>> Le 26/02/2019 à 17:55, Pierre Guillot a écrit :
>> > Thanks! I think to know where the issue is :
>> > 
>> > M= random_matrix(ZZ, 10, sparse= True, density= 0.1)
>> > M._magma_init_(magma)
>> > 
>> > 
>> '_sage_[11]![0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-14,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,8,0,0,0,0]'
>> > 
>> > 
>> > This does not look like a sparse matrix to me : it's been converted to a
>> > "dense" matrix before magma code was produced...
>> > 
>> > no wonder if my 50,000 x 50,000 matrix takes forever to load...
>> > 
>> > If anyone has an easy fix, it would be great. Otherwise, i'll have to 
>> learn
>> > the syntax for sparse matrices in magma, and figure out how magma reads
>> > from a file...
>> > 
>> > 
>> > 
>> > 
>> > 
>> > 
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "sage-support" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to sage-support...@googlegroups.com .
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>> .
>> Visit this group at https://groups.google.com/group/sage-support.
>> For more options, visit https://groups.google.com/d/optout.
>>
>

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Re: [sage-support] about the speed of tha Magma interface

[John Cremona]

On Tue, 26 Feb 2019 at 17:01, Vincent Delecroix <20100.delecr...@gmail.com>
wrote:

> I don't think this has ever been implemented in Sage. You
> have to figure out how to create a sparse matrix in magma
> and write Sage code to produce it. You can get inspiration
> from the current code of _magma_init_
>
>  def _magma_init_(self):
>  P = magma(self.parent())
>  v = [x._magma_init_(magma) for x in self.list()]
>  return '%s![%s]'%(P.name(), ','.join(v))
>
> Vincent
>

This would be a very useful addition (for some people).  Magma constructs
sparse matrices using SparseMatrix() with several interfaces including

(m::RngIntElt, n::RngIntElt, Q::SeqEnum[Tup]) -> MtrxSprs

The m by n sparse matrix, whose entries are given by the tuples in
Q of the form  (specifying that x is at entry (i, j)).

Example:

> M:=SparseMatrix(3,3,[<1,1,1>,<2,2,1>,<3,3,1>]);
> IdentitySparseMatrix(Integers(), 3) eq M;
true




>
> Le 26/02/2019 à 17:55, Pierre Guillot a écrit :
> > Thanks! I think to know where the issue is :
> >
> > M= random_matrix(ZZ, 10, sparse= True, density= 0.1)
> > M._magma_init_(magma)
> >
> >
> '_sage_[11]![0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-14,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,8,0,0,0,0]'
> >
> >
> > This does not look like a sparse matrix to me : it's been converted to a
> > "dense" matrix before magma code was produced...
> >
> > no wonder if my 50,000 x 50,000 matrix takes forever to load...
> >
> > If anyone has an easy fix, it would be great. Otherwise, i'll have to
> learn
> > the syntax for sparse matrices in magma, and figure out how magma reads
> > from a file...
> >
> >
> >
> >
> >
> >
>
> --
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>

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Re: [sage-support] about the speed of tha Magma interface

[Vincent Delecroix]

I don't think this has ever been implemented in Sage. You
have to figure out how to create a sparse matrix in magma
and write Sage code to produce it. You can get inspiration
from the current code of _magma_init_

def _magma_init_(self):
P = magma(self.parent())
v = [x._magma_init_(magma) for x in self.list()]
return '%s![%s]'%(P.name(), ','.join(v))

Vincent

Le 26/02/2019 à 17:55, Pierre Guillot a écrit :

Thanks! I think to know where the issue is :

M= random_matrix(ZZ, 10, sparse= True, density= 0.1)
M._magma_init_(magma)

'_sage_[11]![0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-14,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,8,0,0,0,0]'


This does not look like a sparse matrix to me : it's been converted to a
"dense" matrix before magma code was produced...

no wonder if my 50,000 x 50,000 matrix takes forever to load...

If anyone has an easy fix, it would be great. Otherwise, i'll have to learn
the syntax for sparse matrices in magma, and figure out how magma reads
from a file...








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Re: [sage-support] about the speed of tha Magma interface

[Pierre Guillot]

Thanks! I think to know where the issue is :

M= random_matrix(ZZ, 10, sparse= True, density= 0.1)
M._magma_init_(magma)

'_sage_[11]![0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-14,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,8,0,0,0,0]'


This does not look like a sparse matrix to me : it's been converted to a 
"dense" matrix before magma code was produced...

no wonder if my 50,000 x 50,000 matrix takes forever to load...

If anyone has an easy fix, it would be great. Otherwise, i'll have to learn 
the syntax for sparse matrices in magma, and figure out how magma reads 
from a file...






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Re: [sage-support] about the speed of tha Magma interface

[Vincent Delecroix]

Hi,

Indeed that is a problem with all interfaces that are text
based such as magma (to communicate with Magma Sage uses
an emulation of a console). You can analyze what is sent
to magma by running

sage: m = matrix(2, [1,3,2,4])
sage: m._magma_init_(magma)
'Matrix(IntegerRing(),2,2,StringToIntegerSequence("1 3 2 4"))'

As I don't have magma I can not test it for sparse matrices,
but you can have a look at

sage: m = matrix(2, [0,0,2,0], sparse=True)
sage: m._magma_init_(magma)

For sparse matrices, it might be the case that the
string produced is somehow too big for no good reason. If
you find a smarter way to pass the data that would speed
up the process and could be incorporated into Sage.

Best
Vincent

Le 26/02/2019 à 17:36, Pierre Guillot a écrit :

Hi !

I'm trying to compute the determinant of a sparse, square matrix with
50,000 columns and coefficients in GF(5)["x y z t u"]. I'm trying my luck
with the magma interface, since we have a copy of magma running at my
university.

The first thing surprising me is that, on toy examples, magma seems pretty
slow, but that may be for another question. At least it works.

But when I try

foo= magma(my_matrix)

with the real example, well I seem to have to wait forever. By contrast,
when the matrix was saved as a .sobj file and then re-loaded back, it tooks
less than 10 seconds. Why should it be so hard to enter it into Magma?

is there any workaround that is worth trying? I could somehow directly
write magma code into a file, and then hope that loading that would be
faster, but I'm not sure why i would do better than the existing magma
interface...

thanks!
Pierre



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[sage-support] about the speed of tha Magma interface

[Pierre Guillot]

Hi !

I'm trying to compute the determinant of a sparse, square matrix with 
50,000 columns and coefficients in GF(5)["x y z t u"]. I'm trying my luck 
with the magma interface, since we have a copy of magma running at my 
university.

The first thing surprising me is that, on toy examples, magma seems pretty 
slow, but that may be for another question. At least it works.

But when I try

foo= magma(my_matrix)

with the real example, well I seem to have to wait forever. By contrast, 
when the matrix was saved as a .sobj file and then re-loaded back, it tooks 
less than 10 seconds. Why should it be so hard to enter it into Magma?

is there any workaround that is worth trying? I could somehow directly 
write magma code into a file, and then hope that loading that would be 
faster, but I'm not sure why i would do better than the existing magma 
interface...

thanks!
Pierre

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Re: [sage-support] Viewers in cocalc?

[Vincent Delecroix]

Your question is not about Sage but about a problem
of Sage running in cocalc. On my computer with Sage
installed I have no trouble with plot3d.

SageMath is an aggregation of many softwares and whether
each of them works correctly and interacts correctly
with the others on the online platform that is cocalc is
out of my knowledge.

Though, it might well be related to the thread:

https://groups.google.com/forum/#!topic/sage-devel/QC5-9rexyJo

In other words, try with the option

   plot3d(..., online=True)

Vincent

Le 26/02/2019 à 17:02, David Guichard a écrit :

Well, when I go to

https://github.com/sagemathinc/cocalc/wiki/Support

for Sage questions I get directed to

https://doc.cocalc.com/howto/sage-question.html

and it directs me to "The sage-support mailing list
." which is where I
am now.

My question is about Sage, not any other component of cocalc.

On Tue, Feb 26, 2019 at 12:50 AM Vincent Delecroix <
20100.delecr...@gmail.com> wrote:


This list concerns the SageMath software. If you want support
for cocalc, you should consider writing to their support. They
are very reactive.

Best
Vincent

Le 26/02/2019 à 00:26, david.guichard a écrit :

When I try to specify a viewer in a plot3d I get an error if I try

anything

other than "tachyon". Even viewer='threejs' throws an error, though I

think

the default viewer is threejs. What I'm really looking for is a viewer

that

lets me display an orthogonal projection instead of perspective. I know
Three.js is capable of this, but I can't find a way to specify this to
plot3d. Can I either call a viewer that will do it or tell threejs to do

it?


Thanks,
David



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Re: [sage-support] Viewers in cocalc?

[David Guichard]

Well, when I go to

https://github.com/sagemathinc/cocalc/wiki/Support

for Sage questions I get directed to

https://doc.cocalc.com/howto/sage-question.html

and it directs me to "The sage-support mailing list
." which is where I
am now.

My question is about Sage, not any other component of cocalc.

On Tue, Feb 26, 2019 at 12:50 AM Vincent Delecroix <
20100.delecr...@gmail.com> wrote:

> This list concerns the SageMath software. If you want support
> for cocalc, you should consider writing to their support. They
> are very reactive.
>
> Best
> Vincent
>
> Le 26/02/2019 à 00:26, david.guichard a écrit :
> > When I try to specify a viewer in a plot3d I get an error if I try
> anything
> > other than "tachyon". Even viewer='threejs' throws an error, though I
> think
> > the default viewer is threejs. What I'm really looking for is a viewer
> that
> > lets me display an orthogonal projection instead of perspective. I know
> > Three.js is capable of this, but I can't find a way to specify this to
> > plot3d. Can I either call a viewer that will do it or tell threejs to do
> it?
> >
> > Thanks,
> > David
> >
>
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Re: [sage-support] "Questions about Sage"

[William Stein]

Thanks!!

On Tue, Feb 26, 2019 at 6:06 AM Vincent Delecroix
<20100.delecr...@gmail.com> wrote:
>
> Dear William,
>
> That is a good idea and the list seems to be complete.
>
> * You use both Sage and SageMath. It is a bit confusing.
>
> * I would change the order to reflect where you
>should look at. i.e. put as very last the "report a bug".
>Perhaps also, Sage documentation would be better as
>"one before the last" since it is not that easy to
>browse if you are not used to it.
>
> BTW, what happen with the bug reports at [1]?
>
> [1] https://github.com/sagemathinc/cocalc/wiki/SageBug
>
> Best
> Vincent
>
> Le 26/02/2019 à 04:57, William Stein a écrit :
> > Hi,
> >
> > We put a list of resources for end users asking questions about Sage
> > for the cocalc docs here:
> >
> > https://doc.cocalc.com/howto/sage-question.html?highlight=ask%20sagemath%20org
> >
> > Are we missing anything important?  If so, let me know or click the
> > "Edit in Github" button...
> >
> > William
> >



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Re: [sage-support] "Questions about Sage"

[Vincent Delecroix]

Dear William,

That is a good idea and the list seems to be complete.

* You use both Sage and SageMath. It is a bit confusing.

* I would change the order to reflect where you
  should look at. i.e. put as very last the "report a bug".
  Perhaps also, Sage documentation would be better as
  "one before the last" since it is not that easy to
  browse if you are not used to it.

BTW, what happen with the bug reports at [1]?

[1] https://github.com/sagemathinc/cocalc/wiki/SageBug

Best
Vincent

Le 26/02/2019 à 04:57, William Stein a écrit :

Hi,

We put a list of resources for end users asking questions about Sage
for the cocalc docs here:

https://doc.cocalc.com/howto/sage-question.html?highlight=ask%20sagemath%20org

Are we missing anything important?  If so, let me know or click the
"Edit in Github" button...

William



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Re: [sage-support] Viewers in cocalc?

[Vincent Delecroix]

This list concerns the SageMath software. If you want support
for cocalc, you should consider writing to their support. They
are very reactive.

Best
Vincent

Le 26/02/2019 à 00:26, david.guichard a écrit :

When I try to specify a viewer in a plot3d I get an error if I try anything
other than "tachyon". Even viewer='threejs' throws an error, though I think
the default viewer is threejs. What I'm really looking for is a viewer that
lets me display an orthogonal projection instead of perspective. I know
Three.js is capable of this, but I can't find a way to specify this to
plot3d. Can I either call a viewer that will do it or tell threejs to do it?

Thanks,
David



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