Opened 3 years ago
Closed 3 years ago
#22924 closed enhancement (fixed)
cleaning of linbox for dense integer matrices
Reported by:  vdelecroix  Owned by:  

Priority:  major  Milestone:  sage8.0 
Component:  packages: standard  Keywords:  linbox 
Cc:  cpernet, dlucas  Merged in:  
Authors:  Vincent Delecroix  Reviewers:  Clément Pernet 
Report Upstream:  N/A  Work issues:  
Branch:  0b082c2 (Commits)  Commit:  0b082c2d7aac83d91253a450cd81e7accf13d76b 
Dependencies:  Stopgaps: 
Description (last modified by )
Various cleaning to the linbox interface (sage.libs.linbox
) and Sage dense integer matrices (sage.matrix.matrix_integer_dense
).
 implement a more direct linbox/flint interface in
sage/libs/linbox/linbox_flint_interface.pyx
(supersedes part oflinboxsage.C
inside linbox)
 remove all mpz pointers from
Matrix_integer_dense
(that is the attributesbint _initialized_mpz
,mpz_t * _entrie
andmpz_t ** _rows
) as well as the associated constructors/destructors (int _init_mpz(self)
,int _init_mpz_impl(self)
,int _init_linbox(self)
,void _dealloc_mpz(self)
)
 fix the following error
sage: matrix(ZZ, 2).det(algorithm='padic') Traceback (most recent call last): ... ImportError: No module named matrix_integer_dense_hnf
 add more examples and tests to the documentation
(see #22872 for the linbox task ticket)
Change History (49)
comment:1 Changed 3 years ago by
 Branch set to u/vdelecroix/22924
 Commit set to 38d9da303a72512d2cab94ef0d8219fd03de12aa
comment:2 Changed 3 years ago by
 Commit changed from 38d9da303a72512d2cab94ef0d8219fd03de12aa to 86d8af3dd66ed8c1847452d555953eee7a00f91c
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
86d8af3  Cleaning linbox interface of Matrix_integer_dense

comment:3 Changed 3 years ago by
 Description modified (diff)
 Status changed from new to needs_review
comment:4 Changed 3 years ago by
 Description modified (diff)
comment:5 Changed 3 years ago by
 Component changed from PLEASE CHANGE to packages: standard
comment:6 Changed 3 years ago by
 Commit changed from 86d8af3dd66ed8c1847452d555953eee7a00f91c to 4cae968e969b661488ef07621d29303251732726
comment:7 Changed 3 years ago by
 Commit changed from 4cae968e969b661488ef07621d29303251732726 to 09f62806bc83b5049d90ea481de8abffe61712f0
Branch pushed to git repo; I updated commit sha1. New commits:
09f6280  22924: get rid of spies

comment:8 Changed 3 years ago by
 Commit changed from 09f62806bc83b5049d90ea481de8abffe61712f0 to 69a140e1d299cc6971ad75e868dd9418083bbc0b
comment:9 Changed 3 years ago by
(rebased on 8.0.b4)
comment:10 followup: ↓ 12 Changed 3 years ago by
Great. Let's start with a few remarks:
 Why do need the dependency on #22886 ? That ticket is stalled and is therefore also blocking this one.
 While we are changing a lot of stuff, I wouldn't mind getting rid of these ugly
poly_linbox
method, with a string parametertyp
that determines whether to compute minpoly or charpoly. We should rather only have the 2 methods_minpoly_linbox_
and_charpoly_linbox_
. There is not much duplicated code between these two, especially now after this cleanup.
comment:11 Changed 3 years ago by
 Reviewers set to Clément Pernet
comment:12 in reply to: ↑ 10 ; followup: ↓ 13 Changed 3 years ago by
Replying to cpernet:
Great.
Thanks for having a look!
Let's start with a few remarks:
 Why do need the dependency on #22886 ? That ticket is stalled and is therefore also blocking this one.
I think that Cython compilation fails otherwise (I am trying again right now on top of 8.0.beta4... will take some time since I need to recompile the whole Sage after playing with #22493).
 While we are changing a lot of stuff, I wouldn't mind getting rid of these ugly
poly_linbox
method, with a string parametertyp
that determines whether to compute minpoly or charpoly. We should rather only have the 2 methods_minpoly_linbox_
and_charpoly_linbox_
. There is not much duplicated code between these two, especially now after this cleanup.
The ticket only intends to clean matrix_integer_dense.pyx
. The two functions you mention are actually removed from matrix/matrix_integer_dense.pyx
but kept in libs/linbox/linbox_flint_interface.pyx
(but note that the argument there is an integer). I can get rid of the following function in the interface
# set p to the minpoly or the charpoly of A cdef inline void linbox_fmpz_mat_poly(fmpz_poly_t p, fmpz_mat_t A, int minpoly)
Is that what you want?
comment:13 in reply to: ↑ 12 Changed 3 years ago by
Replying to vdelecroix:
I can get rid of the following function in the interface
# set p to the minpoly or the charpoly of A cdef inline void linbox_fmpz_mat_poly(fmpz_poly_t p, fmpz_mat_t A, int minpoly)Is that what you want?
Ok sorry for the confusion. My remark indeed applies to the new libs/linbox_flint_interface.pyx
.
Sure, it should definitely not be exposed through the new interface as it is an internal trick to factor out code. Then I also suggest to avoid this trick and simply write the two methods for the sake of clarity.
comment:14 Changed 3 years ago by
 Commit changed from 69a140e1d299cc6971ad75e868dd9418083bbc0b to 637fd872a78a7aec0781998a281d4dbbbc0fd7af
comment:15 Changed 3 years ago by
 Dependencies #22886 deleted
No dependency on #22886 anymore (it is needed for cylinbox but it is fine for this ticket).
I cleaned the flint interface a bit more than what you asked for.
comment:16 Changed 3 years ago by
I was wrong (and you were right). There is still def _poly_linbox(self, typ, var='x'):
as a method of Matrix_integer_dense
.
comment:17 followup: ↓ 26 Changed 3 years ago by
By the way, I am adding tests and LinBox has trouble with the characteristic polynomial of the 0 x 0
matrix
sage: matrix([]).charpoly('y', 'linbox') Traceback (most recent call last): ... MemoryError: failed to allocate 2305843008945258512 bytes
Does it qualify as a bug? For now, I will add a special case in the interface LinBox/flint.
EDIT: and it hangs forever for minpoly
.
comment:18 followup: ↓ 24 Changed 3 years ago by
For minpoly
it is written
.. NOTE:: Linbox charpoly disabled on 64bit machines, since it hangs in many cases.
However, I do not see where this actually happens in the code. Do you know what this is?
comment:19 Changed 3 years ago by
 Cc dlucas added
comment:20 Changed 3 years ago by
Un petit timing
sage: m = random_matrix(ZZ, 50) sage: %timeit m._clear_cache(); p = m.charpoly(algorithm='linbox') 100 loops, best of 3: 16.8 ms per loop sage: %timeit m._clear_cache(); p = m.charpoly(algorithm='flint') 10 loops, best of 3: 44.2 ms per loop sage: %timeit m._clear_cache(); p = m.charpoly(algorithm='generic') 10 loops, best of 3: 152 ms per loop
comment:21 Changed 3 years ago by
 Commit changed from 637fd872a78a7aec0781998a281d4dbbbc0fd7af to fde1353a5c22bd3ff3fe50c9df982264b30d505e
Branch pushed to git repo; I updated commit sha1. New commits:
fde1353  22924: clean minpoly/charpoly in Matrix_integer_dense

comment:22 Changed 3 years ago by
All right: Matrix_integer_dense
cleaned and interface fixed on corner cases with commit fde1353
.
comment:23 Changed 3 years ago by
And patchbot is happy (excepted some timeout I am not responsible for).
comment:24 in reply to: ↑ 18 Changed 3 years ago by
Replying to vdelecroix:
For
minpoly
it is written.. NOTE:: Linbox charpoly disabled on 64bit machines, since it hangs in many cases.However, I do not see where this actually happens in the code. Do you know what this is?
It's a super old comment. Some archeology on trac tickets should tell where it comes from but it's safe to remove it.
comment:25 followup: ↓ 28 Changed 3 years ago by
There are a couple of warnings that one could avoid:
[sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:313:49: local variable 'res' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:389:46: local variable 'res' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:394:42: local variable 'res' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:398:42: local variable 'res' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:498:34: local variable 'g' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:532:32: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:534:16: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:562:30: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:564:16: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:717:33: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:736:33: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:756:35: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:1110:39: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:1127:39: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:1150:39: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:1167:39: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:1184:39: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:1217:35: local variable 'r' referenced before assignment [sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:1218:59: local variable 'r' referenced before assignment [
Basically, the variables are passed as "out" arguments, and cython complains that they are not initialized. It is safe to force their value to 0 at declaration (e.g. int res = 0;
) and this would silence out the warning.
comment:26 in reply to: ↑ 17 Changed 3 years ago by
Replying to vdelecroix:
By the way, I am adding tests and LinBox has trouble with the characteristic polynomial of the
0 x 0
matrixsage: matrix([]).charpoly('y', 'linbox') Traceback (most recent call last): ... MemoryError: failed to allocate 2305843008945258512 bytesDoes it qualify as a bug? For now, I will add a special case in the interface LinBox/flint.
EDIT: and it hangs forever for
minpoly
.
This is definitely a bug. Reported upstream: https://github.com/linboxteam/linbox/issues/51
comment:27 followup: ↓ 29 Changed 3 years ago by
In linbox_flint_interface.pyx
lines 84 and 157, you seem to use the method size
of givvector
to get the degree of the corresponding polynomial. While this is very likely to be correct in the current code, the specification do not require that the size of the vector storing the polynomial is ajusted to its degree. One should rather use Givaro::Poly1Dom::degree()
instead.
comment:28 in reply to: ↑ 25 ; followups: ↓ 33 ↓ 38 Changed 3 years ago by
Replying to cpernet:
There are a couple of warnings that one could avoid:
[sagelib8.0.beta4] warning: sage/rings/finite_rings/element_givaro.pyx:313:49: local variable 'res' referenced before assignment ...Basically, the variables are passed as "out" arguments, and cython complains that they are not initialized. It is safe to force their value to 0 at declaration (e.g.
int res = 0;
) and this would silence out the warning.
Yes, but these warnings have nothing to do with this ticket. Feel free to open another one to deal with rings/finite_rings
(and put me in cc if you do).
comment:29 in reply to: ↑ 27 Changed 3 years ago by
Replying to cpernet:
In
linbox_flint_interface.pyx
lines 84 and 157, you seem to use the methodsize
ofgivvector
to get the degree of the corresponding polynomial. While this is very likely to be correct in the current code, the specification do not require that the size of the vector storing the polynomial is ajusted to its degree. One should rather useGivaro::Poly1Dom::degree()
instead.
In LinBox code there are two occurrences of v.size()
in examples/charpoly.C
for a const Polynomial &v
(lines 47 and 57). Idem in examples/minpoly.C
(line 36). Are these also wrong?
How am I supposed to use degree
? I was able to do it 7 lines in Cython... it looks extremely complicated to get such elementary quantity.
cdef GivaroIntegerRing ZZ cdef GivaroDegree deg cdef LinBoxIntegerPolynomialRing * R R = new LinBoxIntegerPolynomialRing(ZZ) R.degree(deg, q) del R cdef size_t length = deg.value() + 1
comment:30 Changed 3 years ago by
 Commit changed from fde1353a5c22bd3ff3fe50c9df982264b30d505e to 6b45893cfec10b3bc20cc44a64233f66e0cf0d8a
comment:31 followup: ↓ 32 Changed 3 years ago by
I implemented your remarks. Though, I do not think that 6b45893
is reasonable.
comment:32 in reply to: ↑ 31 Changed 3 years ago by
Replying to vdelecroix:
I implemented your remarks. Though, I do not think that
6b45893
is reasonable.
Ok this seems indeed quite tedious. After browsing through the current use of size() for degree in LinBox?, I would say it's rather safe to assume that the vector has been resized and therefore that the size
method would return the degree. I was probably being too pedantic, sorry. I suggest to drop 6b45893
.
comment:33 in reply to: ↑ 28 Changed 3 years ago by
Replying to vdelecroix:
Yes, but these warnings have nothing to do with this ticket. Feel free to open another one to deal with
rings/finite_rings
(and put me in cc if you do).
My bad, I thought they were introduced in your new code. Will open a new ticket
comment:34 Changed 3 years ago by
 Commit changed from 6b45893cfec10b3bc20cc44a64233f66e0cf0d8a to a75ec910414f17772072ea13d57fb11117877c16
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
comment:35 followup: ↓ 37 Changed 3 years ago by
Also, I see some new code not directly related to the subject of the ticket (e.g. in _rational_kernel_flint
, rational_kernel_iml
), but this is rather ok for me as it is documentation improvement on routines related to the ticket).
comment:36 followup: ↓ 39 Changed 3 years ago by
Replying to cpernet:
Replying to vdelecroix:
I implemented your remarks. Though, I do not think that
6b45893
is reasonable.Ok this seems indeed quite tedious. After browsing through the current use of size() for degree in LinBox?, I would say it's rather safe to assume that the vector has been resized and therefore that the
size
method would return the degree. I was probably being too pedantic, sorry. I suggest to drop6b45893
.
I dropped it.
It would be fine for me to use degree
however it is horribly complicated. Why is there a class Degree
that is a trivial wrapper around a int64_t
? Why could we not use degree
directly as a method of a polynomial?
comment:37 in reply to: ↑ 35 Changed 3 years ago by
Replying to cpernet:
Also, I see some new code not directly related to the subject of the ticket (e.g. in
_rational_kernel_flint
,rational_kernel_iml
), but this is rather ok for me as it is documentation improvement on routines related to the ticket).
It is. _rational_kernel_iml
now uses fmpz_mat_to_mpz_array
that was introduced in the ticket.
comment:38 in reply to: ↑ 28 Changed 3 years ago by
Replying to vdelecroix:
Feel free to open another one to deal with
rings/finite_rings
(and put me in cc if you do).
Done in #22966.
comment:39 in reply to: ↑ 36 ; followup: ↓ 40 Changed 3 years ago by
Let me try an explanation for this mess (which I agree should be simplified):
Replying to vdelecroix:
Why is there a class
Degree
that is a trivial wrapper around aint64_t
?
I would have said: so as to deal with the degree of the 0 polynomial which is 1 and not size()1=0
Why could we not use
degree
directly as a method of a polynomial?
I assume because in Givaro (and the whole LinBox ecosystem), the container (here givvector
does not know about the semantic). It is the domain of computation (here GivPoly1Dom
who does).
comment:40 in reply to: ↑ 39 ; followup: ↓ 42 Changed 3 years ago by
Replying to cpernet:
Let me try an explanation for this mess (which I agree should be simplified):
Replying to vdelecroix:
Why is there a class
Degree
that is a trivial wrapper around aint64_t
?I would have said: so as to deal with the degree of the 0 polynomial which is 1 and not size()1=0
In LinBox you have size(0) = 1
!? Why would you store the zero at all?
Why could we not use
degree
directly as a method of a polynomial?I assume because in Givaro (and the whole LinBox ecosystem), the container (here
givvector
does not know about the semantic). It is the domain of computation (hereGivPoly1Dom
who does).
I see. This way is indeed more flexible.
comment:41 Changed 3 years ago by
Tell me if there are other improvements to be done on this ticket.
comment:42 in reply to: ↑ 40 Changed 3 years ago by
Replying to vdelecroix:
I would have said: so as to deal with the degree of the 0 polynomial which is 1 and not size()1=0
In LinBox you have
size(0) = 1
!? Why would you store the zero at all?
My mistake. Givaro actually resizes the 0 polynomial to an empty vector, so size1
is always equal to the degree.
After a discussion with JG. Dumas on the topic here are a few clarifications:
 the degree can be accessed in two ways:
 either through `Poly1Dom<..>::degree which silently resize the vector when there are leading zeros.
 direcrly by
P.size()1
when the programmer knows what she does and does not want to pay the price of a resize.
So it's fine to do it with
size()1
as in this ticket, since we know the polynomials handed by LinBox? have correct size in this case.
 The class
Degree
was meant to provide a distinct type than the int64_t returned by size, in order to avoid mixing both approaches. Still the class is not quite satisfactory for the moment (degree (0 + 0)=2 != 1). This has been fixed upstream in https://github.com/linboxteam/givaro/commit/756005d0be64c36513c57403b856d93fc43c8010
comment:43 Changed 3 years ago by
 Status changed from needs_review to positive_review
Ok, the ticket is now fine for me. > positive review.
comment:44 Changed 3 years ago by
 Status changed from positive_review to needs_work
Sorry, two minor documentation typos to be fixed in src/sage/libs/linbox/linbox_flint_interface.pyx
:
 line 10 "linboxSage.C" > "linboxsage.C"
 line 128 "preformed" > "performed"
Back in needs work.
comment:45 Changed 3 years ago by
 Commit changed from a75ec910414f17772072ea13d57fb11117877c16 to 0b082c2d7aac83d91253a450cd81e7accf13d76b
Branch pushed to git repo; I updated commit sha1. New commits:
0b082c2  22924: typos

comment:46 Changed 3 years ago by
 Status changed from needs_work to needs_review
comment:47 Changed 3 years ago by
 Status changed from needs_review to positive_review
Fine then, back to positive review.
comment:48 Changed 3 years ago by
Thanks for the review!
comment:49 Changed 3 years ago by
 Branch changed from u/vdelecroix/22924 to 0b082c2d7aac83d91253a450cd81e7accf13d76b
 Resolution set to fixed
 Status changed from positive_review to closed
New commits:
fix headers
Cleaning linbox interface of Matrix_integer_dense