Opened 22 months ago
Last modified 5 weeks ago
#25993 needs_review enhancement
Upgrade Singular
Reported by:  jdemeyer  Owned by:  

Priority:  major  Milestone:  sage9.2 
Component:  packages: standard  Keywords:  upgrade, Singular 
Cc:  SimonKing, ghtimokau, slelievre, isuruf, saraedum, dkrenn, araichev, cheuberg, behackl, dimpase  Merged in:  
Authors:  Antonio Rojas, Markus Wageringel  Reviewers:  
Report Upstream:  N/A  Work issues:  
Branch:  public/singular413 (Commits)  Commit:  827aa6c8a1d99bd50de6d431085c77164d3a39bb 
Dependencies:  #29465  Stopgaps: 
Description (last modified by )
Tarball 4.1.3: ftp://jim.mathematik.unikl.de/pub/Math/Singular/SOURCES/413/singular4.1.3.tar.gz
Use make SAGE_SPKG="sagespkg o" singularclean build
to automatically download and install.
Change History (85)
comment:1 Changed 22 months ago by
 Dependencies set to #24735
comment:2 Changed 22 months ago by
 Cc SimonKing ghtimokau added
 Description modified (diff)
comment:3 Changed 22 months ago by
 Branch set to u/jdemeyer/ticket/25993
comment:4 Changed 22 months ago by
 Commit set to ec53e6fadfe9cb22a70029f4b9c91576c6c2b1d3
 Description modified (diff)
comment:5 followup: ↓ 20 Changed 22 months ago by
Sigh. So I have to upgrade the group cohomology package earlier than I thought. I'll see what I can do (after grading some exam).
comment:6 followup: ↓ 8 Changed 22 months ago by
The ticket description prominently tells that the group cohomology package is failing, but the title of the ticket is about upgrading Singular.
So, just to be sure about the topic of this ticket:
 Is this ticket about upgrading Singular, which means that a new ticket for upgrading the group cohomology package needs to be created? If this is so, which of the tickets should depend on the other?
 Is this ticket only about upgrading the group cohomology package? Looking at the commits, I suppose that this is not the case.
comment:7 in reply to: ↑ description Changed 22 months ago by
Replying to jdemeyer:
It's not clear to me whether this is a Singular bug or a p_group_cohomology bug.
Most likely it is an API change.
comment:8 in reply to: ↑ 6 ; followup: ↓ 9 Changed 22 months ago by
This ticket is about upgrading Singular. If the p_group_cohomology package must be changed, ideally it should be done in a way which makes it compatible both with Singular 4.1.1p3 as well as earlier versions. In that case, the upgrade of p_group_cohomology can be done on a different ticket and #25993 should depend on that.
Concerning the commit history, only the last commit belongs to this ticket. The rest belongs to #24735 which is an upgrade of Singular to 4.1.1p2.
comment:9 in reply to: ↑ 8 ; followup: ↓ 11 Changed 22 months ago by
comment:10 followup: ↓ 13 Changed 22 months ago by
PS: I recently added a patch to Singular which backports a bugfix that is important to me. Is that bugfix in Singular4.1.1?
comment:11 in reply to: ↑ 9 ; followup: ↓ 12 Changed 22 months ago by
Replying to SimonKing:
I see. Do you know if the breakage already happens in p2?
I know that it does not occur. That's also a good reason to do the upgrade in two steps: first to 4.1.1p2 which works fine and then to 4.1.1p3 (or a later version) once p_group_cohomology is fixed.
comment:12 in reply to: ↑ 11 Changed 22 months ago by
Replying to jdemeyer:
Replying to SimonKing:
I see. Do you know if the breakage already happens in p2?
I know that it does not occur. That's also a good reason to do the upgrade in two steps: first to 4.1.1p2 which works fine and then to 4.1.1p3 (or a later version) once p_group_cohomology is fixed.
Thank you! That sounds like a good plan. And do you know about the backported bug fix?
comment:13 in reply to: ↑ 10 ; followup: ↓ 14 Changed 22 months ago by
Replying to SimonKing:
I recently added a patch to Singular which backports a bugfix that is important to me. Is that bugfix in Singular4.1.1?
That's hard to say if you don't say which patch you mean. In any case, all patches which are currently (in Sage 8.3.rc3) applied to Singular are included in Singular 4.1.1p2.
Note that you said 4.1.1 but I guess you really care about 4.1.1p2 or 4.1.1p3. Despite what the version numbers suggest, experience shows that Singular adds nontrivial changes in such patchreleases.
comment:14 in reply to: ↑ 13 ; followups: ↓ 16 ↓ 18 Changed 22 months ago by
Replying to jdemeyer:
Replying to SimonKing:
I recently added a patch to Singular which backports a bugfix that is important to me. Is that bugfix in Singular4.1.1?
That's hard to say if you don't say which patch you mean. In any case, all patches which are currently (in Sage 8.3.rc3) applied to Singular are included in Singular 4.1.1p2.
It is backport_std.patch
Note that you said 4.1.1 but I guess you really care about 4.1.1p2 or 4.1.1p3. Despite what the version numbers suggest, experience shows that Singular adds nontrivial changes in such patchreleases.
I see. I thought that the "p something" patch level is Sage's addition of patches, not Singular's.
comment:15 Changed 22 months ago by
 Description modified (diff)
 Report Upstream changed from N/A to Fixed upstream, but not in a stable release.
comment:16 in reply to: ↑ 14 Changed 22 months ago by
Replying to SimonKing:
I see. I thought that the "p something" patch level is Sage's addition of patches, not Singular's.
No, Sage's p levels have a dot. So you can have a Singular package version number like 4.1.1p2.p0
(where 4.1.1p2
comes from Singular upstream and .p0
from Sage). I know, it's confusing :)
comment:17 Changed 22 months ago by
 Commit changed from ec53e6fadfe9cb22a70029f4b9c91576c6c2b1d3 to 83c8ac26d40bfa342d4fe37d43ec9db84e1055ba
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
83c8ac2  Upgrade to Singular 4.1.1p3

comment:18 in reply to: ↑ 14 ; followup: ↓ 19 Changed 22 months ago by
Replying to SimonKing:
It is
backport_std.patch
Sorry, I don't know what you mean. Where should I find this patch?
comment:19 in reply to: ↑ 18 Changed 22 months ago by
comment:20 in reply to: ↑ 5 Changed 22 months ago by
Replying to SimonKing:
Sigh. So I have to upgrade the group cohomology package earlier than I thought.
At least this time, it's not the fault of Sage but Singular :)
comment:21 Changed 22 months ago by
 Dependencies changed from #24735 to #24735 #26001
comment:22 Changed 22 months ago by
Is this supposed to pass the nonoptional doctests already? I cherrypicket the last two commits (Upgrade to Singular 4.1.1p3
and Minor fixes to Singular interface
) and added the patch to singular in an attempt to update nix's Singular to p3. I'm getting a segfault while running the doctests:
File "/nix/store/pzc940fjxrhq17j58krwry2y7wi9czh8sagesrc8.3/src/sage/rings/polynomial/plural.pyx", line 396, in sage.rings.polynomial.plural.NCPolynomialRing_plural.__dealloc__ Failed example: R2 = A2.g_algebra({y*x:x*yz, z*x:x*z+2*x, z*y:y*z2*y}, order=TermOrder('degrevlex', 2)) Exception raised: Traceback (most recent call last): File "/nix/store/ic3b215ln47d0js46lyvc7zjizd9jfqppython2.7.15env/lib/python2.7/sitepackages/sage/doctest/forker.py", line 573, in _run self.compile_and_execute(example, compiler, test.globs) File "/nix/store/ic3b215ln47d0js46lyvc7zjizd9jfqppython2.7.15env/lib/python2.7/sitepackages/sage/doctest/forker.py", line 983, in compile_and_execute exec(compiled, globs) File "<doctest sage.rings.polynomial.plural.NCPolynomialRing_plural.__dealloc__[6]>", line 1, in <module> R2 = A2.g_algebra({y*x:x*yz, z*x:x*z+Integer(2)*x, z*y:y*zInteger(2)*y}, order=TermOrder('degrevlex', Integer(2))) File "/nix/store/ic3b215ln47d0js46lyvc7zjizd9jfqppython2.7.15env/lib/python2.7/sitepackages/sage/algebras/free_algebra.py", line 876, in g_algebra order=order, check=check) File "sage/structure/factory.pyx", line 368, in sage.structure.factory.UniqueFactory.__call__ (build/cythonized/sage/structure/factory.c:2046) return self.get_object(version, key, kwds) File "sage/structure/factory.pyx", line 411, in sage.structure.factory.UniqueFactory.get_object (build/cythonized/sage/structure/factory.c:2422) obj = self.create_object(version, key, **extra_args) File "sage/rings/polynomial/plural.pyx", line 173, in sage.rings.polynomial.plural.G_AlgFactory.create_object (build/cythonized/sage/rings/polynomial/plural.cpp:5046) return NCPolynomialRing_plural(base_ring, names, c, d, order, File "sage/rings/polynomial/plural.pyx", line 351, in sage.rings.polynomial.plural.NCPolynomialRing_plural.__init__ (build/cythonized/sage/rings/polynomial/plural.cpp:6406) test = ff.nctools__lib.ndcond(ring = self) File "sage/libs/singular/function.pyx", line 1330, in sage.libs.singular.function.SingularFunction.__call__ (build/cythonized/sage/libs/singular/function.cpp:15332) return call_function(self, args, ring, interruptible, attributes) File "sage/libs/singular/function.pyx", line 1512, in sage.libs.singular.function.call_function (build/cythonized/sage/libs/singular/function.cpp:17285) with opt_ctx: # we are preserving the global options state here File "sage/libs/singular/function.pyx", line 1514, in sage.libs.singular.function.call_function (build/cythonized/sage/libs/singular/function.cpp:17197) sig_on() SignalError: Segmentation fault
comment:23 Changed 21 months ago by
Note that this will also break the build of polymake (not sure if it affects the 3.1 version shipped by Sage)
comment:24 Changed 20 months ago by
 Milestone changed from sage8.4 to sage8.5
comment:25 followup: ↓ 26 Changed 18 months ago by
4.1.1p4 is out, with fixes for the gcd in ZZ and the polymake issue. But (of course) with new problems: the stest function has changed signature and now only accepts two parameters [1]. After porting the Sage code I'm getting floating point exceptions
File "/usr/lib/python2.7/sitepackages/sage/rings/quotient_ring_element.py", line 629, in sage.rings.quotient_ring_element.QuotientRingElement._richcmp_ Failed example: I = F*[x*y+y*z,x^2+x*yy*xy^2]*F Exception raised: Traceback (most recent call last): File "/usr/lib/python2.7/sitepackages/sage/doctest/forker.py", line 671, in _run self.compile_and_execute(example, compiler, test.globs) File "/usr/lib/python2.7/sitepackages/sage/doctest/forker.py", line 1086, in compile_and_execute exec(compiled, globs) File "<doctest sage.rings.quotient_ring_element.QuotientRingElement._richcmp_[7]>", line 1, in <module> I = F*[x*y+y*z,x**Integer(2)+x*yy*xy**Integer(2)]*F File "sage/structure/element.pyx", line 1517, in sage.structure.element.Element.__mul__ (build/cythonized/sage/structure/element.c:12022) return (<Element>left)._mul_(right) File "sage/algebras/letterplace/free_algebra_element_letterplace.pyx", line 604, in sage.algebras.letterplace.free_algebra_element_letterplace.FreeAlgebraElement_letterplace._mul_ (build/cythonized/sage/algebras/letterplace/free_algebra_element_letterplace.cpp:9487) rshift = singular_system("stest",right._poly,left._poly.degree(), ring=A._current_ring) File "sage/libs/singular/function.pyx", line 1330, in sage.libs.singular.function.SingularFunction.__call__ (build/cythonized/sage/libs/singular/function.cpp:15055) return call_function(self, args, ring, interruptible, attributes) File "sage/libs/singular/function.pyx", line 1512, in sage.libs.singular.function.call_function (build/cythonized/sage/libs/singular/function.cpp:16879) with opt_ctx: # we are preserving the global options state here File "sage/libs/singular/function.pyx", line 1514, in sage.libs.singular.function.call_function (build/cythonized/sage/libs/singular/function.cpp:16791) sig_on() FloatingPointError: Floating point exception
[1] https://github.com/Singular/Sources/commit/b00f8a34fb50dbff4746ce45d0680d242f28260c
comment:26 in reply to: ↑ 25 ; followup: ↓ 27 Changed 18 months ago by
Replying to arojas:
4.1.1p4 is out
Really? I don't see it on ftp://jim.mathematik.unikl.de/pub/Math/Singular/SOURCES/411/
comment:27 in reply to: ↑ 26 Changed 18 months ago by
Replying to jdemeyer:
Replying to arojas:
4.1.1p4 is out
Really? I don't see it on ftp://jim.mathematik.unikl.de/pub/Math/Singular/SOURCES/411/
That mirror seems to be outdated
https://service.mathematik.unikl.de/ftp/pub/Math/Singular/SOURCES/411/
comment:28 Changed 18 months ago by
 Dependencies changed from #24735 #26001 to #26001
 Description modified (diff)
 Summary changed from Upgrade to Singular 4.1.1p3 to Upgrade to Singular 4.1.1p4
comment:29 followup: ↓ 30 Changed 17 months ago by
Can you test if it is also breaking the new version of p_group_cohomology (see #26001), which is ready for review?
comment:30 in reply to: ↑ 29 Changed 17 months ago by
Replying to SimonKing:
Can you test if it is also breaking the new version of p_group_cohomology (see #26001), which is ready for review?
I did test: The upgrade to singular4.1.1p3 is not problematic with the new version of p_group_cohomology. I cannot tell about p4, of course.
Anyway, some good news for the start of the new year...
comment:31 Changed 17 months ago by
 Dependencies #26001 deleted
 Description modified (diff)
comment:32 Changed 17 months ago by
 Description modified (diff)
 Report Upstream changed from Fixed upstream, but not in a stable release. to N/A
comment:33 Changed 17 months ago by
 Commit changed from 83c8ac26d40bfa342d4fe37d43ec9db84e1055ba to 4bd32fe685b58802a56a8a6cb4e75b9abe02e94b
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
4bd32fe  Upgrade to Singular 4.1.1p4

comment:34 Changed 17 months ago by
This version compiles, but leads to doctest failures, in particular
sage t src/sage/rings/quotient_ring.py ********************************************************************** File "src/sage/rings/quotient_ring.py", line 89, in sage.rings.quotient_ring Failed example: Q3 = F.quo(F*[F.prod(m) for m in product(F.gens(), repeat=3)]*F) Exception raised: Traceback (most recent call last): File "/usr/local/src/sageconfig/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 671, in _run self.compile_and_execute(example, compiler, test.globs) File "/usr/local/src/sageconfig/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 1086, in compile_and_execute exec(compiled, globs) File "<doctest sage.rings.quotient_ring[20]>", line 1, in <module> Q3 = F.quo(F*[F.prod(m) for m in product(F.gens(), repeat=Integer(3))]*F) File "/usr/local/src/sageconfig/local/lib/python2.7/sitepackages/sage/categories/monoids.py", line 158, in prod return prod(args, self.one()) File "sage/misc/misc_c.pyx", line 144, in sage.misc.misc_c.prod (build/cythonized/sage/misc/misc_c.c:2570) prod = balanced_list_prod(x, 0, n, recursion_cutoff) File "sage/misc/misc_c.pyx", line 180, in sage.misc.misc_c.balanced_list_prod (build/cythonized/sage/misc/misc_c.c:2706) prod *= <object>PySequence_Fast_GET_ITEM(L, k) File "sage/structure/element.pyx", line 1517, in sage.structure.element.Element.__mul__ (build/cythonized/sage/structure/element.c:12023) return (<Element>left)._mul_(right) File "sage/algebras/letterplace/free_algebra_element_letterplace.pyx", line 604, in sage.algebras.letterplace.free_algebra_element_letterplace.FreeAlgebraElement_letterplace._mul_ (build/cythonized/sage/algebras/letterplace/free_algebra_element_letterplace.cpp:9525) rshift = singular_system("stest",right._poly,left._poly.degree(),A._degbound,A.__ngens, ring=A._current_ring) File "sage/libs/singular/function.pyx", line 1330, in sage.libs.singular.function.SingularFunction.__call__ (build/cythonized/sage/libs/singular/function.cpp:15057) return call_function(self, args, ring, interruptible, attributes) File "sage/libs/singular/function.pyx", line 1528, in sage.libs.singular.function.call_function (build/cythonized/sage/libs/singular/function.cpp:17033) raise RuntimeError("error in Singular function call %r:\n%s" % RuntimeError: error in Singular function call 'system': wrong length of parameters(4), expected `poly`,`int` **********************************************************************
comment:35 Changed 17 months ago by
Yes, see comment:25. The letterplace algebra implementation has been completely rewritten in Singular, in particular "stest" can only be used with rings that are explicitely declared as letterplace. In the long term free_algebra_letterplace.pyx should be refactored to use the new implementation, but a faster shortterm solution could be to implement an internal variable shifting method in Sage itself (to replace "stest" usage).
comment:36 Changed 15 months ago by
 Cc slelievre added
 Keywords upgrade Singular added
It seems Singular 412 is out, see the GitHub "releases" page and one official sources directory at unikl:
 https://github.com/Singular/Sources/releases
 https://service.mathematik.unikl.de/ftp/pub/Math/Singular/SOURCES/
So far no mention on the Singular home page or download page:
but I guess they will be updated soon.
comment:37 followup: ↓ 38 Changed 15 months ago by
Relevant changes: system("stest") and system("freegb") are no longer a thing. There is a stest function now, but it's marked static so not accessible from outside the library.
comment:38 in reply to: ↑ 37 ; followup: ↓ 39 Changed 15 months ago by
Replying to arojas:
Relevant changes: system("stest") and system("freegb") are no longer a thing. There is a stest function now, but it's marked static so not accessible from outside the library.
That's quite unfortunate. freegb is needed for free commutative algebras in letterplace implementation. I am not sure if stest is needed there, too.
Any replacement for freegb?
comment:39 in reply to: ↑ 38 ; followup: ↓ 42 Changed 15 months ago by
Replying to SimonKing:
Replying to arojas:
Relevant changes: system("stest") and system("freegb") are no longer a thing. There is a stest function now, but it's marked static so not accessible from outside the library.
That's quite unfortunate. freegb is needed for free commutative algebras in letterplace implementation. I am not sure if stest is needed there, too.
Any replacement for freegb?
Looks like one can simply use std now https://github.com/Singular/Sources/commit/6a0ad754
comment:40 Changed 15 months ago by
 Description modified (diff)
 Summary changed from Upgrade to Singular 4.1.1p4 to Upgrade Singular
comment:41 Changed 12 months ago by
 Cc isuruf saraedum added
comment:42 in reply to: ↑ 39 Changed 5 months ago by
Replying to arojas:
Looks like one can simply use std now https://github.com/Singular/Sources/commit/6a0ad754
Indeed, std
/twostd
can be used for this, but one needs to work over a polynomial ring constructed via `freeAlgebra`, so that certain attributes like the degree bound are set for the computation.
However, I do not see how to make the degrees
option work, as Singular's freeAlgebra
function does not allow for block orders:
sage: F.<a,b,c> = FreeAlgebra(QQ, implementation='letterplace', degrees=(1,2,3)) sage: F.commutative_ring().term_order() Block term order with blocks: (Degree reverse lexicographic term order of length 3, Lexicographic term order of length 1) sage: from sage.libs.singular.function_factory import ff sage: A = ff.freegb__lib.freeAlgebra(F.commutative_ring(), 5) ... RuntimeError: error in Singular function call 'freeAlgebra': only for rings with a global ordering of one block
This is with Singular 4.1.2p1 (freeAlgebra
does not exist in the Singular version that is currently in Sage).
The other failing doctests seem mostly harmless.
comment:43 followups: ↓ 44 ↓ 45 Changed 5 months ago by
 Description modified (diff)
 Milestone changed from sage8.5 to sage9.1
With Singular 4.1.2p2, building Pynac fails with errors like this:
In file included from /amd/compute/mwagerin/git/sage_compute/python3/local/include/factory/factory.h:26, from mpolysingular.cpp:27: /amd/compute/mwagerin/git/sage_compute/python3/local/include/factory/factoryconf.h:21:10: fatal error: factory/globaldefs.h: No such file or directory #include "factory/globaldefs.h" ^~~~~~~~~~~~~~~~~~~~~~
I do not know how to resolve this.
comment:44 in reply to: ↑ 43 Changed 5 months ago by
Replying to ghmwageringel:
With Singular 4.1.2p2, building Pynac fails with errors like this:
In file included from /amd/compute/mwagerin/git/sage_compute/python3/local/include/factory/factory.h:26, from mpolysingular.cpp:27: /amd/compute/mwagerin/git/sage_compute/python3/local/include/factory/factoryconf.h:21:10: fatal error: factory/globaldefs.h: No such file or directory #include "factory/globaldefs.h" ^~~~~~~~~~~~~~~~~~~~~~I do not know how to resolve this.
Does the file exists? If not it looks like a bug in singular's installation. I'll have a look locally when I can.
comment:45 in reply to: ↑ 43 ; followup: ↓ 48 Changed 5 months ago by
Replying to ghmwageringel:
With Singular 4.1.2p2, building Pynac fails with errors like this:
In file included from /amd/compute/mwagerin/git/sage_compute/python3/local/include/factory/factory.h:26, from mpolysingular.cpp:27: /amd/compute/mwagerin/git/sage_compute/python3/local/include/factory/factoryconf.h:21:10: fatal error: factory/globaldefs.h: No such file or directory #include "factory/globaldefs.h" ^~~~~~~~~~~~~~~~~~~~~~I do not know how to resolve this.
This is a bug in singular install: https://git.archlinux.org/svntogit/community.git/tree/trunk/PKGBUILD?h=packages/singular#n42
comment:46 followup: ↓ 47 Changed 5 months ago by
Did you fill a ticket upstream?
comment:47 in reply to: ↑ 46 ; followup: ↓ 49 Changed 5 months ago by
Replying to fbissey:
Did you fill a ticket upstream?
No  i'm tired of filing singular bug reports just to have them ignored.
comment:48 in reply to: ↑ 45 Changed 5 months ago by
Replying to arojas:
This is a bug in singular install: https://git.archlinux.org/svntogit/community.git/tree/trunk/PKGBUILD?h=packages/singular#n42
Thank you. That works.
comment:49 in reply to: ↑ 47 ; followup: ↓ 50 Changed 5 months ago by
comment:50 in reply to: ↑ 49 ; followup: ↓ 51 Changed 5 months ago by
Replying to arojas:
Replying to arojas:
Replying to fbissey:
Did you fill a ticket upstream?
No  i'm tired of filing singular bug reports just to have them ignored.
Seems to be fixed in git master
If you are thinking of https://github.com/Singular/Sources/commit/557b878dd8c840afb5ec95de122ba27a0ec99926 it is in my source for 4.1.2p2 and it obviously doesn't help. Are you thinking of another commit?
comment:51 in reply to: ↑ 50 Changed 5 months ago by
Replying to fbissey:
Replying to arojas:
Replying to arojas:
Replying to fbissey:
Did you fill a ticket upstream?
No  i'm tired of filing singular bug reports just to have them ignored.
Seems to be fixed in git master
If you are thinking of https://github.com/Singular/Sources/commit/557b878dd8c840afb5ec95de122ba27a0ec99926 it is in my source for 4.1.2p2 and it obviously doesn't help. Are you thinking of another commit?
I don't know which commit fixed it, I just compiled git master and checked that the header is installed.
comment:52 Changed 5 months ago by
All right it is actually fixed in the next commit https://github.com/Singular/Sources/commit/10ccdf4ec3a17fc1e6b47d06f9abf4565ae63341
kind of sad.
comment:53 Changed 5 months ago by
I have checked, that commit is all you need to get this particular header.
comment:54 followup: ↓ 55 Changed 5 months ago by
 Work issues set to update letterplace algebras
Regarding the degrees
option of letterplace algebras, Singular should support weighted degree orders naturally now, so Sage's workaround using slack variables should not be necessary anymore. However, I have difficulties to reproduce the old results with Singular's new implementation. The example from letterplace.pyx
:
sage: F.<x,y,z> = FreeAlgebra(QQ, implementation='letterplace', degrees=[1,2,3]) sage: I = F * [x*y+zy*x, x*y*zx^6+y^3] * F sage: I.groebner_basis(Infinity) ... sage: F.degbound() 22
The maximum degree was 22, so the following Singular code should compute the same, as far as I understand, but it fails with an error:
LIB "freegb.lib"; ring r = 0,(x,y,z),wp(1,2,3); def R = freeAlgebra(r, 22); setring R; ideal I = x*y+zy*x, x*y*zx^6+y^3; ideal J = twostd(I); // ? degree bound of Letterplace ring is 22, but at least 23 is needed for this multiplication
Is this a bug in Singular? I think Singular should make sure not to go beyond the degree bound in this computation.
comment:55 in reply to: ↑ 54 Changed 5 months ago by
I have posted this problem to the Singular forums.
comment:56 Changed 5 months ago by
 Branch changed from u/jdemeyer/ticket/25993 to u/ghmwageringel/singular412p1
 Commit changed from 4bd32fe685b58802a56a8a6cb4e75b9abe02e94b to 0c071234ae99343c40735b17280cdf5d0b3a2d6d
 Work issues changed from update letterplace algebras to segfault in plural.pyx
Viktor Levandovskyy has sent a response to the problem, which was very helpful. The ordering I was trying to use is not actually supported. Also, some of the orderings Sage was using in the letterplace computations were not actually supported and, apparently, were silently ignored by Singular. As a consequence, results obtained with the new Letterplace API (which now supports some of the orders) may be a bit different than before. In the case of nonstandard degrees
, a deglex
ordering seems to give similar results as before.
Here is a tentative branch that makes Sage's letterplace functionality work with Singular 4.1.2p1. I followed Antonio's suggestion from comment:35 and his downstream patch about implementing a variable shifting method, and implemented a workaround to call Singular's twostd
with a letterplace polynomial ring constructed via freeAlgebra
. Of course, this should only be seen as a shortterm solution, to maintain backward compatibility where possible.
There is one remaining problem for upgrading to Singular 4.1.2p1. The tests in src/sage/rings/polynomial/plural.pyx
sometimes produce the segmentation fault reported in comment:22, which I do not know how to resolve. For me, the segfault usually occurs during make ptestlong
, but not always when testing the file standalone.
Any help with this is appreciated.
New commits:
0ff7390  25993: upgrade to singular 4.1.2p1

71c871f  25993: rename polynomial shift method to _cycle

0c07123  25993: call new Singular API for letterplace algebras

comment:57 Changed 4 months ago by
Good news, the plural.pyx segfault seems fixed in 4.1.2.p3. There are a few additional test failures, but they look mostly harmless, caused by doc output changes and different generators for some ideals. There's also a small regression in the pc file https://www.singular.unikl.de:8005/trac/ticket/861
comment:58 Changed 4 months ago by
fails its own testsuite on gentoo for stupid reason
make checkTESTS make[4]: Entering directory '/dev/shm/portage/scimathematics/singular4.1.2_p3/work/singular4.1.2/libpolys/polys' make[5]: Entering directory '/dev/shm/portage/scimathematics/singular4.1.2_p3/work/singular4.1.2/libpolys/polys' ../../buildaux/testdriver: line 107: 707661 Segmentation fault (core dumped) "$@" > $log_file 2>&1 FAIL: test ============================================================================ Testsuite summary for libpolys 4.1.2 ============================================================================ # TOTAL: 1 # PASS: 0 # SKIP: 0 # XFAIL: 0 # FAIL: 1 # XPASS: 0 # ERROR: 0 ============================================================================ See polys/testsuite.log
And when I look at the core dump
#0 0x00007f272947b23a in p_Add_q__FieldGeneral_LengthOne_OrdPomog () from /usr/libexec/singular/MOD/p_Procs_FieldGeneral.so #1 0x00005583ef7743b8 in TestSum(ip_sring*, int) () #2 0x00005583ef775c03 in Test(ip_sring*) () #3 0x00005583ef77618f in test_Z13_t_GF() () #4 0x00005583ef77236f in main ()
the stupid thing tries to load a plugin from a previous install rather than the one it just compiled.
Tests pass on a machine with singular removed but it is annoying.
comment:59 Changed 4 months ago by
4.1.2p4 has just been released with a fix for the pkgconfig issue
comment:60 Changed 4 months ago by
My test suite issue is now https://github.com/Singular/Sources/issues/980 but if everything else can be worked out we should proceed. I'll add that flint
detection is stinky and poorly thought out. It kinds of works but leads to messy warnings in the linker in some systems.
comment:61 Changed 3 months ago by
 Branch changed from u/ghmwageringel/singular412p1 to u/ghmwageringel/singular412p4
 Commit changed from 0c071234ae99343c40735b17280cdf5d0b3a2d6d to 9dbc2badedcda7046e37bc5adc2a4768f60318e6
 Description modified (diff)
 Work issues segfault in plural.pyx deleted
I have updated the branch to fix the doctests for Singular 4.1.2p4. The changes are mostly harmless:
 sign changes in the representatives of fraction field elements
 minors now include zero elements (which agrees with the Singular documentation)
 rational points are returned in a different order
 intersection of ideals does not return a Gröbner basis anymore: Neither Sage nor Singular clearly state that the result should be a Gröbner basis, so this change seems fine, but it might be worth checking whether this change was intentional.
New commits:
3af226f  Merge tag '9.1.beta4' into #25993

9dbc2ba  25993: upgrade to singular 4.1.2p4

comment:62 Changed 3 months ago by
 Cc dkrenn araichev cheuberg behackl added
 Work issues set to failing doctests in asymptotics_multivariate_generating_functions.py
The only remaining failing doctests are in asymptotics_multivariate_generating_functions.py
. It would be nice if the authors or anyone familiar with asymptotics could take a look.
Some of these are caused by different representatives being chosen modulo an ideal, which should be fine. However, the relative error does not get small anymore which suggests that there might be a bug on the Sage side.
File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 1576, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.FractionWithFactoredDenominator.? Failed example: decomp = F.asymptotic_decomposition(alpha); decomp Expected: (0, []) + (3/2*r*(1/y + 1)  1/2/y  1/2, [(x*y + x + y  1, 1)]) Got: (0, []) + (2*r*(1/x + 1) + 1/2/x  1/2, [(x*y + x + y  1, 1)]) ********************************************************************** File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 1585, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.FractionWithFactoredDenominator.? Failed example: asy Expected: (1/6000*(3600*sqrt(5)*sqrt(3)*sqrt(2)*sqrt(r)/sqrt(pi) + 463*sqrt(5)*sqrt(3)*sqrt(2)/(sqrt(pi)*sqrt(r)))*432^r, 432, 3/5*sqrt(5)*sqrt(3)*sqrt(2)*sqrt(r)/sqrt(pi) + 463/6000*sqrt(5)*sqrt(3)*sqrt(2)/(sqrt(pi)*sqrt(r))) Got: (1/6000*(3600*sqrt(5)*sqrt(3)*sqrt(2)*sqrt(r)/sqrt(pi)  137*sqrt(5)*sqrt(3)*sqrt(2)/(sqrt(pi)*sqrt(r)))*432^r, 432, 3/5*sqrt(5)*sqrt(3)*sqrt(2)*sqrt(r)/sqrt(pi) + 137/6000*sqrt(5)*sqrt(3)*sqrt(2)/(sqrt(pi)*sqrt(r))) ********************************************************************** File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 1591, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.FractionWithFactoredDenominator.? Failed example: F.relative_error(asy[0], alpha, [1, 2, 4, 8, 16], asy[1]) # abs tol 1e10 Expected: [((4, 3), 2.083333333, [2.092576110], [0.004436533009]), ((8, 6), 2.787374614, [2.790732875], [0.001204811281]), ((16, 12), 3.826259447, [3.827462310], [0.0003143703383]), ((32, 24), 5.328112821, [5.328540787], [0.00008032230388]), ((64, 48), 7.475927885, [7.476079664], [0.00002030232879])] Got: [((4, 3), 2.083333333, [1.783556749], [1.856107239]), ((8, 6), 2.787374614, [2.572223188], [1.922812160]), ((16, 12), 3.826259447, [3.672952629], [1.959932979]), ((32, 24), 5.328112821, [5.219285944], [1.979574968]), ((64, 48), 7.475927885, [7.398824824], [1.989686489])] Tolerance exceeded in 10 of 25: 2.092576110 vs 1.783556749, tolerance 4e0 > 1e10 0.004436533009 vs 1.856107239, tolerance 2e0 > 1e10 2.790732875 vs 2.572223188, tolerance 6e0 > 1e10 0.001204811281 vs 1.922812160, tolerance 2e0 > 1e10 3.827462310 vs 3.672952629, tolerance 8e0 > 1e10 0.0003143703383 vs 1.959932979, tolerance 2e0 > 1e10 5.328540787 vs 5.219285944, tolerance 2e1 > 1e10 0.00008032230388 vs 1.979574968, tolerance 2e0 > 1e10 7.476079664 vs 7.398824824, tolerance 2e1 > 1e10 0.00002030232879 vs 1.989686489, tolerance 2e0 > 1e10 ********************************************************************** File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 1609, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.FractionWithFactoredDenominator.? Failed example: decomp = F.asymptotic_decomposition(alpha); decomp Expected: (0, []) + (16*r*(3/y  4/z)  16/y + 32/z, [(x + 2*y + z  4, 1), (2*x + y + z  4, 1)]) Got: (0, []) + (16*r*(3/x  2/z)  16/x + 16/z, [(x + 2*y + z  4, 1), (2*x + y + z  4, 1)]) ********************************************************************** File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 1620, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.FractionWithFactoredDenominator.? Failed example: asy # long time Expected: (4/3*sqrt(3)*sqrt(r)/sqrt(pi) + 47/216*sqrt(3)/(sqrt(pi)*sqrt(r)), 1, 4/3*sqrt(3)*sqrt(r)/sqrt(pi) + 47/216*sqrt(3)/(sqrt(pi)*sqrt(r))) Got: (4/3*sqrt(3)*sqrt(r)/sqrt(pi)  47/216*sqrt(3)/(sqrt(pi)*sqrt(r)), 1, 4/3*sqrt(3)*sqrt(r)/sqrt(pi)  47/216*sqrt(3)/(sqrt(pi)*sqrt(r))) ********************************************************************** File "src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py", line 1623, in sage.rings.asymptotic.asymptotics_multivariate_generating_functions.FractionWithFactoredDenominator.? Failed example: F.relative_error(asy[0], alpha, [1, 2, 4, 8], asy[1]) # long time Expected: [((3, 3, 2), 0.9812164307, [1.515572606], [0.54458543...]), ((6, 6, 4), 1.576181132, [1.992989399], [0.26444185...]), ((12, 12, 8), 2.485286378, [2.712196351], [0.091301338...]), ((24, 24, 16), 3.700576827, [3.760447895], [0.016178847...])] Got: [((3, 3, 2), 0.9812164307, [1.515572606], [2.544585434]), ((6, 6, 4), 1.576181132, [1.992989399], [2.264441858]), ((12, 12, 8), 2.485286378, [2.712196351], [2.091301338]), ((24, 24, 16), 3.700576827, [3.760447895], [2.016178847])] **********************************************************************
comment:63 followup: ↓ 64 Changed 3 months ago by
Looks like #29247 has broken things again. Getting many failures in sage/algebras/letterplace with this branch on top of 9.1.beta7
comment:64 in reply to: ↑ 63 Changed 3 months ago by
 Dependencies set to #29311
comment:65 Changed 3 months ago by
comment:66 Changed 2 months ago by
 Cc dimpase added
comment:67 followup: ↓ 68 Changed 2 months ago by
Is this ticket going to be ready for 9.1? Otherwise, we may need a ticket for 9.1 with some portability fixes (see #29415)
comment:68 in reply to: ↑ 67 Changed 2 months ago by
 Milestone changed from sage9.1 to sage9.2
Replying to mkoeppe:
Is this ticket going to be ready for 9.1?
Probably not. There are still failing doctests related to asymptotics. Someone should look into that.
But even then, it might be better to merge this in the next release cycle in order to give it some time to get tested.
comment:69 Changed 2 months ago by
 Commit changed from 9dbc2badedcda7046e37bc5adc2a4768f60318e6 to 78f439e57fe3cceb59f7850cde7aa56692351099
comment:70 Changed 2 months ago by
 Dependencies changed from #29311 to #29465
 Status changed from new to needs_review
 Work issues failing doctests in asymptotics_multivariate_generating_functions.py deleted
I found the problem in the asymptotics code. It is caused by an incorrect sign and is resolved by #29465, needing review.
Now this makes all the doctests pass with Singular 4.1.2p4, so this is ready for testing. The optional packages in particular still need to be tested.
Meanwhile, Singular 4.1.2p5 has been released and produces many segmentation faults all over the place, so I guess we stick to 4.1.2p4 for now.
comment:71 Changed 8 weeks ago by
The segfaults are fixed with https://github.com/Singular/Sources/commit/7886c15a361119b200bd15faef4bf5b620d783ad
4.1.3 is out with just one additional, harmless test failure
diff git a/src/sage/libs/singular/function.pyx b/src/sage/libs/singular/function.pyx index b649ab1e64..72f34fd67d 100644  a/src/sage/libs/singular/function.pyx +++ b/src/sage/libs/singular/function.pyx @@ 1308,7 +1308,7 @@ cdef class SingularFunction(SageObject): ... RuntimeError: error in Singular function call 'triangL': The input is no groebner basis.  leaving triang.lib::triangL + leaving triang.lib::triangL (0) Flush any stray output  see :trac:`28622`::
comment:72 Changed 8 weeks ago by
 Branch changed from u/ghmwageringel/singular412p4 to public/singular413
 Commit changed from 78f439e57fe3cceb59f7850cde7aa56692351099 to 8722c0f11e1567dd4598bee604511208ad7f847d
 Description modified (diff)
Thanks for the note. I have updated the branch.
New commits:
8722c0f  25993: upgrade to singular 4.1.3

comment:73 Changed 7 weeks ago by
 Commit changed from 8722c0f11e1567dd4598bee604511208ad7f847d to 5e496abfe428e9ea37db55a8f3a94dc3a462cfa2
comment:74 followups: ↓ 75 ↓ 76 Changed 7 weeks ago by
I have merged 9.1.rc0 and removed the (backported) patch from #29438.
With this, I get the segmentation fault in plural.pyx
from comment:22 again. I am not sure what to do with this. Maybe we could mark it as not tested
and open a new ticket for it.
comment:75 in reply to: ↑ 74 Changed 7 weeks ago by
Replying to ghmwageringel:
I have merged 9.1.rc0 and removed the (backported) patch from #29438.
With this, I get the segmentation fault in
plural.pyx
from comment:22 again. I am not sure what to do with this. Maybe we could mark it asnot tested
and open a new ticket for it.
+1
comment:76 in reply to: ↑ 74 ; followup: ↓ 77 Changed 7 weeks ago by
Replying to ghmwageringel:
I have merged 9.1.rc0 and removed the (backported) patch from #29438.
With this, I get the segmentation fault in
plural.pyx
from comment:22 again.
I can't reproduce that.
I checked out the ticket on top of 9.1.rc0 and run make
according to the ticket description but all tests of src/sage/rings/polynomial/plural.pyx
passed.
Did I miss something? I did that under Windows10 (WSL Ubuntu). The make
logmessages said that Singular 4.1.3 had been build but if I start Singular (through Sage) I get:
SINGULAR / Development A Computer Algebra System for Polynomial Computations / version 4.1.2 0< by: W. Decker, G.M. Greuel, G. Pfister, H. Schoenemann \ Mar 2020 FB Mathematik der Universitaet, D67653 Kaiserslautern \
comment:77 in reply to: ↑ 76 ; followup: ↓ 78 Changed 7 weeks ago by
Replying to soehms:
I can't reproduce that.
I checked out the ticket on top of 9.1.rc0 and run
make
according to the ticket description but all tests ofsrc/sage/rings/polynomial/plural.pyx
passed.
Thanks for taking a look. There is some randomness to this bug. With the current branch, it consistently occurs for me, but has been appearing only from time to time while working on this ticket. If I copy the offending doctest to the top of the file to better isolate the problem, it disappears. I am not even sure if it is really caused by this upgrade – the underlying problem might already exist in Sage without being noticed.
The
make
logmessages said that Singular 4.1.3 had been build but if I start Singular (through Sage) I get:SINGULAR / Development A Computer Algebra System for Polynomial Computations / version 4.1.2 0< by: W. Decker, G.M. Greuel, G. Pfister, H. Schoenemann \ Mar 2020 FB Mathematik der Universitaet, D67653 Kaiserslautern \
Yes, I get that as well. Apparently upstream forgot to change that version number.
comment:78 in reply to: ↑ 77 ; followup: ↓ 81 Changed 7 weeks ago by
Replying to ghmwageringel:
Replying to soehms: There is some randomness to this bug.
That's not good looking!
I tried to reproduce it on another machine (running under Linux Mint 19.1 and Sage with Python 2) but without success, again.
If I copy the offending doctest to the top of the file to better isolate the problem, it disappears.
Does it disappear if you let it in on its position but supress some of the previous doctests, as well?
In my experience such segmentation faults are mostly caused by a previous call of some Cfunction with no prototype and a wrong number of arguments or some usage of a non initialized variable. Anyway, I think this bug will be very difficult to find!
comment:79 Changed 7 weeks ago by
This looks to me as one of these testing framework Heisenbugs we see elsewhere, as well.
comment:80 Changed 7 weeks ago by
 Commit changed from 5e496abfe428e9ea37db55a8f3a94dc3a462cfa2 to 827aa6c8a1d99bd50de6d431085c77164d3a39bb
Branch pushed to git repo; I updated commit sha1. New commits:
827aa6c  25993: disable problematic doctest in plural.pyx

comment:81 in reply to: ↑ 78 ; followup: ↓ 82 Changed 7 weeks ago by
Replying to soehms:
Does it disappear if you let it in on its position but supress some of the previous doctests, as well?
Yes, if I remove the previous block of tests from the previous method, it disappears, too. Even if I move that block of tests from the previous method to the affected method, and thus preserve all tests and their order, everything works fine. Heisenbug indeed. As you cannot replicate it, this problem might not be too serious. Thanks for looking into it, though.
I have disabled the test on the current branch and opened #29528 for it.
comment:82 in reply to: ↑ 81 Changed 6 weeks ago by
Replying to ghmwageringel:
Replying to soehms:
Does it disappear if you let it in on its position but supress some of the previous doctests, as well?
Yes, if I remove the previous block of tests from the previous method, it disappears, too. Even if I move that block of tests from the previous method to the affected method, and thus preserve all tests and their order, everything works fine. Heisenbug indeed. As you cannot replicate it, this problem might not be too serious.
Now, I tried again using the doctest option globaliterations
. With this I was able to reproduce all of your observations (repeatable after 9 loops in the WSL case and 11 loops in the Linux Mint case).
On the other hand, on a 9.1.rc0 installation without that Singular upgrade the segmentation fault didn't occur until loop 500.
comment:83 followup: ↓ 84 Changed 6 weeks ago by
This is just a guess, but this might be related to the problem that the NCPolynomial_plural
elements are sometimes not properly deallocated because the parent ring is not defined anymore, for some reason. Indeed, this change produces a warning in exactly the doctest in __reduce__
which preceeds the problematic one.

src/sage/rings/polynomial/plural.pyx
a b cdef class NCPolynomial_plural(RingElement): 1431 1431 def __dealloc__(self): 1432 1432 # TODO: Warn otherwise! 1433 1433 # for some mysterious reason, various things may be NULL in some cases 1434 1434 if self._parent is not None and (<NCPolynomialRing_plural>self._parent)._ring != NULL and self._poly != NULL: 1435 1435 p_Delete(&self._poly, (<NCPolynomialRing_plural>self._parent)._ring) 1436 elif self._poly != NULL: 1437 print("warning in NCPolynomial_plural.__dealloc__") 1436 1438 1437 1439 def __reduce__(self): 1438 1440 """ 1439 1441 TESTS::
comment:84 in reply to: ↑ 83 Changed 6 weeks ago by
Replying to ghmwageringel:
This is just a guess, but this might be related to the problem that the
NCPolynomial_plural
elements are sometimes not properly deallocated because the parent ring is not defined anymore, for some reason.
There was #13447 dedicated to having proper refcount for libsingular rings. If I recall correctly, the problem is that refcounting in Singular ONLY happens for rings in the interface, i.e. there is no refcount when polynomials are created. However, there is an internal ref counter in Singular that sometimes in very few places in the Singular code is used.
Anyway, perhaps it makes sense to revive that other ticket and finally try and get the refcount problem done.
comment:85 Changed 5 weeks ago by
9.1.rc2 introduces one new test failure:
File "/usr/lib/python3.8/sitepackages/sage/rings/polynomial/multi_polynomial_ideal.py", line 3969, in sage.rings.polynomial.multi_polynomial_ideal.NCPolynomialIdeal.groebner_basis Failed example: ideal(J.transformed_basis()).change_ring(P).interreduced_basis() # testing trac 21884 Expected: [a  60*c^3 + 158/7*c^2 + 8/7*c  1, b + 30*c^3  79/7*c^2 + 3/7*c, c^4  10/21*c^3 + 1/84*c^2 + 1/84*c] Got: // ** redefining xR ( keepring basering;) [a  60*c^3 + 158/7*c^2 + 8/7*c  1, b + 30*c^3  79/7*c^2 + 3/7*c, c^4  10/21*c^3 + 1/84*c^2 + 1/84*c]
Last 10 new commits:
More real > Float porting
Don't check for exact Singular version
Use p_Divide for lcm as suggested by upstream
Backport patch to move singular's NTL handling out of libsingular
Document patch
Remove duplicate cimport
Move patch documentation inside patch itself
rest > reminder
Minor fixes to Singular interface
Upgrade to Singular 4.1.1p3