Upgrade normaliz to 3.5.3 and pynormaliz to 1.12

[mkoeppe]

Among many new features and improvements, these new versions make computations interruptible with ^C.

Source tarballs:

• ​https://github.com/Normaliz/Normaliz/releases/download/v3.5.3/normaliz-3.5.3.tar.gz
• ​https://pypi.python.org/packages/30/48/d2ad6e4defcce3959c66ee541cf5c0eda12186e42ecd68a0531813a16bd0/PyNormaliz-1.12.tar.gz#md5=1ec3419eaa061a0ee4b4f1ffca9cb44d

Upstream bug: ​https://github.com/Normaliz/Normaliz/issues/176

Follow-up ticket with more cutting-edge PyNormaliz version: #25090.

[mkoeppe]

Tested on Mac OS X. Works well except for interrupting (may require newer pynormaliz...) and the doctest failures reported in #23586 (fixing broken pynormaliz doctests).

---

New commits:

​be0b9d2	Upgrade normaliz, pynormaliz
​a6ccc42	normaliz: Back out 22684_cone_reduce_memory_usage.patch

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​5e7a45b

Update PyNormaliz to 1.8

[git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

​f6011b4	Upgrade normaliz to 3.5.1 and pynormaliz to 1.10
​5536407	normaliz: Add flint dependency
​71d2194	normaliz: Back out 22684_cone_reduce_memory_usage.patch
​f2137cc	Polyhedron_normaliz: Adjust doctest to 'uniqueness in output' of normaliz 3.5.1

[tscrim]

I am now getting this crash (looks like an upstream problem):

sage: ieqs = [[0, 2, 0, -1, 0, 0, 0, 0, 0], [0, 0, 2, 0, -1, 0, 0, 0, 0],
....:         [1, -1, 0, 2, -1, 0, 0, 0, 0], [0, 0, -1, -1, 2, -1, 0, 0, 0],
....:         [0, 0, 0, 0, -1, 2, -1, 0, 0], [0, 0, 0, 0, 0, -1, 2, -1, 0],
....:         [0, 0, 0, 0, 0, 0, -1, 2, -1], [2, 0, 0, 0, 0, 0, 0, -1, 2],
....:         [0, -1, 0, 0, 0, 0, 0, 0, 0], [0, 0, -1, 0, 0, 0, 0, 0, 0],
....:         [0, 0, 0, -1, 0, 0, 0, 0, 0], [0, 0, 0, 0, -1, 0, 0, 0, 0],
....:         [0, 0, 0, 0, 0, -1, 0, 0, 0], [0, 0, 0, 0, 0, 0, -1, 0, 0],
....:         [0, 0, 0, 0, 0, 0, 0, -1, 0], [0, 0, 0, 0, 0, 0, 0, 0, -1],
....:         [-1, -1, -1, -1, -1, -1, -1, -1, -1], [3, 1, 0, 0, 0, 0, 0, 0, 0],
....:         [4, 0, 1, 0, 0, 0, 0, 0, 0], [6, 0, 0, 1, 0, 0, 0, 0, 0],
....:         [8, 0, 0, 0, 1, 0, 0, 0, 0], [6, 0, 0, 0, 0, 1, 0, 0, 0],
....:         [4, 0, 0, 0, 0, 0, 1, 0, 0], [2, 0, 0, 0, 0, 0, 0, 1, 0],
....:         [0, 0, 0, 0, 0, 0, 0, 0, 1]]
sage: P = Polyhedron(ieqs=ieqs, backend='normaliz')
sage: P.integral_points()
python2: ./libnormaliz/matrix.cpp:2901: libnormaliz::Matrix<Integer> libnormaliz::Matrix<Integer>::LLL_red(libnormaliz::Matrix<Integer>&, libnormaliz::Matrix<Integer>&) const [with Integer = double]: Assertion `(int) rank()==n' failed.
------------------------------------------------------------------------
/home/travis/sage-build/local/lib/python2.7/site-packages/cysignals/signals.so(+0x574b)[0x7fa5afdf274b]
/home/travis/sage-build/local/lib/python2.7/site-packages/cysignals/signals.so(+0x57b5)[0x7fa5afdf27b5]
/home/travis/sage-build/local/lib/python2.7/site-packages/cysignals/signals.so(+0x849a)[0x7fa5afdf549a]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7fa5bcd37390]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x38)[0x7fa5bc991428]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7fa5bc99302a]
/lib/x86_64-linux-gnu/libc.so.6(+0x2dbd7)[0x7fa5bc989bd7]
/lib/x86_64-linux-gnu/libc.so.6(+0x2dc82)[0x7fa5bc989c82]
/home/travis/sage-build/local/lib/libnormaliz.so.3(_ZNK11libnormaliz6MatrixIdE7LLL_redERS1_S2_+0x5b9)[0x7fa47314f4a9]
/home/travis/sage-build/local/lib/libnormaliz.so.3(_ZNK11libnormaliz6MatrixIdE17LLL_red_transposeERS1_S2_+0x83)[0x7fa47314fdc3]
/home/travis/sage-build/local/lib/libnormaliz.so.3(_ZN11libnormaliz15LLL_coordinatesIxdEENS_25Sublattice_RepresentationIT_EERKNS_6MatrixIT0_EE+0x56)[0x7fa4730cfde6]
/home/travis/sage-build/local/lib/libnormaliz.so.3(_ZN11libnormaliz31LLL_coordinates_without_1st_colIxxEEvRNS_25Sublattice_RepresentationIT_EENS_6MatrixIT0_EES7_b+0x291)[0x7fa4730d0881]
/home/travis/sage-build/local/lib/libnormaliz.so.3(_ZN11libnormaliz14ProjectAndLiftIxxE7computeEbb+0x194)[0x7fa473104e54]
/home/travis/sage-build/local/lib/libnormaliz.so.3(_ZN11libnormaliz4ConeI10__gmp_exprIA1_12__mpz_structS3_EE16project_and_liftERNS_14ConePropertiesERNS_6MatrixIS4_EERKS9_SA_b+0x839)[0x7fa473179b69]
/home/travis/sage-build/local/lib/libnormaliz.so.3(_ZN11libnormaliz4ConeI10__gmp_exprIA1_12__mpz_structS3_EE31try_approximation_or_projectionERNS_14ConePropertiesE+0xf00)[0x7fa4731f5370]
/home/travis/sage-build/local/lib/libnormaliz.so.3(_ZN11libnormaliz4ConeI10__gmp_exprIA1_12__mpz_structS3_EE7computeENS_14ConePropertiesE+0x1e1)[0x7fa4731e8671]
/home/travis/sage-build/local/lib/python2.7/site-packages/PyNormaliz_cpp.so(_Z14_NmzResultImplI10__gmp_exprIA1_12__mpz_structS2_EEP7_objectPN11libnormaliz4ConeIT_EES5_+0x75)[0x7fa4734f6cc5]
/home/travis/sage-build/local/lib/python2.7/site-packages/PyNormaliz_cpp.so(_Z10_NmzResultP7_objectS0_+0x150)[0x7fa4734ed890]

Originally found by

sage: RC = RiggedConfigurations(['E',8,1], [[3,2]])
sage: len(RC.module_generators)
python2: ./libnormaliz/matrix.cpp:2901: libnormaliz::Matrix<Integer> libnormaliz::Matrix<Integer>::LLL_red(libnormaliz::Matrix<Integer>&, libnormaliz::Matrix<Integer>&) const [with Integer = double]: Assertion `(int) rank()==n' failed.

(Mathematical note, through trying to find a smaller example, I am noticing that E₈⁽¹⁾ is special in that it is the only place where I see non-full-dimensional non-empty polytopes in my computations. Well, I also see a 0-dimensional polytope for type D₄⁽³⁾, but that doesn't cause a crash as it is likely special-cased.)

---

Also can you update the comment before --enable-flint to also say you enable flint as it is part of the standard packages of Sage?

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​b8f7abc

normaliz/spkg-install: Explain --enable-flint

[mkoeppe]

I can confirm this crash. Here on Mac OS X, this actually becomes an unhandled SIGABRT:

Assertion failed: ((int) rank()==n), function LLL_red, file ./libnormaliz/matrix.cpp, line 2901.
------------------------------------------------------------------------
0   signals.so                          0x000000010af572d8 print_backtrace + 40
1   ???                                 0x000000010dcac1e0 0x0 + 4526359008
------------------------------------------------------------------------
Unhandled SIGABRT: An abort() occurred.
This probably occurred because a *compiled* module has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Python will now terminate.

[mkoeppe]

Upstream master branch (8db5b68491a105b9185a01c29c2f126f5115e238) has different behavior but does not fix this.

[tmonteil]

I confirm that the packages build and pass self-tests and doctests correctly on both 64 and 32 bit architectures on Debian stretch. I also comfirm that there is a crash on both architectures regarding the test provided by Travis (which should be added in our doctests, once the issue is fixed).

[Winfried]

I am not sure what the matrix ieqs represents. My interpretation: inhomogeneous inequalities, and we want to compute the lattice points in the polytope they define. Under this assumption I have made a Normaliz input file rash.in

amb_space auto
inhom_inequalities
[[0, 2, 0, -1, 0, 0, 0, 0, 0],
...
[0, 0, 0, 0, 0, 0, 0, 0, 1]]
HilbertBasis

Then a run of

normaliz -c crash.in

finishes without any problems in 3.5.1 and the intended 3.5.2. It turns out that the polytope is empty:

0 module generators
1252 Hilbert basis elements of recession monoid
0 vertices of polyhedron
39 extreme rays of recession cone
11 support hyperplanes of polyhedron (homogenized)

embedding dimension = 9
affine dimension of the polyhedron = -1
rank of recession monoid = 8
...

Is my interpretation of the input correct?

[Winfried]

Of course, if the matrix represents inhomogeneous inequalities, what is the RHS? My input above assumes it is the last coordinate. I will now try with the first.

[Winfried]

Unfortunately Normaliz crashes when coordinate 1 is interpreted as the RHS. Will take care of it.

[Winfried]

The problem is solved. Replace line 323 of source/libnormaliz/sublattice_representation.h

by

    if(Vertices.nr_of_rows()==0 || Vertices.rank()<EmbDim){ // use Supps for LLL coordinates

i.e., delete "-1" in this line.

[tscrim]

Replying to Winfried:

The problem is solved. Replace line 323 of source/libnormaliz/sublattice_representation.h

by

    if(Vertices.nr_of_rows()==0 || Vertices.rank()<EmbDim){ // use Supps for LLL coordinates

i.e., delete "-1" in this line.

Great, thank you for figuring it out. I am guessing you are in the process of making a commit upstream or should I do a pull request?

[tscrim]

I've pushed a branch with a fix for this problem. However, I have now come across another crash:

sage: RC = RiggedConfigurations(['E',8,1], [[4,2]])
sage: len(RC.module_generators)
python2: ./libnormaliz/project_and_lift.cpp:75: std::vector<long unsigned int> libnormaliz::ProjectAndLift<IntegerPL, IntegerRet>::order_supps(const libnormaliz::Matrix<Integer>&) [with IntegerPL = long long int; IntegerRet = long long int]: Assertion `Supps.nr_of_rows()>0' failed.
------------------------------------------------------------------------

I have verified that this did at least not crash before (well, up to my patience level of 2 minutes).

However, much more worrying is this:

sage: RC = RiggedConfigurations(['E',8,1], [[5,2]])
sage: %time len(RC.module_generators)
CPU times: user 25 s, sys: 52 ms, total: 25 s
Wall time: 6.95 s
6009

versus before

sage: RC = RiggedConfigurations(['E',8,1], [[5,2]])
sage: %time len(RC.module_generators)
CPU times: user 1min 11s, sys: 320 ms, total: 1min 11s
Wall time: 14.6 s
7066

Although the [5,1] example both returns 75.

I will extract the polytopes and find out which one gives a different number of lattice points. Give me a few minutes.

---

New commits:

​f9f17a4

Added patch to fix upstream issue #176.

[tscrim]

Okay, here is the [4,1] computation to completion:

sage: RC = RiggedConfigurations(['E',8,1], [[4,2]])
sage: %time len(RC.module_generators)
CPU times: user 19min 37s, sys: 5.2 s, total: 19min 42s
Wall time: 4min 37s
288299

[tscrim]

Okay, here is at least the first polytope that goes wrong:

sage: ieqs = [[0, 2, 0, -1, 0, 0, 0, 0, 0],
....:         [0, 0, 2, 0, -1, 0, 0, 0, 0],
....:         [1, -1, 0, 2, -1, 0, 0, 0, 0],
....:         [0, 0, -1, -1, 2, -1, 0, 0, 0],
....:         [0, 0, 0, 0, -1, 2, -1, 0, 0],
....:         [0, 0, 0, 0, 0, -1, 2, -1, 0],
....:         [1, 0, 0, 0, 0, 0, -1, 2, -1],
....:         [0, 0, 0, 0, 0, 0, 0, -1, 2],
....:         [0, -1, 0, 0, 0, 0, 0, 0, 0],
....:         [0, 0, -1, 0, 0, 0, 0, 0, 0],
....:         [0, 0, 0, -1, 0, 0, 0, 0, 0],
....:         [0, 0, 0, 0, -1, 0, 0, 0, 0],
....:         [0, 0, 0, 0, 0, -1, 0, 0, 0],
....:         [0, 0, 0, 0, 0, 0, -1, 0, 0],
....:         [0, 0, 0, 0, 0, 0, 0, -1, 0],
....:         [0, 0, 0, 0, 0, 0, 0, 0, -1],
....:         [-1, -1, -1, -1, -1, -1, -1, -1, -1],
....:         [2, 1, 0, 0, 0, 0, 0, 0, 0],
....:         [4, 0, 1, 0, 0, 0, 0, 0, 0],
....:         [4, 0, 0, 1, 0, 0, 0, 0, 0],
....:         [7, 0, 0, 0, 1, 0, 0, 0, 0],
....:         [6, 0, 0, 0, 0, 1, 0, 0, 0],
....:         [4, 0, 0, 0, 0, 0, 1, 0, 0],
....:         [2, 0, 0, 0, 0, 0, 0, 1, 0],
....:         [1, 0, 0, 0, 0, 0, 0, 0, 1]]
sage: P = Polyhedron(ieqs=ieqs, backend='normaliz')
sage: P.integral_points()
((-2, -2, -4, -5, -4, -3, -2, -1),
 (-2, -2, -4, -5, -4, -3, -2, 0),
 (-1, -2, -3, -4, -3, -2, -2, -1),
 (-1, -2, -3, -4, -3, -2, -1, 0),
 (-1, -1, -2, -2, -2, -2, -2, -1),
 (-1, -1, -2, -2, -1, -1, -1, 0),
 (-1, -1, -2, -2, -1, 0, 0, 0),
 (-1, 0, -2, -2, -2, -2, -2, -1),
 (0, -1, -1, -2, -2, -2, -2, -1),
 (0, 0, -1, -1, -1, -1, -1, 0))
sage: P
A 8-dimensional polyhedron in QQ^8 defined as the convex hull of 134 vertices

versus the new version with the patch:

sage: P.integral_points()
((-1, -2, -3, -4, -3, -2, -1, 0), (0, -1, -1, -2, -2, -2, -2, -1))

[tscrim]

Here's also the example that causes the new crash:

sage: ieqs = [[0, 2, 0, -1, 0, 0, 0, 0, 0],
....:         [0, 0, 2, 0, -1, 0, 0, 0, 0],
....:         [0, -1, 0, 2, -1, 0, 0, 0, 0],
....:         [1, 0, -1, -1, 2, -1, 0, 0, 0],
....:         [0, 0, 0, 0, -1, 2, -1, 0, 0],
....:         [0, 0, 0, 0, 0, -1, 2, -1, 0],
....:         [1, 0, 0, 0, 0, 0, -1, 2, -1],
....:         [0, 0, 0, 0, 0, 0, 0, -1, 2],
....:         [0, -1, 0, 0, 0, 0, 0, 0, 0],
....:         [0, 0, -1, 0, 0, 0, 0, 0, 0],
....:         [0, 0, 0, -1, 0, 0, 0, 0, 0],
....:         [0, 0, 0, 0, -1, 0, 0, 0, 0],
....:         [0, 0, 0, 0, 0, -1, 0, 0, 0],
....:         [0, 0, 0, 0, 0, 0, -1, 0, 0],
....:         [0, 0, 0, 0, 0, 0, 0, -1, 0],
....:         [0, 0, 0, 0, 0, 0, 0, 0, -1],
....:         [-1, -1, -1, -1, -1, -1, -1, -1, -1],
....:         [3, 1, 0, 0, 0, 0, 0, 0, 0],
....:         [4, 0, 1, 0, 0, 0, 0, 0, 0],
....:         [6, 0, 0, 1, 0, 0, 0, 0, 0],
....:         [8, 0, 0, 0, 1, 0, 0, 0, 0],
....:         [6, 0, 0, 0, 0, 1, 0, 0, 0],
....:         [4, 0, 0, 0, 0, 0, 1, 0, 0],
....:         [2, 0, 0, 0, 0, 0, 0, 1, 0],
....:         [1, 0, 0, 0, 0, 0, 0, 0, 1]]
sage: P = Polyhedron(ieqs=ieqs, backend='normaliz')
sage: P.integral_points()
python2: ./libnormaliz/project_and_lift.cpp:75: std::vector<long unsigned int> libnormaliz::ProjectAndLift<IntegerPL, IntegerRet>::order_supps(const libnormaliz::Matrix<Integer>&) [with IntegerPL = long long int; IntegerRet = long long int]: Assertion `Supps.nr_of_rows()>0' failed.
------------------------------------------------------------------------

[mkoeppe]

A hint: If you use P = Polyhedron(ieqs=ieqs, backend='normaliz', verbose=True), the PyNormaliz invocations are shown, making it easier for upstream

[tscrim]

I wasn't aware of that, thank you. Although it does not yield much more information on the new crash:

sage: P = Polyhedron(ieqs=ieqs, backend='normaliz', verbose=True)
# Calling PyNormaliz.NmzCone(['inhom_equations', [], 'inhom_inequalities',
 [[2, 0, -1, 0, 0, 0, 0, 0, 0], [0, 2, 0, -1, 0, 0, 0, 0, 0],
 [-1, 0, 2, -1, 0, 0, 0, 0, 0], [0, -1, -1, 2, -1, 0, 0, 0, 1],
 [0, 0, 0, -1, 2, -1, 0, 0, 0], [0, 0, 0, 0, -1, 2, -1, 0, 0],
 [0, 0, 0, 0, 0, -1, 2, -1, 1], [0, 0, 0, 0, 0, 0, -1, 2, 0],
 [-1, 0, 0, 0, 0, 0, 0, 0, 0], [0, -1, 0, 0, 0, 0, 0, 0, 0],
 [0, 0, -1, 0, 0, 0, 0, 0, 0], [0, 0, 0, -1, 0, 0, 0, 0, 0],
 [0, 0, 0, 0, -1, 0, 0, 0, 0], [0, 0, 0, 0, 0, -1, 0, 0, 0],
 [0, 0, 0, 0, 0, 0, -1, 0, 0], [0, 0, 0, 0, 0, 0, 0, -1, 0],
 [-1, -1, -1, -1, -1, -1, -1, -1, -1], [1, 0, 0, 0, 0, 0, 0, 0, 3],
 [0, 1, 0, 0, 0, 0, 0, 0, 4], [0, 0, 1, 0, 0, 0, 0, 0, 6],
 [0, 0, 0, 1, 0, 0, 0, 0, 8], [0, 0, 0, 0, 1, 0, 0, 0, 6],
 [0, 0, 0, 0, 0, 1, 0, 0, 4], [0, 0, 0, 0, 0, 0, 1, 0, 2],
 [0, 0, 0, 0, 0, 0, 0, 1, 1]]])
sage: P.integral_points()
python2: ./libnormaliz/project_and_lift.cpp:75: std::vector<long unsigned int> libnormaliz::ProjectAndLift<IntegerPL, IntegerRet>::order_supps(const libnormaliz::Matrix<Integer>&) [with IntegerPL = long long int; IntegerRet = long long int]: Assertion `Supps.nr_of_rows()>0' failed.
------------------------------------------------------------------------

Here is also the output for the lattice point computation:

sage: P = Polyhedron(ieqs=ieqs, backend='normaliz', verbose=True)
# Calling PyNormaliz.NmzCone(['inhom_equations', [], 'inhom_inequalities',
 [[2, 0, -1, 0, 0, 0, 0, 0, 0], [0, 2, 0, -1, 0, 0, 0, 0, 0],
 [-1, 0, 2, -1, 0, 0, 0, 0, 1], [0, -1, -1, 2, -1, 0, 0, 0, 0],
 [0, 0, 0, -1, 2, -1, 0, 0, 0], [0, 0, 0, 0, -1, 2, -1, 0, 0],
 [0, 0, 0, 0, 0, -1, 2, -1, 1], [0, 0, 0, 0, 0, 0, -1, 2, 0],
 [-1, 0, 0, 0, 0, 0, 0, 0, 0], [0, -1, 0, 0, 0, 0, 0, 0, 0],
 [0, 0, -1, 0, 0, 0, 0, 0, 0], [0, 0, 0, -1, 0, 0, 0, 0, 0],
 [0, 0, 0, 0, -1, 0, 0, 0, 0], [0, 0, 0, 0, 0, -1, 0, 0, 0],
 [0, 0, 0, 0, 0, 0, -1, 0, 0], [0, 0, 0, 0, 0, 0, 0, -1, 0],
 [-1, -1, -1, -1, -1, -1, -1, -1, -1], [1, 0, 0, 0, 0, 0, 0, 0, 2],
 [0, 1, 0, 0, 0, 0, 0, 0, 4], [0, 0, 1, 0, 0, 0, 0, 0, 4],
 [0, 0, 0, 1, 0, 0, 0, 0, 7], [0, 0, 0, 0, 1, 0, 0, 0, 6],
 [0, 0, 0, 0, 0, 1, 0, 0, 4], [0, 0, 0, 0, 0, 0, 1, 0, 2],
 [0, 0, 0, 0, 0, 0, 0, 1, 1]]])
sage: P.integral_points()
((-1, -2, -3, -4, -3, -2, -1, 0), (0, -1, -1, -2, -2, -2, -2, -1))

[tscrim]

PS - That means the docstring for Polyhedron needs a minor adjustment:

    - ``verbose`` -- boolean (default: ``False``). Whether to print
      verbose output for debugging purposes. Only supported by the cdd
      backends.

[Winfried]

The wrong number of lattice points is a more severe problem. I don't have an explanation for it.

The (first and solved) problem in sublattice_representation.h has nothing to do with it. After the change in sublattice_representation.h:323 a second problem has become visible there in Normaliz' own tests. One must change line 325 to

        if(SuppHelp.rank()<EmbDim-1)

But againthis has nothing to do with the wrong number of lattice points.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​d3f7ceb

New version of patch to fix next crash.

[tscrim]

Replying to Winfried:

The wrong number of lattice points is a more severe problem. I don't have an explanation for it.

I am afraid all I can do is give you examples from my use-case as I do not understand too much about how Normaliz works. Thank you for your continued efforts and quick responses.

The (first and solved) problem in sublattice_representation.h has nothing to do with it. After the change in sublattice_representation.h:323 a second problem has become visible there in Normaliz' own tests. One must change line 325 to

        if(SuppHelp.rank()<EmbDim-1)

But again this has nothing to do with the wrong number of lattice points.

I added that to the patch, but (as you might be aware) I am now getting yet another crash with the same example as in comment:25:

sage: P = Polyhedron(ieqs=ieqs, backend='normaliz', verbose=True)
# Calling PyNormaliz.NmzCone(['inhom_equations', [], 'inhom_inequalities',
 [[2, 0, -1, 0, 0, 0, 0, 0, 0], [0, 2, 0, -1, 0, 0, 0, 0, 0],
 [-1, 0, 2, -1, 0, 0, 0, 0, 0], [0, -1, -1, 2, -1, 0, 0, 0, 1],
 [0, 0, 0, -1, 2, -1, 0, 0, 0], [0, 0, 0, 0, -1, 2, -1, 0, 0],
 [0, 0, 0, 0, 0, -1, 2, -1, 1], [0, 0, 0, 0, 0, 0, -1, 2, 0],
 [-1, 0, 0, 0, 0, 0, 0, 0, 0], [0, -1, 0, 0, 0, 0, 0, 0, 0],
 [0, 0, -1, 0, 0, 0, 0, 0, 0], [0, 0, 0, -1, 0, 0, 0, 0, 0],
 [0, 0, 0, 0, -1, 0, 0, 0, 0], [0, 0, 0, 0, 0, -1, 0, 0, 0],
 [0, 0, 0, 0, 0, 0, -1, 0, 0], [0, 0, 0, 0, 0, 0, 0, -1, 0],
 [-1, -1, -1, -1, -1, -1, -1, -1, -1], [1, 0, 0, 0, 0, 0, 0, 0, 3],
 [0, 1, 0, 0, 0, 0, 0, 0, 4], [0, 0, 1, 0, 0, 0, 0, 0, 6],
 [0, 0, 0, 1, 0, 0, 0, 0, 8], [0, 0, 0, 0, 1, 0, 0, 0, 6],
 [0, 0, 0, 0, 0, 1, 0, 0, 4], [0, 0, 0, 0, 0, 0, 1, 0, 2],
 [0, 0, 0, 0, 0, 0, 0, 1, 1]]])
sage: P
A 8-dimensional polyhedron in QQ^8 defined as the convex hull of 132 vertices
sage: P.integral_points()
python2: ./libnormaliz/project_and_lift.cpp:75: std::vector<long unsigned int> libnormaliz::ProjectAndLift<IntegerPL, IntegerRet>::order_supps(const libnormaliz::Matrix<Integer>&) [with IntegerPL = long long int; IntegerRet = long long int]: Assertion `Supps.nr_of_rows()>0' failed.
------------------------------------------------------------------------

Addendum - It is the same error as before.

[Winfried]

I think all the observed problems are solved. More tomorrow.

[tscrim]

Great, thank you!

[Winfried]

The problem with the wrong number of lattice points (or a failing assertion) was not caused by a severe problem, but by a silly bug. As a temporary fix I suggest to include as lines cone.cpp:3804 and 3805

    if(!is_parallelotope)
        Pair.clear();

So with some surrounding the code there should be

            is_Computed.set(ConeProperty::IsPointed);
        }
    }
    
    if(!is_parallelotope)
        Pair.clear();
    
    if(!inhomogeneous && !isComputed(ConeProperty::Grading))
        return;

I plan to release 3.5.2 at the end of this week. It will contain a more conceptual solution.

Please test.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​737552d

Updating patch with upstream fix for wrong number of lattice points.

[tscrim]

Thank you. I have verified that I get again

sage: RC = RiggedConfigurations(['E',8,1], [[5,2]])
sage: %time len(RC.module_generators)
CPU times: user 27.6 s, sys: 68 ms, total: 27.7 s
Wall time: 7.8 s
7066
sage: RC = RiggedConfigurations(['E',8,1], [[4,2]])
sage: %time len(RC.module_generators)
CPU times: user 5min 6s, sys: 944 ms, total: 5min 7s
Wall time: 1min 36s
288299

and the >2x speedup is very impressive. :) I've updated the patch accordingly.

@mkoeppe Perhaps we should just wait on this upgrade until 3.5.2 is released to avoid the patch since it will be in just a few days?

As far as adding tests go, I think we should explicitly add the polytopes mentioned above rather than the RC code. They are isolated and much faster to test.

[mkoeppe]

Replying to tscrim:

@mkoeppe Perhaps we should just wait on this upgrade until 3.5.2 is released to avoid the patch since it will be in just a few days?

Yes, I think so too.

As far as adding tests go, I think we should explicitly add the polytopes mentioned above rather than the RC code. They are isolated and much faster to test.

I agree.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​530302d	Merge branch 'u/tscrim/upgrade_noramliz_pynormaliz-22984' of git://trac.sagemath.org/sage into u/tscrim/upgrade_noramliz_pynormaliz-22984
​57d40b0	Upgrade Normaliz to 3.5.2.

[tscrim]

Here is with 3.5.2 and the tests I did above now work. Where would a good place be to add the doctests?

[mkoeppe]

I would think the doctests should go to Polyhedron_normaliz.integral_points.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​6ba442d

Adding tests from comment:24,25 of #22984.

[tscrim]

Okay, done.

[tscrim]

ping

[mkoeppe]

19. Gutsche informs us that we should upgrade pynormaliz to 1.12

[jipilab]

All tests passed with sage8.2.beta8.

@Travis: Do you still want to add a comment about the verbose of Polyhedron?

Otherwise, it seems that we need to wait for 1.12 of pynormaliz check everything one last time.

[mkoeppe]

New commits:

​183087a

Upgrade PyNormaliz to 1.12

[jipilab]

New commits:

​7f47ec9

Adapted the polyhedron docstring

[jipilab]

It looks good to me now and all tests pass in the polyhedron folder.

[mkoeppe]

Compilation errors with a specific gcc version with PyNormaliz?. Fixed in normaliz 3.5.3

[mkoeppe]

New commits:

​117e428

Upgrade normaliz to 3.5.3

[jipilab]

Install the latest normaliz and got:

~/sage/src/sage/geometry/polyhedron$ sage -t *.py
Using --optional=4ti2,bliss,latte_int,lidia,lrslib,mpir,normaliz,pynormaliz,python2,sage
Doctesting 25 files.
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------

[tscrim]

Replying to jipilab:

@Travis: Do you still want to add a comment about the verbose of Polyhedron?

It can be on a separate ticket, but the docstring for verbose should also say it is supported for the normaliz backend as well.

[jipilab]

Replying to tscrim:

Replying to jipilab:

@Travis: Do you still want to add a comment about the verbose of Polyhedron?

It can be on a separate ticket, but the docstring for verbose should also say it is supported for the normaliz backend as well.

I went ahead and made the change already... I realized it was not a big deal.

[tscrim]

Ah, thanks. I didn't look at the diffs.

[jipilab]

Merged the forgotten commit.

---

New commits:

​7f47ec9	Adapted the polyhedron docstring
​7057ef4	Merge branch to get docstring adaptation