hpcombi: support Vect16 + PTransf16 + subclasses

[james-d-mitchell]

No description provided.

[james-d-mitchell]

@Joseph-Edwards any chance you can see if you can reproduce the failures on your computer? Everything passes for me compiling with clang or gcc (13.4), so I imagine this might be an architecture issue. You need to add CXXFLAGS="-fpermissive -flax-vector-conversions" to pip before it will compile

[Joseph-Edwards]

@Joseph-Edwards any chance you can see if you can reproduce the failures on your computer?

I'm getting this when running test_cong.py:

Stack trace (most recent call last):
#31   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1bc1642, in 
#30   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1bc1ab5, in Py_RunMain
#29   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1c233f3, in 
#28   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1c234f5, in 
#27   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1c2354f, in 
#26   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1c23d1e, in 
#25   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1c24906, in 
#24   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a7cf61, in 
#23   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a8366e, in PyEval_EvalCode
#22   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a83960, in 
#21   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a52bd5, in 
#20   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a52910, in PyObject_Call
#19   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a14a4d, in 
#18   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a14ed3, in 
#17   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a0cd6a, in 
#16   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1b1bfe6, in 
#15   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1b1c148, in 
#14   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1b1c2ce, in _PyEval_EvalFrameDefault
#13   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a277d1, in 
#12   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1b22146, in 
#11   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a8366e, in PyEval_EvalCode
#10   Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a83960, in 
#9    Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a52bd5, in 
#8    Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1d65180, in 
#7    Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a3c5a6, in _PyObject_MakeTpCall
#6    Object "[...]/libsemigroups_pybind11/.venv/bin/python3", at 0x1a31d7b, in 
#5    Object "[...]/libsemigroups_pybind11/.venv/lib/python3.14/site-packages/_libsemigroups_pybind11.cpython-314-x86_64-linux-gnu.so", at 0x77f0031d2189, in 
#4    Object "[...]/libsemigroups_pybind11/.venv/lib/python3.14/site-packages/_libsemigroups_pybind11.cpython-314-x86_64-linux-gnu.so", at 0x77f003318cc1, in 
#3    Object "[...]/libsemigroups_pybind11/.venv/lib/python3.14/site-packages/_libsemigroups_pybind11.cpython-314-x86_64-linux-gnu.so", at 0x77f003318411, in 
#2    Object "[...]/libsemigroups_pybind11/.venv/lib/python3.14/site-packages/_libsemigroups_pybind11.cpython-314-x86_64-linux-gnu.so", at 0x77f0033180f1, in 
#1    Object "/usr/local/lib/libsemigroups.so.3", at 0x77f008cc059c, in libsemigroups::IsObviouslyInfinite::~IsObviouslyInfinite()
#0    Object "/lib/x86_64-linux-gnu/libc.so.6", at 0x77f00caadd55, in __libc_free
Segmentation fault (Address not mapped to object [0x129])

Investigating now

[Joseph-Edwards]

With debug enabled we get a big more:

#8    Object "/usr/local/lib/libsemigroups.so.3", at 0x76cbba3c801f, in libsemigroups::IsObviouslyInfinite::~IsObviouslyInfinite()
#7    Object "/usr/local/lib/libsemigroups.so.3", at 0x76cbba3caced, in Eigen::Matrix<long, -1, -1, 0, -1, -1>::~Matrix()
#6    Object "/usr/local/lib/libsemigroups.so.3", at 0x76cbba3caccd, in Eigen::PlainObjectBase<Eigen::Matrix<long, -1, -1, 0, -1, -1> >::~PlainObjectBase()
#5    Object "/usr/local/lib/libsemigroups.so.3", at 0x76cbba3cb870, in Eigen::DenseStorage<long, -1, -1, -1, 0>::~DenseStorage()
#4    Object "/usr/local/lib/libsemigroups.so.3", at 0x76cbba3ccfab, in void Eigen::internal::conditional_aligned_delete_auto<long, true>(long*, unsigned long)
#3    Object "/usr/local/lib/libsemigroups.so.3", at 0x76cbba3ce7fb, in void Eigen::internal::conditional_aligned_free<true>(void*)
#2    Object "/usr/local/lib/libsemigroups.so.3", at 0x76cbba3ca53a, in Eigen::internal::aligned_free(void*)
#1    Object "/usr/local/lib/libsemigroups.so.3", at 0x76cbba3ca402, in Eigen::internal::handmade_aligned_free(void*)
#0    Object "/lib/x86_64-linux-gnu/libc.so.6", at 0x76cbc38add55, in __libc_free
Segmentation fault (Address not mapped to object [0x129])

[Joseph-Edwards]

You need to add CXXFLAGS="-fpermissive -flax-vector-conversions" to pip before it will compile

It seems like -flax-vector-conversions is the culprit here. I'm not really sure where to go from here, but this seems to be what is causing the problem (and explains why the errors have nothing to do with HPCombi)

[james-d-mitchell]

I've tried moving the compiler flags into setup.py, if the there's still a seg fault in the linux tests, I'll just add --disable-eigen when we are building libsemigroups. This does leave the question of what to do about the conda feedstocks: libsemigroups currently is compiled there with --enable-eigen, which might mean that the python bindings test fail when installed via conda. We could just disable eigen there too I suppose. We might have to make some releases to check what happens.