{chem}[foss/2023a] RDKit v2024.03.3 #20824

pavelToman · 2024-06-14T13:51:41Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#328

Requires Boost.python from:

{vis}[foss/2023a] micro-sam v1.0.1, torch_em v0.7.1, affogato v0.3.3, ... #20636

boegel

lgtm

…asyconfigs into 20240614155137_new_pr_RDKit2024033

boegel

lgtm

boegel · 2024-06-19T11:49:31Z

@boegelbot please test @ generoso

boegel · 2024-06-19T12:09:43Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3107.skitty.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/boegel/af7a2b4ec0f21f2db259e44e989f37e8 for a full test report.

boegelbot · 2024-06-19T12:10:27Z

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=20824 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20824 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13773

Test results coming soon (I hope)...

- notification for comment with ID 2178501140 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-06-19T12:47:46Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/b82a2e678206c326f723846efad92c6f for a full test report.

boegel · 2024-06-19T16:40:26Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-06-19T16:50:08Z

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=20824 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20824 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4422

Test results coming soon (I hope)...

- notification for comment with ID 2179107309 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-06-19T17:05:40Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/364cb1ed51f94a100b35c845ac252857 for a full test report.

pavelToman · 2024-06-20T08:37:03Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-06-20T08:40:08Z

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=20824 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20824 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4429

Test results coming soon (I hope)...

- notification for comment with ID 2180130927 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-06-20T08:55:20Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/7e1dfa0d4aadc5e46043719e2df99415 for a full test report.

boegel · 2024-07-04T09:59:18Z

Details on failing test below.

@pavelToman Can you check if you can find a clue as to why this is failing, maybe there's patch available?

        Start  27: pyForceFieldConstraints
 27/221 Test  #27: pyForceFieldConstraints ................***Failed    1.04 sec
...[09:07:46] Molecule does not have explicit Hs. Consider calling AddHs()
[09:07:46]

****
Invariant Violation
bad direction in linearSearch
Violation occurred on line 240 in file /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/rdkit-Release_2024_03_3/Code/Numerics/Optimizer/BFGSOpt.h
Failed Expression: status >= 0

======================================================================
FAIL: testUFFAngleConstraints (__main__.TestCase.testUFFAngleConstraints)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/rdkit-Release_2024_03_3/Code/ForceField/Wrap/testConstraints.py", line 164, in testUFFAngleConstraints
    self.assertTrue(r == 0)
AssertionError: False is not true

----------------------------------------------------------------------
Ran 12 tests in 0.633s

FAILED (failures=1)

detailed stracktrace:

----------
Stacktrace:
 0# Invar::Invariant::toString[abi:cxx11]() const in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/lib/libRDKitRDGeneral.so.1
 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/lib/libRDKitRDGeneral.so.1
 2# ForceFields::ForceField::minimize(unsigned int, std::vector<RDKit::Snapshot, std::allocator<RDKit::Snapshot> >*, unsigned int, double, double) in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/lib/libRDKitForceField.so.1
 3# boost::python::objects::caller_py_function_impl<boost::python::detail::caller<int (ForceFields::PyForceField::*)(int, double, double), boost::python::default_call_policies, boost::mpl::vector5<int, ForceFields::PyForceField&, int, double, double> > >::operator()(_object*, _object*) in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/ForceField/rdForceField.so
 4# boost::python::objects::function::call(_object*, _object*) const in /project/def-maintainers/boegelbot/rocky9/zen3/software/Boost.Python/1.82.0-GCC-12.3.0/lib/libboost_python311-mt-x64.so.1.82.0
 5# 0x000014988C0A08C8 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Boost.Python/1.82.0-GCC-12.3.0/lib/libboost_python311-mt-x64.so.1.82.0
 6# boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const in /project/def-maintainers/boegelbot/rocky9/zen3/software/Boost.Python/1.82.0-GCC-12.3.0/lib/libboost_python311-mt-x64.so.1.82.0
 7# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::FileParseException, void (*)(RDKit::FileParseException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::FileParseException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/Chem/rdmolfiles.so
 8# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::BadFileException, void (*)(RDKit::BadFileException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::BadFileException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/Chem/rdmolfiles.so
 9# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::CIPLabeler::MaxIterationsExceeded, void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::CIPLabeler::MaxIterationsExceeded const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/Chem/rdCIPLabeler.so
10# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<RDKit::ConformerException, void (*)(RDKit::ConformerException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(RDKit::ConformerException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/Chem/rdchem.so
11# 0x0000149807DE039C in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/Chem/rdchem.so
12# 0x0000149807DE037C in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/Chem/rdchem.so
13# 0x0000149807DE035C in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/Chem/rdchem.so
14# 0x0000149807DE033C in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/Chem/rdchem.so
15# 0x0000149807DE031C in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/Chem/rdchem.so
16# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Invar::Invariant, void (*)(Invar::Invariant const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Invar::Invariant const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/rdBase.so
17# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<KeyErrorException, void (*)(KeyErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(KeyErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/rdBase.so
18# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ValueErrorException, void (*)(ValueErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ValueErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/rdBase.so
19# boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<IndexErrorException, void (*)(IndexErrorException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(IndexErrorException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) in /dev/shm/boegelbot/RDKit/2024.03.3/foss-2023a/easybuild_obj/rdkit/rdBase.so
20# boost::python::handle_exception_impl(boost::function0<void>) in /project/def-maintainers/boegelbot/rocky9/zen3/software/Boost.Python/1.82.0-GCC-12.3.0/lib/libboost_python311-mt-x64.so.1.82.0
21# 0x000014988C09E272 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Boost.Python/1.82.0-GCC-12.3.0/lib/libboost_python311-mt-x64.so.1.82.0
22# _PyObject_MakeTpCall in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
23# _PyEval_EvalFrameDefault in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
24# 0x000014988CD295AA in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
25# 0x000014988CD66CE6 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
26# _PyEval_EvalFrameDefault in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
27# 0x000014988CD295AA in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
28# _PyObject_FastCallDictTstate in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
29# 0x000014988CD52362 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
30# 0x000014988CD24E3B in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
31# _PyObject_MakeTpCall in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
32# _PyEval_EvalFrameDefault in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
33# 0x000014988CD295AA in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
34# 0x000014988CD66CE6 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
35# _PyEval_EvalFrameDefault in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
36# 0x000014988CD295AA in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
37# _PyObject_FastCallDictTstate in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
38# _PyObject_Call_Prepend in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
39# 0x000014988CDF1260 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
40# _PyObject_MakeTpCall in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
41# _PyEval_EvalFrameDefault in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
42# 0x000014988CD295AA in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
43# 0x000014988CD66CE6 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
44# _PyEval_EvalFrameDefault in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
45# 0x000014988CD295AA in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
46# _PyObject_FastCallDictTstate in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
47# _PyObject_Call_Prepend in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
48# 0x000014988CDF1260 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
49# _PyObject_MakeTpCall in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
50# _PyEval_EvalFrameDefault in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
51# 0x000014988CD295AA in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
52# 0x000014988CD66CE6 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
53# _PyEval_EvalFrameDefault in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
54# 0x000014988CD295AA in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
55# _PyObject_FastCallDictTstate in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
56# _PyObject_Call_Prepend in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
57# 0x000014988CDF1260 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
58# _PyObject_MakeTpCall in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
59# _PyEval_EvalFrameDefault in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
60# 0x000014988CD295AA in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
61# _PyObject_FastCallDictTstate in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
62# 0x000014988CD52362 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
63# 0x000014988CD24E3B in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
64# _PyObject_MakeTpCall in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
65# _PyEval_EvalFrameDefault in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
66# 0x000014988CD295AA in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
67# PyEval_EvalCode in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
68# 0x000014988CDCDB33 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
69# 0x000014988CDCA3BA in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
70# 0x000014988CDEE7E1 in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
71# _PyRun_SimpleFileObject in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
72# _PyRun_AnyFileObject in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
73# Py_RunMain in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
74# Py_BytesMain in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/lib/libpython3.11.so.1.0
75# 0x000014988C829590 in /lib64/libc.so.6
76# __libc_start_main in /lib64/libc.so.6
77# _start in /project/def-maintainers/boegelbot/rocky9/zen3/software/Python/3.11.3-GCCcore-12.3.0/bin/python

boegel · 2024-07-04T10:00:29Z

This seems relevant: rdkit/rdkit#5252

Maybe that fix never actually made it in a release? 🤔

branfosj · 2024-07-04T10:08:32Z

This seems relevant: rdkit/rdkit#5252

Maybe that fix never actually made it in a release? 🤔

That fix is in the code. The failure is further on in the test.

pavelToman · 2024-07-08T11:56:22Z

Open discussion: rdkit/rdkit#7588
Conclusion: we should ignore this one test failing

pavelToman · 2024-07-10T14:33:06Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-07-10T14:40:08Z

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=20824 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20824 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4546

Test results coming soon (I hope)...

- notification for comment with ID 2220681844 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-07-10T14:55:38Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/25c8bbdf9f8ae41951ae2c1bb68c8488 for a full test report.

adding easyconfigs: RDKit-2024.03.3-foss-2023a.eb

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pavelToman mentioned this pull request Jun 17, 2024

OpenFF toolkit vscentrum/vsc-software-stack#328

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boegel approved these changes Jun 18, 2024

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boegel added the update label Jun 18, 2024

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{bio}[foss/2023a] OpenForceField-Toolkit v0.16.0 #20852

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Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

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…asyconfigs into 20240614155137_new_pr_RDKit2024033

boegel previously approved these changes Jun 19, 2024

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ignore failing testUFFAngleConstraints

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pavelToman dismissed boegel’s stale review via bdbf7db July 10, 2024 14:31

ignore failing testUFFAngleConstraints - comments added

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{chem}[foss/2023a] RDKit v2024.03.3 #20824

{chem}[foss/2023a] RDKit v2024.03.3 #20824

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{chem}[foss/2023a] RDKit v2024.03.3 #20824

Are you sure you want to change the base?

{chem}[foss/2023a] RDKit v2024.03.3 #20824

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