From d19f352142d5494557bc53a5c74001ea9760bfaa Mon Sep 17 00:00:00 2001 From: Kazuyoshi Yoshimi Date: Tue, 16 Jun 2026 18:37:41 +0900 Subject: [PATCH 1/2] Fix RXMC replica exchange under NumPy 2 (Python 3.13) find_procrank_from_Trank returned the raw np.argwhere result, a 2-D array (shape (1, 1)). When passed as the MPI source/dest rank, mpi4py converts it with int(); NumPy 2 rejects int() on non-0-dimensional arrays, raising 'only 0-dimensional arrays can be converted to Python scalars' and breaking comm.Recv/Send on Python 3.13. Return a plain Python int instead, and fix the dead 'if i is None' guard (np.argwhere never returns None) to check i.size. Verified locally with Python 3.13 / numpy 2.4.6 / mpi4py 4.1.2: the mock, potts and potts_pamc sampling tests and the unit tests all pass. Co-Authored-By: Claude Opus 4.8 (1M context) --- abics/sampling/rxmc.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/abics/sampling/rxmc.py b/abics/sampling/rxmc.py index 0afdf3b..8bd4b2f 100644 --- a/abics/sampling/rxmc.py +++ b/abics/sampling/rxmc.py @@ -203,10 +203,14 @@ def find_procrank_from_Trank(self, Trank): procrank: int """ i = np.argwhere(self.rank_to_T == Trank) - if i is None: + if i.size == 0: sys.exit("Internal error in TemperatureRX_MPI.find_procrank_from_Trank") else: - return i + # np.argwhere returns a 2-D array (shape (1, 1) here); return a plain + # Python int so it can be used as an MPI source/dest rank. NumPy 2.x + # rejects int() on non-0-dimensional arrays, which previously broke + # comm.Recv/Send on Python 3.13 (numpy>=2). + return int(i[0, 0]) def Xtrial(self, XCscheme): """ From 4be2e300a6689f061276a27f9d093e3434322879 Mon Sep 17 00:00:00 2001 From: Kazuyoshi Yoshimi Date: Tue, 16 Jun 2026 18:37:41 +0900 Subject: [PATCH 2/2] Skip nequip test on Python 3.13 and document the numpy<2 requirement The supported nequip series (<0.7) uses numpy.in1d, removed in NumPy 2, so it needs numpy<2. Python 3.13 has no numpy 1.x wheels, so the nequip path cannot run there. This is an upstream nequip/numpy-2 incompatibility, not an abICS bug. - Exclude the ActiveLearnNequip CI job on Python 3.13 (with a comment) - Note the numpy<2 / no-Python-3.13 limitation in the JA/EN nequip tutorials - Explain the nequip <0.7 cap in pyproject.toml Co-Authored-By: Claude Opus 4.8 (1M context) --- .github/workflows/Test_abICS.yml | 12 ++++++++++++ .../en/source/tutorial/other_models.rst | 18 ++++++++++++++++++ .../ja/source/tutorial/other_models.rst | 19 ++++++++++++++++++- pyproject.toml | 3 +++ .../active_learn_nequip/install_nequip.sh | 15 +++++++++++++++ 5 files changed, 66 insertions(+), 1 deletion(-) diff --git a/.github/workflows/Test_abICS.yml b/.github/workflows/Test_abICS.yml index c23303a..1422547 100644 --- a/.github/workflows/Test_abICS.yml +++ b/.github/workflows/Test_abICS.yml @@ -21,6 +21,18 @@ jobs: exclude: - python-version: '3.13' numpy-version: '1.20.0' + # nequip 0.6.2 (the pinned version) calls the removed numpy.in1d and + # therefore requires numpy<2, but Python 3.13 has no numpy 1.x wheels. + # This is an upstream nequip/numpy-2 incompatibility, not an abICS bug, + # so skip the nequip integration test on Python 3.13. + # + # NOTE for developers: as a result the nequip path is only exercised on + # Python 3.9 (install_nequip.sh pins numpy<2 for that environment); there + # is no numpy-2 / Python 3.13 coverage for nequip. Restoring it requires + # migrating the abICS nequip solver/trainer to nequip >=0.7 (a backwards- + # incompatible rewrite). See the nequip cap in pyproject.toml. + - python-version: '3.13' + testname: ActiveLearnNequip fail-fast: false steps: diff --git a/docs/sphinx/en/source/tutorial/other_models.rst b/docs/sphinx/en/source/tutorial/other_models.rst index beb36d1..e58c6e7 100644 --- a/docs/sphinx/en/source/tutorial/other_models.rst +++ b/docs/sphinx/en/source/tutorial/other_models.rst @@ -17,12 +17,20 @@ Installation of NequIP To use ``nequip``, you need to install NequIP. Currently, NequIP 0.6.2 is supported. +.. note:: + + The supported NequIP (< 0.7) relies on ``numpy.in1d``, which was removed in + NumPy 2, so it requires a ``numpy<2`` environment. Because no NumPy 1.x wheels + are available for Python 3.13, the NequIP path currently cannot be used on + Python 3.13 (please use Python 3.12 or earlier). + Install it with the following command. .. code-block:: bash $ python3 -m pip install wandb $ python3 -m pip install nequip==0.6.2 + $ python3 -m pip install "numpy<2" Also, when installing abICS, you can install NequIP by specifying the [nequip] option. @@ -30,6 +38,11 @@ Also, when installing abICS, you can install NequIP by specifying the [nequip] o $ cd /path/to/abics $ python3 -m pip install '.[nequip]' + $ python3 -m pip install "numpy<2" + +The ``numpy<2`` constraint above is required regardless of the installation +method (the ``[nequip]`` option does not constrain the numpy version, so install +it separately). Preparation of input files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -136,7 +149,12 @@ Currently, nequip-allegro 0.3.0 is supported. .. code-block:: bash $ python3 -m pip install nequip-allegro==0.3.0 + $ python3 -m pip install "numpy<2" + +.. note:: + Allegro runs on top of the same NequIP (< 0.7) stack, so like NequIP it + requires a ``numpy<2`` environment and cannot be used on Python 3.13. Preparation of input files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/docs/sphinx/ja/source/tutorial/other_models.rst b/docs/sphinx/ja/source/tutorial/other_models.rst index b1320d8..62b8c2d 100644 --- a/docs/sphinx/ja/source/tutorial/other_models.rst +++ b/docs/sphinx/ja/source/tutorial/other_models.rst @@ -17,19 +17,31 @@ NequIP のインストール ``nequip`` の利用には、 NequIPのインストールが必要です。 2025年6月現在、NequIP 0.6.2 がサポートされています。 +.. note:: + + サポートされている NequIP (< 0.7) は、NumPy 2 で削除された ``numpy.in1d`` + を利用するため、 ``numpy<2`` の環境が必要です。Python 3.13 には NumPy 1.x の + wheel が存在しないため、現状 NequIP 経路は Python 3.13 では利用できません + (Python 3.12 以前をご利用ください)。 + 下記コマンドにてインストールします。 .. code-block:: bash $ python3 -m pip install wandb $ python3 -m pip install nequip==0.6.2 + $ python3 -m pip install "numpy<2" また、abICSインストール時に ``[nequip]`` オプションを指定すれば、NequIPもインストールされます。 .. code-block:: bash $ cd /path/to/abics - $ python3 -m pip install '.abics[nequip]' + $ python3 -m pip install '.[nequip]' + $ python3 -m pip install "numpy<2" + +いずれのインストール方法でも、上記の ``numpy<2`` 制約が必要です（``[nequip]`` +オプションは numpy のバージョンを制約しないため、別途指定してください）。 インプットファイルの準備 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -135,7 +147,12 @@ Allegro のインストール .. code-block:: bash $ python3 -m pip install nequip-allegro==0.3.0 + $ python3 -m pip install "numpy<2" + +.. note:: + Allegro は上記の NequIP (< 0.7) スタック上で動作するため、NequIP と同じく + ``numpy<2`` の環境が必要で、Python 3.13 では利用できません。 インプットファイルの準備 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/pyproject.toml b/pyproject.toml index 200f784..3f98aca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,6 +20,9 @@ scipy = "^1" mpi4py = ">=3" pymatgen = ">=2022.1.20" qe_tools = "^1.1" +# nequip is capped at <0.7: 0.7+ is a backwards-incompatible rewrite that the +# abICS nequip solver/trainer do not yet support. The supported series uses the +# removed numpy.in1d, so it needs numpy<2 and cannot run on Python 3.13. nequip = {version=">=0.5.6, <0.7", optional=true} [tool.poetry.extras] diff --git a/tests/integration/active_learn_nequip/install_nequip.sh b/tests/integration/active_learn_nequip/install_nequip.sh index afd29ce..44bdc22 100644 --- a/tests/integration/active_learn_nequip/install_nequip.sh +++ b/tests/integration/active_learn_nequip/install_nequip.sh @@ -2,6 +2,13 @@ # This script installs pytorch, nequip, and allegro # into python3 environment +# +# NOTE for developers: +# nequip is pinned to 0.6.2 (and nequip-allegro to 0.3.0) because the abICS +# nequip solver/trainer target the pre-0.7 API. That series uses numpy.in1d, +# which was removed in NumPy 2, so this test only works with numpy<2 and is +# therefore restricted to Python 3.9 in the CI matrix (Python 3.13 has no +# numpy 1.x wheels). Lifting this requires migrating abICS to nequip >=0.7. set -ue @@ -10,6 +17,14 @@ which python3 echo +# Pin numpy<2 up front: nequip 0.6.2 declares "numpy" with no upper bound but +# uses numpy.in1d (removed in NumPy 2). Setting it before the nequip stack keeps +# the subsequent installs resolving against a compatible numpy. +python3 -m pip install "numpy<2" + python3 -m pip install torch==2.5.1 python3 -m pip install nequip==0.6.2 python3 -m pip install nequip-allegro==0.3.0 + +# Re-assert numpy<2 in case any of the above pulled in numpy>=2. +python3 -m pip install "numpy<2"