numba-mpi 1.0.0__tar.gz → 1.1.1__tar.gz

{numba_mpi-1.0.0 → numba_mpi-1.1.1}/.github/workflows/tests+pypi.yml

@@ -33,7 +33,7 @@ jobs:
         pip install -r numba_mpi.egg-info/requires.txt
     - name: Analysing the code with pylint
       run: |
-        pylint --unsafe-load-any-extension=y --disable=fixme $(git ls-files '*.py' | grep -v -e ^tests/paper_listings)
+        pylint --unsafe-load-any-extension=y --disable=fixme,duplicate-code $(git ls-files '*.py' | grep -v -e ^tests/paper_listings)
 
   precommit:
     runs-on: ubuntu-latest
@@ -64,15 +64,15 @@ jobs:
       - uses: mpi4py/setup-mpi@v1
       - name: Build
         run: |
-          pip install pdoc3
+          pip install pdoc
           pip install -e .
-          python -We -m pdoc --html numba_mpi
+          PDOC_ALLOW_EXEC=1 python -We -m pdoc -o html numba_mpi
       - name: Deploy
         if: github.ref == 'refs/heads/main'
         uses: JamesIves/github-pages-deploy-action@4.1.1
         with:
           BRANCH: pdoc
-          FOLDER: html/numba_mpi
+          FOLDER: html
           CLEAN: true
 
   zenodo_json:
@@ -165,9 +165,12 @@ jobs:
           python -We -c "import numba_mpi"
 
       - if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        uses: pypa/gh-action-pypi-publish@unstable/v1
+        uses: pypa/gh-action-pypi-publish@release/v1.12
         with:
+          attestations: false
           repository_url: https://test.pypi.org/legacy/
 
       - if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@unstable/v1
+        uses: pypa/gh-action-pypi-publish@release/v1.12
+        with:
+          attestations: false

{numba_mpi-1.0.0 → numba_mpi-1.1.1}/.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "numba-mpi",
-  "description": "Numba @njittable wrappers for MPI C API tested on Linux, macOS and Windows",
+  "description": "Numba @jittable wrappers for MPI C API tested on Linux, macOS and Windows",
   "creators": [
     {
       "affiliation": "Jagiellonian University, Kraków, Poland",

numba_mpi-1.1.1/CITATION.cff

@@ -0,0 +1,20 @@
+cff-version: 1.2.0
+title: "numba-mpi"
+url: "https://github.com/numba-mpi/numba-mpi"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Derlatka"
+    given-names: "Kacper"
+  - family-names: "Manna"
+    given-names: "Maciej"
+  - family-names: "Bulenok"
+    given-names: "Oleksii"
+  - family-names: "Zwicker"
+    given-names: "David"
+  - family-names: "Arabas"
+    given-names: "Sylwester"
+  doi: "10.1016/j.softx.2024.101897"
+  journal: "SoftwareX"
+  title: "Numba-MPI v1.0: Enabling MPI communication within Numba/LLVM JIT-compiled Python code"
+  year: 2024

{numba_mpi-1.0.0 → numba_mpi-1.1.1}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: numba-mpi
-Version: 1.0.0
-Summary: Numba @njittable MPI wrappers tested on Linux, macOS and Windows
+Version: 1.1.1
+Summary: Numba @jittable MPI wrappers tested on Linux, macOS and Windows
 Home-page: https://github.com/numba-mpi/numba-mpi
 Author: https://github.com/numba-mpi/numba-mpi/graphs/contributors
 License: GPL v3
@@ -19,7 +19,7 @@ Provides-Extra: tests
 Requires-Dist: pytest<8.0.0; extra == "tests"
 Requires-Dist: py-pde; extra == "tests"
 
-# <img src="https://raw.githubusercontent.com/numba-mpi/numba-mpi/main/.github/numba_mpi_logo.svg" style="height:50pt" alt="numba-mpi logo"> numba-mpi
+# <img src="https://raw.githubusercontent.com/numba-mpi/numba-mpi/main/.github/numba_mpi_logo.png" width=128 height=142 alt="numba-mpi logo"> numba-mpi
 
 [![Python 3](https://img.shields.io/static/v1?label=Python&logo=Python&color=3776AB&message=3)](https://www.python.org/)
 [![LLVM](https://img.shields.io/static/v1?label=LLVM&logo=LLVM&color=gold&message=Numba)](https://numba.pydata.org)
@@ -35,9 +35,9 @@ Requires-Dist: py-pde; extra == "tests"
 [![DOI](https://zenodo.org/badge/316911228.svg)](https://zenodo.org/badge/latestdoi/316911228)
 
 ### Overview
-numba-mpi provides Python wrappers to the C MPI API callable from within [Numba JIT-compiled code](https://numba.readthedocs.io/en/stable/user/jit.html) (@njit mode).
+numba-mpi provides Python wrappers to the C MPI API callable from within [Numba JIT-compiled code](https://numba.readthedocs.io/en/stable/user/jit.html) (@jit mode). For an outline of the project, rationale, architecture, and features, refer to: [numba-mpi arXiv e-print](https://doi.org/10.48550/arXiv.2407.13712) (please cite if numba-mpi is used in your research).
 
-Support is provided for a subset of MPI routines covering: `size`/`rank`, `send`/`recv`, `allreduce`, `bcast`, `scatter`/`gather` & `allgather`, `barrier`, `wtime`
+Support is provided for a subset of MPI routines covering: `size`/`rank`, `send`/`recv`, `allreduce`, `reduce`, `bcast`, `scatter`/`gather` & `allgather`, `barrier`, `wtime`
 and basic asynchronous communication with `isend`/`irecv` (only for contiguous arrays); for request handling including `wait`/`waitall`/`waitany` and `test`/`testall`/`testany`.
 
 The API uses NumPy and supports both numeric and character datatypes (e.g., `broadcast`). 
@@ -66,7 +66,7 @@ Features that are not implemented yet include (help welcome!):
 ```python
 import numba, numba_mpi, numpy
 
-@numba.njit()
+@numba.jit()
 def hello():
     src = numpy.array([1., 2., 3., 4., 5.])
     dst_tst = numpy.empty_like(src)

{numba_mpi-1.0.0 → numba_mpi-1.1.1}/README.md

@@ -1,4 +1,4 @@
-# <img src="https://raw.githubusercontent.com/numba-mpi/numba-mpi/main/.github/numba_mpi_logo.svg" style="height:50pt" alt="numba-mpi logo"> numba-mpi
+# <img src="https://raw.githubusercontent.com/numba-mpi/numba-mpi/main/.github/numba_mpi_logo.svg" width=128 height=142 alt="numba-mpi logo"> numba-mpi
 
 [![Python 3](https://img.shields.io/static/v1?label=Python&logo=Python&color=3776AB&message=3)](https://www.python.org/)
 [![LLVM](https://img.shields.io/static/v1?label=LLVM&logo=LLVM&color=gold&message=Numba)](https://numba.pydata.org)
@@ -14,9 +14,9 @@
 [![DOI](https://zenodo.org/badge/316911228.svg)](https://zenodo.org/badge/latestdoi/316911228)
 
 ### Overview
-numba-mpi provides Python wrappers to the C MPI API callable from within [Numba JIT-compiled code](https://numba.readthedocs.io/en/stable/user/jit.html) (@njit mode).
+numba-mpi provides Python wrappers to the C MPI API callable from within [Numba JIT-compiled code](https://numba.readthedocs.io/en/stable/user/jit.html) (@jit mode). For an outline of the project, rationale, architecture, and features, refer to: [numba-mpi arXiv e-print](https://doi.org/10.48550/arXiv.2407.13712) (please cite if numba-mpi is used in your research).
 
-Support is provided for a subset of MPI routines covering: `size`/`rank`, `send`/`recv`, `allreduce`, `bcast`, `scatter`/`gather` & `allgather`, `barrier`, `wtime`
+Support is provided for a subset of MPI routines covering: `size`/`rank`, `send`/`recv`, `allreduce`, `reduce`, `bcast`, `scatter`/`gather` & `allgather`, `barrier`, `wtime`
 and basic asynchronous communication with `isend`/`irecv` (only for contiguous arrays); for request handling including `wait`/`waitall`/`waitany` and `test`/`testall`/`testany`.
 
 The API uses NumPy and supports both numeric and character datatypes (e.g., `broadcast`). 
@@ -45,7 +45,7 @@ Features that are not implemented yet include (help welcome!):
 ```python
 import numba, numba_mpi, numpy
 
-@numba.njit()
+@numba.jit()
 def hello():
     src = numpy.array([1., 2., 3., 4., 5.])
     dst_tst = numpy.empty_like(src)

{numba_mpi-1.0.0 → numba_mpi-1.1.1}/numba_mpi/__init__.py

@@ -13,6 +13,7 @@ from .api.isend import isend
 from .api.operator import Operator
 from .api.rank import rank
 from .api.recv import recv
+from .api.reduce import reduce
 from .api.requests import test, testall, testany, wait, waitall, waitany
 from .api.scatter_gather import allgather, gather, scatter
 from .api.send import send

numba_mpi-1.1.1/numba_mpi/api/reduce.py

@@ -0,0 +1,112 @@
+"""file contains MPI_Reduce() implementations"""
+
+import ctypes
+from numbers import Number
+
+import numpy as np
+from numba.core import types
+from numba.extending import overload
+
+from numba_mpi.common import _MPI_Comm_World_ptr, _MpiComm, _MpiDatatype, _MpiOp, libmpi
+from numba_mpi.utils import _mpi_addr, _mpi_dtype
+
+_MPI_Reduce = libmpi.MPI_Reduce
+_MPI_Reduce.restype = ctypes.c_int
+_MPI_Reduce.argtypes = [
+    ctypes.c_void_p,
+    ctypes.c_void_p,
+    ctypes.c_int,
+    _MpiDatatype,
+    _MpiOp,
+    ctypes.c_int,
+    _MpiComm,
+]
+
+
+def reduce(sendobj, recvobj, operator, root):  # pylint: disable=unused-argument
+    """wrapper for MPI_Reduce
+    Note that complex datatypes and user-defined functions are not properly supported.
+    Returns integer status code (0 == MPI_SUCCESS)
+    """
+    if isinstance(sendobj, Number):
+        # reduce a single number
+        sendobj = np.array([sendobj])
+        status = _MPI_Reduce(
+            sendobj.ctypes.data,
+            recvobj.ctypes.data,
+            sendobj.size,
+            _mpi_dtype(sendobj),
+            _mpi_addr(operator),
+            root,
+            _mpi_addr(_MPI_Comm_World_ptr),
+        )
+
+    elif isinstance(sendobj, np.ndarray):
+        # reduce an array
+        sendobj = np.ascontiguousarray(sendobj)
+        status = _MPI_Reduce(
+            sendobj.ctypes.data,
+            recvobj.ctypes.data,
+            sendobj.size,
+            _mpi_dtype(sendobj),
+            _mpi_addr(operator),
+            root,
+            _mpi_addr(_MPI_Comm_World_ptr),
+        )
+
+    else:
+        raise TypeError(f"Unsupported type {sendobj.__class__.__name__}")
+
+    return status
+
+
+@overload(reduce)
+def ol_reduce(sendobj, recvobj, operator, root):  # pylint: disable=unused-argument
+    """wrapper for MPI_Reduce
+    Note that complex datatypes and user-defined functions are not properly supported.
+    Returns integer status code (0 == MPI_SUCCESS)
+    """
+    if isinstance(sendobj, types.Number):
+        # reduce a single number
+
+        def impl(sendobj, recvobj, operator, root):
+            sendobj = np.array([sendobj])
+
+            status = _MPI_Reduce(
+                sendobj.ctypes.data,
+                recvobj.ctypes.data,
+                sendobj.size,
+                _mpi_dtype(sendobj),
+                _mpi_addr(operator),
+                root,
+                _mpi_addr(_MPI_Comm_World_ptr),
+            )
+
+            # The following no-op prevents numba from too aggressive optimizations
+            # This looks like a bug in numba (tested for version 0.55)
+            sendobj[0]  # pylint: disable=pointless-statement
+
+            return status
+
+    elif isinstance(sendobj, types.Array):
+        # reduce an array
+
+        def impl(sendobj, recvobj, operator, root):
+            sendobj = np.ascontiguousarray(sendobj)
+
+            status = _MPI_Reduce(
+                sendobj.ctypes.data,
+                recvobj.ctypes.data,
+                sendobj.size,
+                _mpi_dtype(sendobj),
+                _mpi_addr(operator),
+                root,
+                _mpi_addr(_MPI_Comm_World_ptr),
+            )
+
+            return status
+
+    else:
+        raise TypeError(f"Unsupported type {sendobj.__class__.__name__}")
+
+    return impl

{numba_mpi-1.0.0 → numba_mpi-1.1.1}/numba_mpi.egg-info/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: numba-mpi
-Version: 1.0.0
-Summary: Numba @njittable MPI wrappers tested on Linux, macOS and Windows
+Version: 1.1.1
+Summary: Numba @jittable MPI wrappers tested on Linux, macOS and Windows
 Home-page: https://github.com/numba-mpi/numba-mpi
 Author: https://github.com/numba-mpi/numba-mpi/graphs/contributors
 License: GPL v3
@@ -19,7 +19,7 @@ Provides-Extra: tests
 Requires-Dist: pytest<8.0.0; extra == "tests"
 Requires-Dist: py-pde; extra == "tests"
 
-# <img src="https://raw.githubusercontent.com/numba-mpi/numba-mpi/main/.github/numba_mpi_logo.svg" style="height:50pt" alt="numba-mpi logo"> numba-mpi
+# <img src="https://raw.githubusercontent.com/numba-mpi/numba-mpi/main/.github/numba_mpi_logo.png" width=128 height=142 alt="numba-mpi logo"> numba-mpi
 
 [![Python 3](https://img.shields.io/static/v1?label=Python&logo=Python&color=3776AB&message=3)](https://www.python.org/)
 [![LLVM](https://img.shields.io/static/v1?label=LLVM&logo=LLVM&color=gold&message=Numba)](https://numba.pydata.org)
@@ -35,9 +35,9 @@ Requires-Dist: py-pde; extra == "tests"
 [![DOI](https://zenodo.org/badge/316911228.svg)](https://zenodo.org/badge/latestdoi/316911228)
 
 ### Overview
-numba-mpi provides Python wrappers to the C MPI API callable from within [Numba JIT-compiled code](https://numba.readthedocs.io/en/stable/user/jit.html) (@njit mode).
+numba-mpi provides Python wrappers to the C MPI API callable from within [Numba JIT-compiled code](https://numba.readthedocs.io/en/stable/user/jit.html) (@jit mode). For an outline of the project, rationale, architecture, and features, refer to: [numba-mpi arXiv e-print](https://doi.org/10.48550/arXiv.2407.13712) (please cite if numba-mpi is used in your research).
 
-Support is provided for a subset of MPI routines covering: `size`/`rank`, `send`/`recv`, `allreduce`, `bcast`, `scatter`/`gather` & `allgather`, `barrier`, `wtime`
+Support is provided for a subset of MPI routines covering: `size`/`rank`, `send`/`recv`, `allreduce`, `reduce`, `bcast`, `scatter`/`gather` & `allgather`, `barrier`, `wtime`
 and basic asynchronous communication with `isend`/`irecv` (only for contiguous arrays); for request handling including `wait`/`waitall`/`waitany` and `test`/`testall`/`testany`.
 
 The API uses NumPy and supports both numeric and character datatypes (e.g., `broadcast`). 
@@ -66,7 +66,7 @@ Features that are not implemented yet include (help welcome!):
 ```python
 import numba, numba_mpi, numpy
 
-@numba.njit()
+@numba.jit()
 def hello():
     src = numpy.array([1., 2., 3., 4., 5.])
     dst_tst = numpy.empty_like(src)

{numba_mpi-1.0.0 → numba_mpi-1.1.1}/numba_mpi.egg-info/SOURCES.txt

@@ -1,10 +1,12 @@
 .gitignore
 .pre-commit-config.yaml
 .zenodo.json
+CITATION.cff
 CODE_OF_CONDUCT.md
 LICENSE
 README.md
 setup.py
+.github/numba_mpi_logo.png
 .github/numba_mpi_logo.svg
 .github/workflows/readme_snippets.yml
 .github/workflows/stale.yml
@@ -28,6 +30,7 @@ numba_mpi/api/isend.py
 numba_mpi/api/operator.py
 numba_mpi/api/rank.py
 numba_mpi/api/recv.py
+numba_mpi/api/reduce.py
 numba_mpi/api/requests.py
 numba_mpi/api/scatter_gather.py
 numba_mpi/api/send.py
@@ -44,6 +47,7 @@ tests/api/test_bcast.py
 tests/api/test_init.py
 tests/api/test_isend_irecv.py
 tests/api/test_rank.py
+tests/api/test_reduce.py
 tests/api/test_scatter_gather.py
 tests/api/test_send_recv.py
 tests/api/test_size.py

{numba_mpi-1.0.0 → numba_mpi-1.1.1}/setup.py

@@ -7,6 +7,9 @@ def get_long_description():
     """returns contents of README.md file"""
     with open("README.md", "r", encoding="utf8") as file:
         long_description = file.read()
+    long_description = long_description.replace(
+        "numba_mpi_logo.svg", "numba_mpi_logo.png"
+    )
     return long_description
 
 
@@ -21,7 +24,7 @@ setup(
     python_requires=">=3.8",
     setup_requires=["setuptools_scm"],
     license="GPL v3",
-    description="Numba @njittable MPI wrappers tested on Linux, macOS and Windows",
+    description="Numba @jittable MPI wrappers tested on Linux, macOS and Windows",
     install_requires=("numba", "numpy", "mpi4py", "psutil"),
     extras_require={"tests": ("pytest<8.0.0", "py-pde")},  # TODO #122
     long_description=get_long_description(),

numba_mpi-1.1.1/tests/api/test_reduce.py

@@ -0,0 +1,54 @@
+# pylint: disable=missing-function-docstring,missing-class-docstring,missing-module-docstring
+import numpy as np
+import pytest
+from numba import njit
+
+import numba_mpi as mpi
+from tests.common import data_types_real
+from tests.utils import get_random_array
+
+
+@njit
+def jit_reduce(sendobj, recvobj, operator, root):
+    """helper function to produce a jitted version of `reduce`"""
+    return mpi.reduce(sendobj, recvobj, operator, root)
+
+
+@pytest.mark.parametrize("reduce", (mpi.reduce, jit_reduce))
+@pytest.mark.parametrize(
+    "op_mpi, op_np",
+    (
+        (mpi.Operator.SUM, np.sum),
+        (mpi.Operator.MIN, np.min),
+        (mpi.Operator.MAX, np.max),
+    ),
+)
+@pytest.mark.parametrize("data_type", data_types_real)
+@pytest.mark.parametrize("root", range(mpi.size()))
+def test_reduce(reduce, op_mpi, op_np, data_type, root):
+    # test arrays
+    src = get_random_array((3,), data_type)
+    rcv = np.empty_like(src)
+    status = reduce(src, rcv, operator=op_mpi, root=root)
+    assert status == mpi.SUCCESS
+    if mpi.rank() == root:
+        expect = op_np(np.tile(src, [mpi.size(), 1]), axis=0)
+        np.testing.assert_equal(rcv, expect)
+
+    # test scalars
+    src = src[0]
+    rcv = np.empty(1, dtype=src.dtype)
+    status = reduce(src, rcv, operator=op_mpi, root=root)
+    assert status == mpi.SUCCESS
+    if mpi.rank() == root:
+        expect = op_np(np.tile(src, [mpi.size(), 1]), axis=0)
+        np.testing.assert_equal(rcv, expect)
+
+    # test 0d arrays
+    src = get_random_array((), data_type)
+    rcv = np.empty_like(src)
+    status = reduce(src, rcv, operator=op_mpi, root=root)
+    assert status == mpi.SUCCESS
+    if mpi.rank() == root:
+        expect = op_np(np.tile(src, [mpi.size(), 1]), axis=0)
+        np.testing.assert_equal(rcv, expect)