numba-mpi 0.43__tar.gz → 1.0.1__tar.gz

{numba_mpi-0.43 → numba_mpi-1.0.1}/.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')
+        pylint --unsafe-load-any-extension=y --disable=fixme $(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:

{numba_mpi-0.43 → numba_mpi-1.0.1}/.pre-commit-config.yaml

@@ -7,12 +7,14 @@ repos:
     rev: 24.1.1
     hooks:
       - id: black
+        exclude: ^tests/paper_listings/
 
   - repo: https://github.com/timothycrosley/isort
     rev: 5.13.2
     hooks:
       - id: isort
         args: ["--profile", "black"]
+        exclude: ^tests/paper_listings/
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
@@ -20,3 +22,4 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: debug-statements
+        exclude: ^tests/paper_listings/

{numba_mpi-0.43 → numba_mpi-1.0.1}/.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-1.0.1/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: "10.48550/arXiv.2407.13712"
+  journal: "arXiv"
+  title: " Enabling MPI communication within Numba/LLVM JIT-compiled Python code using numba-mpi v1.0 "
+  year: 2024

{numba_mpi-0.43/numba_mpi.egg-info → numba_mpi-1.0.1}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: numba-mpi
-Version: 0.43
-Summary: Numba @njittable MPI wrappers tested on Linux, macOS and Windows
+Version: 1.0.1
+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
@@ -17,8 +17,9 @@ Requires-Dist: mpi4py
 Requires-Dist: psutil
 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)
@@ -34,7 +35,7 @@ Requires-Dist: pytest<8.0.0; 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`
 and basic asynchronous communication with `isend`/`irecv` (only for contiguous arrays); for request handling including `wait`/`waitall`/`waitany` and `test`/`testall`/`testany`.
@@ -65,7 +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)
@@ -168,6 +169,7 @@ if numba_mpi.rank() == 0:
     - Intel MPI: https://intel.com/content/www/us/en/developer/tools/oneapi/mpi-library-documentation.html
 - MPI bindings:
     - Python: https://mpi4py.readthedocs.io
+    - Python/JAX: https://mpi4jax.readthedocs.io
     - Julia: https://juliaparallel.org/MPI.jl
     - Rust: https://docs.rs/mpi
     - C++: https://boost.org/doc/html/mpi.html
@@ -175,5 +177,11 @@ if numba_mpi.rank() == 0:
 
 ### Acknowledgements:
 
-Development of numba-mpi has been supported by the [Polish National Science Centre](https://ncn.gov.pl/en) (grant no. 2020/39/D/ST10/01220).
+We thank [all contributors](https://github.com/numba-mpi/numba-mpi/graphs/contributors) and users who reported feedback to the project 
+  through [GitHub issues](https://github.com/numba-mpi/numba-mpi/issues).
+
+Development of numba-mpi has been supported by the [Polish National Science Centre](https://ncn.gov.pl/en) (grant no. 2020/39/D/ST10/01220),
+  the [Max Planck Society](https://www.mpg.de/en) and the [European Union](https://erc.europa.eu/) (ERC, EmulSim, 101044662). 
+We further acknowledge Poland’s high-performance computing infrastructure [PLGrid](https://plgrid.pl) (HPC Centers: [ACK Cyfronet AGH](https://www.cyfronet.pl/en)) 
+  for providing computer facilities and support within computational grant no. PLG/2023/016369.
 

numba_mpi-0.43/PKG-INFO → numba_mpi-1.0.1/README.md

@@ -1,24 +1,4 @@
-Metadata-Version: 2.1
-Name: numba-mpi
-Version: 0.43
-Summary: Numba @njittable 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
-Project-URL: Tracker, https://github.com/numba-mpi/numba-mpi/issues
-Project-URL: Documentation, https://numba-mpi.github.io/numba-mpi
-Project-URL: Source, https://github.com/numba-mpi/numba-mpi
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numba
-Requires-Dist: numpy
-Requires-Dist: mpi4py
-Requires-Dist: psutil
-Provides-Extra: tests
-Requires-Dist: pytest<8.0.0; 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.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)
@@ -34,7 +14,7 @@ Requires-Dist: pytest<8.0.0; 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`
 and basic asynchronous communication with `isend`/`irecv` (only for contiguous arrays); for request handling including `wait`/`waitall`/`waitany` and `test`/`testall`/`testany`.
@@ -65,7 +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)
@@ -168,6 +148,7 @@ if numba_mpi.rank() == 0:
     - Intel MPI: https://intel.com/content/www/us/en/developer/tools/oneapi/mpi-library-documentation.html
 - MPI bindings:
     - Python: https://mpi4py.readthedocs.io
+    - Python/JAX: https://mpi4jax.readthedocs.io
     - Julia: https://juliaparallel.org/MPI.jl
     - Rust: https://docs.rs/mpi
     - C++: https://boost.org/doc/html/mpi.html
@@ -175,5 +156,11 @@ if numba_mpi.rank() == 0:
 
 ### Acknowledgements:
 
-Development of numba-mpi has been supported by the [Polish National Science Centre](https://ncn.gov.pl/en) (grant no. 2020/39/D/ST10/01220).
+We thank [all contributors](https://github.com/numba-mpi/numba-mpi/graphs/contributors) and users who reported feedback to the project 
+  through [GitHub issues](https://github.com/numba-mpi/numba-mpi/issues).
+
+Development of numba-mpi has been supported by the [Polish National Science Centre](https://ncn.gov.pl/en) (grant no. 2020/39/D/ST10/01220),
+  the [Max Planck Society](https://www.mpg.de/en) and the [European Union](https://erc.europa.eu/) (ERC, EmulSim, 101044662). 
+We further acknowledge Poland’s high-performance computing infrastructure [PLGrid](https://plgrid.pl) (HPC Centers: [ACK Cyfronet AGH](https://www.cyfronet.pl/en)) 
+  for providing computer facilities and support within computational grant no. PLG/2023/016369.
 

{numba_mpi-0.43 → numba_mpi-1.0.1}/numba_mpi/__init__.py

@@ -20,6 +20,8 @@ from .api.size import size
 from .api.wtime import wtime
 from .common import RequestType
 
+SUCCESS = 0
+
 try:
     __version__ = version(__name__)
 except PackageNotFoundError:

{numba_mpi-0.43 → numba_mpi-1.0.1}/numba_mpi/api/initialized.py

@@ -17,5 +17,6 @@ def initialized():
     """wrapper for MPI_Initialized()"""
     flag = np.empty((1,), dtype=np.intc)
     status = _MPI_Initialized(flag.ctypes.data)
-    assert status == 0
+    if status != 0:
+        return False
     return bool(flag[0])

{numba_mpi-0.43 → numba_mpi-1.0.1}/numba_mpi/api/rank.py

@@ -15,8 +15,9 @@ _MPI_Comm_rank.argtypes = [_MpiComm, ctypes.c_void_p]
 
 @numba.njit()
 def rank():
-    """wrapper for MPI_Comm_rank()"""
+    """wrapper for MPI_Comm_rank(), in case of failure returns 0"""
     value = np.empty(1, dtype=np.intc)
     status = _MPI_Comm_rank(_mpi_addr(_MPI_Comm_World_ptr), value.ctypes.data)
-    assert status == 0
+    if status != 0:
+        value[0] = 0
     return value[0]

{numba_mpi-0.43 → numba_mpi-1.0.1}/numba_mpi/api/size.py

@@ -15,8 +15,9 @@ _MPI_Comm_size.argtypes = [_MpiComm, ctypes.c_void_p]
 
 @numba.njit()
 def size():
-    """wrapper for MPI_Comm_size()"""
+    """wrapper for MPI_Comm_size(), in case of failure returns 0"""
     value = np.empty(1, dtype=np.intc)
     status = _MPI_Comm_size(_mpi_addr(_MPI_Comm_World_ptr), value.ctypes.data)
-    assert status == 0
+    if status != 0:
+        value[0] = 0
     return value[0]

numba_mpi-0.43/README.md → numba_mpi-1.0.1/numba_mpi.egg-info/PKG-INFO

@@ -1,4 +1,25 @@
-# <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
+Metadata-Version: 2.1
+Name: numba-mpi
+Version: 1.0.1
+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
+Project-URL: Tracker, https://github.com/numba-mpi/numba-mpi/issues
+Project-URL: Documentation, https://numba-mpi.github.io/numba-mpi
+Project-URL: Source, https://github.com/numba-mpi/numba-mpi
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numba
+Requires-Dist: numpy
+Requires-Dist: mpi4py
+Requires-Dist: psutil
+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.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)
@@ -14,7 +35,7 @@
 [![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`
 and basic asynchronous communication with `isend`/`irecv` (only for contiguous arrays); for request handling including `wait`/`waitall`/`waitany` and `test`/`testall`/`testany`.
@@ -45,7 +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)
@@ -148,6 +169,7 @@ if numba_mpi.rank() == 0:
     - Intel MPI: https://intel.com/content/www/us/en/developer/tools/oneapi/mpi-library-documentation.html
 - MPI bindings:
     - Python: https://mpi4py.readthedocs.io
+    - Python/JAX: https://mpi4jax.readthedocs.io
     - Julia: https://juliaparallel.org/MPI.jl
     - Rust: https://docs.rs/mpi
     - C++: https://boost.org/doc/html/mpi.html
@@ -155,5 +177,11 @@ if numba_mpi.rank() == 0:
 
 ### Acknowledgements:
 
-Development of numba-mpi has been supported by the [Polish National Science Centre](https://ncn.gov.pl/en) (grant no. 2020/39/D/ST10/01220).
+We thank [all contributors](https://github.com/numba-mpi/numba-mpi/graphs/contributors) and users who reported feedback to the project 
+  through [GitHub issues](https://github.com/numba-mpi/numba-mpi/issues).
+
+Development of numba-mpi has been supported by the [Polish National Science Centre](https://ncn.gov.pl/en) (grant no. 2020/39/D/ST10/01220),
+  the [Max Planck Society](https://www.mpg.de/en) and the [European Union](https://erc.europa.eu/) (ERC, EmulSim, 101044662). 
+We further acknowledge Poland’s high-performance computing infrastructure [PLGrid](https://plgrid.pl) (HPC Centers: [ACK Cyfronet AGH](https://www.cyfronet.pl/en)) 
+  for providing computer facilities and support within computational grant no. PLG/2023/016369.
 

{numba_mpi-0.43 → numba_mpi-1.0.1}/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
@@ -35,6 +37,7 @@ numba_mpi/api/size.py
 numba_mpi/api/wtime.py
 tests/__init__.py
 tests/common.py
+tests/test_paper_listings.py
 tests/test_version.py
 tests/utils.py
 tests/api/test_allreduce.py
@@ -46,4 +49,11 @@ tests/api/test_rank.py
 tests/api/test_scatter_gather.py
 tests/api/test_send_recv.py
 tests/api/test_size.py
-tests/api/test_wtime.py
+tests/api/test_wtime.py
+tests/paper_listings/exchange.py
+tests/paper_listings/hello.py
+tests/paper_listings/mpi4py_with_error.py
+tests/paper_listings/numba_mpi.py
+tests/paper_listings/py-pde.py
+tests/paper_listings/test.py
+tests/paper_listings/timing.py

{numba_mpi-0.43 → numba_mpi-1.0.1}/numba_mpi.egg-info/requires.txt

@@ -5,3 +5,4 @@ psutil
 
 [tests]
 pytest<8.0.0
+py-pde

{numba_mpi-0.43 → numba_mpi-1.0.1}/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
 
 
@@ -21,9 +24,9 @@ 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")},  # TODO #122
+    extras_require={"tests": ("pytest<8.0.0", "py-pde")},  # TODO #122
     long_description=get_long_description(),
     long_description_content_type="text/markdown",
     packages=find_packages(include=["numba_mpi", "numba_mpi.*"]),

{numba_mpi-0.43 → numba_mpi-1.0.1}/tests/api/test_allreduce.py

@@ -4,7 +4,7 @@ import pytest
 from numba import njit
 
 import numba_mpi as mpi
-from tests.common import MPI_SUCCESS, data_types_real
+from tests.common import data_types_real
 from tests.utils import get_random_array
 
 
@@ -29,7 +29,7 @@ def test_allreduce(allreduce, op_mpi, op_np, data_type):
     src = get_random_array((3,), data_type)
     rcv = np.empty_like(src)
     status = allreduce(src, rcv, operator=op_mpi)
-    assert status == MPI_SUCCESS
+    assert status == mpi.SUCCESS
     expect = op_np(np.tile(src, [mpi.size(), 1]), axis=0)
     np.testing.assert_equal(rcv, expect)
 
@@ -37,7 +37,7 @@ def test_allreduce(allreduce, op_mpi, op_np, data_type):
     src = src[0]
     rcv = np.empty(1, dtype=src.dtype)
     status = allreduce(src, rcv, operator=op_mpi)
-    assert status == MPI_SUCCESS
+    assert status == mpi.SUCCESS
     expect = op_np(np.tile(src, [mpi.size(), 1]), axis=0)
     np.testing.assert_equal(rcv, expect)
 
@@ -45,6 +45,6 @@ def test_allreduce(allreduce, op_mpi, op_np, data_type):
     src = get_random_array((), data_type)
     rcv = np.empty_like(src)
     status = allreduce(src, rcv, operator=op_mpi)
-    assert status == MPI_SUCCESS
+    assert status == mpi.SUCCESS
     expect = op_np(np.tile(src, [mpi.size(), 1]), axis=0)
     np.testing.assert_equal(rcv, expect)

{numba_mpi-0.43 → numba_mpi-1.0.1}/tests/api/test_barrier.py

@@ -3,7 +3,6 @@ import numba
 import pytest
 
 import numba_mpi
-from tests.common import MPI_SUCCESS
 
 
 @numba.njit()
@@ -15,4 +14,4 @@ def jit_barrier():
 def test_barrier(barrier):
     status = barrier()
 
-    assert status == MPI_SUCCESS
+    assert status == numba_mpi.SUCCESS

{numba_mpi-0.43 → numba_mpi-1.0.1}/tests/api/test_bcast.py

@@ -4,7 +4,7 @@ import numpy as np
 import pytest
 
 import numba_mpi as mpi
-from tests.common import MPI_SUCCESS, data_types
+from tests.common import data_types
 from tests.utils import get_random_array
 
 
@@ -25,7 +25,7 @@ def test_bcast_np_array(data_type, bcast):
 
     status = bcast(data, root)
 
-    assert status == MPI_SUCCESS
+    assert status == mpi.SUCCESS
 
     np.testing.assert_equal(data, datatobcast)
 
@@ -43,5 +43,5 @@ def test_bcast_string(stringtobcast):
         data = datatobcast
 
     status = mpi.bcast(data, root)
-    assert status == MPI_SUCCESS
+    assert status == mpi.SUCCESS
     assert str(data) == str(datatobcast)

{numba_mpi-0.43 → numba_mpi-1.0.1}/tests/api/test_isend_irecv.py

@@ -7,7 +7,7 @@ import pytest
 from mpi4py.MPI import ANY_SOURCE, ANY_TAG, COMM_WORLD
 
 import numba_mpi as mpi
-from tests.common import MPI_SUCCESS, data_types
+from tests.common import data_types
 from tests.utils import get_random_array
 
 TEST_WAIT_FULL_IN_SECONDS = 0.3
@@ -69,23 +69,23 @@ def test_isend_irecv(isnd, ircv, wait, data_type):
 
     if mpi.rank() == 0:
         status, req = isnd(src, dest=1, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         req_exp = COMM_WORLD.Isend(src, dest=1, tag=22)
 
         status = wait(req)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         req_exp.wait()
 
     elif mpi.rank() == 1:
         status, req = ircv(dst_tst, source=0, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         req_exp = COMM_WORLD.Irecv(dst_exp, source=0, tag=22)
 
         status = wait(req)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         req_exp.wait()
 
@@ -106,11 +106,11 @@ def test_send_default_tag(isnd, ircv, wait):
 
     if mpi.rank() == 0:
         status, req = isnd(src, dest=1)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         wait(req)
     elif mpi.rank() == 1:
         status, req = ircv(dst_tst, source=0, tag=0)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         wait(req)
 
         np.testing.assert_equal(dst_tst, src)
@@ -129,11 +129,11 @@ def test_recv_default_tag(isnd, ircv, wait):
 
     if mpi.rank() == 0:
         status, req = isnd(src, dest=1, tag=44)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         wait(req)
     elif mpi.rank() == 1:
         status, req = ircv(dst_tst, source=0)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         wait(req)
 
         np.testing.assert_equal(dst_tst, src)
@@ -152,11 +152,11 @@ def test_recv_default_source(isnd, ircv, wait):
 
     if mpi.rank() == 0:
         status, req = isnd(src, dest=1, tag=44)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         wait(req)
     elif mpi.rank() == 1:
         status, req = ircv(dst_tst, tag=44)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         wait(req)
 
         np.testing.assert_equal(dst_tst, src)
@@ -179,21 +179,21 @@ def test_isend_irecv_waitall(isnd, ircv, wall, data_type):
     reqs = np.zeros((2,), dtype=mpi.RequestType)
     if mpi.rank() == 0:
         status, reqs[0:1] = isnd(src1, dest=1, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, reqs[1:2] = isnd(src2, dest=1, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         status = wall(reqs)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
     elif mpi.rank() == 1:
         status, reqs[0:1] = ircv(dst1, source=0, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, reqs[1:2] = ircv(dst2, source=0, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         status = wall(reqs)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         np.testing.assert_equal(dst1, src1)
         np.testing.assert_equal(dst2, src2)
@@ -214,21 +214,21 @@ def test_isend_irecv_waitall_tuple(isnd, ircv, wall):
 
     if mpi.rank() == 0:
         status, req_1 = isnd(src1, dest=1, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, req_2 = isnd(src2, dest=1, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         status = wall((req_1, req_2))
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
     elif mpi.rank() == 1:
         status, req_1 = ircv(dst1, source=0, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, req_2 = ircv(dst2, source=0, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         status = wall((req_1, req_2))
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         np.testing.assert_equal(dst1, src1)
         np.testing.assert_equal(dst2, src2)
@@ -248,15 +248,15 @@ def test_isend_irecv_waitall_exchange(isnd, ircv, wall):
     reqs = np.zeros((2,), dtype=mpi.RequestType)
     if mpi.rank() == 0:
         status, reqs[0:1] = isnd(src, dest=1, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, reqs[1:2] = ircv(dst, source=1, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
     elif mpi.rank() == 1:
         status, reqs[0:1] = isnd(src, dest=0, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, reqs[1:2] = ircv(dst, source=0, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
     wall(reqs)
 
@@ -303,19 +303,19 @@ def test_isend_irecv_waitany(isnd, ircv, wany, wall, data_type):
     reqs = np.zeros((2,), dtype=mpi.RequestType)
     if mpi.rank() == 0:
         status, reqs[0:1] = isnd(src1, dest=1, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, reqs[1:2] = isnd(src2, dest=1, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         wall(reqs)
 
     elif mpi.rank() == 1:
         status, reqs[0:1] = ircv(dst1, source=0, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, reqs[1:2] = ircv(dst2, source=0, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         status, index = wany(reqs)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         if index == 0:
             np.testing.assert_equal(dst1, src1)
@@ -341,14 +341,14 @@ def test_isend_irecv_test(isnd, ircv, tst, wait):
     if mpi.rank() == 0:
         time.sleep(TEST_WAIT_FULL_IN_SECONDS)
         status, req = isnd(src, dest=1, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         wait(req)
     elif mpi.rank() == 1:
         status, req = ircv(dst, source=0, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         status, flag = tst(req)
-        while status == MPI_SUCCESS and not flag:
+        while status == mpi.SUCCESS and not flag:
             time.sleep(TEST_WAIT_INCREMENT_IN_SECONDS)
             status, flag = tst(req)
 
@@ -379,20 +379,20 @@ def test_isend_irecv_testall(isnd, ircv, tall, wall):
         time.sleep(TEST_WAIT_FULL_IN_SECONDS)
 
         status, reqs[0:1] = isnd(src1, dest=1, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, reqs[1:2] = isnd(src2, dest=1, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         wall(reqs)
 
     elif mpi.rank() == 1:
         status, reqs[0:1] = ircv(dst1, source=0, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, reqs[1:2] = ircv(dst2, source=0, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         status, flag = tall(reqs)
-        while status == MPI_SUCCESS and not flag:
+        while status == mpi.SUCCESS and not flag:
             time.sleep(TEST_WAIT_INCREMENT_IN_SECONDS)
             status, flag = tall(reqs)
 
@@ -425,20 +425,20 @@ def test_isend_irecv_testany(isnd, ircv, tany, wall):
         time.sleep(TEST_WAIT_FULL_IN_SECONDS)
 
         status, reqs[0:1] = isnd(src1, dest=1, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, reqs[1:2] = isnd(src2, dest=1, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         wall(reqs)
 
     elif mpi.rank() == 1:
         status, reqs[0:1] = ircv(dst1, source=0, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         status, reqs[1:2] = ircv(dst2, source=0, tag=22)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         status, flag, index = tany(reqs)
-        while status == MPI_SUCCESS and not flag:
+        while status == mpi.SUCCESS and not flag:
             time.sleep(TEST_WAIT_INCREMENT_IN_SECONDS)
             status, flag, index = tany(reqs)
 

{numba_mpi-0.43 → numba_mpi-1.0.1}/tests/api/test_scatter_gather.py

@@ -4,7 +4,7 @@ import numpy as np
 import pytest
 
 import numba_mpi as mpi
-from tests.common import MPI_SUCCESS, data_types
+from tests.common import data_types
 from tests.utils import get_random_array
 
 
@@ -41,7 +41,7 @@ def test_scatter(data_type, scatter, send_count, data_size):
     recv_data = np.empty(send_count, data_type).astype(dtype=data_type)
     status = scatter(send_data, recv_data, send_count, root)
 
-    assert status == MPI_SUCCESS
+    assert status == mpi.SUCCESS
     np.testing.assert_equal(
         recv_data, data[rank * send_count : (rank + 1) * send_count]
     )
@@ -71,7 +71,7 @@ def test_gather(data_type, gather, recv_count, data_size):
 
     status = gather(send_data, recv_data, recv_count, root)
 
-    assert status == MPI_SUCCESS
+    assert status == mpi.SUCCESS
     valid_range = slice(0, mpi.size() * recv_count)
     if rank == root:
         np.testing.assert_equal(data[valid_range], recv_data[valid_range])
@@ -98,6 +98,6 @@ def test_allgather(data_type, allgather, recv_count, data_size):
 
     status = allgather(send_data, recv_data, recv_count)
 
-    assert status == MPI_SUCCESS
+    assert status == mpi.SUCCESS
     valid_range = slice(0, mpi.size() * recv_count)
     np.testing.assert_equal(data[valid_range], recv_data[valid_range])

{numba_mpi-0.43 → numba_mpi-1.0.1}/tests/api/test_send_recv.py

@@ -4,7 +4,7 @@ import pytest
 from mpi4py.MPI import COMM_WORLD
 
 import numba_mpi as mpi
-from tests.common import MPI_SUCCESS, data_types
+from tests.common import data_types
 from tests.utils import get_random_array
 
 
@@ -26,11 +26,11 @@ def test_send_recv(snd, rcv, fortran_order, data_type):
 
     if mpi.rank() == 0:
         status = snd(src, dest=1, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         COMM_WORLD.Send(src, dest=1, tag=22)
     elif mpi.rank() == 1:
         status = rcv(dst_tst, source=0, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
         COMM_WORLD.Recv(dst_exp, source=0, tag=22)
 
         np.testing.assert_equal(dst_tst, src)
@@ -47,10 +47,10 @@ def test_send_recv_noncontiguous(snd, rcv, data_type):
 
     if mpi.rank() == 0:
         status = snd(src[::2], dest=1, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
     elif mpi.rank() == 1:
         status = rcv(dst_tst[::2], source=0, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         np.testing.assert_equal(dst_tst[1::2], 0)
         np.testing.assert_equal(dst_tst[::2], src[::2])
@@ -66,10 +66,10 @@ def test_send_0d_arrays(snd, rcv, data_type):
 
     if mpi.rank() == 0:
         status = snd(src, dest=1, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
     elif mpi.rank() == 1:
         status = rcv(dst_tst, source=0, tag=11)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         np.testing.assert_equal(dst_tst, src)
 
@@ -83,10 +83,10 @@ def test_send_default_tag(snd, rcv):
 
     if mpi.rank() == 0:
         status = snd(src, dest=1)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
     elif mpi.rank() == 1:
         status = rcv(dst_tst, source=0, tag=0)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         np.testing.assert_equal(dst_tst, src)
 
@@ -100,10 +100,10 @@ def test_recv_default_tag(snd, rcv):
 
     if mpi.rank() == 0:
         status = snd(src, dest=1, tag=44)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
     elif mpi.rank() == 1:
         status = rcv(dst_tst, source=0)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         np.testing.assert_equal(dst_tst, src)
 
@@ -117,9 +117,9 @@ def test_recv_default_source(snd, rcv):
 
     if mpi.rank() == 0:
         status = snd(src, dest=1, tag=44)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
     elif mpi.rank() == 1:
         status = rcv(dst_tst, tag=44)
-        assert status == MPI_SUCCESS
+        assert status == mpi.SUCCESS
 
         np.testing.assert_equal(dst_tst, src)

{numba_mpi-0.43 → numba_mpi-1.0.1}/tests/common.py

@@ -1,8 +1,6 @@
 # pylint: disable=missing-function-docstring,missing-class-docstring,missing-module-docstring
 import numpy as np
 
-MPI_SUCCESS = 0
-
 data_types_real = [
     int,
     np.int32,

numba_mpi-1.0.1/tests/paper_listings/exchange.py

@@ -0,0 +1,26 @@
+import numpy as np
+import numba_mpi as mpi
+import numba
+
+@numba.jit(nopython=True)
+def exchange_data(src_data):
+    dst_data = np.empty_like(src_data)
+    reqs = np.zeros((2,), dtype=mpi.RequestType)
+
+    if mpi.rank() == 0:
+        status, reqs[0:1] = mpi.isend(src_data, dest=1, tag=11)
+        assert status == mpi.SUCCESS
+        status, reqs[1:2] = mpi.irecv(dst_data, source=1, tag=22)
+        assert status == mpi.SUCCESS
+    elif mpi.rank() == 1:
+        status, reqs[0:1] = mpi.isend(src_data, dest=0, tag=22)
+        assert status == mpi.SUCCESS
+        status, reqs[1:2] = mpi.irecv(dst_data, source=0, tag=11)
+        assert status == mpi.SUCCESS
+
+    mpi.waitall(reqs)
+    return dst_data
+
+if mpi.rank() < 2:
+    src_data = np.random.rand(10000)
+    dst_data = exchange_data(src_data)

numba_mpi-1.0.1/tests/paper_listings/hello.py

@@ -0,0 +1,13 @@
+import numba, timeit
+
+@numba.jit(nopython=True)
+def get_pi_part(n_intervals=1000000, rank=0, size=1):
+    h = 1 / n_intervals
+    partial_sum = 0.0
+    for i in range(rank + 1, n_intervals, size):
+        x = h * (i - 0.5)
+        partial_sum += 4 / (1 + x**2)
+    return h * partial_sum
+
+time = lambda fun: min(timeit.repeat(fun, number=1, repeat=5))
+print(f"speedup: {time(get_pi_part.py_func) / time(get_pi_part):.3g}")

numba_mpi-1.0.1/tests/paper_listings/mpi4py_with_error.py

@@ -0,0 +1,19 @@
+import mpi4py, numba, numpy as np
+
+N_TIMES = 10000
+RTOL = 1e-3
+
+def pi_mpi4py(n_intervals):
+    pi = np.array([0.])
+    part = np.empty_like(pi)
+    for _ in range(N_TIMES):
+        part[0] = get_pi_part(n_intervals,
+            mpi4py.MPI.COMM_WORLD.rank, mpi4py.MPI.COMM_WORLD.size)
+        mpi4py.MPI.COMM_WORLD.Allreduce(part,
+            (pi, mpi4py.MPI.DOUBLE), op=mpi4py.MPI.SUM)
+        assert abs(pi[0] - np.pi) / np.pi < RTOL
+
+try:
+    numba.jit(pi_mpi4py, nopython=True)(1)
+except Exception as ex:
+    print(ex)

numba_mpi-1.0.1/tests/paper_listings/numba_mpi.py

@@ -0,0 +1,10 @@
+import numba_mpi
+
+@numba.jit(nopython=True)
+def pi_numba_mpi(n_intervals):
+    pi = np.array([0.])
+    part = np.empty_like(pi)
+    for _ in range(N_TIMES):
+        part[0] = get_pi_part(n_intervals, numba_mpi.rank(), numba_mpi.size())
+        numba_mpi.allreduce(part, pi, numba_mpi.Operator.SUM)
+        assert abs(pi[0] - np.pi) / np.pi < RTOL

numba_mpi-1.0.1/tests/paper_listings/py-pde.py

@@ -0,0 +1,13 @@
+import pde
+
+grid = pde.UnitGrid([16, 16])
+state = pde.ScalarField.random_uniform(grid, 0.49, 0.51)
+eq = pde.PDE({"c": "laplace(c**3-c-laplace(c))-0.01*(c-0.5)"})
+
+final_state = eq.solve(
+    state,
+    t_range=1e4,
+    adaptive=True,
+    solver="explicit_mpi",
+    decomposition=[2, -1],
+)

numba_mpi-1.0.1/tests/paper_listings/test.py

@@ -0,0 +1,31 @@
+import numpy as np
+import pytest
+import numba_mpi as mpi
+from tests.common import data_types
+from tests.utils import get_random_array
+
+@pytest.mark.parametrize("snd, rcv", (
+    (mpi.send, mpi.recv),
+    (mpi.send.py_func, mpi.recv.py_func))
+)
+@pytest.mark.parametrize("fortran_order", [True, False])
+@pytest.mark.parametrize("data_type", data_types)
+def test_send_recv(snd, rcv, fortran_order, data_type):
+    src = get_random_array((3, 3), data_type)
+    if fortran_order:
+        src = np.asfortranarray(src, dtype=data_type)
+    else:
+        src = src.astype(dtype=data_type)
+    dst_exp = np.empty_like(src)
+    dst_tst = np.empty_like(src)
+
+    if mpi.rank() == 0:
+        status = snd(src, dest=1, tag=11)
+        assert status == mpi.SUCCESS
+        COMM_WORLD.Send(src, dest=1, tag=22)
+    elif mpi.rank() == 1:
+        status = rcv(dst_tst, source=0, tag=11)
+        assert status == mpi.SUCCESS
+        COMM_WORLD.Recv(dst_exp, source=0, tag=22)
+        np.testing.assert_equal(dst_tst, src)
+        np.testing.assert_equal(dst_exp, src)

numba_mpi-1.0.1/tests/paper_listings/timing.py

@@ -0,0 +1,19 @@
+from matplotlib import pyplot
+
+plot_x = [x for x in range(1, 11)]
+plot_y = {'numba_mpi': [], 'mpi4py': []}
+for x in plot_x:
+    for impl in plot_y:
+        plot_y[impl].append(min(timeit.repeat(
+            f"pi_{impl}(n_intervals={N_TIMES // x})",
+            globals=locals(),
+            number=1,
+            repeat=10
+        )))
+
+if numba_mpi.rank() == 0:
+    pyplot.plot(
+        plot_x,
+        np.array(plot_y['mpi4py'])/np.array(plot_y['numba_mpi']),
+        marker='o'
+    )

numba_mpi-1.0.1/tests/test_paper_listings.py

@@ -0,0 +1,37 @@
+""" checks if listings from the paper run OK """
+
+import pathlib
+
+import pytest
+
+import numba_mpi
+
+
+@pytest.mark.parametrize(
+    "files",
+    (
+        ("hello.py", "mpi4py_with_error.py", "numba_mpi.py", "timing.py"),
+        ("exchange.py",),
+        ("test.py",),
+        pytest.param(
+            ("py-pde.py",),
+            marks=pytest.mark.skipif(numba_mpi.size() != 2, reason="hardcoded"),
+        ),
+    ),
+)
+@pytest.mark.skipif(numba_mpi.size() == 1, reason="listings assume more than 1 worker")
+def test_paper_listings(files):
+    """concatenates code from all files and executes it in global scope"""
+    code = ""
+    for file in files:
+        with open(
+            pathlib.Path(__file__).parent / "paper_listings" / file, encoding="utf-8"
+        ) as stream:
+            code += "".join(stream.readlines())
+        code += "\n"
+    try:
+        exec(code, globals())  # pylint: disable=exec-used
+    except Exception as ex:
+        for line_num, line in enumerate(code.split("\n"), start=1):
+            print(line_num, ":", line)
+        raise ex