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.flake8
View file @ 5600b6b6
[flake8]
max-line-length=120
exclude=pystencils/jupyter.py,
pystencils/plot.py
pystencils/session.py
exclude=src/pystencils/jupyter.py,
src/pystencils/plot.py
src/pystencils/session.py
ignore = W293 W503 W291 C901 E741
.gitattributes
View file @ 5600b6b6
pystencils/_version.py export-subst
src/pystencils/_version.py export-subst
.gitignore
View file @ 5600b6b6
......@@ -5,7 +5,7 @@ __pycache__
*.vti
/build
/dist
/*.egg-info
*.egg-info
.cache
_build
/html_doc
......@@ -15,15 +15,16 @@ _build
_local_tmp
RELEASE-VERSION
test-report
pystencils/boundaries/createindexlistcython.c
pystencils/boundaries/createindexlistcython.*.so
pystencils_tests/tmp
pystencils_tests/var
pystencils_tests/kerncraft_inputs/.2d-5pt.c_kerncraft/
pystencils_tests/kerncraft_inputs/.3d-7pt.c_kerncraft/
src/pystencils/boundaries/createindexlistcython.c
src/pystencils/boundaries/createindexlistcython.*.so
tests/tmp
tests/var
tests/kerncraft_inputs/.2d-5pt.c_kerncraft/
tests/kerncraft_inputs/.3d-7pt.c_kerncraft/
report.xml
coverage_report/
# macOS
**/.DS_Store
*.uuid
.gitlab-ci.yml
View file @ 5600b6b6
stages:
- pretest
- test
- nightly
- docs
- deploy
# -------------------------- Templates ------------------------------------------------------------------------------------
# Base configuration for jobs meant to run at every commit
.every-commit:
rules:
- if: $CI_PIPELINE_SOURCE != "schedule"
# Configuration for jobs meant to run on each commit to pycodegen/pystencils/master
.every-commit-master:
rules:
- if: '$CI_PIPELINE_SOURCE != "schedule" && $CI_PROJECT_PATH == "pycodegen/pystencils" && $CI_COMMIT_BRANCH == "master"'
# Base configuration for jobs meant to run at a schedule
.scheduled:
rules:
- if: $CI_PIPELINE_SOURCE == "schedule"
# -------------------------- Tests ------------------------------------------------------------------------------------
# Normal test - runs on every commit all but "long run" tests
tests-and-coverage:
stage: pretest
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
before_script:
- pip install -e .
script:
- pip install sympy --upgrade
- env
- pip list
- export NUM_CORES=$(nproc --all)
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- mkdir public
- py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. -m "not longrun" --html test-report/index.html --junitxml=report.xml
- python3 -m coverage xml
- pytest -v -n $NUM_CORES --cov-report html --cov-report xml --cov-report term --cov=. -m "not longrun" --html test-report/index.html --junitxml=report.xml
- python -m coverage xml
tags:
- docker
- cuda11
- AVX
coverage: /Total coverage:\s\d+.\d+\%/
artifacts:
when: always
paths:
- coverage_report
- test-report
reports:
cobertura: coverage.xml
coverage_report:
coverage_format: cobertura
path: coverage.xml
junit: report.xml
# pipeline with latest python version
latest-python:
# Normal test with longruns
tests-and-coverage-with-longrun:
stage: test
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
when: manual
allow_failure: true
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
before_script:
- pip install sympy --upgrade
- pip install -e .
script:
- env
- pip list
......@@ -50,75 +73,66 @@ latest-python:
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- mkdir public
- py.test -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
- py.test -v -n $NUM_CORES
tags:
- docker
- cuda11
- AVX
artifacts:
when: always
reports:
junit: report.xml
# Nightly test - runs "long run" jobs only
test-longrun:
# pipeline with latest python version
latest-python:
stage: test
only:
variables:
- $ENABLE_NIGHTLY_BUILDS
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
before_script:
- pip install -e .
script:
- env
- pip list
- pip install -e .
- export NUM_CORES=$(nproc --all)
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. --html test-report/index.html --junitxml=report.xml
- mkdir public
- py.test -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
tags:
- docker
- cuda11
- AVX
artifacts:
when: always
paths:
- coverage_report
- test-report
reports:
junit: report.xml
# Minimal tests in windows environment
minimal-windows:
stage: test
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
tags:
- win
script:
- export NUM_CORES=$(nproc --all)
- source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
- source activate pystencils
- pip install joblib
- pip list
- python -c "import numpy"
- py.test -v -m "not (notebook or longrun)"
#minimal-windows:
# stage: test
# tags:
# - win
# script:
# - export NUM_CORES=$(nproc --all)
# - source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
# - source activate pystencils
# - pip install joblib
# - pip list
# - python -c "import numpy"
# - py.test -v -m "not (notebook or longrun)"
ubuntu:
stage: test
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
before_script:
- apt-get -y remove python3-sympy
- ln -s /usr/include/locale.h /usr/include/xlocale.h
- pip3 install `grep -Eo 'sympy[>=]+[0-9\.]+' setup.py | sed 's/>/=/g'`
# - pip3 install `grep -Eo 'sympy[>=]+[0-9\.]+' setup.py | sed 's/>/=/g'`
- pip3 install -e .
script:
- export NUM_CORES=$(nproc --all)
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- sed -i 's/--doctest-modules //g' pytest.ini
- env
- pip3 list
- pytest-3 -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
- pip list
- pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
tags:
- docker
- cuda11
......@@ -130,10 +144,11 @@ ubuntu:
.multiarch_template:
stage: test
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
extends: .every-commit
allow_failure: true
before_script: &multiarch_before_script
# - pip3 install -v .
- export PYTHONPATH=src
- python3 -c "import pystencils as ps; ps.cpu.cpujit.read_config()"
- sed -i '/^fail_under.*/d' pytest.ini
script:
......@@ -143,20 +158,26 @@ ubuntu:
- sed -i 's/--doctest-modules //g' pytest.ini
- env
- pip3 list
- pytest-3 -v -n $NUM_CORES --junitxml=report.xml pystencils_tests/test_*vec*.py pystencils_tests/test_random.py
- python3 -m pytest -v -n $NUM_CORES --cov-report html --cov-report xml --cov=. --junitxml=report.xml tests/test_*vec*.py tests/test_random.py tests/test_half_precision.py
- python3 -m coverage xml
tags:
- docker
- AVX
artifacts:
when: always
paths:
- coverage_report
reports:
coverage_report:
coverage_format: cobertura
path: coverage.xml
junit: report.xml
arm64v8:
extends: .multiarch_template
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64
variables:
PYSTENCILS_SIMD: "neon"
QEMU_CPU: "cortex-a76"
before_script:
- *multiarch_before_script
- sed -i s/march=native/march=armv8-a/g ~/.config/pystencils/config.json
......@@ -164,51 +185,41 @@ arm64v8:
ppc64le:
extends: .multiarch_template
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ppc64le
variables:
PYSTENCILS_SIMD: "vsx"
before_script:
- *multiarch_before_script
- sed -i s/mcpu=native/mcpu=power8/g ~/.config/pystencils/config.json
arm64v9:
# Compiler support for SVE is still pretty rough: GCC 10+11 produce incorrect code for fixed-width vectors,
# while Clang 12 produces memory-corrupting heisenbugs unless we enable the address sanitizer.
# In the RNG tests, GCC 10+11 produce an internal compiler error.
# The memory corruption seems to only happen with qemu-user, not with qemu-system.
# Once the compilers and QEMU have improved, this job should be cleaned up to match the others.
# SVE support is still unreliable in GCC 11 (incorrect code for fixed-width vectors, internal compiler errors).
# For half precision Clang is necessary
extends: .multiarch_template
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64
variables:
PYSTENCILS_SIMD: "sve256,sve512,sve"
ASAN_OPTIONS: detect_leaks=0
LD_PRELOAD: /usr/lib/aarch64-linux-gnu/libasan.so.6
before_script:
- *multiarch_before_script
- sed -i s/march=native/march=armv8-a+sve/g ~/.config/pystencils/config.json
- sed -i s/march=native/march=armv9-a+sve2+sme/g ~/.config/pystencils/config.json
- sed -i s/g\+\+/clang++/g ~/.config/pystencils/config.json
riscv64:
# The RISC-V vector extension is still experimental and needs special compiler flags.
# Once they are officially released, this job should be cleaned up to match the others.
# RISC-V vector extension are currently not supported by GCC.
extends: .multiarch_template
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/riscv64
variables:
# explicitly set SIMD as detection requires QEMU >= 8.1
PYSTENCILS_SIMD: "rvv"
QEMU_CPU: "rv64,v=true"
QEMU_CPU: "rv64,v=true,zicboz=true"
before_script:
- *multiarch_before_script
- sed -i 's/march=native/march=rv64imfdv0p10 -menable-experimental-extensions/g' ~/.config/pystencils/config.json
- sed -i s/g\+\+/clang++/g ~/.config/pystencils/config.json
- sed -i 's/fopenmp/fopenmp=libgomp -I\/usr\/include\/riscv64-linux-gnu/g' ~/.config/pystencils/config.json
- sed -i 's/march=native/march=rv64imfdvzicboz/g' ~/.config/pystencils/config.json
- sed -i s/g\+\+/clang++-15/g ~/.config/pystencils/config.json
minimal-conda:
stage: pretest
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
before_script:
- pip install -e .
script:
- python setup.py quicktest
- python quicktest.py
tags:
- docker
- cuda
......@@ -216,13 +227,13 @@ minimal-conda:
minimal-sympy-master:
stage: test
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
before_script:
- pip install -e .
script:
- python -m pip install --upgrade git+https://github.com/sympy/sympy.git
- python setup.py quicktest
- python quicktest.py
allow_failure: true
tags:
- docker
......@@ -248,7 +259,6 @@ pycodegen-integration:
- cd ..
- pip install -e pystencils/
- pip install -e lbmpy/
- pip install -e pygrandchem/
- cmake --version
- ./install_walberla.sh
- export NUM_CORES=$(nproc --all)
......@@ -258,14 +268,12 @@ pycodegen-integration:
- py.test -v -n $NUM_CORES --junitxml=report.xml .
- cd ../lbmpy
- py.test -v -n $NUM_CORES --junitxml=report.xml .
- cd ../pygrandchem
- py.test -v -n $NUM_CORES --junitxml=report.xml .
- cd ../walberla/build/
- make -j $NUM_CORES CodegenJacobiCPU CodegenJacobiGPU CodegenPoissonCPU CodegenPoissonGPU MicroBenchmarkGpuLbm LbCodeGenerationExample
- make -j $NUM_CORES multiphaseCPU multiphaseGPU FluctuatingMRT FlowAroundSphereCodeGen
- make -j $NUM_CORES multiphaseCPU multiphaseGPU FluctuatingMRT FlowAroundSphereCodeGen FieldLayoutAndVectorizationTest GeneratedOutflowBC
- cd apps/benchmarks/UniformGridGPU
- make -j $NUM_CORES
- cd ../UniformGridGenerated
- cd ../UniformGridCPU
- make -j $NUM_CORES
tags:
- docker
......@@ -276,26 +284,57 @@ pycodegen-integration:
reports:
junit: pycodegen/*/report.xml
# -------------------- Scheduled Tasks --------------------------------------------------------------------------
# Nightly test against the latest (pre-release) version of SymPy published on PyPI
nightly-sympy:
stage: nightly
needs: []
extends: .scheduled
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
before_script:
- pip install -e .
- pip install --upgrade --pre sympy
script:
- env
- pip list
- export NUM_CORES=$(nproc --all)
- mkdir -p ~/.config/matplotlib
- echo "backend:template" > ~/.config/matplotlib/matplotlibrc
- mkdir public
- pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
tags:
- docker
- AVX
- cuda
artifacts:
when: always
reports:
junit: report.xml
# -------------------- Linter & Documentation --------------------------------------------------------------------------
flake8-lint:
stage: pretest
except:
variables:
- $ENABLE_NIGHTLY_BUILDS
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
script:
- flake8 pystencils
- flake8 src/pystencils
tags:
- docker
build-documentation:
stage: test
stage: docs
extends: .every-commit
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation
needs: []
before_script:
- pip install -e .
script:
- export PYTHONPATH=`pwd`
- mkdir html_doc
- sphinx-build -b html doc html_doc
- sphinx-build -W -b html doc html_doc
......@@ -308,7 +347,9 @@ build-documentation:
pages:
image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
extends: .every-commit-master
stage: deploy
needs: ["tests-and-coverage", "build-documentation"]
script:
- ls -l
- mv coverage_report html_doc
......@@ -318,5 +359,3 @@ pages:
- public
tags:
- docker
only:
- master@pycodegen/pystencils
MANIFEST.in
View file @ 5600b6b6
include README.md
include COPYING.txt
include AUTHORS.txt
include CONTRIBUTING.md
CHANGELOG.md
global-include *.pyx
include versioneer.py
include pystencils/_version.py
include CHANGELOG.md
README.md
View file @ 5600b6b6
......@@ -52,7 +52,7 @@ pip install pystencils[interactive]
Without `[interactive]` you get a minimal version with very little dependencies.
All options:
- `gpu`: use this if an NVIDIA GPU is available and CUDA is installed
- `gpu`: use this if an NVIDIA or AMD GPU is available and CUDA or ROCm is installed
- `alltrafos`: pulls in additional dependencies for loop simplification e.g. libisl
- `bench_db`: functionality to store benchmark result in object databases
- `interactive`: installs dependencies to work in Jupyter including image I/O, plotting etc.
......@@ -63,7 +63,7 @@ Options can be combined e.g.
pip install pystencils[interactive, gpu, doc]
```
pystencils is also fully compatible with Windows machines. If working with visual studio and pycuda makes sure to run example files first to ensure that pycuda can find the compiler's executable.
pystencils is also fully compatible with Windows machines. If working with visual studio and cupy makes sure to run example files first to ensure that cupy can find the compiler's executable.
Documentation
-------------
......@@ -81,4 +81,7 @@ Many thanks go to the [contributors](https://i10git.cs.fau.de/pycodegen/pystenci
If you use pystencils in a publication, please cite the following articles:
Overview:
- M. Bauer et al, Code Generation for Massively Parallel Phase-Field Simulations. Association for Computing Machinery, 2019. https://doi.org/10.1145/3295500.3356186
\ No newline at end of file
- M. Bauer et al, Code Generation for Massively Parallel Phase-Field Simulations. Association for Computing Machinery, 2019. https://doi.org/10.1145/3295500.3356186
Performance Modelling:
- D. Ernst et al, Analytical performance estimation during code generation on modern GPUs. Journal of Parallel and Distributed Computing, 2023. https://doi.org/10.1016/j.jpdc.2022.11.003
binder/environment.yml
View file @ 5600b6b6
......@@ -7,7 +7,7 @@
# conda env create -f conda_environment_user.yml
# . activate pystencils
#
# If you have CUDA installed and want to use your GPU, uncomment the last line to install pycuda
# If you have CUDA or ROCm installed and want to use your GPU, uncomment the last line to install cupy
#
# ----------------------------------------------------------------------------------------------------------------------
......@@ -32,4 +32,4 @@ dependencies:
- ipy_table # HTML tables for jupyter notebooks
- pyevtk # VTK output for serial simulations
- blitzdb # file-based No-SQL database to store simulation results
#- pycuda # add this if you have CUDA installed
#- cupy # add this if you have CUDA or ROCm installed
conftest.py
View file @ 5600b6b6
......@@ -8,7 +8,7 @@ import nbformat
import pytest
from nbconvert import PythonExporter
from pystencils.boundaries.createindexlistcython import * # NOQA
from pystencils.boundaries.createindexlist import * # NOQA
# Trigger config file reading / creation once - to avoid race conditions when multiple instances are creating it
# at the same time
from pystencils.cpu import cpujit
......@@ -40,47 +40,48 @@ def add_path_to_ignore(path):
collect_ignore = [os.path.join(SCRIPT_FOLDER, "doc", "conf.py"),
os.path.join(SCRIPT_FOLDER, "pystencils", "opencl", "opencl.autoinit")]
add_path_to_ignore('pystencils_tests/benchmark')
os.path.join(SCRIPT_FOLDER, "src", "pystencils", "opencl", "opencl.autoinit")]
add_path_to_ignore('tests/benchmark')
add_path_to_ignore('_local_tmp')
try:
import pycuda
import cupy
except ImportError:
collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_cudagpu.py")]
add_path_to_ignore('pystencils/gpucuda')
collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_gpu.py")]
add_path_to_ignore('src/pystencils/gpu')
try:
import waLBerla
except ImportError:
collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_aligned_array.py"),
os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_datahandling_parallel.py"),
collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_aligned_array.py"),
os.path.join(SCRIPT_FOLDER, "tests/test_datahandling_parallel.py"),
os.path.join(SCRIPT_FOLDER, "doc/notebooks/03_tutorial_datahandling.ipynb"),
os.path.join(SCRIPT_FOLDER, "pystencils/datahandling/parallel_datahandling.py"),
os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_small_block_benchmark.ipynb")]
os.path.join(SCRIPT_FOLDER, "src/pystencils/datahandling/parallel_datahandling.py"),
os.path.join(SCRIPT_FOLDER, "tests/test_small_block_benchmark.ipynb")]
try:
import blitzdb
except ImportError:
add_path_to_ignore('pystencils/runhelper')
collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_parameterstudy.py")]
add_path_to_ignore('src/pystencils/runhelper')
collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_parameterstudy.py")]
collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_json_serializer.py")]
try:
import islpy
except ImportError:
collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils/integer_set_analysis.py")]
collect_ignore += [os.path.join(SCRIPT_FOLDER, "src/pystencils/integer_set_analysis.py")]
try:
import graphviz
except ImportError:
collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils/backends/dot.py")]
collect_ignore += [os.path.join(SCRIPT_FOLDER, "src/pystencils/backends/dot.py")]
collect_ignore += [os.path.join(SCRIPT_FOLDER, "doc/notebooks/01_tutorial_getting_started.ipynb")]
try:
import pyevtk
except ImportError:
collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils/datahandling/vtk.py")]
collect_ignore += [os.path.join(SCRIPT_FOLDER, "src/pystencils/datahandling/vtk.py")]
collect_ignore += [os.path.join(SCRIPT_FOLDER, 'setup.py')]
......
doc/conf.py 100644 → 100755
View file @ 5600b6b6
......@@ -26,14 +26,14 @@ templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
copyright = f'{datetime.datetime.now().year}, Martin Bauer'
author = 'Martin Bauer'
copyright = f'{datetime.datetime.now().year}, Martin Bauer, Markus Holzer, Frederik Hennig'
author = 'Martin Bauer, Markus Holzer, Frederik Hennig'
# The short X.Y version (including .devXXXX, rcX, b1 suffixes if present)
version = re.sub(r'(\d+\.\d+)\.\d+(.*)', r'\1\2', pystencils.__version__)
version = re.sub(r'(\.dev\d+).*?$', r'\1', version)
# The full version, including alpha/beta/rc tags.
release = pystencils.__version__
language = None
language = 'en'
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
default_role = 'any'
pygments_style = 'sphinx'
......
doc/notebooks/01_tutorial_getting_started.ipynb
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doc/notebooks/demo_wave_equation.ipynb
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doc/sphinx/kernel_compile_and_call.rst
View file @ 5600b6b6
......@@ -27,11 +27,11 @@ Code printing
GPU Indexing
-------------
.. autoclass:: pystencils.gpucuda.AbstractIndexing
.. autoclass:: pystencils.gpu.AbstractIndexing
:members:
.. autoclass:: pystencils.gpucuda.BlockIndexing
.. autoclass:: pystencils.gpu.BlockIndexing
:members:
.. autoclass:: pystencils.gpucuda.LineIndexing
.. autoclass:: pystencils.gpu.LineIndexing
:members:
pyproject.toml 0 → 100644
View file @ 5600b6b6
[project]
name = "pystencils"
description = "Speeding up stencil computations on CPUs and GPUs"
dynamic = ["version"]
readme = "README.md"
authors = [
{ name = "Martin Bauer" },
{ name = "Jan Hönig " },
{ name = "Markus Holzer" },
{ name = "Frederik Hennig" },
{ email = "cs10-codegen@fau.de" },
]
license = { file = "COPYING.txt" }
requires-python = ">=3.10"
dependencies = ["sympy>=1.9,<=1.12.1", "numpy>=1.8.0", "appdirs", "joblib", "pyyaml", "fasteners"]
classifiers = [
"Development Status :: 4 - Beta",
"Framework :: Jupyter",
"Topic :: Software Development :: Code Generators",
"Topic :: Scientific/Engineering :: Physics",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
]
[project.urls]
"Bug Tracker" = "https://i10git.cs.fau.de/pycodegen/pystencils/-/issues"
"Documentation" = "https://pycodegen.pages.i10git.cs.fau.de/pystencils/"
"Source Code" = "https://i10git.cs.fau.de/pycodegen/pystencils"
[project.optional-dependencies]
gpu = ['cupy']
alltrafos = ['islpy', 'py-cpuinfo']
bench_db = ['blitzdb', 'pymongo', 'pandas']
interactive = [
'matplotlib',
'ipy_table',
'imageio',
'jupyter',
'pyevtk',
'rich',
'graphviz',
]
use_cython = [
'Cython'
]
doc = [
'sphinx',
'sphinx_rtd_theme',
'nbsphinx',
'sphinxcontrib-bibtex',
'sphinx_autodoc_typehints',
'pandoc',
]
tests = [
'pytest',
'pytest-cov',
'pytest-html',
'ansi2html',
'pytest-xdist',
'flake8',
'nbformat',
'nbconvert',
'ipython',
'matplotlib',
'py-cpuinfo',
'randomgen>=1.18',
]
[build-system]
requires = [
"setuptools>=61",
"versioneer[toml]>=0.29",
# 'Cython'
]
build-backend = "setuptools.build_meta"
[tool.setuptools.package-data]
pystencils = [
"include/*.h",
"boundaries/createindexlistcython.pyx"
]
[tool.setuptools.packages.find]
where = ["src"]
include = ["pystencils", "pystencils.*"]
namespaces = false
[tool.versioneer]
# See the docstring in versioneer.py for instructions. Note that you must
# re-run 'versioneer.py setup' after changing this section, and commit the
# resulting files.
VCS = "git"
style = "pep440"
versionfile_source = "src/pystencils/_version.py"
versionfile_build = "pystencils/_version.py"
tag_prefix = "release/"
parentdir_prefix = "pystencils-"
pystencils/datahandling/pycuda.py deleted 100644 → 0
View file @ 1acd3925
try:
import pycuda.gpuarray as gpuarray
except ImportError:
gpuarray = None
import numpy as np
import pystencils
class PyCudaArrayHandler:
def __init__(self):
import pycuda.autoinit # NOQA
def zeros(self, shape, dtype=np.float64, order='C'):
cpu_array = np.zeros(shape=shape, dtype=dtype, order=order)
return self.to_gpu(cpu_array)
def ones(self, shape, dtype=np.float64, order='C'):
cpu_array = np.ones(shape=shape, dtype=dtype, order=order)
return self.to_gpu(cpu_array)
def empty(self, shape, dtype=np.float64, layout=None):
if layout:
cpu_array = pystencils.field.create_numpy_array_with_layout(shape=shape, dtype=dtype, layout=layout)
return self.to_gpu(cpu_array)
else:
return gpuarray.empty(shape, dtype)
@staticmethod
def to_gpu(array):
return gpuarray.to_gpu(array)
@staticmethod
def upload(array, numpy_array):
array.set(numpy_array)
@staticmethod
def download(array, numpy_array):
array.get(numpy_array)
def randn(self, shape, dtype=np.float64):
cpu_array = np.random.randn(*shape).astype(dtype)
return self.to_gpu(cpu_array)
from_numpy = to_gpu
class PyCudaNotAvailableHandler:
def __getattribute__(self, name):
raise NotImplementedError("Unable to initiaize PyCuda! "
"Try to run `import pycuda.autoinit` to check whether PyCuda is working correctly!")
pystencils/include/PyStencilsField.h deleted 100644 → 0
View file @ 1acd3925
#pragma once
extern "C++" {
#ifdef __CUDA_ARCH__
template <typename DTYPE_T, std::size_t DIMENSION> struct PyStencilsField {
DTYPE_T *data;
DTYPE_T shape[DIMENSION];
DTYPE_T stride[DIMENSION];
};
#else
#include <array>
template <typename DTYPE_T, std::size_t DIMENSION> struct PyStencilsField {
DTYPE_T *data;
std::array<DTYPE_T, DIMENSION> shape;
std::array<DTYPE_T, DIMENSION> stride;
};
#endif
}