Compare revisions

[flake8]

max-line-length=120

exclude=lbmpy/plot.py

        lbmpy/session.py

ignore = W293 W503 W291

exclude=src/lbmpy/plot.py

        src/lbmpy/session.py

ignore = W293 W503 W291 C901 E741

src/lbmpy/_version.py export-subst

__pycache__

.ipynb_checkpoints

.coverage

.coverage*

*.pyc

*.vti

/build

/html_doc

/dist

/*.egg-info

*.egg-info

.cache

_build

/.idea

.cache

_local_tmp

**/.vscode

**/pylintrc

*.bak

*.tmp

/tests/db

doc/bibtex.json

/db

/src/lbmpy/phasefield/simplex_projection.*.so

/src/lbmpy/phasefield/simplex_projection.c

test-report

report.xml

# macOS

**/.DS_Store

*.uuid

# benchmark database

/tests/benchmark/db

 No newline at end of file

stages:

  - test

  - "Code Quality"

  - "Tests"

  - "Prerelease-Tests"

  - integration

  - nightly

  - docs

  - deploy

# --------------------------  Code Quality --------------------------------------------------------------------------------

# --------------------------  Tests ------------------------------------------------------------------------------------

# Linter for code formatting

flake8-lint:

  stage: "Code Quality"

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:alpine

  script:

    - nox -s lint

  tags:

    - docker

# --------------------------  Tests --------------------------------------------------------------------------------

# Normal test - runs on every commit all but "long run" tests

tests-and-coverage:

  stage: test

  except:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

testsuite-cuda-py3.10:

  stage: "Tests"

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:ubuntu24.04-cuda12.6

  needs: []

  script:

    - export NUM_CORES=$(nproc --all)

    - mkdir -p ~/.config/matplotlib

    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc

    - mkdir public

    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils

    - py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=. -m "not longrun"

    - nox -s "testsuite_gpu-3.10(cupy12)"

  tags:

    - docker

    - cuda

    - cudaComputeCapability6.1

    - AVX

  coverage: /Total coverage:\s\d+.\d+\%/

  artifacts:

    when: always

    paths:

      - coverage_report

      - test-report

    reports:

      coverage_report:

        coverage_format: cobertura

        path: coverage.xml

      junit: report.xml

# Nightly test  - runs "long run" jobs only

test-longrun:

  stage: test

  only:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

testsuite-cpu-py3.13:

  stage: "Tests"

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:alpine

  needs: []

  script:

    - export NUM_CORES=$(nproc --all)

    - mkdir -p ~/.config/matplotlib

    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc

    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils

    - py.test -v -n $NUM_CORES --cov-report html --cov-report term --cov=.

    - nox -s "testsuite_cpu-3.13"

  tags:

    - docker

    - cuda

    - 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

# Normal test with longruns

tests-and-coverage-with-longrun:

  stage: "Tests"

  when: manual

  allow_failure: true

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

  script:

    - source /cygdrive/c/Users/build/Miniconda3/Scripts/activate

    - source activate pystencils_dev

    - env

    - conda env list

    # - pip install sympy --upgrade

    - export NUM_CORES=$(nproc --all)

    - mkdir -p ~/.config/matplotlib

    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc

    - mkdir public

    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils

    - python -c "import numpy"

    - python setup.py quicktest

minimal-ubuntu:

  stage: test

  except:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_ubuntu

    - env

    - pip list

    - py.test -v -n $NUM_CORES

  tags:

    - docker

    - cuda

    - cudaComputeCapability6.1

    - AVX

# --------------------------  Nightly and Pre-Release Tests --------------------------------------------------------------------------------

# Test against latest pystencils 2.0 development version

pystencils-2.0dev:

  stage: "Prerelease-Tests"

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:ubuntu24.04-cuda12.6

  allow_failure: true

  needs: []

  script:

    - pip3 install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils

    - python3 setup.py quicktest

    - mkdir -p ~/.config/matplotlib

    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc

    - nox -s "testsuite_pystencils2(cupy12)"

  tags:

    - docker

    - AVX

    - cuda

    - cudaComputeCapability6.1

  artifacts:

    when: always

    paths:

      - test-report

    reports:

      junit: report.xml

minimal-conda:

  stage: test

  except:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda

minimal-sympy-master:

  stage: "Prerelease-Tests"

  needs: []

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/nox:alpine

  script:

    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils

    - python setup.py quicktest

    - nox -s quicktest -P 3.13 -- --sympy-master

  allow_failure: true

  tags:

    - docker

# pycodegen-integration:

#   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

#   stage: integration

#   when: manual

#   allow_failure: true

#   script:

#     - env

#     - pip list

#     - git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pycodegen.git

#     - cd pycodegen

#     - git submodule sync --recursive

#     - git submodule update --init --recursive

#     - git submodule foreach git fetch origin   # compare the latest master version!

#     - git submodule foreach git reset --hard origin/master

#     - cd lbmpy

#     - git remote add test $CI_REPOSITORY_URL

#     - git fetch test

#     - git reset --hard $CI_COMMIT_SHA

#     - cd ..

#     - pip install -e pystencils/

#     - pip install -e lbmpy/

#     - ./install_walberla.sh

#     # build all integration tests

#     - cd walberla/build/

#     - make -j $NUM_CORES MicroBenchmarkGpuLbm LbCodeGenerationExample

#     - cd apps/benchmarks/UniformGridGPU

#     - make -j $NUM_CORES

#     - cd ../UniformGridCPU

#     - make -j $NUM_CORES

# -------------------- Linter & Documentation --------------------------------------------------------------------------

#   tags:

#     - docker

#     - cuda

#     - cudaComputeCapability6.1

#     - AVX

flake8-lint:

  stage: test

  except:

    variables:

      - $ENABLE_NIGHTLY_BUILDS

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

# -------------------- Scheduled Tasks --------------------------------------------------------------------------

nightly-sympy:

  stage: nightly

  rules:

    - if: $CI_PIPELINE_SOURCE == "schedule"

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python

  before_script:

    - pip install -e .

    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils

    - pip install --upgrade --pre sympy

  script:

    - flake8 lbmpy

    - 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

    - cudaComputeCapability6.1

  artifacts:

    when: always

    reports:

      junit: report.xml

# -------------------- Documentation and deploy ------------------------------------------------------------------------

build-documentation:

  stage: test

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

  stage: docs

  needs: []

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/documentation

  before_script:

    - pip install -e .

  script:

    - export PYTHONPATH=`pwd`

    - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils

  tags:

    - docker

    - cuda

    - cudaComputeCapability6.1

  artifacts:

    paths:

      - html_doc

pages:

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full

  rules:

    - if: '$CI_PIPELINE_SOURCE != "schedule" && $CI_PROJECT_PATH == "pycodegen/lbmpy" && $CI_COMMIT_BRANCH == "master"'

  stage: deploy

  needs: ["testsuite-cuda-py3.10", "build-documentation"]

  script:

    - ls -l

    - mv coverage_report html_doc

      - public

  tags:

    - docker

  only:

    - master@pycodegen/lbmpy

Contributors:

-------------

  - Martin Bauer <martin.bauer@fau.de>

  - Markus Holzer <markus.holzer@fau.de>

  - Michael Kuron <mkuron@icp.uni-stuttgart.de>

  - Stephan Seitz <stephan.seitz@fau.de>

  - Frederik Hennig <frederik.hennig@fau.de>

  - Helen Schottenhamml <helen.schottenhamml@fau.de>

  - Rudolf Weeber <weeber@icp.uni-stuttgart.de>

  - Christian Godenschwager <christian.godenschwager@fau.de>

  - Jan Hönig <jan.hoenig@fau.de>

  - Philipp Suffa <philipp.suffa@fau.de>

# Change Log

## Unreleased

### Removed

* Removing OpenCL support because it is not supported by pystencils anymore

# Contributing

lbmpy is built on the open-source python framework [pystencils](https://pypi.org/project/pystencils/). Please consider the [contribution guideline](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/CONTRIBUTING.md) of pystencils for contributing to lbmpy.

 No newline at end of file

include README.md

include COPYING.txt

include AUTHORS.txt

include CONTRIBUTING.md

include CHANGELOG.md

lbmpy

=====

[![Docs](https://img.shields.io/badge/read-the_docs-brightgreen.svg)](http://pycodegen.pages.walberla.net/lbmpy)

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mabau/lbmpy/master?filepath=doc%2Fnotebooks)

[![Docs](https://img.shields.io/badge/read-the_docs-brightgreen.svg)](http://pycodegen.pages.i10git.cs.fau.de/lbmpy)

[![pipeline status](https://i10git.cs.fau.de/pycodegen/lbmpy/badges/master/pipeline.svg)](https://i10git.cs.fau.de/pycodegen/lbmpy/commits/master)

[![coverage report](https://i10git.cs.fau.de/pycodegen/lbmpy/badges/master/coverage.svg)](http://pycodegen.pages.walberla.net/lbmpy/coverage_report)

[![coverage report](https://i10git.cs.fau.de/pycodegen/lbmpy/badges/master/coverage.svg)](http://pycodegen.pages.i10git.cs.fau.de/lbmpy/coverage_report)

Run fast fluid simulations based on the lattice Boltzmann method in Python.

Run fast fluid simulations based on the lattice Boltzmann method in Python on CPUs and GPUs.

lbmpy creates highly optimized LB compute kernels in C or CUDA, for a wide variety of different collision operators, including MRT,

entropic, and cumulant schemes.

![alt text](doc/img/logo.png)

All collision operators can be easily adapted, for example, to integrate turbulence models, custom force terms, or multi-phase models. 

It even comes with an integrated Chapman Enskog analysis based on sympy!

Common test scenarios can be set up quickly:

```python

from pystencils import Target

from lbmpy.session import *

ch = create_channel(domain_size=(300, 100, 100), force=1e-7, method=Method.TRT,

                    equilibrium_order=2, compressible=True,

                    relaxation_rates=[1.97, 1.6], optimization={'target': Target.GPU})

```

To find out more, check out the interactive [tutorial notebooks online with binder](https://mybinder.org/v2/gh/mabau/lbmpy/master?filepath=doc%2Fnotebooks).

Installation

------------

For local installation use pip:

```bash

export PIP_EXTRA_INDEX_URL=https://www.walberla.net/pip

pip install lbmpy[interactive]

```

Without `[interactive]` you get a minimal version with very little dependencies.

All options:

-  `gpu`: use this if nVidia GPU is available and CUDA is installed

- `gpu`: use this if a NVIDIA GPU is available and CUDA is installed

- `opencl`: use this to enable the target `opencl` (execution using OpenCL)

- `alltrafos`: pulls in additional dependencies for loop simplification e.g. libisl

- `interactive`: installs dependencies to work in Jupyter including image I/O, plotting etc.

Documentation

-------------

Read the docs [here](http://pycodegen.pages.walberla.net/lbmpy) and

Read the docs [here](http://pycodegen.pages.i10git.cs.fau.de/lbmpy) and

check out the Jupyter notebooks in `doc/notebooks`. 

Contributing

-------

To see how to open issues, submit bug reports, create feature requests or submit your additions to lbmpy please refer to

[contribution documentation](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/CONTRIBUTING.md) of pystencils since lbmpy is heavily build on pystencils.

Many thanks go to the [contributors](https://i10git.cs.fau.de/pycodegen/lbmpy/-/blob/master/AUTHORS.txt) of lbmpy.

### Please cite us

If you use lbmpy in a publication, please cite the following articles:

Overview:

  - F. Hennig et al, Advanced Automatic Code Generation for Multiple Relaxation-Time Lattice Boltzmann Methods. SIAM Journal on Scientific Computing, 2023. https://doi.org/10.1137/22M1531348 ([Preprint](https://arxiv.org/abs/2211.02435))

  - M. Bauer et al, lbmpy: Automatic code generation for efficient parallel lattice Boltzmann methods. Journal of Computational Science, 2021. https://doi.org/10.1016/j.jocs.2020.101269 ([Preprint](https://arxiv.org/abs/2001.11806))

Multiphase:

   - M. Holzer et al, Highly efficient lattice Boltzmann multiphase simulations of immiscible fluids at high-density ratios on CPUs and GPUs through code generation. The International Journal of High Performance Computing Applications, 2021. https://doi.org/10.1177/10943420211016525

### Further Reading

- F. Hennig et al, Automatic Code Generation for the Cumulant Lattice Boltzmann Method. ICMMES, 2021. [Poster Link](https://www.researchgate.net/publication/353224406_Automatic_Code_Generation_for_the_Cumulant_Lattice_Boltzmann_Method)

build-essential

graphviz

ffmpeg

# ----------------------------------------------------------------------------------------------------------------------

# Environment with all dependencies to use pystencils

#

#

# Download conda at https://conda.io/miniconda.html and create this environment by running:

#     conda env create -f conda_environment_user.yml

#     . activate pystencils

#

# If you have CUDA or ROCm installed and want to use your GPU, uncomment the last line to install cupy

#

# ----------------------------------------------------------------------------------------------------------------------

name: pystencils

dependencies:

  # Basic dependencies:

  - python >= 3.6

  - numpy

  - sympy >= 1.1

  - appdirs # to find default cache directory on each platform

  - joblib # caching on hard-disk, this is optional, but if not installed lbmpy is really slow

  - cython # speed up boundary list computation (optional)

  - matplotlib

  - imageio

  - pandas

  - scipy

  - pip

  - pip:

      - islpy # used to optimize staggered kernels

      - py-cpuinfo # get cpu info like cache sizes, supported vector instruction sets, ...

      - graphviz  # can show abstract syntax trees as formatted graphs

      - ipy_table  # HTML tables for jupyter notebooks

      - pyevtk # VTK output for serial simulations

      - blitzdb # file-based No-SQL database to store simulation results

      - pystencils

      #- cupy # add this if you have CUDA or ROCm installed

#!/bin/bash

python3 setup.py develop

export MPMATH_NOGMPY=1

exec "$@"

 No newline at end of file

import tempfile

import runpy

import sys

import warnings

import platform

import pathlib

import nbformat

import nbconvert

import sympy

from lbmpy._compat import IS_PYSTENCILS_2

# Trigger config file reading / creation once - to avoid race conditions when multiple instances are creating it

# at the same time

if not IS_PYSTENCILS_2:

    from pystencils.cpu import cpujit

# trigger cython imports - there seems to be a problem when multiple processes try to compile the same cython file

# at the same time

try:

    import pyximport

    pyximport.install(language_level=3)

    from lbmpy.phasefield.simplex_projection import simplex_projection_2d  # NOQA

except ImportError:

    pass

from lbmpy.phasefield.simplex_projection import simplex_projection_2d  # NOQA

SCRIPT_FOLDER = os.path.dirname(os.path.realpath(__file__))

sys.path.insert(0, os.path.abspath('lbmpy'))

# the Ubuntu pipeline uses an older version of pytest which uses deprecated functionality.

# This leads to many warinings in the test and coverage pipeline.

pytest_numeric_version = [int(x, 10) for x in pytest.__version__.split('.')]

pytest_numeric_version.reverse()

pytest_version = sum(x * (100 ** i) for i, x in enumerate(pytest_numeric_version))

def add_path_to_ignore(path):

    if not os.path.exists(path):

collect_ignore = [os.path.join(SCRIPT_FOLDER, "doc", "conf.py"),

                  os.path.join(SCRIPT_FOLDER, "doc", "img", "mb_discretization", "maxwell_boltzmann_stencil_plot.py")]

add_path_to_ignore('pystencils_tests/benchmark')

add_path_to_ignore('_local_tmp')

if IS_PYSTENCILS_2:

    #   TODO: Fix these step-by-step

    collect_ignore += [

        os.path.join(SCRIPT_FOLDER, "doc", "notebooks", "10_tutorial_conservative_allen_cahn_two_phase.ipynb"),

        os.path.join(SCRIPT_FOLDER, "tests", "test_compiled_in_boundaries.ipynb")

    ]

try:

    import pycuda

    import cupy

except ImportError:

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_cpu_gpu_equivalence.py")]

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_cpu_gpu_equivalence.py")]

try:

    import waLBerla

except ImportError:

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_serial_scenarios.py")]

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "lbmpy_tests/test_datahandling_parallel.py")]

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_datahandling_parallel.py")]

try:

    import blitzdb

except ImportError:

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/benchmark"),

                       os.path.join(SCRIPT_FOLDER,

                                    "tests/full_scenarios/kida_vortex_flow/scenario_kida_vortex_flow.py"),

                       os.path.join(SCRIPT_FOLDER, "tests/full_scenarios/shear_wave/scenario_shear_wave.py"),

                       os.path.join(SCRIPT_FOLDER, "tests/test_json_serializer.py"),

                       os.path.join(SCRIPT_FOLDER, "src/lbmpy/db.py")]

if platform.system().lower() == 'windows':

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_quicktests.py")]

sver = sympy.__version__.split(".")

if int(sver[0]) == 1 and int(sver[1]) < 2:

    add_path_to_ignore('tests/phasefield')

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "tests/test_n_phase_boyer_noncoupled.ipynb")]

collect_ignore += [os.path.join(SCRIPT_FOLDER, 'setup.py')]

            collect_ignore.append(f)

import nbformat

from nbconvert import PythonExporter

class IPythonMockup:

    def run_line_magic(self, *args, **kwargs):

        pass

        # disable matplotlib output

        exec("import matplotlib.pyplot as p; "

             "p.close('all'); "

             "p.switch_backend('Template')", global_dict)

        # in notebooks there is an implicit plt.show() - if this is not called a warning is shown when the next

        # plot is created. This warning is suppressed here

        # Also animations cannot be shown, which also leads to a warning.

        exec("import warnings;"

             "warnings.filterwarnings('ignore', 'Adding an axes using the same arguments as a previous.*')",

             "warnings.filterwarnings('ignore', 'Adding an axes using the same arguments as a previous.*');"

             "warnings.filterwarnings('ignore', 'Animation was deleted without rendering anything.*');",

             global_dict)

        with tempfile.NamedTemporaryFile() as f:

            f.write(self.code.encode())

            f.flush()

            runpy.run_path(f.name, init_globals=global_dict, run_name=self.name)

        #   Close any open figures

        exec("import matplotlib.pyplot as p; "

             "p.close('all')", global_dict)

class IPyNbFile(pytest.File):

    def collect(self):

        exporter = PythonExporter()

        exporter = nbconvert.PythonExporter()

        exporter.exclude_markdown = True

        exporter.exclude_input_prompt = True

        notebook_contents = self.fspath.open()

        notebook_contents = self.fspath.open(encoding='utf-8')

        with warnings.catch_warnings():

            warnings.filterwarnings("ignore", "IPython.core.inputsplitter is deprecated")

            notebook = nbformat.read(notebook_contents, 4)

            code, _ = exporter.from_notebook_node(notebook)

            if pytest_version >= 50403:

                yield IPyNbTest.from_parent(name=self.name, parent=self, code=code)

            else:

                yield IPyNbTest(self.name, self, code)

    def teardown(self):

        pass

if pytest_version >= 70000:

    #   Since pytest 7.0, usage of `py.path.local` is deprecated and `pathlib.Path` should be used instead

    import pathlib

    def pytest_collect_file(file_path: pathlib.Path, parent):

        glob_exprs = ["*demo*.ipynb", "*tutorial*.ipynb", "test_*.ipynb"]

        if any(file_path.match(g) for g in glob_exprs):

            return IPyNbFile.from_parent(path=file_path, parent=parent)

else:

    def pytest_collect_file(path, parent):

        glob_exprs = ["*demo*.ipynb", "*tutorial*.ipynb", "test_*.ipynb"]

        if any(path.fnmatch(g) for g in glob_exprs):

            if pytest_version >= 50403:

                return IPyNbFile.from_parent(fspath=path, parent=parent)

            else:

                return IPyNbFile(path, parent)

import sphinx_rtd_theme

import os

import sys

import re

import lbmpy

sys.path.insert(0, os.path.abspath('.'))

from version_from_git import version_number_from_git

extensions = [

    'sphinx.ext.autodoc',

source_suffix = '.rst'

master_doc = 'index'

copyright = '{}, Martin Bauer'.format(datetime.datetime.now().year)

author = 'Martin Bauer'

version = version_number_from_git()

release = version_number_from_git()

language = None

copyright = f'{datetime.datetime.now().year}, Martin Bauer, Markus Holzer, Frederik Hennig'