Compare revisions

[flake8]

max-line-length=120

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*

*.pyc

*.vti

/build

/html_doc

/dist

*.egg-info

.cache

_build

/.idea

_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:

  - "Code Quality"

  - "Tests"

  - "Prerelease-Tests"

  - integration

  - nightly

  - docs

  - deploy

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

# 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

testsuite-cuda-py3.10:

  stage: "Tests"

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

  needs: []

  script:

    - mkdir -p ~/.config/matplotlib

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

    - 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

testsuite-cpu-py3.13:

  stage: "Tests"

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

  needs: []

  script:

    - mkdir -p ~/.config/matplotlib

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

    - nox -s "testsuite_cpu-3.13"

  tags:

    - docker

    - AVX

  artifacts:

    when: always

    paths:

      - test-report

    reports:

      junit: report.xml

# 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:

    # - 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

    - 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:

    - 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-sympy-master:

  stage: "Prerelease-Tests"

  needs: []

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

  script:

    - 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

#   tags:

#     - docker

#     - cuda

#     - cudaComputeCapability6.1

#     - AVX

# -------------------- 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:

    - 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: 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

    - mkdir html_doc

    - sphinx-build -W -b html doc html_doc

  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

    - mv html_doc public  # folder has to be named "public" for gitlab to publish it

  artifacts:

    paths:

      - public

  tags:

    - docker

[settings]

line_length=100

balanced_wrapping=True

multi_line_output=4

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

=====

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

[![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.i10git.cs.fau.de/lbmpy/coverage_report)

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

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.

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.

Options can be combined e.g.

```bash

pip install pystencils[interactive,gpu,doc]

pip install lbmpy[interactive,gpu,doc]

```

Documentation

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

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

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 os

import pytest

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

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):

        return

    global collect_ignore

    collect_ignore += [os.path.join(SCRIPT_FOLDER, path, f) for f in os.listdir(os.path.join(SCRIPT_FOLDER, 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('_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 cupy

except ImportError:

    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, "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')]

for root, sub_dirs, files in os.walk('.'):

    for f in files:

        if f.endswith(".ipynb") and not any(f.startswith(k) for k in ['demo', 'tutorial', 'test', 'doc']):

            collect_ignore.append(f)

class IPythonMockup:

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

        pass

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

        pass

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

        pass

    def __bool__(self):

        return False

class IPyNbTest(pytest.Item):

    def __init__(self, name, parent, code):

        super(IPyNbTest, self).__init__(name, parent)

        self.code = code

        self.add_marker('notebook')

    def runtest(self):

        global_dict = {'get_ipython': lambda: IPythonMockup(),

                       'is_test_run': True}

        # 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', '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 = nbconvert.PythonExporter()

        exporter.exclude_markdown = True

        exporter.exclude_input_prompt = True

        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)

#!/usr/bin/env python3

# -*- coding: utf-8 -*-

#

import datetime

import sphinx_rtd_theme