.flake8

 [flake8]
 max-line-length=120
-exclude=pystencils/jupytersetup.py,
-        pystencils/plot2d.py
-        pystencils/session.py
-ignore = W293 W503 W291
+exclude=src/pystencils/jupyter.py,
+        src/pystencils/plot.py
+        src/pystencils/session.py
+ignore = W293 W503 W291 C901 E741

.gitattributes

+src/pystencils/_version.py export-subst

.gitignore

 __pycache__
 .ipynb_checkpoints
-.coverage
+.coverage*
 *.pyc
 *.vti
 /build
 /dist
-/*.egg-info
+*.egg-info
 .cache
 _build
+/html_doc
 /.idea
+.vscode
 .cache
-_local_tmp
+_local_tmp
\ No newline at end of file
+RELEASE-VERSION
+test-report
+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

 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: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/software/pystencils/full
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
+  before_script:
+    - pip install -e .
   script:
+    - env
+    - pip list
     - export NUM_CORES=$(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"
+    - 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
-    - cuda
+    - cuda11
     - 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:
+# Normal test with longruns
+tests-and-coverage-with-longrun:
   stage: test
-  only:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/software/pystencils/full
+  when: manual
+  allow_failure: true
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3
+  before_script:
+    - pip install sympy --upgrade
+    - pip install -e .
   script:
+    - env
+    - pip list
     - export NUM_CORES=$(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=.
+    - mkdir public
+    - py.test -v -n $NUM_CORES
+  tags:
+    - docker
+    - cuda11
+    - AVX
+
+# pipeline with latest python version
+latest-python:
+  stage: test
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
+  before_script:
+    - pip install -e .
+  script:
+    - env
+    - pip list
+    - pip install -e .
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - mkdir public
+    - py.test -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
   tags:
     - docker
-    - cuda
     - AVX
   artifacts:
-    paths:
-      - coverage_report
+    when: always
+    reports:
+      junit: report.xml
+
 
 # Minimal tests in windows environment
-minimal-windows:
+#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:
-      - $ENABLE_NIGHTLY_BUILDS
-  tags:
-    - win
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ubuntu
+  before_script:
+    - ln -s /usr/include/locale.h /usr/include/xlocale.h
+    - pip3 install -e .
   script:
-    - source /cygdrive/c/Users/build/Miniconda3/Scripts/activate
-    - source activate pystencils_dev
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - sed -i 's/--doctest-modules //g' pytest.ini
     - env
-    - conda env list
-    - python -c "import numpy"
-    - python setup.py quicktest
+    - pip list
+    - pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml
+  tags:
+    - docker
+    - cuda11
+    - AVX
+  artifacts:
+    when: always
+    reports:
+      junit: report.xml
 
-minimal-ubuntu:
+.multiarch_template:
   stage: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/software/pystencils/minimal_ubuntu
+  extends: .every-commit
+  allow_failure: true
+  before_script: &multiarch_before_script
+    # - pip3 install -v .
+    - export PYTHONPATH=src
+    - python3 -c "import pystencils as ps; ps.cpu.cpujit.read_config()"
+    - sed -i '/^fail_under.*/d' pytest.ini
   script:
-    - python3 setup.py quicktest
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - sed -i 's/--doctest-modules //g' pytest.ini
+    - env
+    - pip3 list
+    - 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:
+    QEMU_CPU: "cortex-a76"
+  before_script:
+    - *multiarch_before_script
+    - sed -i s/march=native/march=armv8-a/g ~/.config/pystencils/config.json
+
+ppc64le:
+  extends: .multiarch_template
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ppc64le
+  before_script:
+    - *multiarch_before_script
+    - sed -i s/mcpu=native/mcpu=power8/g ~/.config/pystencils/config.json
+
+arm64v9:
+  # 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
+  before_script:
+    - *multiarch_before_script
+    - 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:
+  # 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,zicboz=true"
+  before_script:
+    - *multiarch_before_script
+    - 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
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
+  before_script:
+    - pip install -e .
+  script:
+    - python quicktest.py
+  tags:
+    - docker
+    - cuda
+
+
+minimal-sympy-master:
   stage: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/software/pystencils/minimal_conda
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/minimal_conda
+  before_script:
+    - pip install -e .
   script:
-    - python setup.py quicktest
+    - python -m pip install --upgrade git+https://github.com/sympy/sympy.git
+    - python quicktest.py
+  allow_failure: true
   tags:
     - docker
+    - cuda
 
 
+pycodegen-integration:
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
+  stage: test
+  when: manual
+  allow_failure: true
+  script:
+    - 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 pystencils
+    - git remote add test $CI_REPOSITORY_URL
+    - git fetch test
+    - git reset --hard $CI_COMMIT_SHA
+    - cd ..
+    - pip install -e pystencils/
+    - pip install -e lbmpy/
+    - cmake --version
+    - ./install_walberla.sh
+    - export NUM_CORES=$(nproc --all)
+    - mkdir -p ~/.config/matplotlib
+    - echo "backend:template" > ~/.config/matplotlib/matplotlibrc
+    - cd pystencils
+    - py.test -v -n $NUM_CORES --junitxml=report.xml .
+    - cd ../lbmpy
+    - 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 FieldLayoutAndVectorizationTest GeneratedOutflowBC
+    - cd apps/benchmarks/UniformGridGPU
+    - make -j $NUM_CORES
+    - cd ../UniformGridCPU
+    - make -j $NUM_CORES
+  tags:
+    - docker
+    - cuda11
+    - AVX
+  artifacts:
+    when: always
+    reports:
+      junit: pycodegen/*/report.xml
+
+
+# -------------------- Scheduled Tasks --------------------------------------------------------------------------
+
+
+# Nightly test against the latest (pre-release) version of SymPy published on PyPI
+nightly-sympy:
+  stage: nightly
+  needs: []
+  extends: .scheduled
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/latest_python
+  before_script:
+    - pip install -e .
+    - pip install --upgrade --pre sympy
+  script:
+    - env
+    - pip list
+    - export NUM_CORES=$(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: test
-  except:
-    variables:
-      - $ENABLE_NIGHTLY_BUILDS
-  image: i10git.cs.fau.de:5005/software/pystencils/full
+  stage: pretest
+  extends: .every-commit
+  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   script:
-    - flake8 pystencils
+    - flake8 src/pystencils
   tags:
     - docker
-    - cuda
 
 
 build-documentation:
-  stage: test
-  image: i10git.cs.fau.de:5005/software/pystencils/full
+  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
   tags:
     - docker
-    - cuda
   artifacts:
     paths:
       - html_doc
 
 
 pages:
-  image: i10git.cs.fau.de:5005/software/pystencils/full
+  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
@@ -129,5 +359,3 @@ pages:
       - public
   tags:
     - docker
-  only:
-    - master@pycodegen/pystencils

.isort.cfg

+[settings]
+line_length=100
+balanced_wrapping=True
+multi_line_output=4
+known_third_party=sympy

AUTHORS.txt

+
+Contributors:
+-------------
+
+  - Martin Bauer <martin.bauer@fau.de>
+  - Markus Holzer <markus.holzer@fau.de>
+  - Stephan Seitz <stephan.seitz@fau.de>
+  - Michael Kuron <mkuron@icp.uni-stuttgart.de>
+  - Jan Hönig <jan.hoenig@fau.de>
+  - Julian Hammer <julian.hammer@fau.de>
+  - Nils Kohl <nils.kohl@fau.de>
+  - Frederik Hennig <frederik.hennig@fau.de>
+  - Dominik Ernst <dominik.ernst@fau.de>
+  - Christian Godenschwager <christian.godenschwager@fau.de>
+  - Dominik Thoennes <dominik.thoennes@fau.de>

CHANGELOG.md

+# Change Log
+
+## Unreleased
+
+### Removed
+* LLVM backend because it was not used much and not good integrated in pystencils.
+* OpenCL backend because it was not used much and not good integrated in pystencils.

CONTRIBUTING.md

+# Contributing
+
+Contributions to pystencils are always welcome, and they are greatly appreciated!
+A list of open problems can be found [here]( https://i10git.cs.fau.de/pycodegen/pystencils/-/issues).
+Of course, it is also always appreciated to bring own ideas and problems to the community!
+
+
+Please submit all contributions to the official [GitLab repository](https://i10git.cs.fau.de/pycodegen/pystencils) in the form of a Merge Request. Please do not submit git diffs or files containing the changes.
+There also exists a GitHub repository, which is only a mirror to the GitLab repository. Contributions to the GitHub repository are not considered.
+
+`pystencils` is an open-source python package under the license of  AGPL3. Thus we consider the act of contributing to the code by submitting a Merge Request as the "Sign off" or agreement to the AGPL3 license.
+
+You can contribute in many different ways:
+
+## Types of Contributions
+
+### Report Bugs
+
+Report bugs at [https://i10git.cs.fau.de/pycodegen/pystencils/-/issues](https://i10git.cs.fau.de/pycodegen/pystencils/-/issues).
+
+For pystencils, it is often necessary to provide the python and [SymPy](https://www.sympy.org/en/index.html) versions used and hardware information like the
+processor architecture and the compiler version used to compile the generated kernels.
+
+### Fix Issues
+
+Look through the GitLab issues. Different tags are indicating the status of the issues.
+The "bug" tag indicates problems with pystencils, while the "feature" tag shows ideas that should be added in the future.
+
+### Write Documentation
+
+The documentation of pystencils can be found [here](https://pycodegen.pages.i10git.cs.fau.de/pystencils/). Jupyter notebooks are used to provide an
+interactive start to pystencils. It is always appreciated if new document notebooks are provided
+since this helps others a lot.
+
+## Get Started!
+
+Ready to contribute? Here is how to set up `pystencils` for local development.
+
+1. Fork the `pystencils` repo on GitLab.
+2. Clone your fork locally:
+```bash
+    $ git clone https://i10git.cs.fau.de/your-name/pystencils
+```
+3. Install your local copy into a virtualenv. It is also recommended to use anaconda or miniconda to manage the python environments.
+```bash
+    $ mkvirtualenv pystencils
+    $ cd pystencils/
+    $ pip install -e .
+```
+4. Create a branch for local development:
+```bash
+    $ git checkout -b name-of-your-bugfix-or-feature
+```
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the
+   tests
+```bash
+    $ flake8 pystencils
+    $ py.test -v -n $NUM_CORES -m "not longrun" .
+   
+```
+
+   To get all packages needed for development, a requirements list can be found [here](https://i10git.cs.fau.de/pycodegen/pycodegen/-/blob/master/conda_environment_dev.yml). This includes flake8 and pytest.
+
+6. Commit your changes and push your branch to GitHub::
+```bash
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+```
+7. Submit a Merge Request on GitLab.
+
+## Merge Request Guidelines
+
+Before you submit a Merge Request, check that it meets these guidelines:
+
+1. All functionality that is implemented through this Merge Request should be covered by unit tests. These are implemented in `pystencil_tests`
+2. If the Merge Request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring.
+3. If you have a maintainer status for `pystencils`, you can merge Merge Requests to the master branch. However, every Merge Request needs to be reviewed by another developer. Thus it is not allowed to merge a Merge Request, which is submitted by oneself.
+
+## Tips
+
+To run a subset of tests:
+```bash
+$ py.test my_test.py
+```
\ No newline at end of file

MANIFEST.in

-include README.md
-include COPYING.txt
+include AUTHORS.txt
+include CONTRIBUTING.md
+include CHANGELOG.md

README.md

 pystencils
 ==========
 
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mabau/pystencils/master?filepath=doc%2Fnotebooks)
+[![Docs](https://img.shields.io/badge/read-the_docs-brightgreen.svg)](https://pycodegen.pages.i10git.cs.fau.de/pystencils)
+[![pypi-package](https://badge.fury.io/py/pystencils.svg)](https://badge.fury.io/py/pystencils)
 [![pipeline status](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/pipeline.svg)](https://i10git.cs.fau.de/pycodegen/pystencils/commits/master)
-[![coverage report](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/coverage.svg)](https://i10git.cs.fau.de/pycodegen/pystencils/commits/master)
-[coverage report](http://pycodegen.pages.walberla.net/pystencils/coverage_report)
+[![coverage report](https://i10git.cs.fau.de/pycodegen/pystencils/badges/master/coverage.svg)](http://pycodegen.pages.i10git.cs.fau.de/pystencils/coverage_report)
 
 Run blazingly fast stencil codes on numpy arrays.
 
-*pystencils* uses sympy to define stencil operations, that can be executed on numpy array.
-It runs faster than normal numpy code and even as Cython and numba.
+*pystencils* uses sympy to define stencil operations, that can be executed on numpy arrays.
+Exploiting the stencil structure makes *pystencils* run faster than normal numpy code and even as Cython and numba,
+[as demonstrated in this notebook](https://pycodegen.pages.i10git.cs.fau.de/pystencils/notebooks/demo_benchmark.html).
+
 
 Here is a code snippet that computes the average of neighboring cells:
 ```python
@@ -17,7 +21,7 @@ import numpy as np
 
 f, g = ps.fields("f, g : [2D]")
 stencil = ps.Assignment(g[0, 0],
-                        (f[1, 0] + f[-1, 0] + f[0, 1] + f[0, -1]) / 4)
+                       (f[1, 0] + f[-1, 0] + f[0, 1] + f[0, -1]) / 4)
 kernel = ps.create_kernel(stencil).compile()
 
 f_arr = np.random.rand(1000, 1000)
@@ -29,15 +33,15 @@ kernel(f=f_arr, g=g_arr)
 It comes with automatic finite difference discretization for PDEs:
 
 ```python
+import pystencils as ps
+import sympy as sp
+
 c, v = ps.fields("c, v(2): [2D]")
 adv_diff_pde = ps.fd.transient(c) - ps.fd.diffusion(c, sp.symbols("D")) + ps.fd.advection(c, v)
 discretize = ps.fd.Discretization2ndOrder(dx=1, dt=0.01)
 discretization = discretize(adv_diff_pde)
 ```
 
-Look at the [documentation](http://pycodegen.pages.walberla.net/pystencils) to learn more.
-
-
 Installation
 ------------
 
@@ -48,7 +52,7 @@ pip install pystencils[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 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.
@@ -56,12 +60,28 @@ All options:
 
 Options can be combined e.g.
 ```bash
-pip install pystencils[interactive,gpu,doc]
-```    
+pip install pystencils[interactive, gpu, doc]
+```
 
+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
 -------------
 
-Read the docs [here](http://pycodegen.pages.walberla.net/pystencils) and
-check out the Jupyter notebooks in `doc/notebooks`.
+Read the docs [here](https://pycodegen.pages.i10git.cs.fau.de/pystencils) and
+check out the Jupyter notebooks in `doc/notebooks`. The **Changelog** of pystencils can be found [here](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/CHANGELOG.md).
+
+Authors
+-------
+
+Many thanks go to the [contributors](https://i10git.cs.fau.de/pycodegen/pystencils/-/blob/master/AUTHORS.txt) of pystencils.
+
+### Please cite us
+
+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
+
+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/apt.txt

+build-essential
+graphviz
+ffmpeg

binder/environment.yml

+
+# ----------------------------------------------------------------------------------------------------------------------
+# 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 >= 3.8
+  - 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
+      #- cupy # add this if you have CUDA or ROCm installed

binder/start

+#!/bin/bash
+
+python3 setup.py develop
+
+exec "$@"
\ No newline at end of file

conftest.py

 import os
-import pytest
-import tempfile
 import runpy
 import sys
+import tempfile
+import warnings
+
+import nbformat
+import pytest
+from nbconvert import PythonExporter
+
+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
@@ -14,12 +20,17 @@ try:
     pyximport.install(language_level=3)
 except ImportError:
     pass
-from pystencils.boundaries.createindexlistcython import *  # NOQA
 
 
 SCRIPT_FOLDER = os.path.dirname(os.path.realpath(__file__))
 sys.path.insert(0, os.path.abspath('pystencils'))
 
+# 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):
@@ -28,34 +39,49 @@ def add_path_to_ignore(path):
     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")]
-add_path_to_ignore('pystencils_tests/benchmark')
+collect_ignore = [os.path.join(SCRIPT_FOLDER, "doc", "conf.py"),
+                  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/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 llvmlite
+    import waLBerla
 except ImportError:
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, 'pystencils_tests/backends/llvm.py')]
-    add_path_to_ignore('pystencils/llvm')
+    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, "src/pystencils/datahandling/parallel_datahandling.py"),
+                       os.path.join(SCRIPT_FOLDER, "tests/test_small_block_benchmark.ipynb")]
 
 try:
-    import kerncraft
+    import blitzdb
 except ImportError:
-    collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_kerncraft_coupling.py")]
-    add_path_to_ignore('pystencils/kerncraft_coupling')
+    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 blitzdb
+    import islpy
 except ImportError:
-    add_path_to_ignore('pystencils/runhelper')
+    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, "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, "src/pystencils/datahandling/vtk.py")]
 
 collect_ignore += [os.path.join(SCRIPT_FOLDER, 'setup.py')]
 
@@ -65,10 +91,6 @@ for root, sub_dirs, files in os.walk('.'):
             collect_ignore.append(f)
 
 
-import nbformat
-from nbconvert import PythonExporter
-
-
 class IPythonMockup:
     def run_line_magic(self, *args, **kwargs):
         pass
@@ -89,6 +111,7 @@ class IPyNbTest(pytest.Item):
         self.code = code
         self.add_marker('notebook')
 
+    @pytest.mark.filterwarnings("ignore:IPython.core.inputsplitter is deprecated")
     def runtest(self):
         global_dict = {'get_ipython': lambda: IPythonMockup(),
                        'is_test_run': True}
@@ -114,10 +137,16 @@ class IPyNbFile(pytest.File):
         exporter.exclude_markdown = True
         exporter.exclude_input_prompt = True
 
-        notebook_contents = self.fspath.open()
-        notebook = nbformat.read(notebook_contents, 4)
-        code, _ = exporter.from_notebook_node(notebook)
-        yield IPyNbTest(self.name, self, code)
+        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
@@ -126,4 +155,7 @@ class IPyNbFile(pytest.File):
 def pytest_collect_file(path, parent):
     glob_exprs = ["*demo*.ipynb", "*tutorial*.ipynb", "test_*.ipynb"]
     if any(path.fnmatch(g) for g in glob_exprs):
-        return IPyNbFile(path, parent)
+        if pytest_version >= 50403:
+            return IPyNbFile.from_parent(fspath=path, parent=parent)
+        else:
+            return IPyNbFile(path, parent)

doc/conf.py

@@ -4,10 +4,11 @@
 import datetime
 import sphinx_rtd_theme
 import os
+import re
 import sys
 
 sys.path.insert(0, os.path.abspath('.'))
-from version_from_git import version_number_from_git
+import pystencils
 
 extensions = [
     'sphinx.ext.autodoc',
@@ -25,11 +26,14 @@ templates_path = ['_templates']
 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'
+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 = 'en'
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
 default_role = 'any'
 pygments_style = 'sphinx'
@@ -47,13 +51,14 @@ nbsphinx_execute = 'never'
 nbsphinx_codecell_lexer = 'python3'
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'python': ('https://docs.python.org/3.6', None),
+intersphinx_mapping = {'python': ('https://docs.python.org/3.8', None),
                        'numpy': ('https://docs.scipy.org/doc/numpy/', None),
                        'matplotlib': ('https://matplotlib.org/', None),
                        'sympy': ('https://docs.sympy.org/latest/', None),
                        }
 
 autodoc_member_order = 'bysource'
+bibtex_bibfiles = ['sphinx/pystencils.bib']
 
 project = 'pystencils'
-html_logo = "img/logo.png"
+html_logo = 'img/logo.png'

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doc/index.rst

@@ -14,5 +14,6 @@ pystencils can help you to generate blazingly fast code for image processing, nu
 
 .. image:: /img/pystencils_arch_block_diagram.svg
     :height: 450px
+    :align: center
 
 

doc/notebooks/02_tutorial_basic_kernels.ipynb

 %% Cell type:code id: tags:
 
 ``` python
 from pystencils.session import *
 ```
 
 %% Cell type:markdown id: tags:
 
 # Tutorial 02: Basic Kernel generation with *pystencils*
 
 Now that you have an [overview of pystencils](01_tutorial_getting_started.ipynb),
 this tutorial shows in more detail how to formulate, optimize and run stencil kernels.
 
 ## 1) Kernel Definition
 
 ### a) Defining kernels with assignment lists and the  `kernel` decorator
 
 *pystencils* gets a symbolic formulation of the kernel. This can be either an `Assignment` or a sequence of `Assignment`s that follow a set of restrictions.
 
 Lets first create a kernel that consists of multiple assignments:
 
 %% Cell type:code id: tags:
 
 ``` python
 src_arr = np.zeros([20, 30])
 dst_arr = np.zeros_like(src_arr)
 
 dst, src = ps.fields(dst=dst_arr, src=src_arr)
 ```
 
 %% Cell type:code id: tags:
 
 ``` python
 grad_x, grad_y = sp.symbols("grad_x, grad_y")
 
 symbolic_description = [
     ps.Assignment(grad_x, (src[1, 0] - src[-1, 0]) / 2),
     ps.Assignment(grad_y, (src[0, 1] - src[0, -1]) / 2),
     ps.Assignment(dst[0, 0], grad_x + grad_y),
 ]
 kernel = ps.create_kernel(symbolic_description)
 symbolic_description
 ```
 
 %% Output
 
-    $$\left [ grad_{x} \leftarrow \frac{{{src}_{E}}}{2} - \frac{{{src}_{W}}}{2}, \quad grad_{y} \leftarrow \frac{{{src}_{N}}}{2} - \frac{{{src}_{S}}}{2}, \quad {{dst}_{C}} \leftarrow grad_{x} + grad_{y}\right ]$$
+
+    $\displaystyle \left[ grad_{x} \leftarrow_{} \frac{{src}_{(1,0)}}{2} - \frac{{src}_{(-1,0)}}{2}, \  grad_{y} \leftarrow_{} \frac{{src}_{(0,1)}}{2} - \frac{{src}_{(0,-1)}}{2}, \  {dst}_{(0,0)} \leftarrow_{} grad_{x} + grad_{y}\right]$
     ⎡         src_E   src_W            src_N   src_S                         ⎤
     ⎢gradₓ := ───── - ─────, grad_y := ───── - ─────, dst_C := gradₓ + grad_y⎥
     ⎣           2       2                2       2                           ⎦
 
 %% Cell type:markdown id: tags:
 
 We created subexpressions, using standard sympy symbols on the left hand side, to split the kernel into multiple assignments. Defining a kernel using a list of `Assignment`s is quite tedious and hard to read.
 To simplify the formulation of a kernel, *pystencils* offers the `kernel` decorator, that transforms a normal Python function with `@=` assignments into an assignment list that can be passed to `create_kernel`.
 
 %% Cell type:code id: tags:
 
 ``` python
 @ps.kernel
 def symbolic_description_using_function():
     grad_x @= (src[1, 0] - src[-1, 0]) / 2
     grad_y @= (src[0, 1] - src[0, -1]) / 2
     dst[0, 0] @= grad_x + grad_y
 symbolic_description_using_function
 ```
 
 %% Output
 
-    $$\left [ grad_{x} \leftarrow \frac{{{src}_{E}}}{2} - \frac{{{src}_{W}}}{2}, \quad grad_{y} \leftarrow \frac{{{src}_{N}}}{2} - \frac{{{src}_{S}}}{2}, \quad {{dst}_{C}} \leftarrow grad_{x} + grad_{y}\right ]$$
+
+    $\displaystyle \left[ grad_{x} \leftarrow_{} \frac{{src}_{(1,0)}}{2} - \frac{{src}_{(-1,0)}}{2}, \  grad_{y} \leftarrow_{} \frac{{src}_{(0,1)}}{2} - \frac{{src}_{(0,-1)}}{2}, \  {dst}_{(0,0)} \leftarrow_{} grad_{x} + grad_{y}\right]$
     ⎡         src_E   src_W            src_N   src_S                         ⎤
     ⎢gradₓ := ───── - ─────, grad_y := ───── - ─────, dst_C := gradₓ + grad_y⎥
     ⎣           2       2                2       2                           ⎦
 
 %% Cell type:markdown id: tags:
 
 The decorated function can contain any Python code, only the `@=` operator, and the ternary inline `if-else` operator have different meaning.
 
 ### b) Ternary 'if' with `Piecewise`
 
 The ternary operator maps to `sympy.Piecewise` functions, that can be used to introduce branching into the kernel. Piecewise defined functions must give a value for every input, i.e. there must be a 'otherwise' clause in the end that is indicated by the condition `True`. Piecewise objects are standard sympy terms that can be integrated into bigger expressions:
 
 %% Cell type:code id: tags:
 
 ``` python
 sp.Piecewise((1.0, src[0,1] > 0), (0.0, True)) + src[1, 0]
 ```
 
 %% Output
 
-    $${{src}_{E}} + \begin{cases} 1.0 & \text{for}\: {{src}_{N}} > 0 \\0.0 & \text{otherwise} \end{cases}$$
+
+    $\displaystyle {src}_{(1,0)} + \begin{cases} 1.0 & \text{for}\: {src}_{(0,1)} > 0 \\0.0 & \text{otherwise} \end{cases}$
             ⎛⎧1.0  for src_N > 0⎞
     src_E + ⎜⎨                  ⎟
             ⎝⎩0.0    otherwise  ⎠
 
 %% Cell type:markdown id: tags:
 
 Piecewise objects are created by the `kernel` decorator for ternary if-else statements.
 
 %% Cell type:code id: tags:
 
 ``` python
 @ps.kernel
 def kernel_with_piecewise():
     grad_x @= (src[1, 0] - src[-1, 0]) / 2 if src[-1, 0] > 0 else 0.0
 kernel_with_piecewise
 ```
 
 %% Output
 
-    $$\left [ grad_{x} \leftarrow \begin{cases} \frac{{{src}_{E}}}{2} - \frac{{{src}_{W}}}{2} & \text{for}\: {{src}_{W}} > 0 \\0.0 & \text{otherwise} \end{cases}\right ]$$
+
+    $\displaystyle \left[ grad_{x} \leftarrow_{} \begin{cases} \frac{{src}_{(1,0)}}{2} - \frac{{src}_{(-1,0)}}{2} & \text{for}\: {src}_{(-1,0)} > 0 \\0.0 & \text{otherwise} \end{cases}\right]$
     ⎡         ⎧src_E   src_W               ⎤
     ⎢         ⎪───── - ─────  for src_W > 0⎥
     ⎢gradₓ := ⎨  2       2                 ⎥
     ⎢         ⎪                            ⎥
     ⎣         ⎩     0.0         otherwise  ⎦
 
 %% Cell type:markdown id: tags:
 
 ### c) Assignment level optimizations using `AssignmentCollection`
 
 When the kernels get larger and more complex, it is helpful to organize the list of assignment into a more structured way. The `AssignmentCollection` offers optimizating transformation on a list of assignments. It holds two assignment lists, one for subexpressions and one for the main assignments. Main assignments are typically those that write to an array.
 
 %% Cell type:code id: tags:
 
 ``` python
 @ps.kernel
 def somewhat_longer_dummy_kernel(s):
     s.a @= src[0, 1] + src[-1, 0]
     s.b @= 2 * src[1, 0] + src[0, -1]
     s.c @= src[0, 1] + 2 * src[1, 0] + src[-1, 0] + src[0, -1] - src[0,0]
     dst[0, 0] @= s.a + s.b + s.c
 
 ac = ps.AssignmentCollection(main_assignments=somewhat_longer_dummy_kernel[-1:],
                              subexpressions=somewhat_longer_dummy_kernel[:-1])
 ac
 ```
 
 %% Output
 
-    Equation Collection for dst_C
+    AssignmentCollection: dst_C, <- f(src_C, src_W, src_S, src_N, src_E)
 
 %% Cell type:code id: tags:
 
 ``` python
 ac.operation_count
 ```
 
 %% Output
 
-    {'adds': 8, 'muls': 2, 'divs': 0}
+    {'adds': 8,
+     'muls': 2,
+     'divs': 0,
+     'sqrts': 0,
+     'fast_sqrts': 0,
+     'fast_inv_sqrts': 0,
+     'fast_div': 0}
 
 %% Cell type:markdown id: tags:
 
 The `pystencils.simp` submodule offers several functions to optimize a collection of assignments.
 It also offers functionality to group optimization into strategies and evaluate them.
 In this example we reduce the number of operations by reusing existing subexpressions to get rid of two unnecessary floating point additions. For more information about assignment collections and simplifications see the [demo notebook](demo_assignment_collection.ipynb).
 
 %% Cell type:code id: tags:
 
 ``` python
 opt_ac = ps.simp.subexpression_substitution_in_existing_subexpressions(ac)
 opt_ac
 ```
 
 %% Output
 
-    Equation Collection for dst_C
+    AssignmentCollection: dst_C, <- f(src_C, src_W, src_S, src_N, src_E)
 
 %% Cell type:code id: tags:
 
 ``` python
 opt_ac.operation_count
 ```
 
 %% Output
 
-    {'adds': 6, 'muls': 1, 'divs': 0}
+    {'adds': 6,
+     'muls': 1,
+     'divs': 0,
+     'sqrts': 0,
+     'fast_sqrts': 0,
+     'fast_inv_sqrts': 0,
+     'fast_div': 0}
 
 %% Cell type:markdown id: tags:
 
 ### d) Ghost layers and iteration region
 
 When creating a kernel with neighbor accesses, *pystencils* automatically restricts the iteration region, such that all accesses are safe.
 
 %% Cell type:code id: tags:
 
 ``` python
 kernel = ps.create_kernel(ps.Assignment(dst[0,0], src[2, 0] + src[-1, 0]))
 ps.show_code(kernel)
 ```
 
 %% Output
 
 
-    FUNC_PREFIX void kernel(double * RESTRICT fd_dst, double * RESTRICT const fd_src)
-    {
-       for (int ctr_0 = 2; ctr_0 < 18; ctr_0 += 1)
-       {
-          double * RESTRICT fd_dst_C = 30*ctr_0 + fd_dst;
-          double * RESTRICT const fd_src_2E = 30*ctr_0 + fd_src + 60;
-          double * RESTRICT const fd_src_W = 30*ctr_0 + fd_src - 30;
-          for (int ctr_1 = 2; ctr_1 < 28; ctr_1 += 1)
-          {
-             fd_dst_C[ctr_1] = fd_src_2E[ctr_1] + fd_src_W[ctr_1];
-          }
-       }
-    }
 
 %% Cell type:markdown id: tags:
 
 When no additional ghost layer information is given, *pystencils* looks at all neighboring field accesses and introduces the required number of ghost layers **for all directions**. In the example above the largest neighbor accesses was ``src[2, 0]``, so theoretically we would need 2 ghost layers only the the end of the x coordinate.
 By default *pystencils* introduces 2 ghost layers at all borders of the domain. The next cell shows how to change this behavior. Be careful with manual ghost layer specification, wrong values may lead to SEGFAULTs.
 
 %% Cell type:code id: tags:
 
 ``` python
 gl_spec = [(0, 2),   # 0 ghost layers at the left, 2 at the right border
            (1, 0)]   # 1 ghost layer at the lower y, one at the upper y coordinate
 kernel = ps.create_kernel(ps.Assignment(dst[0,0], src[2, 0] + src[-1, 0]), ghost_layers=gl_spec)
 ps.show_code(kernel)
 ```
 
 %% Output
 
 
-    FUNC_PREFIX void kernel(double * RESTRICT fd_dst, double * RESTRICT const fd_src)
-    {
-       for (int ctr_0 = 0; ctr_0 < 18; ctr_0 += 1)
-       {
-          double * RESTRICT fd_dst_C = 30*ctr_0 + fd_dst;
-          double * RESTRICT const fd_src_2E = 30*ctr_0 + fd_src + 60;
-          double * RESTRICT const fd_src_W = 30*ctr_0 + fd_src - 30;
-          for (int ctr_1 = 1; ctr_1 < 30; ctr_1 += 1)
-          {
-             fd_dst_C[ctr_1] = fd_src_2E[ctr_1] + fd_src_W[ctr_1];
-          }
-       }
-    }
 
 %% Cell type:markdown id: tags:
 
 ## 2 ) Restrictions
 
 
 ### a) Independence Restriction
 
 *pystencils* only works for kernels where each array element can be updated independently from all other elements. This restriction ensures that the kernels can be easily parallelized and also be run on the GPU. Trying to define kernels where the results depends on the iteration order, leads to a ValueError.
 
 %% Cell type:code id: tags:
 
 ``` python
 invalid_description = [
     ps.Assignment(dst[1, 0], src[1, 0] + src[-1, 0]),
     ps.Assignment(dst[0, 0], src[1, 0] - src[-1, 0]),
 ]
 try:
     invalid_kernel = ps.create_kernel(invalid_description)
     assert False, "Should never be executed"
 except ValueError as e:
     print(e)
 ```
 
 %% Output
 
     Field dst is written at two different locations
 
 %% Cell type:markdown id: tags:
 
 The independence restriction makes sure that the kernel can be safely parallelized by checking the following conditions: If a field is modified inside the kernel, it may only be modified at a single spatial position. In that case the field may also only be read at this position. Fields that are not modified may be read at multiple neighboring positions.
 
 Specifically, this rule allows for in-place updates that don't access neighbors.
 
 %% Cell type:code id: tags:
 
 ``` python
 valid_kernel = ps.create_kernel(ps.Assignment(src[0,0], 2*src[0,0] + 42))
 ```
 
 %% Cell type:markdown id: tags:
 
 If a field stores multiple values per cell, as in the next example, this restriction only applies for accesses with the same index.
 
 %% Cell type:code id: tags:
 
 ``` python
 v = ps.fields("v(2): double[2D]")
 valid_kernel = ps.create_kernel([ps.Assignment(v[0,0](1), 2*v[0,0](1) + 42),
-                                 ps.Assignment(v[0,1](0), 2*v[1,0](0) + 42)])
+                                 ps.Assignment(v[0,1](0), 2*v[0,1](0) + 42)])
 ```
 
 %% Cell type:markdown id: tags:
 
 ### b) Static Single Assignment Form
 
 All assignments that don't write to a field must be in SSA form
 1. Each sympy symbol may only occur once as a left-hand-side (fields can be written multiple times)
 2. A symbol has to be defined before it is used. If it is never defined it is introduced as function parameter
 
 The next cell demonstrates the first SSA restriction:
 
 %% Cell type:code id: tags:
 
 ``` python
 @ps.kernel
 def not_allowed():
     a, b = sp.symbols("a b")
     a @= src[0, 0]
     b @= a + 3
     a @= src[-1, 0]
     dst[0, 0] @= a + b
 try:
     ps.create_kernel(not_allowed)
     assert False
 except ValueError as e:
     print(e)
 ```
 
 %% Output
 
     Assignments not in SSA form, multiple assignments to a
 
 %% Cell type:markdown id: tags:
 
-However, for right hand sides that are Field.Accesses this is allowed:
+Also it is not allowed to write a field at the same location
 
 %% Cell type:code id: tags:
 
 ``` python
 @ps.kernel
-def allowed():
+def not_allowed():
     dst[0, 0] @= src[0, 1] + src[1, 0]
     dst[0, 0] @= 2 * dst[0, 0]
-ps.create_kernel(allowed)
+
+try:
+    ps.create_kernel(not_allowed)
+    assert False
+except ValueError as e:
+    print(e)
 ```
 
 %% Output
 
-    KernelFunction kernel([<double * RESTRICT fd_dst>, <double * RESTRICT const fd_src>])
+    Field dst is written twice at the same location
+
+%% Cell type:markdown id: tags:
+
+This situation should be resolved by introducing temporary variables
+
+%% Cell type:code id: tags:
+
+``` python
+tmp_var = sp.Symbol("a")
+
+@ps.kernel
+def allowed():
+    tmp_var @= src[0, 1] + src[1, 0]
+    dst[0, 0] @= 2 * tmp_var
+
+
+ast = ps.create_kernel(allowed)
+ps.show_code(ast)
+```
+
+%% Output
+
+