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.flake8

+3 −3
Original line number Original line Diff line number Diff line 
[flake8]

[flake8]

max-line-length=120

max-line-length=120

exclude=pystencils/jupyter.py,

exclude=src/pystencils/jupyter.py,

        pystencils/plot.py

        src/pystencils/plot.py

        pystencils/session.py

        src/pystencils/session.py

ignore = W293 W503 W291 C901 E741
 
ignore = W293 W503 W291 C901 E741

.gitattributes

+1 −1
Original line number Original line Diff line number Diff line 
pystencils/_version.py export-subst
 
src/pystencils/_version.py export-subst

.gitignore

+8 −7
Original line number Original line Diff line number Diff line
@@ -5,7 +5,7 @@ __pycache__ 
*.vti

*.vti

/build

/build

/dist

/dist

/*.egg-info

*.egg-info

.cache

.cache

_build

_build

/html_doc

/html_doc
@@ -15,15 +15,16 @@ _build 
_local_tmp

_local_tmp

RELEASE-VERSION

RELEASE-VERSION

test-report

test-report

pystencils/boundaries/createindexlistcython.c

src/pystencils/boundaries/createindexlistcython.c

pystencils/boundaries/createindexlistcython.*.so

src/pystencils/boundaries/createindexlistcython.*.so

pystencils_tests/tmp

tests/tmp

pystencils_tests/var

tests/var

pystencils_tests/kerncraft_inputs/.2d-5pt.c_kerncraft/

tests/kerncraft_inputs/.2d-5pt.c_kerncraft/

pystencils_tests/kerncraft_inputs/.3d-7pt.c_kerncraft/

tests/kerncraft_inputs/.3d-7pt.c_kerncraft/

report.xml

report.xml

coverage_report/

coverage_report/









# macOS

# macOS

**/.DS_Store

**/.DS_Store

*.uuid

.gitlab-ci.yml

+137 −97
Original line number Original line Diff line number Diff line 
stages:

stages:

  - pretest

  - pretest

  - test

  - test

  - nightly

  - docs

  - deploy

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

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





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

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

tests-and-coverage:

tests-and-coverage:

  stage: pretest

  stage: pretest

  except:

  extends: .every-commit

    variables:

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3

      - $ENABLE_NIGHTLY_BUILDS

  before_script:

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

    - pip install -e .

  script:

  script:

    - pip install sympy --upgrade

    - env

    - env

    - pip list

    - pip list

    - export NUM_CORES=$(nproc --all)

    - export NUM_CORES=$(nproc --all)

    - mkdir -p ~/.config/matplotlib

    - mkdir -p ~/.config/matplotlib

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

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

    - mkdir public

    - 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

    - 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

    - python3 -m coverage xml

    - python -m coverage xml

  tags:

  tags:

    - docker

    - docker

    - cuda11

    - cuda11

    - AVX

    - AVX

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

  artifacts:

  artifacts:

    when: always

    when: always

    paths:

    paths:

      - coverage_report

      - coverage_report

      - test-report

      - test-report

    reports:

    reports:

      cobertura: coverage.xml

      coverage_report:

        coverage_format: cobertura

        path: coverage.xml

      junit: report.xml

      junit: report.xml





# pipeline with latest python version

# Normal test with longruns

latest-python:

tests-and-coverage-with-longrun:

  stage: test

  stage: test

  except:

  when: manual

    variables:

  allow_failure: true

      - $ENABLE_NIGHTLY_BUILDS

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full:cupy12.3

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

  before_script:

    - pip install sympy --upgrade

    - pip install -e .

  script:

  script:

    - env

    - env

    - pip list

    - pip list
@@ -50,74 +73,66 @@ latest-python: 
    - mkdir -p ~/.config/matplotlib

    - mkdir -p ~/.config/matplotlib

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

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

    - mkdir public

    - mkdir public

    - py.test -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml

    - py.test -v -n $NUM_CORES

  tags:

  tags:

    - docker

    - docker

    - cuda11

    - AVX

    - AVX

  artifacts:

    when: always

    reports:

      junit: report.xml





# Nightly test  - runs "long run" jobs only

# pipeline with latest python version

test-longrun:

latest-python:

  stage: test

  stage: test

  only:

  extends: .every-commit

    variables:

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

      - $ENABLE_NIGHTLY_BUILDS

  before_script:

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

    - pip install -e .

  script:

  script:

    - env

    - pip list

    - pip install -e .

    - export NUM_CORES=$(nproc --all)

    - export NUM_CORES=$(nproc --all)

    - mkdir -p ~/.config/matplotlib

    - mkdir -p ~/.config/matplotlib

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

    - 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:

  tags:

    - docker

    - docker

    - cuda11

    - AVX

    - AVX

  artifacts:

  artifacts:

    when: always

    when: always

    paths:

      - coverage_report

      - test-report

    reports:

    reports:

      junit: report.xml

      junit: report.xml







# Minimal tests in windows environment

# Minimal tests in windows environment

minimal-windows:

#minimal-windows:

  stage: test

#  stage: test

  except:

#  tags:

    variables:

#    - win

      - $ENABLE_NIGHTLY_BUILDS

#  script:

  tags:

#    - export NUM_CORES=$(nproc --all)

    - win

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

  script:

#    - source activate pystencils

    - export NUM_CORES=$(nproc --all)

#    - pip install joblib

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

#    - pip list

    - source activate pystencils

#    - python -c "import numpy"

    - pip install joblib

#    - py.test -v -m "not (notebook or longrun)"

    - pip list

    - python -c "import numpy"

    - py.test -v -m "not (notebook or longrun)"





ubuntu:

ubuntu:

  stage: test

  stage: test

  except:

  extends: .every-commit

    variables:

      - $ENABLE_NIGHTLY_BUILDS

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

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

  before_script:

  before_script:

    # - apt-get -y remove python3-sympy

    - ln -s /usr/include/locale.h /usr/include/xlocale.h

    - ln -s /usr/include/locale.h /usr/include/xlocale.h

    # - pip3 install `grep -Eo 'sympy[>=]+[0-9\.]+' setup.py | sed 's/>/=/g'`

    - pip3 install -e .

  script:

  script:

    - export NUM_CORES=$(nproc --all)

    - export NUM_CORES=$(nproc --all)

    - mkdir -p ~/.config/matplotlib

    - mkdir -p ~/.config/matplotlib

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

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

    - sed -i 's/--doctest-modules //g' pytest.ini

    - sed -i 's/--doctest-modules //g' pytest.ini

    - env

    - env

    - pip3 list

    - pip list

    - pytest-3 -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml

    - pytest -v -n $NUM_CORES -m "not longrun" --junitxml=report.xml

  tags:

  tags:

    - docker

    - docker

    - cuda11

    - cuda11
@@ -129,10 +144,11 @@ ubuntu: 




.multiarch_template:

.multiarch_template:

  stage: test

  stage: test

  except:

  extends: .every-commit

    variables:

  allow_failure: true

      - $ENABLE_NIGHTLY_BUILDS

  before_script: &multiarch_before_script

  before_script: &multiarch_before_script

    # - pip3 install -v .

    - export PYTHONPATH=src

    - python3 -c "import pystencils as ps; ps.cpu.cpujit.read_config()"

    - python3 -c "import pystencils as ps; ps.cpu.cpujit.read_config()"

    - sed -i '/^fail_under.*/d' pytest.ini

    - sed -i '/^fail_under.*/d' pytest.ini

  script:

  script:
@@ -142,72 +158,68 @@ ubuntu: 
    - sed -i 's/--doctest-modules //g' pytest.ini

    - sed -i 's/--doctest-modules //g' pytest.ini

    - env

    - env

    - pip3 list

    - 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 --reruns 2 --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:

  tags:

    - docker

    - docker

    - AVX

    - multiarch

  artifacts:

  artifacts:

    when: always

    when: always

    paths:

      - coverage_report

    reports:

    reports:

      coverage_report:

        coverage_format: cobertura

        path: coverage.xml

      junit: report.xml

      junit: report.xml





arm64v8:

arm64v8:

  extends: .multiarch_template

  extends: .multiarch_template

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64

  variables:

  variables:

    PYSTENCILS_SIMD: "neon"

    QEMU_CPU: "cortex-a76"

  before_script:

  before_script:

    - *multiarch_before_script

    - *multiarch_before_script

    - sed -i s/march=native/march=armv8-a/g ~/.config/pystencils/config.json





ppc64le:

ppc64le:

  extends: .multiarch_template

  extends: .multiarch_template

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ppc64le

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/ppc64le

  variables:

    PYSTENCILS_SIMD: "vsx"

  before_script:

  before_script:

    - *multiarch_before_script

    - *multiarch_before_script

    - sed -i s/mcpu=native/mcpu=power8/g ~/.config/pystencils/config.json





arm64v9:

arm64v9:

  # Compiler support for SVE is still pretty rough: GCC 10+11 produce incorrect code for fixed-width vectors,

  # SVE support is still unreliable in GCC 13 (incorrect code for fixed-width vectors, internal compiler errors).

  # while Clang 12 produces memory-corrupting heisenbugs unless we enable the address sanitizer.

  # For half precision Clang is necessary

  # 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.

  extends: .multiarch_template

  extends: .multiarch_template

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/arm64

  variables:

  variables:

    PYSTENCILS_SIMD: "sve256,sve512,sve"

    # disable pointer authentication to speed up emulation by 3x

    ASAN_OPTIONS: detect_leaks=0

    QEMU_CPU: "max,pauth-impdef=on"

    LD_PRELOAD: /usr/lib/aarch64-linux-gnu/libasan.so.6

  before_script:

  before_script:

    - *multiarch_before_script

    - *multiarch_before_script

    - sed -i s/march=native/march=armv8-a+sve/g ~/.config/pystencils/config.json

    - sed -i s/g\+\+/clang++/g ~/.config/pystencils/config.json

    - sed -i s/g\+\+/clang++/g ~/.config/pystencils/config.json





riscv64:

riscv64:

  # The RISC-V vector extension is still experimental and needs special compiler flags.

  # RISC-V vector extension support is incomplete in GCC 13.

  # Once they are officially released, this job should be cleaned up to match the others.

  extends: .multiarch_template

  extends: .multiarch_template

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/riscv64

  image: i10git.cs.fau.de:5005/pycodegen/pycodegen/riscv64

  variables:

  variables:

    # explicitly set SIMD as detection requires QEMU >= 8.1

    PYSTENCILS_SIMD: "rvv"

    PYSTENCILS_SIMD: "rvv"

    QEMU_CPU: "rv64,v=true"

    QEMU_CPU: "rv64,v=true,zicboz=true"

  before_script:

  before_script:

    - *multiarch_before_script

    - *multiarch_before_script

    - sed -i 's/march=native/march=rv64imfdv0p10 -menable-experimental-extensions/g' ~/.config/pystencils/config.json

    - sed -i 's/march=native/march=rv64imfdvzicboz/g' ~/.config/pystencils/config.json

    - sed -i s/g\+\+/clang++/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





minimal-conda:

minimal-conda:

  stage: pretest

  stage: pretest

  except:

  extends: .every-commit

    variables:

      - $ENABLE_NIGHTLY_BUILDS

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

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

  before_script:

    - pip install -e .

  script:

  script:

    - python setup.py quicktest

    - python quicktest.py

  tags:

  tags:

    - docker

    - docker

    - cuda

    - cuda
@@ -215,13 +227,13 @@ minimal-conda: 




minimal-sympy-master:

minimal-sympy-master:

  stage: test

  stage: test

  except:

  extends: .every-commit

    variables:

      - $ENABLE_NIGHTLY_BUILDS

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

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

  before_script:

    - pip install -e .

  script:

  script:

    - python -m pip install --upgrade git+https://github.com/sympy/sympy.git

    - python -m pip install --upgrade git+https://github.com/sympy/sympy.git

    - python setup.py quicktest

    - python quicktest.py

  allow_failure: true

  allow_failure: true

  tags:

  tags:

    - docker

    - docker
@@ -247,7 +259,6 @@ pycodegen-integration: 
    - cd ..

    - cd ..

    - pip install -e pystencils/

    - pip install -e pystencils/

    - pip install -e lbmpy/

    - pip install -e lbmpy/

    - pip install -e pygrandchem/

    - cmake --version

    - cmake --version

    - ./install_walberla.sh

    - ./install_walberla.sh

    - export NUM_CORES=$(nproc --all)

    - export NUM_CORES=$(nproc --all)
@@ -257,14 +268,12 @@ pycodegen-integration: 
    - py.test -v -n $NUM_CORES --junitxml=report.xml .

    - py.test -v -n $NUM_CORES --junitxml=report.xml .

    - cd ../lbmpy

    - cd ../lbmpy

    - py.test -v -n $NUM_CORES --junitxml=report.xml .

    - py.test -v -n $NUM_CORES --junitxml=report.xml .

    - cd ../pygrandchem

    - py.test -v -n $NUM_CORES --junitxml=report.xml .

    - cd ../walberla/build/

    - cd ../walberla/build/

    - make -j $NUM_CORES CodegenJacobiCPU CodegenJacobiGPU CodegenPoissonCPU CodegenPoissonGPU MicroBenchmarkGpuLbm LbCodeGenerationExample

    - 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

    - cd apps/benchmarks/UniformGridGPU

    - make -j $NUM_CORES

    - make -j $NUM_CORES

    - cd ../UniformGridGenerated

    - cd ../UniformGridCPU

    - make -j $NUM_CORES

    - make -j $NUM_CORES

  tags:

  tags:

    - docker

    - docker
@@ -275,26 +284,57 @@ pycodegen-integration: 
    reports:

    reports:

      junit: pycodegen/*/report.xml

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

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









flake8-lint:

flake8-lint:

  stage: pretest

  stage: pretest

  except:

  extends: .every-commit

    variables:

      - $ENABLE_NIGHTLY_BUILDS

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

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

  script:

  script:

    - flake8 pystencils

    - flake8 src/pystencils

  tags:

  tags:

    - docker

    - docker









build-documentation:

build-documentation:

  stage: test

  stage: docs

  extends: .every-commit

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

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

  needs: []

  before_script:

    - pip install -e .

  script:

  script:

    - export PYTHONPATH=`pwd`

    - mkdir html_doc

    - mkdir html_doc

    - sphinx-build -b html doc  html_doc

    - sphinx-build -b html doc  html_doc

    - sphinx-build -W -b html doc  html_doc

    - sphinx-build -W -b html doc  html_doc
@@ -307,7 +347,9 @@ build-documentation: 




pages:

pages:

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

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

  extends: .every-commit-master

  stage: deploy

  stage: deploy

  needs: ["tests-and-coverage", "build-documentation"]

  script:

  script:

    - ls -l

    - ls -l

    - mv coverage_report html_doc

    - mv coverage_report html_doc
@@ -317,5 +359,3 @@ pages: 
      - public

      - public

  tags:

  tags:

    - docker
 
    - docker
 
  only:

    - master@pycodegen/pystencils

MANIFEST.in

+1 −6
Original line number Original line Diff line number Diff line 
include README.md

include COPYING.txt

include AUTHORS.txt

include AUTHORS.txt

include CONTRIBUTING.md

include CONTRIBUTING.md

CHANGELOG.md

include CHANGELOG.md
 
global-include *.pyx

include versioneer.py

include pystencils/_version.py

README.md

+6 −3
Original line number Original line Diff line number Diff line
@@ -52,7 +52,7 @@ pip install pystencils[interactive] 
Without `[interactive]` you get a minimal version with very little dependencies.

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





All options:

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

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

- `bench_db`: functionality to store benchmark result in object databases

- `bench_db`: functionality to store benchmark result in object databases

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

- `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]

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

Documentation

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

-------------
@@ -82,3 +82,6 @@ If you use pystencils in a publication, please cite the following articles: 




Overview:

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

  - 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

+2 −2
Original line number Original line Diff line number Diff line
@@ -7,7 +7,7 @@ 
#     conda env create -f conda_environment_user.yml

#     conda env create -f conda_environment_user.yml

#     . activate pystencils

#     . 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

      - ipy_table  # HTML tables for jupyter notebooks

      - pyevtk # VTK output for serial simulations

      - pyevtk # VTK output for serial simulations

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

      - 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

+16 −19
Original line number Original line Diff line number Diff line
@@ -8,7 +8,7 @@ import nbformat 
import pytest

import pytest

from nbconvert import PythonExporter

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

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

# at the same time

# at the same time

from pystencils.cpu import cpujit

from pystencils.cpu import cpujit
@@ -40,51 +40,48 @@ def add_path_to_ignore(path): 








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

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

                  os.path.join(SCRIPT_FOLDER, "pystencils", "opencl", "opencl.autoinit")]

                  os.path.join(SCRIPT_FOLDER, "src", "pystencils", "opencl", "opencl.autoinit")]

add_path_to_ignore('pystencils_tests/benchmark')

add_path_to_ignore('tests/benchmark')

add_path_to_ignore('_local_tmp')

add_path_to_ignore('_local_tmp')









try:

try:

    import pycuda

    import cupy

except ImportError:

except ImportError:

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

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

    add_path_to_ignore('pystencils/gpucuda')

    add_path_to_ignore('src/pystencils/gpu')





try:

try:

    import waLBerla

    import waLBerla

except ImportError:

except ImportError:

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_aligned_array.py"),

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

                       os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_datahandling_parallel.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, "doc/notebooks/03_tutorial_datahandling.ipynb"),

                       os.path.join(SCRIPT_FOLDER, "pystencils/datahandling/parallel_datahandling.py"),

                       os.path.join(SCRIPT_FOLDER, "src/pystencils/datahandling/parallel_datahandling.py"),

                       os.path.join(SCRIPT_FOLDER, "pystencils_tests/test_small_block_benchmark.ipynb")]

                       os.path.join(SCRIPT_FOLDER, "tests/test_small_block_benchmark.ipynb")]





try:

try:

    import blitzdb

    import blitzdb

except ImportError:

except ImportError:

    add_path_to_ignore('pystencils/runhelper')

    add_path_to_ignore('src/pystencils/runhelper')

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

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

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





try:

try:

    import islpy

    import islpy

except ImportError:

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:

try:

    import graphviz

    import graphviz

except ImportError:

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")]

    collect_ignore += [os.path.join(SCRIPT_FOLDER, "doc/notebooks/01_tutorial_getting_started.ipynb")]





try:

try:

    import pyevtk

    import pyevtk

except ImportError:

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")]



# TODO: Remove if Ubuntu 18.04 is no longer supported

if pytest_version < 50403:

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





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

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

doc/conf.py

100644 → 100755
+3 −3
Original line number Original line Diff line number Diff line
@@ -26,14 +26,14 @@ templates_path = ['_templates'] 
source_suffix = '.rst'

source_suffix = '.rst'

master_doc = 'index'

master_doc = 'index'





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

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

author = 'Martin Bauer'

author = 'Martin Bauer, Markus Holzer, Frederik Hennig'

# The short X.Y version (including .devXXXX, rcX, b1 suffixes if present)

# 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'(\d+\.\d+)\.\d+(.*)', r'\1\2', pystencils.__version__)

version = re.sub(r'(\.dev\d+).*?$', r'\1', version)

version = re.sub(r'(\.dev\d+).*?$', r'\1', version)

# The full version, including alpha/beta/rc tags.

# The full version, including alpha/beta/rc tags.

release = pystencils.__version__

release = pystencils.__version__

language = None

language = 'en'

exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']

exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']

default_role = 'any'

default_role = 'any'

pygments_style = 'sphinx'

pygments_style = 'sphinx'

doc/sphinx/kernel_compile_and_call.rst

+6 −6
Original line number Original line Diff line number Diff line
@@ -11,11 +11,11 @@ Creating kernels 
.. autoclass:: pystencils.CreateKernelConfig

.. autoclass:: pystencils.CreateKernelConfig

    :members:

    :members:





.. autofunction:: pystencils.create_domain_kernel

.. autofunction:: pystencils.kernelcreation.create_domain_kernel





.. autofunction:: pystencils.create_indexed_kernel

.. autofunction:: pystencils.kernelcreation.create_indexed_kernel





.. autofunction:: pystencils.create_staggered_kernel

.. autofunction:: pystencils.kernelcreation.create_staggered_kernel









Code printing

Code printing
@@ -27,11 +27,11 @@ Code printing 
GPU Indexing

GPU Indexing

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

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





.. autoclass:: pystencils.gpucuda.AbstractIndexing

.. autoclass:: pystencils.gpu.AbstractIndexing

   :members:

   :members:





.. autoclass:: pystencils.gpucuda.BlockIndexing

.. autoclass:: pystencils.gpu.BlockIndexing

   :members:

   :members:





.. autoclass:: pystencils.gpucuda.LineIndexing

.. autoclass:: pystencils.gpu.LineIndexing

   :members:
 
   :members:

pyproject.toml

0 → 100644
+98 −0
Original line number Original line Diff line number Diff line 
[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/backends/cuda_known_functions.txt

deleted100644 → 0
+0 −294
Original line number Original line Diff line number Diff line 
__prof_trigger

printf



__syncthreads

__syncthreads_count

__syncthreads_and

__syncthreads_or

__syncwarp

__threadfence

__threadfence_block

__threadfence_system



atomicAdd

atomicSub

atomicExch

atomicMin

atomicMax

atomicInc

atomicDec

atomicAnd

atomicOr

atomicXor

atomicCAS



__all_sync

__any_sync

__ballot_sync

__active_mask



__shfl_sync

__shfl_up_sync

__shfl_down_sync

__shfl_xor_sync



__match_any_sync

__match_all_sync



__isGlobal

__isShared

__isConstant

__isLocal



tex1Dfetch

tex1D

tex2D

tex3D



sqrtf

rsqrtf

cbrtf

rcbrtf

hypotf

rhypotf

norm3df

rnorm3df

norm4df

rnorm4df

normf

rnormf

expf

exp2f

exp10f

expm1f

logf

log2f

log10f

log1pf

sinf

cosf

tanf

sincosf

sinpif

cospif

sincospif

asinf

acosf

atanf

atan2f

sinhf

coshf

tanhf

asinhf

acoshf

atanhf

powf

erff

erfcf

erfinvf

erfcinvf

erfcxf

normcdff

normcdfinvf

lgammaf

tgammaf

fmaf

frexpf

ldexpf

scalbnf

scalblnf

logbf

ilogbf

j0f

j1f

jnf

y0f

y1f

ynf

cyl_bessel_i0f

cyl_bessel_i1f

fmodf

remainderf

remquof

modff

fdimf

truncf

roundf

rintf

nearbyintf

ceilf

floorf

lrintf

lroundf

llrintf

llroundf



sqrt

rsqrt

cbrt

rcbrt

hypot

rhypot

norm3d

rnorm3d

norm4d

rnorm4d

norm

rnorm

exp

exp2

exp10

expm1

log

log2

log10

log1p

sin

cos

tan

sincos

sinpi

cospi

sincospi

asin

acos

atan

atan2

sinh

cosh

tanh

asinh

acosh

atanh

pow

erf

erfc

erfinv

erfcinv

erfcx

normcdf

normcdfinv

lgamma

tgamma

fma

frexp

ldexp

scalbn

scalbln

logb

ilogb

j0

j1

jn

y0

y1

yn

cyl_bessel_i0

cyl_bessel_i1

fmod

remainder

remquo

mod

fdim

trunc

round

rint

nearbyint

ceil

floor

lrint

lround

llrint

llround



__fdividef

__sinf

__cosf

__tanf

__sincosf

__logf

__log2f

__log10f

__expf

__exp10f

__powf



__fadd_rn

__fsub_rn

__fmul_rn

__fmaf_rn

__frcp_rn

__fsqrt_rn

__frsqrt_rn

__fdiv_rn



__fadd_rz

__fsub_rz

__fmul_rz

__fmaf_rz

__frcp_rz

__fsqrt_rz

__frsqrt_rz

__fdiv_rz



__fadd_ru

__fsub_ru

__fmul_ru

__fmaf_ru

__frcp_ru

__fsqrt_ru

__frsqrt_ru

__fdiv_ru



__fadd_rd

__fsub_rd

__fmul_rd

__fmaf_rd

__frcp_rd

__fsqrt_rd

__frsqrt_rd

__fdiv_rd



__fdividef

__expf

__exp10f

__logf

__log2f

__log10f

__sinf

__cosf

__sincosf

__tanf

__powf



__dadd_rn

__dsub_rn

__dmul_rn

__fma_rn

__ddiv_rn

__drcp_rn

__dsqrt_rn



__dadd_rz

__dsub_rz

__dmul_rz

__fma_rz

__ddiv_rz

__drcp_rz

__dsqrt_rz



__dadd_ru

__dsub_ru

__dmul_ru

__fma_ru

__ddiv_ru

__drcp_ru

__dsqrt_ru



__dadd_rd

__dsub_rd

__dmul_rd

__fma_rd

__ddiv_rd

__drcp_rd

__dsqrt_rd

pystencils/data_types.py

deleted100644 → 0
+0 −814

File deleted.

Preview size limit exceeded, changes collapsed.

pystencils/datahandling/pycuda.py

deleted100644 → 0
+0 −52
Original line number Original line Diff line number Diff line 
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

deleted100644 → 0
+0 −19
Original line number Original line Diff line number Diff line 
#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

}

pystencils/include/opencl_stdint.h

deleted100644 → 0
+0 −15
Original line number Original line Diff line number Diff line 
#ifndef OPENCL_STDINT

#define OPENCL_STDINT



typedef unsigned int      uint_t;



typedef signed char       int8_t;

typedef signed short      int16_t;

typedef signed int        int32_t;

typedef signed long int   int64_t;

typedef unsigned char     uint8_t;

typedef unsigned short    uint16_t;

typedef unsigned int      uint32_t;

typedef unsigned long int uint64_t;



#endif

pystencils_tests/test_address_of.py

deleted100644 → 0
+0 −48
Original line number Original line Diff line number Diff line 
"""

Test of pystencils.data_types.address_of

"""

import sympy as sp

import pystencils

from pystencils.data_types import PointerType, address_of, cast_func, create_type

from pystencils.simp.simplifications import sympy_cse





def test_address_of():

    x, y = pystencils.fields('x,y: int64[2d]')

    s = pystencils.TypedSymbol('s', PointerType(create_type('int64')))



    assert address_of(x[0, 0]).canonical() == x[0, 0]

    assert address_of(x[0, 0]).dtype == PointerType(x[0, 0].dtype, restrict=True)

    assert address_of(sp.Symbol("a")).dtype == PointerType('void', restrict=True)



    assignments = pystencils.AssignmentCollection({

        s: address_of(x[0, 0]),

        y[0, 0]: cast_func(s, create_type('int64'))

    }, {})



    ast = pystencils.create_kernel(assignments)

    pystencils.show_code(ast)



    assignments = pystencils.AssignmentCollection({

        y[0, 0]: cast_func(address_of(x[0, 0]), create_type('int64'))

    }, {})



    ast = pystencils.create_kernel(assignments)

    pystencils.show_code(ast)





def test_address_of_with_cse():

    x, y = pystencils.fields('x,y: int64[2d]')

    s = pystencils.TypedSymbol('s', PointerType(create_type('int64')))



    assignments = pystencils.AssignmentCollection({

        y[0, 0]: cast_func(address_of(x[0, 0]), create_type('int64')) + s,

        x[0, 0]: cast_func(address_of(x[0, 0]), create_type('int64')) + 1

    }, {})



    ast = pystencils.create_kernel(assignments)

    pystencils.show_code(ast)

    assignments_cse = sympy_cse(assignments)



    ast = pystencils.create_kernel(assignments_cse)

    pystencils.show_code(ast)

pystencils_tests/test_complex_numbers.py

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

#

# Copyright © 2019 Stephan Seitz <stephan.seitz@fau.de>

#

# Distributed under terms of the GPLv3 license.

"""



"""



import itertools



import numpy as np

import pytest

import sympy

from sympy.functions import im, re



import pystencils

from pystencils import AssignmentCollection

from pystencils.data_types import TypedSymbol, create_type



X, Y = pystencils.fields('x, y: complex64[2d]')

A, B = pystencils.fields('a, b: float32[2d]')

S1, S2, T = sympy.symbols('S1, S2, T')



TEST_ASSIGNMENTS = [

    AssignmentCollection({X[0, 0]: 1j}),

    AssignmentCollection({

        S1: re(Y.center),

        S2: im(Y.center),

        X[0, 0]: 2j * S1 + S2

    }),

    AssignmentCollection({

        A.center: re(Y.center),

        B.center: im(Y.center),

    }),

    AssignmentCollection({

        Y.center: re(Y.center) + X.center + 2j,

    }),

    AssignmentCollection({

        T: 2 + 4j,

        Y.center: X.center / T,

    })

]



SCALAR_DTYPES = ['float32', 'float64']





@pytest.mark.parametrize("assignment, scalar_dtypes",

                         itertools.product(TEST_ASSIGNMENTS, (np.float32,)))

@pytest.mark.parametrize('target', (pystencils.Target.CPU, pystencils.Target.GPU))

def test_complex_numbers(assignment, scalar_dtypes, target):

    ast = pystencils.create_kernel(assignment,

                                   target=target,

                                   data_type=scalar_dtypes)

    code = pystencils.get_code_str(ast)



    print(code)

    assert "Not supported" not in code



    if target == pystencils.Target.GPU:

        pytest.importorskip('pycuda')



    kernel = ast.compile()

    assert kernel is not None





X, Y = pystencils.fields('x, y: complex128[2d]')

A, B = pystencils.fields('a, b: float64[2d]')

S1, S2 = sympy.symbols('S1, S2')

T128 = TypedSymbol('ts', create_type('complex128'))



TEST_ASSIGNMENTS = [

    AssignmentCollection({X[0, 0]: 1j}),

    AssignmentCollection({

        S1: re(Y.center),

        S2: im(Y.center),

        X[0, 0]: 2j * S1 + S2

    }),

    AssignmentCollection({

        A.center: re(Y.center),

        B.center: im(Y.center),

    }),

    AssignmentCollection({

        Y.center: re(Y.center) + X.center + 2j,

    }),

    AssignmentCollection({

        T128: 2 + 4j,

        Y.center: X.center / T128,

    })

]



SCALAR_DTYPES = ['float64']





@pytest.mark.parametrize("assignment", TEST_ASSIGNMENTS)

@pytest.mark.parametrize('target', (pystencils.Target.CPU, pystencils.Target.GPU))

def test_complex_numbers_64(assignment, target):

    ast = pystencils.create_kernel(assignment,

                                   target=target,

                                   data_type='double')

    code = pystencils.get_code_str(ast)



    print(code)

    assert "Not supported" not in code



    if target == pystencils.Target.GPU:

        pytest.importorskip('pycuda')



    kernel = ast.compile()

    assert kernel is not None





@pytest.mark.parametrize('dtype', (np.float32, np.float64))

@pytest.mark.parametrize('target', (pystencils.Target.CPU, pystencils.Target.GPU))

@pytest.mark.parametrize('with_complex_argument', ('with_complex_argument', False))

def test_complex_execution(dtype, target, with_complex_argument):



    complex_dtype = f'complex{64 if dtype ==np.float32 else 128}'

    x, y = pystencils.fields(f'x, y:  {complex_dtype}[2d]')



    x_arr = np.zeros((20, 30), complex_dtype)

    y_arr = np.zeros((20, 30), complex_dtype)



    if with_complex_argument:

        a = pystencils.TypedSymbol('a', create_type(complex_dtype))

    else:

        a = (2j+1)



    assignments = AssignmentCollection({

        y.center: x.center + a

    })



    if target == pystencils.Target.GPU:

        pytest.importorskip('pycuda')

        from pycuda.gpuarray import zeros

        x_arr = zeros((20, 30), complex_dtype)

        y_arr = zeros((20, 30), complex_dtype)



    kernel = pystencils.create_kernel(assignments, target=target, data_type=dtype).compile()



    if with_complex_argument:

        kernel(x=x_arr, y=y_arr, a=2j+1)

    else:

        kernel(x=x_arr, y=y_arr)



    if target == pystencils.Target.GPU:

        y_arr = y_arr.get()

    assert np.allclose(y_arr, 2j+1)

pystencils_tests/test_create_kernel_backwards_compability.py

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Original line number Original line Diff line number Diff line 
import pytest



import pystencils as ps

import numpy as np





# This test aims to trigger deprication warnings. Thus the warnings should not be displayed in the warning summary.

def test_create_kernel_backwards_compatibility():

    size = (30, 20)



    src_field_string = np.random.rand(*size)

    src_field_enum = np.copy(src_field_string)

    src_field_config = np.copy(src_field_string)

    dst_field_string = np.zeros(size)

    dst_field_enum = np.zeros(size)

    dst_field_config = np.zeros(size)



    f = ps.Field.create_from_numpy_array("f", src_field_enum)

    d = ps.Field.create_from_numpy_array("d", dst_field_enum)



    jacobi = ps.Assignment(d[0, 0], (f[1, 0] + f[-1, 0] + f[0, 1] + f[0, -1]) / 4)

    ast_enum = ps.create_kernel(jacobi, target=ps.Target.CPU).compile()

    with pytest.warns(DeprecationWarning):

        ast_string = ps.create_kernel(jacobi, target='cpu').compile()

    # noinspection PyTypeChecker

    with pytest.warns(DeprecationWarning):

        ast_config = ps.create_kernel(jacobi, config=ps.CreateKernelConfig(target='cpu')).compile()

    ast_enum(f=src_field_enum, d=dst_field_enum)

    ast_string(f=src_field_string, d=dst_field_string)

    ast_config(f=src_field_config, d=dst_field_config)



    error = np.sum(np.abs(dst_field_enum - dst_field_string))

    np.testing.assert_almost_equal(error, 0.0)

    error = np.sum(np.abs(dst_field_enum - dst_field_config))

    np.testing.assert_almost_equal(error, 0.0)

pystencils_tests/test_cuda_known_functions.py

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Original line number Original line Diff line number Diff line 
import sympy



import pytest



import pystencils

from pystencils.astnodes import get_dummy_symbol

from pystencils.backends.cuda_backend import CudaSympyPrinter

from pystencils.data_types import address_of

from pystencils.enums import Target





def test_cuda_known_functions():

    printer = CudaSympyPrinter()

    print(printer.known_functions)



    x, y = pystencils.fields('x,y: float32 [2d]')



    assignments = pystencils.AssignmentCollection({

        get_dummy_symbol(): sympy.Function('atomicAdd')(address_of(y.center()), 2),

        y.center():  sympy.Function('rsqrtf')(x[0, 0])

    })



    ast = pystencils.create_kernel(assignments, target=Target.GPU)

    pytest.importorskip('pycuda')

    pystencils.show_code(ast)

    kernel = ast.compile()

    assert(kernel is not None)





def test_cuda_but_not_c():

    x, y = pystencils.fields('x,y: float32 [2d]')



    assignments = pystencils.AssignmentCollection({

        get_dummy_symbol(): sympy.Function('atomicAdd')(address_of(y.center()), 2),

        y.center():  sympy.Function('rsqrtf')(x[0, 0])

    })



    ast = pystencils.create_kernel(assignments, target=Target.CPU)

    pystencils.show_code(ast)





def test_cuda_unknown():

    x, y = pystencils.fields('x,y: float32 [2d]')



    assignments = pystencils.AssignmentCollection({

        get_dummy_symbol(): sympy.Function('wtf')(address_of(y.center()), 2),

    })



    ast = pystencils.create_kernel(assignments, target=Target.GPU)

    pystencils.show_code(ast)

pystencils_tests/test_dot_printer.ipynb

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Original line number Original line Diff line number Diff line 
%% Cell type:code id: tags:



``` python

import pytest

pytest.importorskip('graphviz')

```



%% Cell type:code id: tags:



``` python

from pystencils.session import *

from pystencils.astnodes import Block, Conditional

```



%% Cell type:code id: tags:



``` python

src, dst = ps.fields("src, dst: double[2D]", layout='c')



true_block = Block([ps.Assignment(dst[0, 0], src[-1, 0])])

false_block = Block([ps.Assignment(dst[0, 0], src[1, 0])])

ur = [true_block, Conditional(dst.center() > 0.0, true_block, false_block)]



ast = ps.create_kernel(ur)

```



%% Cell type:code id: tags:



``` python

ps.to_dot(ast, graph_style={'size': "9.5,12.5"})

```



%% Output



img src="data:image/svg+xml;utf8,<?xml version="1.0" encoding="UTF-8" standalone="no"?><!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN""http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"><!-- Generated by graphviz version 2.40.1 (20161225.0304)--><!-- Title: %3 Pages: 1 --><svg width="684pt" height="290pt"viewBox="0.00 0.00 684.00 289.51" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g id="graph0" class="graph" transform="scale(.4128 .4128) rotate(0) translate(4 697.3797)"><title>%3</title><polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-697.3797 1653.0784,-697.3797 1653.0784,4 -4,4"/><!-- 140060050351120 --><g id="node1" class="node"><title>140060050351120</title><ellipse fill="#a056db" stroke="#000000" cx="243.1436" cy="-675.3797" rx="111.5806" ry="18"/><text text-anchor="middle" x="243.1436" y="-671.6797" font-family="Times,serif" font-size="14.00" fill="#000000">Func: kernel (dst,src)</text></g><!-- 140060034299536 --><g id="node19" class="node"><title>140060034299536</title><ellipse fill="#dbc256" stroke="#000000" cx="243.1436" cy="-603.3797" rx="37.0935" ry="18"/><text text-anchor="middle" x="243.1436" y="-599.6797" font-family="Times,serif" font-size="14.00" fill="#000000">Block</text></g><!-- 140060050351120&#45;&gt;140060034299536 --><g id="edge18" class="edge"><title>140060050351120&#45;&gt;140060034299536</title><path fill="none" stroke="#000000" d="M243.1436,-657.2111C243.1436,-649.5107 243.1436,-640.3541 243.1436,-631.7964"/><polygon fill="#000000" stroke="#000000" points="246.6437,-631.793 243.1436,-621.793 239.6437,-631.793 246.6437,-631.793"/></g><!-- 140060034299984 --><g id="node2" class="node"><title>140060034299984</title><ellipse fill="#3498db" stroke="#000000" cx="243.1436" cy="-531.3797" rx="86.3847" ry="18"/><text text-anchor="middle" x="243.1436" y="-527.6797" font-family="Times,serif" font-size="14.00" fill="#000000">Loop over dim 0</text></g><!-- 140060034299664 --><g id="node18" class="node"><title>140060034299664</title><ellipse fill="#dbc256" stroke="#000000" cx="243.1436" cy="-459.3797" rx="37.0935" ry="18"/><text text-anchor="middle" x="243.1436" y="-455.6797" font-family="Times,serif" font-size="14.00" fill="#000000">Block</text></g><!-- 140060034299984&#45;&gt;140060034299664 --><g id="edge16" class="edge"><title>140060034299984&#45;&gt;140060034299664</title><path fill="none" stroke="#000000" d="M243.1436,-513.2111C243.1436,-505.5107 243.1436,-496.3541 243.1436,-487.7964"/><polygon fill="#000000" stroke="#000000" points="246.6437,-487.793 243.1436,-477.793 239.6437,-487.793 246.6437,-487.793"/></g><!-- 140060034380240 --><g id="node3" class="node"><title>140060034380240</title><ellipse fill="#56db7f" stroke="#000000" cx="72.1436" cy="-387.3797" rx="72.2875" ry="18"/><text text-anchor="middle" x="72.1436" y="-383.6797" font-family="Times,serif" font-size="14.00" fill="#000000">_data_dst_00</text></g><!-- 140060034381584 --><g id="node4" class="node"><title>140060034381584</title><ellipse fill="#56db7f" stroke="#000000" cx="243.1436" cy="-387.3797" rx="81.4863" ry="18"/><text text-anchor="middle" x="243.1436" y="-383.6797" font-family="Times,serif" font-size="14.00" fill="#000000">_data_src_0m1</text></g><!-- 140060034300688 --><g id="node5" class="node"><title>140060034300688</title><ellipse fill="#3498db" stroke="#000000" cx="429.1436" cy="-387.3797" rx="86.3847" ry="18"/><text text-anchor="middle" x="429.1436" y="-383.6797" font-family="Times,serif" font-size="14.00" fill="#000000">Loop over dim 1</text></g><!-- 140060034298960 --><g id="node17" class="node"><title>140060034298960</title><ellipse fill="#dbc256" stroke="#000000" cx="429.1436" cy="-315.3797" rx="37.0935" ry="18"/><text text-anchor="middle" x="429.1436" y="-311.6797" font-family="Times,serif" font-size="14.00" fill="#000000">Block</text></g><!-- 140060034300688&#45;&gt;140060034298960 --><g id="edge12" 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class="node"><title>140060034299472</title><ellipse fill="#56bd7f" stroke="#000000" cx="857.1436" cy="-202.6899" rx="372.7906" ry="58.8803"/><text text-anchor="middle" x="857.1436" y="-228.9899" font-family="Times,serif" font-size="14.00" fill="#000000">else: </text><text text-anchor="middle" x="857.1436" y="-213.9899" font-family="Times,serif" font-size="14.00" fill="#000000"> Block _data_dst_00 ← _data_dst + _stride_dst_0*ctr_0</text><text text-anchor="middle" x="857.1436" y="-198.9899" font-family="Times,serif" font-size="14.00" fill="#000000">_data_src_01 ← _data_src + _stride_src_0*ctr_0 + _stride_src_0</text><text text-anchor="middle" x="857.1436" y="-183.9899" font-family="Times,serif" font-size="14.00" fill="#000000">_data_dst_00[_stride_dst_1*ctr_1] ← _data_src_01[_stride_src_1*ctr_1]</text><text text-anchor="middle" x="857.1436" y="-168.9899" font-family="Times,serif" font-size="14.00" fill="#000000"> </text></g><!-- 140060037556304 --><g id="node12" 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