Merge branch 'master' of https://github.com/Parallel-in-Time/pySDC

Author: pancetta

.github/workflows/ci_pipeline.yml

@@ -25,7 +25,7 @@ jobs:
         with:
           environment-file: ${{ env.YML }}
           create-args: >-
-              python=3.12
+              python=3.13
       - name: Code reformatting with black
         run: |
           black pySDC  --check --diff --color
@@ -39,7 +39,7 @@ jobs:
       fail-fast: false
       matrix:
         env: ['base', 'fenics', 'mpi4py', 'petsc', 'pytorch']
-        python: ['3.9', '3.10', '3.11', '3.12']
+        python: ['3.9', '3.10', '3.11', '3.12', '3.13']
     defaults:
       run:
         shell: bash -l {0}
@@ -55,6 +55,9 @@ jobs:
       - name: Install additional packages as needed
         run: |
           micromamba install -y --file etc/environment-tests.yml --freeze-installed
+      - name: Install pySDC as a package in the current environment
+        run: |
+          pip install --no-deps -e .
       - name: Run pytest for CPU stuff
         run: |
           echo "print('Loading sitecustomize.py...')
@@ -67,7 +70,7 @@ jobs:
           mv .coverage coverage_${{ matrix.env }}.dat
       - name: Uploading artifacts
         uses: actions/upload-artifact@v4
-        if: matrix.python == '3.12'
+        if: matrix.python == '3.13'
         with:
           name: test-artifacts-cpu-${{ matrix.env }}
           path: |
@@ -95,7 +98,6 @@ jobs:
           - Second_orderSDC
           - soft_failure
           - TOMS
-        python: ['3.9', '3.10', '3.11', '3.12']
     defaults:
       run:
         shell: bash -l {0}
@@ -106,8 +108,6 @@ jobs:
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: "pySDC/projects/${{ matrix.env }}/environment.yml"
-          create-args: >-
-              python=${{ matrix.python }}
       - name: Install additional packages as needed
         run: |
           micromamba install -y --file etc/environment-tests.yml --freeze-installed
@@ -123,7 +123,6 @@ jobs:
           mv .coverage coverage_${{ matrix.env }}.dat
       - name: Uploading artifacts
         uses: actions/upload-artifact@v4
-        if: matrix.python == '3.12'
         with:
           name: test-artifacts-project-${{ matrix.env }}
           path: |
@@ -166,6 +165,69 @@ jobs:
           path: |
             data_libpressio
             coverage_libpressio.dat
+
+  user_firedrake_tests:
+    runs-on: ubuntu-latest
+    container:
+      image: firedrakeproject/firedrake-vanilla-default:latest
+      options: --user root
+      volumes:
+        - ${{ github.workspace }}:/repositories
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Fix HOME
+        # For unknown reasons GitHub actions overwrite HOME to /github/home
+        # which will break everything unless fixed
+        # (https://github.com/actions/runner/issues/863)
+        run: echo "HOME=/home/firedrake" >> "$GITHUB_ENV"
+      - name: Checkout pySDC
+        uses: actions/checkout@v4
+        with: 
+          path: ./pySDC
+      - name: Checkout gusto
+        uses: actions/checkout@v4
+        with:
+          repository: firedrakeproject/gusto
+          path: ./gusto_repo
+      - name: Create virtual environment
+        # pass '--system-site-packages' so Firedrake can be found
+        run: python3 -m venv --system-site-packages venv-pySDC
+
+      - name: Install pySDC
+        run: |
+          . venv-pySDC/bin/activate
+          pip install -e /repositories/pySDC
+          # test installation
+          python -c "import pySDC; print(f'pySDC module: {pySDC}')"
+      - name: Install gusto
+        run: |
+          . venv-pySDC/bin/activate
+          pip install -e /repositories/gusto_repo
+          # test installation
+          python -c "import gusto; print(f'gusto module: {gusto}')"
+      - name: run pytest
+        run: |
+          . venv-pySDC/bin/activate
+          firedrake-clean
+          cd ./pySDC
+          python -m coverage run -m pytest --continue-on-collection-errors -v --durations=0 /repositories/pySDC/pySDC/tests -m firedrake
+        timeout-minutes: 45
+      - name: Make coverage report
+        run: |
+
+          cd ./pySDC
+          mv data ../data_firedrake
+          coverage combine
+          mv .coverage ../coverage_firedrake.dat
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-artifacts-firedrake
+          path: |
+            data_firedrake
+            coverage_firedrake.dat
          
   user_monodomain_tests_linux:
     runs-on: ubuntu-latest

.github/workflows/gitlab_ci.yml

@@ -106,7 +106,7 @@ jobs:
           echo "Merge the two parts of the Merge-Request to test the resulting version"
           git merge "${{ github.event.pull_request.head.sha }}"
       - name: Mirror and wait for Gitlab-CI
-        uses: jakob-fritz/[email protected]
+        uses: jakob-fritz/[email protected].1
         env:
           MODE: 'all'  # Either 'mirror', 'get_status', 'get_artifact', or 'all'
           GITLAB_TOKEN: ${{ secrets.GITLAB_SECRET }}

.gitignore

@@ -10,6 +10,8 @@ step_*.png
 *.swp
 *_data.json
 !_dataRef.json
+*.pysdc
+*.vtr
 
 # Created by https://www.gitignore.io
 

.gitlab-ci.yml

@@ -27,24 +27,8 @@ prepare_JUWELS:
     - shell
   script:
     - mkdir -p benchmarks
-    - module --force purge
-    - module load Stages/2024
-    - module load GCC
-    - module load OpenMPI
-    - module load FFTW
-    - module load mpi4py
-    - module load SciPy-Stack
-    - module load CuPy
     - jutil env activate -p ${JUWELS_PROJECT}
-    - python -m venv --clear $SCRATCH/.venv/pySDC
-    - source $SCRATCH/.venv/pySDC/bin/activate
-    - pip install -e .
-    - pip install pytest-benchmark coverage
-    - git submodule add -f https://github.com/brownbaerchen/mpi4py-fft.git
-    - cd mpi4py-fft
-    - git checkout cupy_implementation
-    - FFTW_LIBRARY_DIR="/p/software/juwels/stages/2024/software/FFTW/3.3.10-GCC-12.3.0/lib64" pip install --force-reinstall .
-    - cd ../
+    - source ./etc/venv_juwels/setup.sh
 
 
 test_JUWELS:
@@ -77,16 +61,8 @@ test_JUWELS:
       - sbatch.out
   before_script:
     - mkdir -p benchmarks
-    - module --force purge
-    - module load Stages/2024
-    - module load GCC
-    - module load OpenMPI
-    - module load FFTW
-    - module load mpi4py
-    - module load SciPy-Stack
-    - module load CuPy
     - jutil env activate -p ${JUWELS_PROJECT}
-    - source $SCRATCH/.venv/pySDC/bin/activate
+    - source ./etc/venv_juwels/activate.sh
   script:
     - bash etc/check_node_avail.sh || PARTITION_AVAIL=$?
     - if [ -n "$PARTITION_AVAIL" ] ; then exit $PARTITION_AVAIL ; fi

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 :arrow_left: [Back to main page](./README.md)
 
+-   April 11, 2025: Version 5.6 adds a framework for MPI-parallel I/O, developed by [\@tlunet](https://github.com/tlunet), making it easier to visualize the data obtained with pySDC on HPC machines in software such as ParaView.
+    Also, pySDC is now compatible with the finite element library [Firedrake](https://github.com/firedrakeproject/firedrake) and the geophysical fluid dynamics library
+    [Gusto](https://github.com/firedrakeproject/gusto), thanks to [\@jshipton](https://github.com/jshipton) and [\@brownbaerchen](https://github.com/brownbaerchen).
+    The former allows to setup PDEs with finite element discretizations in pySDC and then solve in time with SDC and PFASST, while the latter allows to setup a geophysical fluid dynamics problem and then use pySDC with any SDC setup as a timestepper in Gusto.
 -   June 24, 2024: Major summer cleanup with Version 5.5. [\@tlunet](https://github.com/tlunet) extracted all quadrature-related stuff into his new standalone code 
     [qmat](https://github.com/Parallel-in-Time/qmat), which makes pySDC much more focussed and both parts easier to maintain. 
     [\@lisawim](https://github.com/lisawim) worked a lot on the DAE sweepers (including an MPI-parallel version), while [\@brownbaerchen](https://github.com/brownbaerchen) has fun with GPUs.

CITATION.cff

@@ -28,11 +28,15 @@ authors:
     given-names: Jakob
     orcid: https://orcid.org/0000-0001-6280-8396
     affiliation: "Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany"
+  - family-names: Shipton
+    given-names: Jemma
+    orcid: https://orcid.org/0000-0002-8635-0831
+    affiliation: "Department of Mathematics and Statistics, University of Exeter, Exeter, UK"
 
 
-version: 5.5.2
+version: 5.6
 doi: 10.5281/zenodo.594191
-date-released: 2024-09-23
+date-released: 2025-04-11
 keywords: 
   - "parallel-in-time"
   - "spectral deferred corrections"

README.md

@@ -5,6 +5,8 @@
 [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
 [![SQAaaS badge shields.io](https://img.shields.io/badge/sqaaas%20software-silver-lightgrey)](https://api.eu.badgr.io/public/assertions/aS8J0NDTTjCyYP6iVufviQ "SQAaaS silver badge achieved")
 [![PyPI - Downloads](https://img.shields.io/pypi/dm/pySDC?logo=pypi)](https://pypistats.org/packages/pysdc)
+[![HiRSE Code Promo Badge](https://img.shields.io/badge/Promo-8db427?label=HiRSE&labelColor=005aa0&link=https%3A%2F%2Fgo.fzj.de%2FCodePromo)](https://go.fzj.de/CodePromo)
+[![SWH](https://archive.softwareheritage.org/badge/origin/https://github.com/Parallel-in-Time/pySDC/)](https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/Parallel-in-Time/pySDC)
 
 # Welcome to pySDC!
 
@@ -19,8 +21,8 @@ implemented.
 
 -   Variants of SDC: explicit, implicit, IMEX, multi-implicit, Verlet,
     multi-level, diagonal, multi-step
--   Variants of PFASST: virtual parallel or MPI-based parallel,
-    classical of multigrid perspective
+-   Variants of PFASST: virtually parallel or MPI-based parallel,
+    classical or multigrid perspective
 -   8 tutorials: from setting up a first collocation problem to SDC,
     PFASST and advanced topics
 -   Projects: many documented projects with defined and tested outcomes
@@ -43,12 +45,11 @@ The code is hosted on GitHub, see
 will give you a core version of `pySDC` to work with,
 working with the developer version is most often the better choice. We
 thus recommend to checkout the code from GitHub and install the
-dependencies e.g. by using a [conda](https://conda.io/en/latest/)
-environment. For this, `pySDC` ships with environment files
-which can be found in the folder `etc/`. Use these as e.g.
+dependencies e.g. by using [micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html). For this, `pySDC` ships with environment files
+which can be found in the folder `etc/` or within the projects. Use these as e.g.
 
 ``` bash
-conda env create -f etc/environment-base.yml
+micromamba create -f etc/environment-base.yml
 ```
 
 If you want to install the developer version using `pip` directly from the GitHub repository, use this:
@@ -102,7 +103,8 @@ The current software release can be cited using Zenodo:
 
 `pySDC` code was originally developed by [Robert Speck (@pancetta)](https://github.com/pancetta),
 and is now maintained and developed by a small community of scientists interested in SDC methods.
-Checkout the [Changelog](./CHANGELOG.md) to see pySDC's evolution since 2016.
+Checkout the [Changelog](./CHANGELOG.md) to see pySDC's evolution since 2016. It has a
+software management plan (SWP), too, see [here](https://smw.dsw.elixir-europe.org/wizard/projects/c3dda921-b7b0-4f4d-b5dc-778b9780552d).
 
 Any contribution is dearly welcome! If you want to contribute, please take the time to read our [Contribution Guidelines](./CONTRIBUTING.md)
 (and don't forget to take a peek at our nice [Code of Conduct](./CODE_OF_CONDUCT.md) :wink:).
@@ -112,13 +114,13 @@ Any contribution is dearly welcome! If you want to contribute, please take the t
 This project has received funding from the [European High-Performance
 Computing Joint Undertaking](https://eurohpc-ju.europa.eu/) (JU) under
 grant agreement No 955701 ([TIME-X](https://www.time-x-eurohpc.eu/))
-and grant agreement No 101118139.
+and grant agreement No 101118139. 
 The JU receives support from the European Union's Horizon 2020 research
 and innovation programme and Belgium, France, Germany, and Switzerland.
 This project also received funding from the [German Federal Ministry of
 Education and Research](https://www.bmbf.de/bmbf/en/home/home_node.html)
 (BMBF) grants  16HPC047 and 16ME0679K. Supported by the European Union - NextGenerationEU. 
-The project also received help from the [Helmholtz Platform for Research Software Engineering - Preparatory Study (HiRSE_PS)](https://www.helmholtz-hirse.de/).
+The project also received help from the [Joint Lab "Helmholtz Information -  Research Software Engineering" (HiRSE)](https://www.helmholtz-hirse.de/).
 
 <p align="center">
   <img src="./docs/img/EuroHPC.jpg" height="105"/> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

docs/source/conf.py

@@ -70,9 +70,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '5.5'
+version = '5.6'
 # The full version, including alpha/beta/rc tags.
-release = '5.5.2'
+release = '5.6'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/index.rst

@@ -25,6 +25,7 @@ Tutorial
    tutorial/step_6.rst
    tutorial/step_7.rst
    tutorial/step_8.rst
+   tutorial/step_9.rst
 
 Playgrounds
 -----------
@@ -53,6 +54,7 @@ Projects
    projects/compression.rst
    projects/second_order.rst
    projects/monodomain.rst
+   projects/GPU.rst
 
 
 API documentation

docs/source/projects/GPU.rst

@@ -0,0 +1 @@
+.. include:: /../../pySDC/projects/GPU/README.rst