Merge branch 'master' into neuralpint

Author: tlunet

.github/workflows/ci_pipeline.yml

@@ -169,6 +169,58 @@ jobs:
           path: |
             data_libpressio
             coverage_libpressio.dat
+
+  user_firedrake_tests:
+    runs-on: ubuntu-latest
+    container:
+      image: firedrakeproject/firedrake-vanilla:latest
+      options: --user root
+      volumes:
+        - ${{ github.workspace }}:/repositories
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - 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: Install pySDC
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          python -m pip install --no-deps -e /repositories/pySDC
+          python -m pip install qmat
+      - name: Install gusto
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          python -m pip install -e /repositories/gusto_repo
+      - name: run pytest
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          firedrake-clean
+          cd ./pySDC
+          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: |
+          . /home/firedrake/firedrake/bin/activate
+
+          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 }}

README.md

@@ -19,8 +19,8 @@ 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 +43,11 @@ 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:

docs/source/tutorial/doc_step_7_E.rst

@@ -0,0 +1,3 @@
+Full code: `pySDC/tutorial/step_7/E_pySDC_with_Firedrake.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/tutorial/step_7/E_pySDC_with_Firedrake.py>`_
+
+.. literalinclude:: ../../../pySDC/tutorial/step_7/E_pySDC_with_Firedrake.py

docs/source/tutorial/doc_step_7_F.rst

@@ -0,0 +1,4 @@
+Full code: `pySDC/tutorial/step_7/F_pySDC_with_Gusto.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/tutorial/step_7/F_pySDC_with_Gusto.py>`_
+Find a suitable plotting script here: `pySDC/tutorial/step_7/F_2_plot_pySDC_with_Gusto_result.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/tutorial/step_7/F_2_plot_pySDC_with_Gusto_result.py>`_
+
+.. literalinclude:: ../../../pySDC/tutorial/step_7/F_pySDC_with_Gusto.py

etc/environment-petsc.yml

@@ -9,7 +9,7 @@ dependencies:
   - matplotlib>=3.0
   - dill>=0.2.6
   - mpich
-  - petsc4py
+  - petsc4py<3.22
   - mpi4py>=3.0.0
   - pip
   - pip:

pySDC/core/space_transfer.py

@@ -27,17 +27,17 @@ class SpaceTransfer(object):
         coarse_prob (pySDC.Problem.ptype): reference to the coarse problem
     """
 
-    def __init__(self, fine_prob, coarse_prob, space_transfer_params):
+    def __init__(self, fine_prob, coarse_prob, params):
         """
         Initialization routine
 
         Args:
             fine_prob (pySDC.Problem.ptype): reference to the fine problem
             coarse_prob (pySDC.Problem.ptype): reference to the coarse problem
-            space_transfer_params (dict): user-defined parameters
+            params (dict): user-defined parameters
         """
 
-        self.params = _Pars(space_transfer_params)
+        self.params = _Pars(params)
 
         # set up logger
         self.logger = logging.getLogger('space-transfer')

pySDC/helpers/fieldsIO.py

@@ -49,6 +49,7 @@
 import os
 import numpy as np
 from typing import Type, TypeVar
+import logging
 
 T = TypeVar("T")
 
@@ -69,11 +70,26 @@ class MPI:
 DTYPES = {
     0: np.float64,  # double precision
     1: np.complex128,
-    2: np.float128,  # quadruple precision
-    3: np.complex256,
-    4: np.float32,  # single precision
-    5: np.complex64,
 }
+try:
+    DTYPES.update(
+        {
+            2: np.float128,  # quadruple precision
+            3: np.complex256,
+        }
+    )
+except AttributeError:
+    logging.getLogger('FieldsIO').debug('Warning: Quadruple precision not available on this machine')
+try:
+    DTYPES.update(
+        {
+            4: np.float32,  # single precision
+            5: np.complex64,
+        }
+    )
+except AttributeError:
+    logging.getLogger('FieldsIO').debug('Warning: Single precision not available on this machine')
+
 DTYPES_AVAIL = {val: key for key, val in DTYPES.items()}
 
 # Header dtype
@@ -106,7 +122,7 @@ def __init__(self, dtype, fileName):
                 self.dtype = key
                 avail = True
                 break
-        assert avail, f"{dtype=} not available"
+        assert avail, f"{dtype=} not available. Supported on this machine: {list(DTYPES_AVAIL.keys())}"
         self.fileName = fileName
         self.initialized = False
 

pySDC/helpers/firedrake_ensemble_communicator.py

@@ -0,0 +1,75 @@
+from mpi4py import MPI
+import firedrake as fd
+import numpy as np
+
+
+class FiredrakeEnsembleCommunicator:
+    """
+    Ensemble communicator for performing multiple similar distributed simulations with Firedrake, see https://www.firedrakeproject.org/firedrake/parallelism.html
+    This is intended to do space-time parallelism in pySDC.
+    This class wraps the time communicator. All requests that are not overloaded are passed to the time communicator. For instance, `ensemble.rank` will return the rank in the time communicator.
+    Some operations are overloaded to use the interface of the MPI communicator but handles communication with the ensemble communicator instead.
+    """
+
+    def __init__(self, comm, space_size):
+        """
+        Args:
+            comm (MPI.Intracomm): MPI communicator, which will be split into time and space communicators
+            space_size (int): Size of the spatial communicators
+
+        Attributes:
+            ensemble (firedrake.Ensemble): Ensemble communicator
+        """
+        self.ensemble = fd.Ensemble(comm, space_size)
+        self.comm_wold = comm
+
+    def Split(self, *args, **kwargs):
+        return FiredrakeEnsembleCommunicator(self.comm_wold.Split(*args, **kwargs), space_size=self.space_comm.size)
+
+    @property
+    def space_comm(self):
+        return self.ensemble.comm
+
+    @property
+    def time_comm(self):
+        return self.ensemble.ensemble_comm
+
+    def __getattr__(self, name):
+        return getattr(self.time_comm, name)
+
+    def Reduce(self, sendbuf, recvbuf, op=MPI.SUM, root=0):
+        if type(sendbuf) in [np.ndarray]:
+            self.ensemble.ensemble_comm.Reduce(sendbuf, recvbuf, op, root)
+        else:
+            assert op == MPI.SUM
+            self.ensemble.reduce(sendbuf, recvbuf, root=root)
+
+    def Allreduce(self, sendbuf, recvbuf, op=MPI.SUM):
+        if type(sendbuf) in [np.ndarray]:
+            self.ensemble.ensemble_comm.Allreduce(sendbuf, recvbuf, op)
+        else:
+            assert op == MPI.SUM
+            self.ensemble.allreduce(sendbuf, recvbuf)
+
+    def Bcast(self, buf, root=0):
+        if type(buf) in [np.ndarray]:
+            self.ensemble.ensemble_comm.Bcast(buf, root)
+        else:
+            self.ensemble.bcast(buf, root=root)
+
+    def Irecv(self, buf, source, tag=MPI.ANY_TAG):
+        if type(buf) in [np.ndarray, list]:
+            return self.ensemble.ensemble_comm.Irecv(buf=buf, source=source, tag=tag)
+        return self.ensemble.irecv(buf, source, tag=tag)[0]
+
+    def Isend(self, buf, dest, tag=MPI.ANY_TAG):
+        if type(buf) in [np.ndarray, list]:
+            return self.ensemble.ensemble_comm.Isend(buf=buf, dest=dest, tag=tag)
+        return self.ensemble.isend(buf, dest, tag=tag)[0]
+
+    def Free(self):
+        del self
+
+
+def get_ensemble(comm, space_size):
+    return fd.Ensemble(comm, space_size)