Test sympde branch terminal_expressions_for_NS

.github/workflows/continuous-integration.yml

@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ 3.8, 3.9, '3.10', '3.11' ]
+        python-version: [ 3.9, '3.10', '3.11', '3.12' ]
         isMerge:
           - ${{ github.event_name == 'push' && github.ref == 'refs/heads/devel' }}
         exclude:
@@ -25,6 +25,8 @@ jobs:
         include:
           - os: macos-latest
             python-version: '3.10'
+          - os: macos-latest
+            python-version: '3.12'
 
     name: ${{ matrix.os }} / Python ${{ matrix.python-version }}
 
@@ -96,7 +98,12 @@ jobs:
 
       - name: Download a specific release of PETSc
         run: |
-          git clone --depth 1 --branch v3.20.5 https://gitlab.com/petsc/petsc.git
+          if [[ "${{ matrix.python-version }}" == "3.12" ]]; then
+            git clone --depth 1 --branch v3.21.3 https://gitlab.com/petsc/petsc.git
+          else
+            git clone --depth 1 --branch v3.20.5 https://gitlab.com/petsc/petsc.git
+          fi
+
 
       - name: Install PETSc with complex support, and test it
         working-directory: ./petsc
@@ -116,14 +123,27 @@ jobs:
 
       - name: Install Python dependencies
         run: |
-          export CC="mpicc" HDF5_MPI="ON"
+          export CC="mpicc"
+          export HDF5_MPI="ON"
           python -m pip install -r requirements.txt
           python -m pip install -r requirements_extra.txt --no-build-isolation
           python -m pip list
 
-      - name: Check h5py installation
+      - name: Check parallel h5py installation
+        run: |
+            python -c "
+            from mpi4py import MPI
+            import h5py
+            # This particular instantiation of h5py.File will fail if parallel h5py isn't installed
+            f = h5py.File('parallel_test.hdf5', 'w', driver='mpio', comm=MPI.COMM_WORLD)
+            print(f)"
+
+      - name: Download a development version of sympde
+        working-directory: /tmp
         run: |
-            python -c "from h5py import File; print(File)"
+          wget https://github.com/pyccel/sympde/archive/refs/heads/terminal_expressions_for_NS.zip
+          unzip ./terminal_expressions_for_NS.zip
+          python3 -m pip install ./sympde-terminal_expressions_for_NS          
 
       - name: Install project
         run: |

.github/workflows/documentation.yml

@@ -36,21 +36,23 @@ jobs:
         make -C docs clean
         make -C docs html
         python docs/update_links.py
-    - name: Setup Pages
-      uses: actions/configure-pages@v3
-    - name: Upload artifact
-      uses: actions/upload-pages-artifact@v1
-      with:
-        path: 'docs/build/html'
 
-  deploy_docs:
-    if: github.event_name != 'pull_request'
-    needs: build_docs
-    runs-on: ubuntu-latest
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    steps:
-    - name: Deploy to GitHub Pages
-      id: deployment
-      uses: actions/deploy-pages@v2
+    # Disable docs deployment for now as we're in psydac fork repo
+    # - name: Setup Pages
+    #   uses: actions/configure-pages@v3
+    # - name: Upload artifact
+    #   uses: actions/upload-pages-artifact@v1
+    #   with:
+    #     path: 'docs/build/html'
+
+  # deploy_docs:
+  #   if: github.event_name != 'pull_request'
+  #   needs: build_docs
+  #   runs-on: ubuntu-latest
+  #   environment:
+  #     name: github-pages
+  #     url: ${{ steps.deployment.outputs.page_url }}
+  #   steps:
+  #   - name: Deploy to GitHub Pages
+  #     id: deployment
+  #     uses: actions/deploy-pages@v2

.gitignore

@@ -5,6 +5,7 @@
 *.lock
 __psydac__/
 __*pyccel__/
+docs/source/modules/STUBDIR/*
 
 build
 *build*

docs/source/modules/feec.multipatch.rst

@@ -9,5 +9,9 @@ feec.multipatch
 
     multipatch.api
     multipatch.fem_linear_operators
+    multipatch.multipatch_domain_utilities
+    multipatch.non_matching_operators
     multipatch.operators
+    multipatch.plotting_utilities
     multipatch.utilities
+    multipatch.utils_conga_2d

examples/maxwell_2d_multi_patch.py

@@ -129,11 +129,12 @@ def run_maxwell_2d(uex, f, alpha, domain, ncells, degree, k=None, kappa=None, co
     N = 20
 
     mappings = OrderedDict([(P.logical_domain, P.mapping) for P in domain.interior])
-    mappings_list = [m.get_callable_mapping() for m in mappings.values()]
+    mappings_list = [m for m in mappings.values()]
+    call_mappings_list = [m.get_callable_mapping() for m in mappings_list]
 
     Eex_x   = lambdify(domain.coordinates, Eex[0])
     Eex_y   = lambdify(domain.coordinates, Eex[1])
-    Eex_log = [pull_2d_hcurl([Eex_x, Eex_y], f) for f in mappings_list]
+    Eex_log = [pull_2d_hcurl([Eex_x, Eex_y], f) for f in call_mappings_list]
 
     etas, xx, yy    = get_plotting_grid(mappings, N=20)
     grid_vals_hcurl = lambda v: get_grid_vals(v, etas, mappings_list, space_kind='hcurl')

mesh/generate_pipe.py

@@ -1,5 +1,7 @@
 import numpy as np
 
+raise NotImplementedError("igakit is no longer imported to support python 3.12")
+
 from igakit.cad import circle, ruled, bilinear, join
 from psydac.cad.geometry             import Geometry, export_nurbs_to_hdf5, refine_nurbs
 

mesh/multipatch/create_magnet.py

@@ -1,5 +1,7 @@
 import numpy as np
 
+raise NotImplementedError("igakit is no longer imported to support python 3.12")
+
 from psydac.cad.multipatch import export_multipatch_nurbs_to_hdf5
 from igakit.cad import bilinear
 from igakit.cad import circle

psydac/api/discretization.py

@@ -102,7 +102,7 @@ def get_max_degree_of_one_space(Vh):
     Vh : FemSpace
         The finite element space under investigation.
 
-    Results
+    Returns
     -------
     list[int]
         The maximum polynomial degre of Vh with respect to each coordinate.
@@ -133,7 +133,7 @@ def get_max_degree(*spaces):
     *spaces : tuple[FemSpace]
         The finite element spaces under investigation.
 
-    Results
+    Returns
     -------
     list[int]
         The maximum polynomial degree across all spaces, with respect to each

psydac/api/fem.py

@@ -767,7 +767,9 @@ def allocate_matrices(self, backend=None):
                         elif use_prolongation:
                             Ps  = [knot_insertion_projection_operator(trs, trs.get_refined_space(ncells)) for trs in trial_fem_space.spaces]
                             P   = BlockLinearOperator(trial_fem_space.vector_space, trial_fem_space.get_refined_space(ncells).vector_space)
-                            for ni,Pi in enumerate(Ps):P[ni,ni] = Pi
+                            for ni,Pi in enumerate(Ps):
+                                P[ni,ni] = Pi
+
                             mat = ComposedLinearOperator(trial_space, test_space, mat, P)
 
                     self._matrix[i,j] = mat

psydac/api/postprocessing.py

@@ -953,12 +953,9 @@ def _reconstruct_spaces(self):
         for subdomain_names, space_dict in subdomains_to_spaces.items():
             if space_dict == {}:
                 continue
-            ncells_dict = {interior_name: interior_names_to_ncells[interior_name] for interior_name in subdomain_names}
-            # No need for a a dict until PR about non-conforming meshes is merged
-            # Check for conformity
-            ncells =  list(ncells_dict.values())[0]
-            assert all(ncells_patch == ncells for ncells_patch in ncells_dict.values())
 
+            ncells = {interior_name: interior_names_to_ncells[interior_name] for interior_name in subdomain_names}
+
             subdomain    = domain.get_subdomain(subdomain_names)
             space_name_0 = list(space_dict.keys())[0]
             periodic     = space_dict[space_name_0][2].get('periodic', None)

psydac/api/settings.py

@@ -13,7 +13,7 @@
 
 PSYDAC_BACKEND_GPYCCEL  = {'name': 'pyccel',
                        'compiler': 'GNU',
-                       'flags'   : '-O3 -march=native -mtune=native -ffast-math',
+                       'flags'   : '-O3 -ffast-math',
                        'folder'  : '__gpyccel__',
                        'tag'     : 'gpyccel',
                        'openmp'  : False}
@@ -41,8 +41,22 @@
 # ...
 
 # Platform-dependent flags
-if platform.machine() == 'x86_64':
-    PSYDAC_BACKEND_GPYCCEL['flags'] += ' -mavx'
+if platform.system() == "Darwin" and platform.machine() == 'arm64':
+    # Apple silicon requires architecture-specific flags (see https://github.com/pyccel/psydac/pull/411)
+    import subprocess # nosec B404
+    cpu_brand = subprocess.check_output(['sysctl','-n','machdep.cpu.brand_string']).decode('utf-8') # nosec B603, B607
+    if "Apple M1" in cpu_brand:
+        PSYDAC_BACKEND_GPYCCEL['flags'] += ' -mcpu=apple-m1'
+    else:
+        # TODO: Support later Apple CPU models. Perhaps the CPU naming scheme could be easily guessed
+        # based on the output of 'sysctl -n machdep.cpu.brand_string', but I wouldn't rely on this
+        # guess unless it has been manually verified. Loud errors are better than silent failures!
+        raise SystemError(f"Unsupported Apple CPU '{cpu_brand}'.")
+else:
+    # Default architecture flags
+    PSYDAC_BACKEND_GPYCCEL['flags'] += ' -march=native -mtune=native'
+    if platform.machine() == 'x86_64':
+        PSYDAC_BACKEND_GPYCCEL['flags'] += ' -mavx'
 
 #==============================================================================
 
@@ -53,4 +67,4 @@
     'pyccel-intel' : PSYDAC_BACKEND_IPYCCEL,
     'pyccel-pgi'   : PSYDAC_BACKEND_PGPYCCEL,
     'pyccel-nvidia': PSYDAC_BACKEND_NVPYCCEL,
-}
+}

psydac/api/tests/build_domain.py

@@ -1,10 +1,16 @@
 # coding: utf-8
 
+# todo: this file has a lot of redundant code with psydac/feec/multipatch/multipatch_domain_utilities.py
+# it should probably be removed in the future
+
 import numpy as np
 
 from sympde.topology import Square, Domain
 from sympde.topology import IdentityMapping, PolarMapping, AffineMapping, Mapping
 
+# remove after sympde PR #155 is merged and call Domain.join instead
+from psydac.feec.multipatch.multipatch_domain_utilities import sympde_Domain_join
+
 #==============================================================================
 # small extension to SymPDE:
 class TransposedPolarMapping(Mapping):
@@ -20,6 +26,7 @@ class TransposedPolarMapping(Mapping):
     _ldim        = 2
     _pdim        = 2
 
+# todo: remove this
 def create_domain(patches, interfaces, name):
     connectivity = []
     patches_interiors = [D.interior for D in patches]
@@ -54,6 +61,8 @@ def flip_axis(name='no_name', c1=0., c2=0.):
     )
 
 #==============================================================================
+
+# todo: use build_multipatch_domain instead
 def build_pretzel(domain_name='pretzel', r_min=None, r_max=None):
     """
     design pretzel-like domain
@@ -189,23 +198,29 @@ def build_pretzel(domain_name='pretzel', r_min=None, r_max=None):
                     domain_14,
                     ])
 
-    interfaces = [
-        [domain_1.get_boundary(axis=1, ext=+1), domain_5.get_boundary(axis=1, ext=-1),  1],
-        [domain_5.get_boundary(axis=1, ext=+1), domain_6.get_boundary(axis=1, ext=1),   1],
-        [domain_6.get_boundary(axis=1, ext=-1), domain_2.get_boundary(axis=1, ext=-1),  1],
-        [domain_2.get_boundary(axis=1, ext=+1), domain_7.get_boundary(axis=1, ext=-1),  1],
-        [domain_7.get_boundary(axis=1, ext=+1), domain_3.get_boundary(axis=1, ext=-1),  1],
-        [domain_3.get_boundary(axis=1, ext=+1), domain_9.get_boundary(axis=1, ext=-1),  1],
-        [domain_9.get_boundary(axis=1, ext=+1), domain_4.get_boundary(axis=1, ext=-1),  1],
-        [domain_4.get_boundary(axis=1, ext=+1), domain_12.get_boundary(axis=1, ext=1),  1],
-        [domain_12.get_boundary(axis=1, ext=-1), domain_1.get_boundary(axis=1, ext=-1), 1],
-        [domain_6.get_boundary(axis=0, ext=-1), domain_13.get_boundary(axis=0, ext=1),  1],
-        [domain_7.get_boundary(axis=0, ext=-1), domain_13.get_boundary(axis=0, ext=-1), 1],
-        [domain_5.get_boundary(axis=0, ext=-1), domain_14.get_boundary(axis=0, ext=-1), 1],
-        [domain_12.get_boundary(axis=0, ext=-1), domain_14.get_boundary(axis=0, ext=+1),1],
+    axis_0 = 0
+    axis_1 = 1
+    ext_0 = -1
+    ext_1 = +1
+
+    connectivity = [
+        [(domain_1,  axis_1, ext_1), (domain_5,  axis_1, ext_0), 1],
+        [(domain_5,  axis_1, ext_1), (domain_6,  axis_1, ext_1), 1],
+        [(domain_6,  axis_1, ext_0), (domain_2,  axis_1, ext_0), 1],
+        [(domain_2,  axis_1, ext_1), (domain_7,  axis_1, ext_0), 1],
+        [(domain_7,  axis_1, ext_1), (domain_3,  axis_1, ext_0), 1],
+        [(domain_3,  axis_1, ext_1), (domain_9,  axis_1, ext_0), 1],
+        [(domain_9,  axis_1, ext_1), (domain_4,  axis_1, ext_0), 1],
+        [(domain_4,  axis_1, ext_1), (domain_12, axis_1, ext_1), 1],
+        [(domain_12, axis_1, ext_0), (domain_1,  axis_1, ext_0), 1],
+        [(domain_6,  axis_0, ext_0), (domain_13, axis_0, ext_1), 1],
+        [(domain_7,  axis_0, ext_0), (domain_13, axis_0, ext_0), 1],
+        [(domain_5,  axis_0, ext_0), (domain_14, axis_0, ext_0), 1],
+        [(domain_12, axis_0, ext_0), (domain_14, axis_0, ext_1), 1],
         ]
 
+    # domain = Domain.join(patches, connectivity, name=domain_name)
+    domain = sympde_Domain_join(patches, connectivity, name=domain_name)
 
-    domain = create_domain(patches, interfaces, domain_name)
     return domain