debug

.github/workflows/build.yml

@@ -107,7 +107,7 @@ jobs:
 
     - name: Run tests
       if: always()
-      run: python3 -m pytest --junit-xml=test-results-${{ env.BUILD_IDENTIFIER }}.xml tests/
+      run: python3 -m pytest --junit-xml=test-results-${{ env.BUILD_IDENTIFIER }}.xml  -k "testParallelGMG[4-interval-P3-false]" tests/
 
     - name: Run flake8
       if: always()
@@ -221,7 +221,7 @@ jobs:
 
     - name: Run tests
       if: always()
-      run: python3 -m pytest --junit-xml=test-results-${{ runner.os }}-${{ matrix.py-version }}.xml tests/
+      run: python3 -m pytest --junit-xml=test-results-${{ runner.os }}-${{ matrix.py-version }}.xml -k "testParallelGMG[4-interval-P3-false]" tests/
 
     - name: Run flake8
       if: always()

.github/workflows/container.yml

@@ -32,114 +32,114 @@ jobs:
         echo "IMAGE_TAGS=pr-${{ github.event.number }}" >> $GITHUB_ENV
         echo "TEST_IMAGE_TAG=pr-${{ github.event.number }}" >> $GITHUB_ENV
 
-    - name: Check out
-      if: always()
-      uses: actions/[email protected]
-      with:
-        fetch-depth: 0
-
-    # - uses: hadolint/[email protected]
-    #   with:
-    #     dockerfile: Dockerfile
-    #     ignore: 'DL3008,DL3013'
-    #     verbose: true
-
-    - name: Build Image
-      id: build_image
-      uses: redhat-actions/buildah-build@v2
-      with:
-        image: ${{ env.IMAGE_NAME }}
-        tags: ${{ env.IMAGE_TAGS }}
-        containerfiles: |
-          ./Dockerfile
-        build-args: |
-          PYNUCLEUS_BUILD_PARALLELISM=4
-
-    - name: Push To GHCR
-      if: (github.event_name == 'pull_request') && (github.actor != 'dependabot[bot]')
-      uses: redhat-actions/push-to-registry@v2
-      id: push-pr
-      with:
-        image: ${{ steps.build_image.outputs.image }}
-        tags: ${{ env.IMAGE_TAGS }}
-        registry: ${{ env.IMAGE_REGISTRY }}
-        username: ${{ env.REGISTRY_USER }}
-        password: ${{ env.REGISTRY_PASSWORD }}
-        extra-args: |
-          --disable-content-trust
-
-    - name: Run tests
-      run: |
-        podman run \
-        -e MPIEXEC_FLAGS="--allow-run-as-root --oversubscribe" \
-        --workdir /pynucleus \
-        --rm \
-        --entrypoint='["python3", "-m", "pytest", "--junit-xml", "test-results.xml"]' \
-        ${{ steps.build_image.outputs.image }}:${{ env.TEST_IMAGE_TAG }}
-
-    - name: Push To GHCR
-      if: github.event_name == 'push'
-      uses: redhat-actions/push-to-registry@v2
-      id: push
-      with:
-        image: ${{ steps.build_image.outputs.image }}
-        tags: ${{ steps.build_image.outputs.tags }}
-        registry: ${{ env.IMAGE_REGISTRY }}
-        username: ${{ env.REGISTRY_USER }}
-        password: ${{ env.REGISTRY_PASSWORD }}
-        extra-args: |
-          --disable-content-trust
-
-    - name: Echo outputs
-      if: github.event_name == 'push'
-      run: |
-        echo "${{ toJSON(steps.push.outputs) }}"
-
-  container-test:
-    needs: container
-
-    strategy:
-      matrix:
-        include:
-          - runner: 'ubuntu-latest'
-
-    name: Container test ${{ matrix.runner }}
-    runs-on: ${{ matrix.runner }}
-
-    steps:
-    - name: Check out
-      uses: actions/[email protected]
-
-    - name: Install podman-compose
-      run: pip install podman-compose
-
-    - name: Run container test
-      run: podman-compose run quick-test
-
-  update-binder-image:
-    needs: container
-    if: github.event_name == 'push'
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout binder branch
-        uses: actions/[email protected]
-        with:
-          ref: binder
-
-      - name: Modify Dockerfile
-        run: |
-          python generateDockerfile.py ${{ env.IMAGE_REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.TEST_IMAGE_TAG }}
-
-      - name: Create PR
-        uses: peter-evans/create-pull-request@v6
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          commit-message: "Update Dockerfile"
-          title: "Update Dockerfile"
-          body: |
-            This PR updates the Dockerfile for binder.
-          branch: binder-update
-          base: binder
-          delete-branch: true
+    # - name: Check out
+  #     if: always()
+  #     uses: actions/[email protected]
+  #     with:
+  #       fetch-depth: 0
+
+  #   # - uses: hadolint/[email protected]
+  #   #   with:
+  #   #     dockerfile: Dockerfile
+  #   #     ignore: 'DL3008,DL3013'
+  #   #     verbose: true
+
+  #   - name: Build Image
+  #     id: build_image
+  #     uses: redhat-actions/buildah-build@v2
+  #     with:
+  #       image: ${{ env.IMAGE_NAME }}
+  #       tags: ${{ env.IMAGE_TAGS }}
+  #       containerfiles: |
+  #         ./Dockerfile
+  #       build-args: |
+  #         PYNUCLEUS_BUILD_PARALLELISM=4
+
+  #   - name: Push To GHCR
+  #     if: (github.event_name == 'pull_request') && (github.actor != 'dependabot[bot]')
+  #     uses: redhat-actions/push-to-registry@v2
+  #     id: push-pr
+  #     with:
+  #       image: ${{ steps.build_image.outputs.image }}
+  #       tags: ${{ env.IMAGE_TAGS }}
+  #       registry: ${{ env.IMAGE_REGISTRY }}
+  #       username: ${{ env.REGISTRY_USER }}
+  #       password: ${{ env.REGISTRY_PASSWORD }}
+  #       extra-args: |
+  #         --disable-content-trust
+
+  #   - name: Run tests
+  #     run: |
+  #       podman run \
+  #       -e MPIEXEC_FLAGS="--allow-run-as-root --oversubscribe" \
+  #       --workdir /pynucleus \
+  #       --rm \
+  #       --entrypoint='["python3", "-m", "pytest", "--junit-xml", "test-results.xml"]' \
+  #       ${{ steps.build_image.outputs.image }}:${{ env.TEST_IMAGE_TAG }}
+
+  #   - name: Push To GHCR
+  #     if: github.event_name == 'push'
+  #     uses: redhat-actions/push-to-registry@v2
+  #     id: push
+  #     with:
+  #       image: ${{ steps.build_image.outputs.image }}
+  #       tags: ${{ steps.build_image.outputs.tags }}
+  #       registry: ${{ env.IMAGE_REGISTRY }}
+  #       username: ${{ env.REGISTRY_USER }}
+  #       password: ${{ env.REGISTRY_PASSWORD }}
+  #       extra-args: |
+  #         --disable-content-trust
+
+  #   - name: Echo outputs
+  #     if: github.event_name == 'push'
+  #     run: |
+  #       echo "${{ toJSON(steps.push.outputs) }}"
+
+  # container-test:
+  #   needs: container
+
+  #   strategy:
+  #     matrix:
+  #       include:
+  #         - runner: 'ubuntu-latest'
+
+  #   name: Container test ${{ matrix.runner }}
+  #   runs-on: ${{ matrix.runner }}
+
+  #   steps:
+  #   - name: Check out
+  #     uses: actions/[email protected]
+
+  #   - name: Install podman-compose
+  #     run: pip install podman-compose
+
+  #   - name: Run container test
+  #     run: podman-compose run quick-test
+
+  # update-binder-image:
+  #   needs: container
+  #   if: github.event_name == 'push'
+
+  #   runs-on: ubuntu-latest
+
+  #   steps:
+  #     - name: Checkout binder branch
+  #       uses: actions/[email protected]
+  #       with:
+  #         ref: binder
+
+  #     - name: Modify Dockerfile
+  #       run: |
+  #         python generateDockerfile.py ${{ env.IMAGE_REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.TEST_IMAGE_TAG }}
+
+  #     - name: Create PR
+  #       uses: peter-evans/create-pull-request@v6
+  #       with:
+  #         token: ${{ secrets.GITHUB_TOKEN }}
+  #         commit-message: "Update Dockerfile"
+  #         title: "Update Dockerfile"
+  #         body: |
+  #           This PR updates the Dockerfile for binder.
+  #         branch: binder-update
+  #         base: binder
+  #         delete-branch: true

.github/workflows/documentation-ci.yml

@@ -26,49 +26,49 @@ jobs:
     - name: Check out repo
       uses: actions/[email protected]
 
-    - name: Pull ccache cache
-      id: ccache-restore
-      uses: actions/cache/restore@v4
-      with:
-        path: /home/runner/.cache/ccache
-        key: ccache-documentation-ci
+    # - name: Pull ccache cache
+    #   id: ccache-restore
+    #   uses: actions/cache/restore@v4
+    #   with:
+    #     path: /home/runner/.cache/ccache
+    #     key: ccache-documentation-ci
 
-    - uses: actions/setup-python@v5
-      with:
-        python-version: '3.11'
+    # - uses: actions/setup-python@v5
+    #   with:
+    #     python-version: '3.11'
 
-    - name: Install Ubuntu packages
-      run: |
-        sudo apt-get update
-        sudo apt-get install mpi-default-bin mpi-default-dev libmetis-dev libparmetis-dev libsuitesparse-dev ccache
+    # - name: Install Ubuntu packages
+    #   run: |
+    #     sudo apt-get update
+    #     sudo apt-get install mpi-default-bin mpi-default-dev libmetis-dev libparmetis-dev libsuitesparse-dev ccache
 
-    - name: Install Python dependencies
-      run: make prereq && make prereq-extra
+    # - name: Install Python dependencies
+    #   run: make prereq && make prereq-extra
 
-    - name: Install
-      run: make dev
+    # - name: Install
+    #   run: make dev
 
-    - name: Remove ccache cache
-      if: ${{ steps.ccache-restore.outputs.cache-hit }}
-      shell: bash
-      env:
-        GH_TOKEN: ${{ github.token }}
-      run: |
-        gh extension install actions/gh-actions-cache
-        gh actions-cache delete ccache --confirm
-      continue-on-error: true
+    # - name: Remove ccache cache
+    #   if: ${{ steps.ccache-restore.outputs.cache-hit }}
+    #   shell: bash
+    #   env:
+    #     GH_TOKEN: ${{ github.token }}
+    #   run: |
+    #     gh extension install actions/gh-actions-cache
+    #     gh actions-cache delete ccache --confirm
+    #   continue-on-error: true
 
-    - name: Push ccache cache
-      uses: actions/cache/save@v4
-      with:
-        path: /home/runner/.cache/ccache
-        key: ccache-documentation-ci
+    # - name: Push ccache cache
+    #   uses: actions/cache/save@v4
+    #   with:
+    #     path: /home/runner/.cache/ccache
+    #     key: ccache-documentation-ci
 
-    - name: Build documentation
-      run: |
-        make docs
+    # - name: Build documentation
+    #   run: |
+    #     make docs
 
-    - name: Upload artifact
-      uses: actions/upload-artifact@v4
-      with:
-        path: 'docs/build'
+    # - name: Upload artifact
+    #   uses: actions/upload-artifact@v4
+    #   with:
+    #     path: 'docs/build'

fem/PyNucleus_fem/algebraicOverlaps.pyx

@@ -86,6 +86,7 @@ cdef class algebraicOverlap:
             INDEX_t[::1] shared_dofs = self.shared_dofs
         for j in range(self.num_shared_dofs):
             self.myExchangeOut[j] = vec[shared_dofs[j]]
+        assert np.all(np.isfinite(self.exchangeOut))
         self.tagNoSend += 1
         return self.comm.Isend(self.myExchangeOut,
                                dest=self.otherSubdomainNo,
@@ -108,6 +109,7 @@ cdef class algebraicOverlap:
             INDEX_t[::1] shared_dofs = self.shared_dofs
         for j in range(self.num_shared_dofs):
             vec[shared_dofs[j]] += self.myExchangeIn[j]
+        assert np.all(np.isfinite(self.exchangeIn))
 
     cdef MPI.Request sendComplex(self,
                                  const COMPLEX_t[::1] vec,
@@ -553,7 +555,7 @@ cdef class algebraicOverlapManager:
         shared_dofs = set()
         for otherSubdomain in self.overlaps:
             shared_dofs |= set(list(np.array(self.overlaps[otherSubdomain].shared_dofs)))
-        return np.array(list(shared_dofs), dtype=INDEX)
+        return np.array(sorted(shared_dofs), dtype=INDEX)
 
     def prepareDistribute(self):
         cdef:
@@ -1082,6 +1084,7 @@ cdef class algebraicOverlapManager:
             algebraicOverlapOneSidedPutLockAll ov1SPLA
         MPI.Request.Waitall(requestsSend)
         del requestsSend[:]
+        assert np.all(np.isfinite(vec))
         requestsOneSidedGet = []
         requestsOneSidedPut = []
         requestsOneSidedPutLockAll = []