Dokken/ci h5py fixes

.github/workflows/book_stable.yml

@@ -9,7 +9,6 @@ on:
     branches: ["release"]
 env:
   HDF5_MPI: "ON"
-  HDF5_DIR: "/usr/local/"
   H5PY_SETUP_REQUIRES: 0
   DEB_PYTHON_INSTALL_LAYOUT: deb_system
   LIBGL_ALWAYS_SOFTWARE: 1
@@ -29,6 +28,12 @@ jobs:
       - name: Install common packages
         uses: ./.github/actions/install-dependencies
 
+      - name: Configure HDF5 MPI Environment
+        run: |
+          # Evaluate architecture dynamically and write to GITHUB_ENV
+          ARCH_TRIPLET=$(gcc -print-multiarch)
+          echo "HDF5_LIBDIR=/usr/lib/${ARCH_TRIPLET}/hdf5/openmpi" >> $GITHUB_ENV
+
       - name: Install book deps
         run: |
           python3 -m pip install --break-system-packages -U pip setuptools pkgconfig poetry-core poetry_dynamic_versioning

.github/workflows/test_nightly.yml

@@ -20,19 +20,29 @@ jobs:
     container: ghcr.io/fenics/dolfinx/lab:nightly
 
     env:
-      HDF5_MPI: "ON"
-      H5PY_SETUP_REQUIRES: 0
-      HDF5_DIR: "/usr/local/"
       PYVISTA_OFF_SCREEN: true
       PYVISTA_JUPYTER_BACKEND: html
       LIBGL_ALWAYS_SOFTWARE: 1
+      CC: "mpicc"
+      HDF5_MPI: "ON"
+      HDF5_INCLUDEDIR: "/usr/include/hdf5/openmpi"
+      H5PY_SETUP_REQUIRES: 0
+      OMPI_ALLOW_RUN_AS_ROOT: 1
+      OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+      PRTE_MCA_rmaps_default_mapping_policy: :oversubscribe
 
     steps:
       - uses: actions/checkout@v7
 
       - name: Special handling of some installation
         uses: ./.github/actions/install-dependencies
 
+      - name: Configure HDF5 MPI Environment
+        run: |
+          # Evaluate architecture dynamically and write to GITHUB_ENV
+          ARCH_TRIPLET=$(gcc -print-multiarch)
+          echo "HDF5_LIBDIR=/usr/lib/${ARCH_TRIPLET}/hdf5/openmpi" >> $GITHUB_ENV
+
       - name: Install requirements
         run: |
           python3 -m pip install --break-system-packages -U pip setuptools pkgconfig poetry-core poetry-core poetry-dynamic-versioning
@@ -46,7 +56,7 @@ jobs:
         run: |
           export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH
           export PETSC_ARCH=linux-gnu-complex128-32
-          export PYTHONPATH=/usr/local/dolfinx-complex/lib/python3.12/dist-packages:$PYTHONPATH
+          export PYTHONPATH=/usr/local/dolfinx-complex/lib/python/dist-packages:$PYTHONPATH
           export LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH
           python3 complex_mode.py
           mpirun -n 2 python3 complex_mode.py

.github/workflows/test_stable.yml

@@ -11,13 +11,18 @@ jobs:
     runs-on: ubuntu-latest
     container: ghcr.io/fenics/dolfinx/lab:stable
     env:
-      HDF5_MPI: "ON"
-      HDF5_DIR: "/usr/local/"
-      H5PY_SETUP_REQUIRES: "0"
+
       DEB_PYTHON_INSTALL_LAYOUT: deb_system
       PYVISTA_OFF_SCREEN: true
       PYVISTA_JUPYTER_BACKEND: html
       LIBGL_ALWAYS_SOFTWARE: 1
+      CC: "mpicc"
+      HDF5_MPI: "ON"
+      HDF5_INCLUDEDIR: "/usr/include/hdf5/openmpi"
+      H5PY_SETUP_REQUIRES: 0
+      OMPI_ALLOW_RUN_AS_ROOT: 1
+      OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+      PRTE_MCA_rmaps_default_mapping_policy: :oversubscribe
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

docker/Dockerfile

@@ -7,14 +7,14 @@ ARG TARGETPLATFORM
 
 ENV DEB_PYTHON_INSTALL_LAYOUT=deb_system
 ENV HDF5_MPI="ON"
-ENV HDF5_DIR="/usr/local"
+ENV OMPI_ALLOW_RUN_AS_ROOT=1
+ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+ENV PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
 
 WORKDIR /tmp/
 # Requirements for pyvista (gl1 and render1) and jupyterlab (nodejs and curl)
 RUN apt-get update && apt-get install -y libgl1-mesa-dev mesa-utils curl
-# RUN curl -sL https://deb.nodesource.com/setup_18.x -o nodesource_setup.sh && \
-#     bash nodesource_setup.sh && \
-#     apt -y install nodejs
+
 
 # Install netgen from source
 RUN  apt-get update && \
@@ -36,6 +36,13 @@ ENV PYTHONPATH=$NETGENDIR/../lib/python3.12/site-packages:${PYTHONPATH}:${PYTHON
 # Install vtk
 RUN python3 -m pip install vtk
 
+RUN ARCH_TRIPLET=$(gcc -print-multiarch) && \
+    export CC="mpicc" && \
+    export HDF5_MPI="ON" && \
+    export HDF5_INCLUDEDIR="/usr/include/hdf5/openmpi" && \
+    export HDF5_LIBDIR="/usr/lib/${ARCH_TRIPLET}/hdf5/openmpi" && \
+    pip install --no-binary=h5py h5py --no-build-isolation --no-cache-dir
+
 ADD pyproject.toml /tmp/pyproject.toml
 WORKDIR /tmp
 # As we install netgen from source we don't need the netgen deps here