Spack-Based HPC Development Environment

This workspace builds a Docker image with a Spack environment for MFEM (and optionally deal.II) and presents installed software via a view. It supports active development against local source trees under /code.

Files

• Dockerfile: see Dockerfile.base — builds the image, installs packages via Spack, and configures auto-activation.
• Spack environment: spack.yaml — declares specs, view location, and develop entries for building from local sources.

Build the Image

# From the repo root
docker build -f Dockerfile.base -t hpc-dev .

Run the Container

# Start an interactive login shell with the Spack environment active
docker run -it --rm hpc-dev

# Mount a host directory (Windows path example) to /mnt in the container
docker run -it --rm -v D:\docker_ws:/mnt hpc-dev

Development Workflow (MFEM)

• Source location: /code/mfem (cloned during build).
• Spack is configured to build MFEM from /code/mfem with variants via develop: in spack.yaml.

Rebuild after making changes:

# Inside the container
cd /opt/hpc-env
. /opt/spack/share/spack/setup-env.sh
spack env activate .
spack install --force mfem@master+examples+miniapps

Use installed artifacts from the view:

# Binaries / headers / libraries (copy/symlink view)
ls /opt/views/view/bin
ls /opt/views/view/include
ls /opt/views/view/lib /opt/views/view/lib64

# Example: confirm mfem install
mfem-config --prefix

Optional: Development Workflow (deal.II)

If you enabled the dealii develop entry:

• Clone source into /code/dealii (similar to MFEM):

# Modify Dockerfile to clone deal.II or clone after container start
cd /code
git clone --depth=1 https://github.com/dealii/dealii.git dealii

• Rebuild:

cd /opt/hpc-env
. /opt/spack/share/spack/setup-env.sh
spack env activate .
spack install --force dealii@9.7.1~adol-c~arborx~arpack~assimp~cgal+complex~cuda~doc~examples~ginkgo~gmsh+gsl~hdf5~int64~ipo+kokkos+metis+mpi+muparser~nanoflann~netcdf~optflags+p4est+petsc+platform-introspection+python+scalapack+simplex+slepc~sundials~symengine+taskflow~threads~trilinos~vtk build_type=Release

Environment & View

• The Spack view is configured at /opt/views/view.
• The Docker image appends activation commands to /etc/profile.d/z10_spack_environment.sh, so login shells start with the environment enabled.
• activate.sh (if used) exports common variables like CMAKE_PREFIX_PATH, PETSC_DIR, SLEPC_DIR, and sets PATH, LD_LIBRARY_PATH, etc.

Image Size & Cleanup

The Dockerfile runs:

spack clean --all
find /opt/software -type d -name build -exec rm -rf {} + 2>/dev/null || true

This removes cached sources and build directories, reducing image size while keeping installed binaries/headers/libs in the view.

Troubleshooting

• If the environment isn’t active, source profile:

source /etc/profile

• If mfem-config isn’t found, ensure /opt/views/view/bin is on PATH or activate the env:

. /opt/spack/share/spack/setup-env.sh
spack env activate /opt/hpc-env

• For path mismatches, verify develop: entries in spack.yaml match actual source locations (e.g., /code/mfem, /code/dealii).

Notes

• With unified concretization (unify: true / together), shared dependencies (MPI, PETSc, SLEPc) are resolved once. Adjust variants if conflicts arise.
• Prefer a single MPI implementation (e.g., MPICH) across all specs for ABI compatibility.