More documentation, add container modifications

.github/workflows/spacktainer.yaml

@@ -74,6 +74,7 @@ jobs:
           # - multiscale-run
           - neurodamus-hippocampus
           - neurodamus-neocortex
+          - neurodamus-thalamus
           - system-benchmarks
     runs-on:
       - codebuild-spacktainers-tf-${{ github.run_id }}-${{ github.run_attempt }}
@@ -94,6 +95,9 @@ jobs:
           # Triggers building the 'builder' image, otherwise it is optimized away
           COPY --from=builder /etc/debian_version /etc/debian_version
           EOF
+          if [[ -f Dockerfile.epilogue ]]; then
+          cat Dockerfile.epilogue >> Dockerfile
+          fi
       - name: build ${{ matrix.spacktainer }}
         uses: ./.github/actions/build_container
         with:

README.md

@@ -11,6 +11,9 @@ This repository aims to be the one-stop shop for all of our container needs.
 
 The only files you should have to edit as an end-user are located in the `container_definitions` folder. There's a subfolder per architecture (currently supported: `amd64` and `arm64`) under which both `spack.yaml` (in subdirectories) and `def` files can live.
 * A `spack.yaml` file file defines a Spack container - in it you can define the Spack specs as you would in a Spack environment. If you have specific requirements for dependencies, you can add `spack: packages: ...` keys to define those, again, as in a Spack environment.
+* If a `Dockerfile.epilogue` is present in the container directory, it will be appended to
+the auto-generated `Dockerfile`. This can be used to, e.g., include compilers in the final
+container and perform other fine-tuning.
 * A def file defines a singularity container that will be built from an existing container on docker-hub. nexus-storage is already defined for amd64 as an example.
 
 In both cases, the filename will be used as the name of your container. In case of a YAML file, the container version will be derived from the first package in your spec. In case of a def file, the version will be the same as the tag on docker hub.

container_definitions/amd64/neurodamus-hippocampus/Dockerfile.epilogue

@@ -0,0 +1,3 @@
+RUN apt-get update \
+    && apt-get install -y gcc g++ make \
+    && rm -rf /var/lib/apt/lists/*

container_definitions/amd64/neurodamus-neocortex/Dockerfile.epilogue

@@ -0,0 +1,3 @@
+RUN apt-get update \
+    && apt-get install -y gcc g++ make \
+    && rm -rf /var/lib/apt/lists/*

container_definitions/amd64/neurodamus-thalamus/Dockerfile.epilogue

@@ -0,0 +1,3 @@
+RUN apt-get update \
+    && apt-get install -y gcc g++ make \
+    && rm -rf /var/lib/apt/lists/*

container_definitions/amd64/neurodamus-thalamus/spack.yaml

@@ -0,0 +1,8 @@
+spack:
+  specs:
+    - neurodamus-models model=thalamus +coreneuron+caliper
+    - py-neurodamus
+  packages:
+    all:
+      providers:
+        mpi: [mpich]