From af3cb230800b24cfa5fa802e9c4ce29bf922baae Mon Sep 17 00:00:00 2001
From: Matthias Wolf <matthias.wolf@epfl.ch>
Date: Wed, 11 Dec 2024 16:33:08 +0100
Subject: [PATCH] More documentation, add container modifications (#9)

Allows to append instructions to the container, used here to install compilers.
---
 .github/workflows/spacktainer.yaml                        | 4 ++++
 README.md                                                 | 3 +++
 .../amd64/neurodamus-hippocampus/Dockerfile.epilogue      | 3 +++
 .../amd64/neurodamus-neocortex/Dockerfile.epilogue        | 3 +++
 .../amd64/neurodamus-thalamus/Dockerfile.epilogue         | 3 +++
 .../amd64/neurodamus-thalamus/spack.yaml                  | 8 ++++++++
 6 files changed, 24 insertions(+)
 create mode 100644 container_definitions/amd64/neurodamus-hippocampus/Dockerfile.epilogue
 create mode 100644 container_definitions/amd64/neurodamus-neocortex/Dockerfile.epilogue
 create mode 100644 container_definitions/amd64/neurodamus-thalamus/Dockerfile.epilogue
 create mode 100644 container_definitions/amd64/neurodamus-thalamus/spack.yaml

diff --git a/.github/workflows/spacktainer.yaml b/.github/workflows/spacktainer.yaml
index e438357..0aa0e99 100644
--- a/.github/workflows/spacktainer.yaml
+++ b/.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:
diff --git a/README.md b/README.md
index c73fc56..93164a1 100644
--- a/README.md
+++ b/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.
diff --git a/container_definitions/amd64/neurodamus-hippocampus/Dockerfile.epilogue b/container_definitions/amd64/neurodamus-hippocampus/Dockerfile.epilogue
new file mode 100644
index 0000000..8a5ff9a
--- /dev/null
+++ b/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/*
diff --git a/container_definitions/amd64/neurodamus-neocortex/Dockerfile.epilogue b/container_definitions/amd64/neurodamus-neocortex/Dockerfile.epilogue
new file mode 100644
index 0000000..8a5ff9a
--- /dev/null
+++ b/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/*
diff --git a/container_definitions/amd64/neurodamus-thalamus/Dockerfile.epilogue b/container_definitions/amd64/neurodamus-thalamus/Dockerfile.epilogue
new file mode 100644
index 0000000..8a5ff9a
--- /dev/null
+++ b/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/*
diff --git a/container_definitions/amd64/neurodamus-thalamus/spack.yaml b/container_definitions/amd64/neurodamus-thalamus/spack.yaml
new file mode 100644
index 0000000..f4ab3ff
--- /dev/null
+++ b/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]