Use package repository for CI (#75)

Author: twsearle

.github/workflows/ci.yml

@@ -5,7 +5,10 @@ on:
     branches: [develop]
   pull_request:
     branches: [develop]
-
+  workflow_dispatch:
+env:
+    REGISTRY: ghcr.io
+    IMAGE_NAME: twsearle/orca-jedi/ci-almalinux9:v1.7.0
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -15,40 +18,79 @@ jobs:
         with:
           lfs: true
 
+      - name: checkout orca-jedi
+        uses: actions/checkout@v3
+        with:
+          path: ci/orca-jedi
+          repository: MetOffice/orca-jedi
+          token: ${{ secrets.GHCR_PAT }}
+          lfs: true
+
       - name: checkout jedicmake
         uses: actions/checkout@v3
         with:
           path: ci/jedicmake
           repository: JCSDA-internal/jedi-cmake
           submodules: true
-          token: ${{ secrets.GH_PAT }}
+          token: ${{ secrets.GHCR_PAT }}
 
       - name: checkout oops
         uses: actions/checkout@v3
         with:
           path: ci/oops
           repository: JCSDA-internal/oops
-          token: ${{ secrets.GH_PAT }}
+          token: ${{ secrets.GHCR_PAT }}
+
+      - name: checkout vader
+        uses: actions/checkout@v3
+        with:
+          path: ci/vader
+          repository: JCSDA-internal/vader
+          token: ${{ secrets.GHCR_PAT }}
+
+      - name: checkout saber
+        uses: actions/checkout@v3
+        with:
+          path: ci/saber
+          repository: JCSDA-internal/saber
+          token: ${{ secrets.GHCR_PAT }}
 
       - name: checkout ioda
         uses: actions/checkout@v3
         with:
           path: ci/ioda
           repository: JCSDA-internal/ioda
-          token: ${{ secrets.GH_PAT }}
+          token: ${{ secrets.GHCR_PAT }}
 
       - name: checkout ufo
         uses: actions/checkout@v3
         with:
           path: ci/ufo
           repository: JCSDA-internal/ufo
-          token: ${{ secrets.GH_PAT }}
+          token: ${{ secrets.GHCR_PAT }}
+
+      - name: checkout atlas-data
+        uses: actions/checkout@v3
+        with:
+          path: ci/atlas-data
+          repository: MetOffice/atlas-data
+          lfs: true
+          token: ${{ secrets.GHCR_PAT }}
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: twsearle
+          password: ${{ secrets.GHCR_PAT }}
 
+      - name: Pull Docker image
+        run: docker pull ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
       - name: build and test
         run: |
           docker run --rm \
-            --entrypoint=/usr/local/src/nemo-feedback/ci/build.sh \
-            --workdir=/usr/local/src/nemo-feedback/ci \
-            --volume $PWD:/usr/local/src/nemo-feedback \
-            'jcsda/docker-gnu-openmpi-dev:latest'
+            --entrypoint=/usr/local/src/orca-jedi/ci/build-and-test.sh \
+            --workdir=/usr/local/src/orca-jedi/ci \
+            --volume $PWD:/usr/local/src/orca-jedi \
+            ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}

ci/CMakeLists.txt

@@ -2,18 +2,26 @@
 
 cmake_minimum_required( VERSION 3.18 FATAL_ERROR )
 
-project( nemo-feedback-ci VERSION 0.1 LANGUAGES C CXX Fortran )
+project( nemo-feedback-ci VERSION 1.0 LANGUAGES C CXX Fortran )
 
 set( ENABLE_MPI ON CACHE BOOL "Compile with MPI" )
 set( ENABLE_OMP ON CACHE BOOL "Compile with OpenMP" )
 
+LIST( APPEND ATLAS_TEST_ENVIRONMENT
+    ATLAS_ORCA_CACHING=1
+    ATLAS_CACHE_PATH=${CMAKE_BINARY_DIR}/share
+    PLUGINS_MANIFEST_PATH=${CMAKE_BINARY_DIR}/share/plugins )
+
 add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/jedicmake" EXCLUDE_FROM_ALL)
 if(NOT DEFINED jedicmake_DIR)
   set(jedicmake_DIR "${CMAKE_BINARY_DIR}/jedicmake")
 endif()
 
 add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/oops" EXCLUDE_FROM_ALL)
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/vader" EXCLUDE_FROM_ALL)
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/saber" EXCLUDE_FROM_ALL)
 add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/ioda" EXCLUDE_FROM_ALL)
 add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/ufo" EXCLUDE_FROM_ALL)
+add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/orca-jedi" EXCLUDE_FROM_ALL)
 add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/nemo-feedback")
 enable_testing()

ci/Dockerfile

@@ -0,0 +1,66 @@
+#!/bin/bash
+set -euo pipefail
+
+finally() {
+    trap '' ERR
+    trap '' EXIT
+    if [[ -d "${WORKD:-}" ]]; then
+        cd /
+        rm -fr "${WORKD}"
+    fi
+}
+
+HERE="$(cd "$(dirname "$0")" && pwd)"
+THIS="$(basename "$0")"
+NPROC=${NPROC:-2}
+WORKD="$(mktemp -d "${THIS}-XXXXXX" -t)"
+
+trap finally ERR
+trap finally EXIT
+
+cd "${WORKD}"
+
+if [[ -f /opt/spack-environment/activate.sh ]]; then
+    source /opt/spack-environment/activate.sh
+fi
+
+# -- Enable OpenMPI over subscription -----------------------------------------
+if command -v ompi_info &>/dev/null; then
+    echo "Check support for MPI_THREAD_MULTIPLE"
+    ompi_info | grep -i 'thread support'
+    ompi_vn=$(ompi_info | awk '/Ident string:/ {print $3}')
+    case $ompi_vn in
+        4.*) export OMPI_MCA_rmaps_base_oversubscribe=1 ;;
+        5.*) export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe ;;
+    esac
+fi
+
+atlas_orca_v=$(atlas --info |
+  sed -n 's/ *atlas-orca version (\([0-9]*\.[0-9]*\.[0-9]*\)).*/\1/p')
+
+echo "
+-------------------------------
+gcc version $(gcc -dumpversion ||:)
+$(ecbuild --version ||:)
+atlas version $(atlas --version ||:)
+atlas-orca version ${atlas_orca_v:-:}
+eckit version $(eckit-version ||:)
+ectrans version $(ectrans --version ||:)
+fckit version $(fckit --version ||:)
+fiat version $(fiat --version ||:)
+odc version $(odc --version ||:)
+-------------------------------
+"
+
+rm -f "${HERE}/nemo-feedback"
+ln -s '..' "${HERE}/nemo-feedback"
+ecbuild -S "${HERE}"
+make -j "${NPROC}"
+
+env OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 \
+    OOPS_TRACE=1 OOPS_DEBUG=1 \
+    LD_LIBRARY_PATH="${HERE}/lib:${LD_LIBRARY_PATH}" \
+    ATLAS_DATA_PATH="${HERE}/atlas-data" \
+    ctest -j "${NPROC}" -V --output-on-failure --test-dir "./nemo-feedback"
+
+exit