Change HDF5 develop to use cmake and fix CI integration (#136)

jeanbez · web-flow · commit bbbf4c5f7a0b · 2025-07-25T17:16:38.000-07:00
* update CI versions and change HDF5 develop to use cmake

* change upload version

* fix CI

* change HDF5 compilation flags

* update VOL ASYNC version in CI and drop debug

* fix CI

* add build log for E3SM

* add build log for E3SM

* fix action syntax

* bump version

* update E3SM dependecy

* update GitHub Ubuntu CI image version

* fix NERSC integration

* fix typo

* improve CI usage

* fix CI

* changes in GitLab CI integration

* change build
diff --git a/.github/workflows/clang-format-check.yml b/.github/workflows/clang-format-check.yml
@@ -9,7 +9,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Run clang-format style check for C programs.
-      uses: DoozyX/clang-format-lint-action@v0.11
+      uses: DoozyX/clang-format-lint-action@v0.18.2
       with:
         source: '.'
         extensions: 'c,h,cpp,hpp'
diff --git a/.github/workflows/clang-format-fix.yml b/.github/workflows/clang-format-fix.yml
@@ -10,7 +10,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Run clang-format style check for C programs.
-      uses: DoozyX/clang-format-lint-action@v0.11
+      uses: DoozyX/clang-format-lint-action@v0.18.2
       with:
         source: '.'
         extensions: 'c,h,cpp,hpp'
diff --git a/.github/workflows/h5bench-hdf5-1.10.4.yml b/.github/workflows/h5bench-hdf5-1.10.4.yml
@@ -9,9 +9,13 @@ on:
     branches:
       - master
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   h5bench:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     container:
       image: hpcio/hdf5-1.10.4
     timeout-minutes: 60
@@ -217,13 +221,9 @@ jobs:
           cd build
           ./h5bench --debug --abort-on-failure ../samples/sync-macsio.json
 
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
-
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: test
           path: build/storage/**/std*
diff --git a/.github/workflows/h5bench-hdf5-1.10.7.yml b/.github/workflows/h5bench-hdf5-1.10.7.yml
@@ -9,9 +9,13 @@ on:
     branches:
       - master
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   h5bench:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     container:
       image: hpcio/hdf5-1.10.7
     timeout-minutes: 60
@@ -217,13 +221,9 @@ jobs:
           cd build
           ./h5bench --debug --abort-on-failure ../samples/sync-macsio.json
 
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
-
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: test
           path: build/h5bench_e3sm-prefix/src/h5bench_e3sm-stamp/*
diff --git a/.github/workflows/h5bench-hdf5-1.10.8.yml b/.github/workflows/h5bench-hdf5-1.10.8.yml
@@ -9,9 +9,13 @@ on:
     branches:
       - master
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   h5bench:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     container:
       image: hpcio/hdf5-1.10.8
     timeout-minutes: 60
@@ -217,13 +221,9 @@ jobs:
           cd build
           ./h5bench --debug --abort-on-failure ../samples/sync-macsio.json
 
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
-
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: test
           path: build/storage/**/std*
diff --git a/.github/workflows/h5bench-hdf5-1.12.0.yml b/.github/workflows/h5bench-hdf5-1.12.0.yml
@@ -9,9 +9,13 @@ on:
     branches:
       - master
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   h5bench:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     container:
       image: hpcio/hdf5-1.12.0
     timeout-minutes: 60
@@ -252,13 +256,9 @@ jobs:
           cd build
           ./h5bench --debug --abort-on-failure ../samples/sync-macsio.json
 
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
-
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: test
           path: build/storage/**/std*
diff --git a/.github/workflows/h5bench-hdf5-1.14.0.yml b/.github/workflows/h5bench-hdf5-1.14.0.yml
@@ -9,9 +9,13 @@ on:
     branches:
       - master
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   h5bench:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     container:
       image: hpcio/hdf5-1.14.0
     timeout-minutes: 60
@@ -507,13 +511,9 @@ jobs:
 
           ./h5bench --debug --abort-on-failure ../samples/async-amrex.json
 
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
-
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: test
           path: build*/storage/**/std*
diff --git a/.github/workflows/h5bench-hdf5-1.14.1.yml b/.github/workflows/h5bench-hdf5-1.14.1.yml
@@ -9,9 +9,13 @@ on:
     branches:
       - master
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   h5bench:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     container:
       image: hpcio/hdf5-1.14.1
     timeout-minutes: 60
@@ -507,13 +511,9 @@ jobs:
 
           ./h5bench --debug --abort-on-failure ../samples/async-amrex.json
 
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
-
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: test
           path: build*/storage/**/std*
diff --git a/.github/workflows/h5bench-hdf5-develop-test.yml b/.github/workflows/h5bench-hdf5-develop-test.yml
@@ -5,9 +5,13 @@ on:
 
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   h5bench:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     timeout-minutes: 60
     env:
       OMPI_ALLOW_RUN_AS_ROOT: 1
@@ -28,21 +32,29 @@ jobs:
           git clone https://github.com/HDFGroup/hdf5.git
 
           # VOL-ASYNC
-          git clone --recursive https://github.com/hpc-io/vol-async.git --branch v1.7 /opt/vol-async
+          git clone --recursive https://github.com/hpc-io/vol-async.git --branch v1.9 /opt/vol-async
 
           python3 -m pip install pytest
 
       - name: Build HDF5 develop
         run: |
           export HDF5_DIR=/opt/hdf5
-          export HDF5_LIBTOOL=/usr/bin/libtoolize
-          
+
           mkdir $HDF5_DIR
+          mkdir hdf5/build
 
-          cd hdf5
+          cd hdf5/build
 
-          ./autogen.sh
-          ./configure --prefix=$HDF5_DIR --enable-parallel --enable-threadsafe --enable-unsupported
+          cmake \
+            -DCMAKE_INSTALL_PREFIX=$HDF5_DIR \
+            -DHDF5_ENABLE_PARALLEL=ON \
+            -DHDF5_ENABLE_THREADSAFE=ON \
+            -DHDF5_ALLOW_UNSUPPORTED=ON \
+            -DBUILD_TESTING=OFF \
+            -DHDF5_BUILD_HL_LIB=OFF \
+            -DHDF5_BUILD_EXAMPLES=OFF \
+            -DHDF5_BUILD_TOOLS:BOOL=OFF \
+            -DCMAKE_C_COMPILER=mpicc ..
 
           make -j 2
           make install
@@ -146,14 +158,12 @@ jobs:
 
           ctest --verbose .
 
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
-
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: test
-          path: build*/storage/**/std*
+          path: |
+            build*/storage/**/std*
+            build*/h5bench_e3sm-prefix/src/h5bench_e3sm-stamp/h5bench_e3sm-build-*.log
           retention-days: 5
diff --git a/.github/workflows/h5bench-hdf5-develop.yml b/.github/workflows/h5bench-hdf5-develop.yml
@@ -7,7 +7,7 @@ on:
 
 jobs:
   h5bench:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     timeout-minutes: 60
     env:
       OMPI_ALLOW_RUN_AS_ROOT: 1
@@ -28,19 +28,27 @@ jobs:
           git clone https://github.com/HDFGroup/hdf5.git
 
           # VOL-ASYNC
-          git clone --recursive https://github.com/hpc-io/vol-async.git --branch v1.7 /opt/vol-async
+          git clone --recursive https://github.com/hpc-io/vol-async.git --branch v1.9 /opt/vol-async
 
       - name: Build HDF5 develop
         run: |
           export HDF5_DIR=/opt/hdf5
-          export HDF5_LIBTOOL=/usr/bin/libtoolize
-          
+
           mkdir $HDF5_DIR
+          mkdir hdf5/build
 
-          cd hdf5
+          cd hdf5/build
 
-          ./autogen.sh
-          ./configure --prefix=$HDF5_DIR --enable-parallel --enable-threadsafe --enable-unsupported
+          cmake \
+            -DCMAKE_INSTALL_PREFIX=$HDF5_DIR \
+            -DHDF5_ENABLE_PARALLEL=ON \
+            -DHDF5_ENABLE_THREADSAFE=ON \
+            -DHDF5_ALLOW_UNSUPPORTED=ON \
+            -DBUILD_TESTING=OFF \
+            -DHDF5_BUILD_HL_LIB=OFF \
+            -DHDF5_BUILD_EXAMPLES=OFF \
+            -DHDF5_BUILD_TOOLS:BOOL=OFF \
+            -DCMAKE_C_COMPILER=mpicc ..
 
           make -j 2
           make install
@@ -148,10 +156,6 @@ jobs:
 
           ./h5bench --debug --abort-on-failure ../samples/async-write-read-contig-1d-small.json
         
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
-
       - name: Test h5bench SYNC write 1D contiguous (memory) strided (file)
         run: |
           export HDF5_HOME=/opt/hdf5
@@ -639,14 +643,12 @@ jobs:
 
           ./h5bench --debug --abort-on-failure ../samples/async-amrex.json
 
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
-
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: test
-          path: build*/storage/**/std*
+          path: |
+            build*/storage/**/std*
+            build*/h5bench_e3sm-prefix/src/h5bench_e3sm-stamp/h5bench_e3sm-build-*.log
           retention-days: 5
diff --git a/.github/workflows/nersc.yml b/.github/workflows/nersc.yml
@@ -1,14 +1,40 @@
 name: NERSC
 
 on:
-  workflow_dispatch:
-  push:
+  pull_request
+
+env:
+  PR_NUMBER: ${{ github.event.number }}
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
 
 jobs:
-  synchronize:
-    runs-on: ubuntu-20.04
-    timeout-minutes: 5
+  authorize:
+    runs-on: ubuntu-latest
     steps:
-      - name: Synchronize NERSC CI
+      - run: true
+
+  sync-with-nersc:
+    needs: authorize
+    runs-on: ubuntu-latest
+    timeout-minutes: 2
+    
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          
+      - name: Setup git
+        run: |
+          git config --global user.name "h5bench BOT"
+          git config --global user.email "h5bench@example.com"
+    
+      - name: Create PR branch
         run: |
-          curl --request POST --header "PRIVATE-TOKEN: ${{ secrets.NERSC_GITLAB_TOKEN }}" "${{ secrets.NERSC_GITLAB_URL }}"
+          PR_SHA=$(git rev-parse --short "$GITHUB_SHA")
+          git fetch origin pull/${PR_NUMBER}/head:PR-${PR_SHA}
+          git remote add gitlab https://${{ secrets.GITLAB_TOKEN_NAME }}:${{ secrets.GITLAB_TOKEN }}@${{ secrets.GITLAB_URL }}
+          git checkout PR-${PR_SHA}
+          git push -f -u gitlab PR-${PR_SHA}
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
diff --git a/e3sm b/e3sm
