Parallel-NetCDF · wkliao · Jan 14, 2023 · May 27, 2023 · May 27, 2023
diff --git a/.github/workflows/cache_async_vol.yml b/.github/workflows/cache_async_vol.yml
@@ -19,7 +19,7 @@ on:
       - 'tests/*'
 
 env:
-   MPICH_VERSION: 4.0.2
+   MPICH_VERSION: 4.1.1
    ARGOBOTS_VERSION: 1.1
    ASYNC_VOL_VERSION: 1.4
    HDF5_VERSION: 1.14.1-2

diff --git a/.github/workflows/logvol_master.yml b/.github/workflows/logvol_master.yml
@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - master
-      - github_action
     paths-ignore:
       - '**/*.md'
       - '**/*.txt'
@@ -60,7 +59,6 @@ jobs:
                         --disable-doxygen-doc \
                         --disable-doxygen-man \
                         --disable-doxygen-html \
-                        --disable-hltools \
                         --disable-tools \
                         --disable-tests \
                         CC=mpicc

diff --git a/.github/workflows/logvol_master_mpich.yml b/.github/workflows/logvol_master_mpich.yml
@@ -0,0 +1,140 @@
+name: LogVOL master + MPICH
+
+on:
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - '**/*.md'
+      - '**/*.txt'
+      - '**/*.jpg'
+      - '**/*.png'
+      - 'tests/*'
+      - 'datasets/*'
+  pull_request:
+    branches: master
+    paths-ignore:
+      - '**/*.md'
+      - '**/*.txt'
+      - '**/*.jpg'
+      - '**/*.png'
+      - 'tests/*'
+      - 'datasets/*'
+
+env:
+   MPICH_VERSION: 4.1.1
+   HDF5_VERSION: 1.14.1-2
+
+jobs:
+    build:
+      runs-on: ubuntu-latest
+      timeout-minutes: 60
+      steps:
+        - uses: actions/checkout@v3
+        - name: Set up dependencies
+          run: |
+            sudo apt-get update
+            sudo apt-get -y install automake autoconf libtool libtool-bin m4 cmake
+            # The MPICH installed on github actions is too slow
+            # sudo apt-get install mpich
+            # mpicc -v
+            # zlib
+            sudo apt-get -y install zlib1g-dev
+        - name: Add global env variables into GITHUB_ENV
+          run: |
+            set -x
+            echo "MPICH_DIR=${GITHUB_WORKSPACE}/MPICH" >> $GITHUB_ENV
+            echo "HDF5_ROOT=${GITHUB_WORKSPACE}/HDF5" >> $GITHUB_ENV
+            echo "LOGVOL_DIR=${GITHUB_WORKSPACE}/LOGVOL" >> $GITHUB_ENV
+            echo "HDF5_PLUGIN_PATH=${GITHUB_WORKSPACE}/LOGVOL/lib" >> $GITHUB_ENV
+            echo "HDF5_USE_FILE_LOCKING=FALSE" >> $GITHUB_ENV
+        - name: Build MPICH ${{ env.MPICH_VERSION }}
+          if: ${{ success() }}
+          run: |
+            cd ${GITHUB_WORKSPACE}
+            rm -rf ${MPICH_DIR} ; mkdir ${MPICH_DIR} ; cd ${MPICH_DIR}
+            wget -q https://www.mpich.org/static/downloads/${MPICH_VERSION}/mpich-${MPICH_VERSION}.tar.gz
+            gzip -dc mpich-${MPICH_VERSION}.tar.gz | tar -xf -
+            cd mpich-${MPICH_VERSION}
+            ./configure --prefix=${MPICH_DIR} \
+                        --silent \
+                        --enable-romio \
+                        --with-file-system=ufs \
+                        --with-device=ch3:sock \
+                        --disable-fortran \
+                        CC=gcc
+            make -s LIBTOOLFLAGS=--silent V=1 -j 8 install > qout 2>&1
+            make -s -j 8 distclean >> qout 2>&1
+        - name: Install HDF5
+          if: ${{ success() }}
+          run: |
+            cd ${GITHUB_WORKSPACE}
+            rm -rf ${HDF5_ROOT} ; mkdir ${HDF5_ROOT} ; cd ${HDF5_ROOT}
+            VER_MAJOR=${HDF5_VERSION%.*}
+            VER_NOPATCH=${HDF5_VERSION%-*} # remove patch version
+            wget -cq https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${VER_MAJOR}/hdf5-${VER_NOPATCH}/src/hdf5-${HDF5_VERSION}.tar.gz
+            tar -zxf hdf5-${HDF5_VERSION}.tar.gz
+            cd hdf5-${HDF5_VERSION}
+            ./configure --prefix=${HDF5_ROOT} \
+                        --silent \
+                        --enable-hl \
+                        --enable-parallel \
+                        --enable-build-mode=production \
+                        --disable-doxygen-doc \
+                        --disable-doxygen-man \
+                        --disable-doxygen-html \
+                        --disable-hltools \
+                        --disable-tools \
+                        --disable-tests \
+                        CC=${MPICH_DIR}/bin/mpicc
+            make -s LIBTOOLFLAGS=--silent V=1 -j 8 install > qout 2>&1
+            make -s distclean >> qout 2>&1
+        - name: Dump HDF5 config.log file
+          if: ${{ failure() }}
+          run: |
+            cat ${HDF5_ROOT}/hdf5-${HDF5_VERSION}/config.log
+        - name: Install Log VOL connector from its master branch
+          if: ${{ success() }}
+          run: |
+            cd ${GITHUB_WORKSPACE}
+            rm -rf vol-log-based
+            git clone -q https://github.com/DataLib-ECP/vol-log-based.git
+            cd vol-log-based
+            autoreconf -i
+            ./configure --prefix=${LOGVOL_DIR} \
+                        --silent \
+                        --with-hdf5=${HDF5_ROOT} \
+                        --with-mpi=${MPICH_DIR}
+            make -s LIBTOOLFLAGS=--silent V=1 -j 8 install > qout 2>&1
+            make -s distclean >> qout 2>&1
+        - name: Build and check E3SM_IO with HDF5 Log VOL connector only
+          if: ${{ success() }}
+          run: |
+            cd ${GITHUB_WORKSPACE}
+            rm -rf ./test_output
+            autoreconf -i
+            ./configure --with-hdf5=${HDF5_ROOT} \
+                        --with-logvol=${LOGVOL_DIR} \
+                        --with-mpi=${MPICH_DIR} \
+                        CFLAGS=-fno-var-tracking-assignments \
+                        CXXFLAGS=-fno-var-tracking-assignments
+            make -j 8
+            make check
+        - name: Dump log files if E3SM_IO with HDF5 Log VOL connector test failed
+          if: ${{ failure() }}
+          run: |
+            cd ${GITHUB_WORKSPACE}
+            cat test.sh.log utils/*.log
+            cat config.log
+        - name: Test E3SM_IO -- parallel runs
+          if: ${{ success() }}
+          run: |
+            cd ${GITHUB_WORKSPACE}
+            make ptest
+        - name: Test make distcheck
+          if: ${{ success() }}
+          run: |
+            cd ${GITHUB_WORKSPACE}
+            make distcheck DISTCHECK_CONFIGURE_FLAGS="--with-hdf5=${HDF5_ROOT} --with-logvol=${LOGVOL_DIR} CC=${MPICH_DIR}/bin/mpicc CXX=${MPICH_DIR}/bin/mpicxx CFLAGS=-fno-var-tracking-assignments CXXFLAGS=-fno-var-tracking-assignments"
+            make distclean
+
diff --git a/.github/workflows/mpich_static.yml b/.github/workflows/mpich_static.yml
@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - master
-      - github_action
     paths-ignore:
       - '**/*.md'
       - '**/*.txt'
@@ -23,7 +22,7 @@ on:
       - 'datasets/*'
 
 env:
-   MPICH_VERSION: 4.0.2
+   MPICH_VERSION: 4.1.1
    PNETCDF_VERSION: 1.12.3
    HDF5_VERSION: 1.14.1-2
    NETCDF4_VERSION: 4.9.0
@@ -104,7 +103,6 @@ jobs:
                         --disable-doxygen-doc \
                         --disable-doxygen-man \
                         --disable-doxygen-html \
-                        --disable-hltools \
                         --disable-tools \
                         --disable-tests \
                         --disable-shared \

diff --git a/.github/workflows/ubuntu_ompi.yml b/.github/workflows/ubuntu_ompi.yml
@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - master
-      - github_action
     paths-ignore:
       - '**/*.md'
       - '**/*.txt'
@@ -80,7 +79,6 @@ jobs:
                         --disable-doxygen-doc \
                         --disable-doxygen-man \
                         --disable-doxygen-html \
-                        --disable-hltools \
                         --disable-tools \
                         --disable-tests \
                         CC=mpicc