Update PIO from pio2_6_2 to pio2_6_5

I did this update by simply copying the ParallelIO repository (checked
out at pio2_6_5) to here, and then deleting the .git directory. I
confirmed that, prior to this update, there were no diffs from the
ParallelIO repository (at pio2_6_2), so it is safe to do the update in
this simple manner.

Changes here:

pio2_6_3: Merge pull request #1982 from alperaltuntas/bugfix_debug
- fix minor bugs in pio_nc4.c

pio2_6_4: Bug fix release. Fixes issues with large datasets and with
autoconf/cmake configure option.

pio2_6_5: Updated for compatibility with netcdf-c 4.9.3 and cygwin.

Resolves #353

Author: billsacks

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildhdf5/action.yml

@@ -34,7 +34,7 @@ inputs:
 runs:
   using: composite
   steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         repository: HDFGroup/hdf5
         path: hdf5-src
@@ -50,7 +50,10 @@ runs:
         -DHDF5_ENABLE_PARALLEL=${{ inputs.enable_parallel }} \
         -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
         -DBUILD_TESTING=${{ inputs.enable_testing }} \
+        -DHDF5_ENABLE_DEPRICATED_SYMBOLS=OFF \
+        -DHDF5_BUILD_EXAMPLES=OFF \
         -DHDF5_BUILD_TOOLS=OFF \
+        -DCMAKE_BUILD_TYPE=REL \
         ../
         make
         make install

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildmpich/action.yml

@@ -13,7 +13,7 @@ inputs:
 runs:
   using: composite
   steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         repository: pmodels/mpich
         path: mpich-src

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildnetcdf/action.yml

@@ -45,7 +45,7 @@ inputs:
 runs:
   using: composite
   steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         repository: Unidata/netcdf-c
         path: netcdf-c-src

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildnetcdff/action.yml

@@ -19,7 +19,7 @@ inputs:
 runs:
   using: composite
   steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         repository: Unidata/netcdf-fortran
         path: netcdf-fortran-src

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildopenmpi/action.yml

@@ -13,7 +13,7 @@ inputs:
 runs:
   using: composite
   steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         repository: open-mpi/ompi
         path: openmpi-src

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/buildpnetcdf/action.yml

@@ -2,7 +2,7 @@ description: 'Build the pnetcdf library'
 inputs:
   pnetcdf_version:
     description: 'Tag in the pnetcdf repository to use'
-    default: checkpoint.1.12.3
+    default: checkpoint.1.14.0
     required: False
     type: string
   install_prefix:
@@ -23,7 +23,7 @@ inputs:
 runs:
   using: composite
   steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         repository: Parallel-NetCDF/PnetCDF
         path: pnetcdf-src

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/intelcompilers/action.yml

@@ -2,22 +2,20 @@ description: 'Install Intel Compilers'
 runs:
   using: composite
   steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: setup repo
       shell: bash
       run: |
-        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-        rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-        sudo echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+        #wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        # download the key to system keyring
+        wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+        #sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        #rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
         sudo apt-get update
     - name: install
       shell: bash
       run: |
-        sudo apt-get install -y intel-oneapi-common-vars
-        sudo apt-get install -y intel-oneapi-compiler-fortran
-        sudo apt-get install -y intel-oneapi-mkl
-        sudo apt-get install -y intel-oneapi-mpi
-        sudo apt-get install -y intel-oneapi-mpi-devel
+        sudo apt-get install intel-oneapi-hpc-toolkit
         source /opt/intel/oneapi/setvars.sh
-        printenv >> $GITHUB_ENV
+        source /opt/intel/oneapi/compiler/latest/env/vars.sh intel64

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/parallelio_autotools/action.yml

@@ -2,7 +2,7 @@ description: 'Build the parallelio library using cmake'
 inputs:
   parallelio_version:
     description: 'Tag in the parallelio repository to use'
-    default: pio2_5_10
+    default: pio2_6_3
     required: False
     type: string
   shared_libraries:
@@ -101,12 +101,12 @@ runs:
   using: composite
   steps:
     - name: Check if already present
-      uses: andstor/file-existence-action@v2
+      uses: andstor/file-existence-action@v3
       with:
        files: ${{ inputs.src_path }}
     - name: get parallelio
       if: ${{ steps.check_files.outputs.files_exists != 'true' }}
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: NCAR/ParallelIO
         path: ${{ inputs.src_path }}

src/Infrastructure/IO/PIO/ParallelIO/.github/actions/parallelio_cmake/action.yml

@@ -2,7 +2,7 @@ description: 'Build the parallelio library using cmake'
 inputs:
   parallelio_version:
     description: 'Tag in the parallelio repository to use'
-    default: pio2_5_9
+    default: pio2_6_3
     required: False
     type: string
   shared_libraries:
@@ -110,7 +110,7 @@ inputs:
 runs:
   using: composite
   steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         repository: NCAR/ParallelIO
         path: parallelio-src

src/Infrastructure/IO/PIO/ParallelIO/.github/workflows/autotools.yml

@@ -19,7 +19,7 @@ jobs:
       LDFLAGS: "-L/usr/lib/x86_64-linux-gnu -lnetcdf_mpi -lpnetcdf"
       FCFLAGS: "-Wall -Werror -fallow-argument-mismatch -Wno-conversion"
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Installs
       run: |
         set -x
@@ -54,4 +54,4 @@ jobs:
 
 #    - name: Setup tmate session
 #      if: ${{ failure() }}
-#      uses: mxschmitt/action-tmate@v3
+#      uses: mxschmitt/action-tmate@v4