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Merge pull request #1995 from jedwards4b/fillvalue_fix.wif
Fillvalue fix.wif
2 parents fcb8529 + 6b60bc8 commit b38e34e

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-49
lines changed

‎.github/actions/buildhdf5/action.yml

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@@ -34,7 +34,7 @@ inputs:
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runs:
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using: composite
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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repository: HDFGroup/hdf5
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path: hdf5-src

‎.github/actions/buildmpich/action.yml

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

‎.github/actions/buildnetcdf/action.yml

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

‎.github/actions/buildnetcdff/action.yml

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

‎.github/actions/buildopenmpi/action.yml

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

‎.github/actions/buildpnetcdf/action.yml

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

‎.github/actions/parallelio_autotools/action.yml

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

‎.github/actions/parallelio_cmake/action.yml

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

‎.github/workflows/cmake.yml

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@@ -19,7 +19,7 @@ jobs:
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# LDFLAGS: "-static-libasan"
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# ASAN_OPTIONS: "detect_odr_violation=0"
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Installs
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run: |
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set -x

‎.github/workflows/cmake_ubuntu_latest.yml

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@@ -23,7 +23,7 @@ jobs:
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PNETCDF_VERSION: checkpoint.1.12.3
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FCFLAGS: "-fallow-argument-mismatch"
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Installs
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run: |
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set -x
@@ -36,7 +36,7 @@ jobs:
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- name: cache-pnetcdf
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id: cache-pnetcdf
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/pnetcdf
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key: pnetcdf-${{ runner.os }}-${{ env.PNETCDF_VERSION }}

‎.github/workflows/netcdf_hdf5_no_pnetcdf_ncint_mpich.yml

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@@ -19,13 +19,13 @@ jobs:
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FFLAGS: "-fallow-argument-mismatch"
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FCFLAGS: "-fallow-argument-mismatch"
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Installs
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run: |
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sudo apt-get install doxygen graphviz wget gfortran libjpeg-dev libz-dev libcurl4-gnutls-dev
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- name: cache-mpich
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id: cache-mpich
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/work/ParallelIO/ParallelIO/mpich
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key: mpich-${{ runner.os }}-${{ env.MPICH_VERSION }}
@@ -39,7 +39,7 @@ jobs:
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- name: cache-hdf5
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id: cache-hdf5
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/work/ParallelIO/ParallelIO/hdf5
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key: hdf5-${{ runner.os }}-${{ env.HDF5_VERSION }}-mpich-${{ env.MPICH_VERSION }}
@@ -55,7 +55,7 @@ jobs:
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- name: cache-netcdf
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id: cache-netcdf
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/work/ParallelIO/ParallelIO/netcdf
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key: netcdf-${{ runner.os }}-${{ env.NETCDF_C_VERSION }}-${{ env.NETCDF_FORTRAN_VERSION }}-mpich-${{ env.MPICH_VERSION }}-hdf5-${{ env.HDF5_VERSION }}
@@ -79,7 +79,7 @@ jobs:
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- name: cache-netcdf-fortran
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id: cache-netcdf-fortran
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/netcdf-fortran
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key: netcdf-fortran-${{ runner.os }}-${{ env.NETCDF_FORTRAN_VERSION }}-mpich-${{ env.MPICH_VERSION }}-hdf5-${{ env.HDF5_VERSION }}

‎.github/workflows/netcdf_hdf5_pnetcdf_ncint_mpich_asan.yml

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@@ -20,13 +20,13 @@ jobs:
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FCFLAGS: "-fallow-argument-mismatch"
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FFLAGS: "-fallow-argument-mismatch"
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Installs
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run: |
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sudo apt-get install doxygen graphviz wget gfortran libjpeg-dev libz-dev
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- name: cache-mpich
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id: cache-mpich
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/mpich
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key: mpich-${{ runner.os }}-${{ env.MPICH_VERSION }}
@@ -40,7 +40,7 @@ jobs:
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- name: cache-hdf5
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id: cache-hdf5
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/hdf5
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key: hdf5-${{ runner.os }}-${{ env.HDF5_VERSION }}-mpich-${{ env.MPICH_VERSION }}
@@ -55,7 +55,7 @@ jobs:
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mpi_path: $HOME/mpich
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- name: cache-netcdf-c
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id: cache-netcdf-c
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/netcdf-c
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key: netcdf-c-${{ runner.os }}-${{ env.NETCDF_C_VERSION }}-mpich-${{ env.MPICH_VERSION }}-hdf5-${{ env.HDF5_VERSION }}
@@ -69,7 +69,7 @@ jobs:
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- name: cache-netcdf-fortran
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id: cache-netcdf-fortran
72-
uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/netcdf-fortran
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key: netcdf-fortran-${{ runner.os }}-${{ env.NETCDF_F_VERSION }}-mpich-${{ env.MPICH_VERSION }}-hdf5-${{ env.HDF5_VERSION_MAJOR }}.${{ env.HDF5_VERSION_PATCH }}
@@ -84,7 +84,7 @@ jobs:
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- name: cache-pnetcdf
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id: cache-pnetcdf
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/pnetcdf
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key: pnetcdf-${{ runner.os }}-${{ env.PNETCDF_VERSION }}-mpich-${{ env.MPICH_VERSION }}

‎.github/workflows/netcdf_pnetcdf_openmpi.yml

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@@ -22,13 +22,13 @@ jobs:
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FCFLAGS: "-fallow-argument-mismatch"
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FFLAGS: "-fallow-argument-mismatch"
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steps:
25-
- uses: actions/checkout@v3
25+
- uses: actions/checkout@v4
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- name: Installs
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run: |
2828
sudo apt-get install doxygen graphviz wget gfortran libjpeg-dev libz-dev
2929
- name: cache-openmpi
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id: cache-openmpi
31-
uses: actions/cache@v3
31+
uses: actions/cache@v4
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with:
3333
path: ~/work/ParallelIO/ParallelIO/openmpi
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key: openmpi-${{ runner.os }}-${{ env.OPENMPI_VERSION }}
@@ -42,7 +42,7 @@ jobs:
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4343
- name: cache-hdf5
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id: cache-hdf5
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/work/ParallelIO/ParallelIO/hdf5
4848
key: hdf5-${{ runner.os }}-${{ env.HDF5_VERSION }}-openmpi-${{ env.OPENMPI_VERSION }}
@@ -58,7 +58,7 @@ jobs:
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- name: cache-netcdf
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id: cache-netcdf
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uses: actions/cache@v3
61+
uses: actions/cache@v4
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with:
6363
path: ~/work/ParallelIO/ParallelIO/netcdf
6464
key: netcdf-${{ runner.os }}-${{ env.NETCDF_C_VERSION }}-${{ env.NETCDF_FORTRAN_VERSION }}-openmpi-${{ env.OPENMPI_VERSION }}-hdf5-${{ env.HDF5_VERSION }}
@@ -73,7 +73,7 @@ jobs:
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# - name: Setup tmate session
7575
# if: ${{ failure() }}
76-
# uses: mxschmitt/action-tmate@v3
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# uses: mxschmitt/action-tmate@v4
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7878
- name: Build NetCDF Fortran
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if: steps.cache-netcdf.outputs.cache-hit != 'true'
@@ -85,7 +85,7 @@ jobs:
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# - name: cache-pnetcdf
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# id: cache-pnetcdf
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# uses: actions/cache@v3
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# uses: actions/cache@v4
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# with:
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# path: ~/pnetcdf
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# key: pnetcdf-${{ runner.os }}-${{ env.PNETCDF_VERSION }}-openmpi-${{ env.OPENMPI_VERSION_MAJOR }}.${{ env.OPENMPI_VERSION_PATCH }}

‎.github/workflows/strict_autotools_ubuntu_latest.yml

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FCFLAGS: "-fallow-argument-mismatch -Wall"
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PNETCDF_VERSION: checkpoint.1.12.3
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Installs
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run: |
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set -x
@@ -29,7 +29,7 @@ jobs:
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- name: cache-pnetcdf
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id: cache-pnetcdf
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ~/work/ParallelIO/ParallelIO/pnetcdf
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key: pnetcdf-${{ runner.os }}-${{ env.PNETCDF_VERSION }}-openmpi

‎CMakeLists.txt

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@@ -10,7 +10,7 @@ project (PIO C)
1010
# The project version number.
1111
set(VERSION_MAJOR 2 CACHE STRING "Project major version number.")
1212
set(VERSION_MINOR 6 CACHE STRING "Project minor version number.")
13-
set(VERSION_PATCH 2 CACHE STRING "Project patch version number.")
13+
set(VERSION_PATCH 5 CACHE STRING "Project patch version number.")
1414
mark_as_advanced(VERSION_MAJOR VERSION_MINOR VERSION_PATCH)
1515

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# Create version info in autotools parlance for pio_meta.h.
@@ -352,7 +352,7 @@ CHECK_C_SOURCE_COMPILES("
352352
#if !NC_HAS_SZIP_WRITE
353353
choke me
354354
#endif
355-
int main() {return 0;}" HAVE_SZIP_WRITE)
355+
int main() {return 0;}" USE_SZIP)
356356

357357
###
358358
# Check to see if parallel filters are supported by HDF5/netcdf-c.

‎configure.ac

+3-3
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@@ -2,7 +2,7 @@
22
## Ed Hartnett 8/16/17
33

44
# Initialize autoconf and automake.
5-
AC_INIT(pio, 2.6.2)
5+
AC_INIT(pio, 2.6.5)
66
AC_CONFIG_SRCDIR(src/clib/pio_darray.c)
77
AM_INIT_AUTOMAKE([foreign serial-tests])
88

@@ -11,15 +11,15 @@ AM_INIT_AUTOMAKE([foreign serial-tests])
1111
# AC_DEFINE_UNQUOTED for config.h.
1212
AC_SUBST([PIO_VERSION_MAJOR]) PIO_VERSION_MAJOR=2
1313
AC_SUBST([PIO_VERSION_MINOR]) PIO_VERSION_MINOR=6
14-
AC_SUBST([PIO_VERSION_PATCH]) PIO_VERSION_PATCH=2
14+
AC_SUBST([PIO_VERSION_PATCH]) PIO_VERSION_PATCH=5
1515
AC_DEFINE_UNQUOTED([PIO_VERSION_MAJOR], [$PIO_VERSION_MAJOR], [PIO major version])
1616
AC_DEFINE_UNQUOTED([PIO_VERSION_MINOR], [$PIO_VERSION_MINOR], [PIO minor version])
1717
AC_DEFINE_UNQUOTED([PIO_VERSION_PATCH], [$PIO_VERSION_PATCH], [PIO patch version])
1818

1919
# Once more for the documentation.
2020
AC_SUBST([VERSION_MAJOR], [2])
2121
AC_SUBST([VERSION_MINOR], [6])
22-
AC_SUBST([VERSION_PATCH], [2])
22+
AC_SUBST([VERSION_PATCH], [5])
2323

2424

2525
# The m4 directory holds macros for autoconf.

‎src/clib/pio.h

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@@ -27,6 +27,9 @@
2727
(((NC_VERSION_MAJOR == Maj) && (NC_VERSION_MINOR == Min) && (NC_VERSION_PATCH >= Pat)) || \
2828
((NC_VERSION_MAJOR == Maj) && (NC_VERSION_MINOR > Min)) || (NC_VERSION_MAJOR > Maj))
2929

30+
#ifndef NC_FillValue
31+
#define NC_FillValue _FillValue
32+
#endif
3033

3134
/** PIO_OFFSET is an integer type of size sufficient to represent the
3235
* size (in bytes) of the largest file supported by MPI. This is not

‎src/clib/pio_nc.c

+4-4
Original file line numberDiff line numberDiff line change
@@ -2322,7 +2322,7 @@ PIOc_def_var(int ncid, const char *name, nc_type xtype, int ndims,
23222322
*
23232323
* When the fill mode for the file is NC_FILL, then fill values are
23242324
* used for missing data. This function sets the fill value to be used
2325-
* for a variable. If no specific fill value is set (as a _FillValue
2325+
* for a variable. If no specific fill value is set (as a NC_FillValue
23262326
* attribute), then the default fill values from netcdf.h are used.
23272327
*
23282328
* NetCDF-4 and pnetcdf files allow setting fill_mode (to NC_FILL or
@@ -2430,7 +2430,7 @@ PIOc_def_var_fill(int ncid, int varid, int fill_mode, const void *fill_valuep)
24302430
{
24312431
ierr = nc_set_fill(file->fh, NC_FILL, NULL);
24322432
if (!ierr)
2433-
ierr = nc_put_att(file->fh, varid, _FillValue, xtype, 1, fill_valuep);
2433+
ierr = nc_put_att(file->fh, varid, NC_FillValue, xtype, 1, fill_valuep);
24342434
}
24352435
}
24362436
else
@@ -2477,7 +2477,7 @@ PIOc_inq_var_fill(int ncid, int varid, int *no_fill, void *fill_valuep)
24772477
{
24782478
iosystem_desc_t *ios; /* Pointer to io system information. */
24792479
file_desc_t *file; /* Pointer to file information. */
2480-
nc_type xtype; /* Type of variable and its _FillValue attribute. */
2480+
nc_type xtype; /* Type of variable and its NC_FillValue attribute. */
24812481
PIO_Offset type_size; /* Size in bytes of this variable's type. */
24822482
int mpierr = MPI_SUCCESS, mpierr2; /* Return code from MPI function codes. */
24832483
int ierr = PIO_NOERR; /* Return code from function calls. */
@@ -2574,7 +2574,7 @@ PIOc_inq_var_fill(int ncid, int varid, int *no_fill, void *fill_valuep)
25742574

25752575
if (!ierr && fill_valuep)
25762576
{
2577-
ierr = nc_get_att(file->fh, varid, _FillValue, fill_valuep);
2577+
ierr = nc_get_att(file->fh, varid, NC_FillValue, fill_valuep);
25782578
if (ierr == NC_ENOTATT)
25792579
{
25802580
char char_fill_value = NC_FILL_CHAR;

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