Merge pull request #1995 from jedwards4b/fillvalue_fix.wif

Fillvalue fix.wif

.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

.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

.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

.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

.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

.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

.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 }}

.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

.github/workflows/cmake.yml

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

.github/workflows/cmake_ubuntu_latest.yml

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

.github/workflows/netcdf_hdf5_no_pnetcdf_ncint_mpich.yml

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

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

.github/workflows/netcdf_pnetcdf_openmpi.yml

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

.github/workflows/strict_autotools_ubuntu_latest.yml

@@ -20,7 +20,7 @@ jobs:
       FCFLAGS: "-fallow-argument-mismatch -Wall"
       PNETCDF_VERSION: checkpoint.1.12.3
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Installs
       run: |
         set -x
@@ -29,7 +29,7 @@ jobs:
 
     - name: cache-pnetcdf
       id: cache-pnetcdf
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/work/ParallelIO/ParallelIO/pnetcdf
         key: pnetcdf-${{ runner.os }}-${{ env.PNETCDF_VERSION }}-openmpi

CMakeLists.txt

@@ -10,7 +10,7 @@ project (PIO C)
 # The project version number.
 set(VERSION_MAJOR   2   CACHE STRING "Project major version number.")
 set(VERSION_MINOR   6   CACHE STRING "Project minor version number.")
-set(VERSION_PATCH   2   CACHE STRING "Project patch version number.")
+set(VERSION_PATCH   5   CACHE STRING "Project patch version number.")
 mark_as_advanced(VERSION_MAJOR VERSION_MINOR VERSION_PATCH)
 
 # Create version info in autotools parlance for pio_meta.h.
@@ -352,7 +352,7 @@ CHECK_C_SOURCE_COMPILES("
 #if !NC_HAS_SZIP_WRITE
       choke me
 #endif
-int main() {return 0;}" HAVE_SZIP_WRITE)
+int main() {return 0;}" USE_SZIP)
 
 ###
 # Check to see if parallel filters are supported by HDF5/netcdf-c.

configure.ac

@@ -2,7 +2,7 @@
 ## Ed Hartnett 8/16/17
 
 # Initialize autoconf and automake.
-AC_INIT(pio, 2.6.2)
+AC_INIT(pio, 2.6.5)
 AC_CONFIG_SRCDIR(src/clib/pio_darray.c)
 AM_INIT_AUTOMAKE([foreign serial-tests])
 
@@ -11,15 +11,15 @@ AM_INIT_AUTOMAKE([foreign serial-tests])
 # AC_DEFINE_UNQUOTED for config.h.
 AC_SUBST([PIO_VERSION_MAJOR]) PIO_VERSION_MAJOR=2
 AC_SUBST([PIO_VERSION_MINOR]) PIO_VERSION_MINOR=6
-AC_SUBST([PIO_VERSION_PATCH]) PIO_VERSION_PATCH=2
+AC_SUBST([PIO_VERSION_PATCH]) PIO_VERSION_PATCH=5
 AC_DEFINE_UNQUOTED([PIO_VERSION_MAJOR], [$PIO_VERSION_MAJOR], [PIO major version])
 AC_DEFINE_UNQUOTED([PIO_VERSION_MINOR], [$PIO_VERSION_MINOR], [PIO minor version])
 AC_DEFINE_UNQUOTED([PIO_VERSION_PATCH], [$PIO_VERSION_PATCH], [PIO patch version])
 
 # Once more for the documentation.
 AC_SUBST([VERSION_MAJOR], [2])
 AC_SUBST([VERSION_MINOR], [6])
-AC_SUBST([VERSION_PATCH], [2])
+AC_SUBST([VERSION_PATCH], [5])
 
 
 # The m4 directory holds macros for autoconf.

src/clib/pio.h

@@ -27,6 +27,9 @@
     (((NC_VERSION_MAJOR == Maj) && (NC_VERSION_MINOR == Min) && (NC_VERSION_PATCH >= Pat)) || \
      ((NC_VERSION_MAJOR == Maj) && (NC_VERSION_MINOR > Min)) || (NC_VERSION_MAJOR > Maj))
 
+#ifndef NC_FillValue
+#define NC_FillValue _FillValue
+#endif
 
 /** PIO_OFFSET is an integer type of size sufficient to represent the
  * size (in bytes) of the largest file supported by MPI. This is not

src/clib/pio_nc.c

@@ -2322,7 +2322,7 @@ PIOc_def_var(int ncid, const char *name, nc_type xtype, int ndims,
  *
  * When the fill mode for the file is NC_FILL, then fill values are
  * used for missing data. This function sets the fill value to be used
- * for a variable. If no specific fill value is set (as a _FillValue
+ * for a variable. If no specific fill value is set (as a NC_FillValue
  * attribute), then the default fill values from netcdf.h are used.
  *
  * 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)
             {
                 ierr = nc_set_fill(file->fh, NC_FILL, NULL);
                 if (!ierr)
-                    ierr = nc_put_att(file->fh, varid, _FillValue, xtype, 1, fill_valuep);
+                    ierr = nc_put_att(file->fh, varid, NC_FillValue, xtype, 1, fill_valuep);
             }
         }
         else
@@ -2477,7 +2477,7 @@ PIOc_inq_var_fill(int ncid, int varid, int *no_fill, void *fill_valuep)
 {
     iosystem_desc_t *ios;  /* Pointer to io system information. */
     file_desc_t *file;     /* Pointer to file information. */
-    nc_type xtype;         /* Type of variable and its _FillValue attribute. */
+    nc_type xtype;         /* Type of variable and its NC_FillValue attribute. */
     PIO_Offset type_size;  /* Size in bytes of this variable's type. */
     int mpierr = MPI_SUCCESS, mpierr2;  /* Return code from MPI function codes. */
     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)
 
             if (!ierr && fill_valuep)
             {
-                ierr = nc_get_att(file->fh, varid, _FillValue, fill_valuep);
+                ierr = nc_get_att(file->fh, varid, NC_FillValue, fill_valuep);
                 if (ierr == NC_ENOTATT)
                 {
                     char char_fill_value = NC_FILL_CHAR;