Merge pull request #1997 from briandobbins/qsort_comparator_64bit_fix

Fixes in issue in the qsort comparison function

.github/actions/buildhdf5/action.yml

@@ -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

.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

.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

CMakeLists.txt

@@ -29,18 +29,18 @@ include(CheckSymbolExists)
 
 # Determine the configure date.
 IF(DEFINED ENV{SOURCE_DATE_EPOCH})
-	EXECUTE_PROCESS(
-	  COMMAND "date" "-u" "-d" "@$ENV{SOURCE_DATE_EPOCH}"
-	  OUTPUT_VARIABLE CONFIG_DATE
-	  )
+        EXECUTE_PROCESS(
+          COMMAND "date" "-u" "-d" "@$ENV{SOURCE_DATE_EPOCH}"
+          OUTPUT_VARIABLE CONFIG_DATE
+          )
 ELSE()
-	EXECUTE_PROCESS(
-	  COMMAND date
-	  OUTPUT_VARIABLE CONFIG_DATE
-	  )
+        EXECUTE_PROCESS(
+          COMMAND date
+          OUTPUT_VARIABLE CONFIG_DATE
+          )
 ENDIF()
 IF(CONFIG_DATE)
-	string(STRIP ${CONFIG_DATE} CONFIG_DATE)
+        string(STRIP ${CONFIG_DATE} CONFIG_DATE)
 ENDIF()
 
 # A function used to create autotools-style 'yes/no' definitions.
@@ -363,9 +363,9 @@ if (HAVE_NETCDF_PAR)
 #if !NC_HAS_PAR_FILTERS
     choke me
 #endif
-int main() {return 0;}" HAVE_PAR_FILTERS)
+int main() {return 0;}" PIO_HAS_PAR_FILTERS)
 else()
-  set(HAVE_PAR_FILTERS 0)
+  set(PIO_HAS_PAR_FILTERS 0)
 endif()
 
 ###
@@ -486,7 +486,7 @@ set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
 INSTALL(FILES "${PIO_BINARY_DIR}/libpio.settings"
   DESTINATION lib
   COMPONENT libraries)
-  
+
 #####
 # Create pio_meta.h include file.
 #####

configure.ac

@@ -38,7 +38,7 @@ fi
 LD=ld # Required for MPE to work.
 LT_INIT
 
-# Find and learn about install 
+# Find and learn about install
 AC_PROG_INSTALL
 
 # Find and learn about the C compiler.
@@ -294,7 +294,7 @@ AC_MSG_CHECKING([whether netCDF provides parallel filter support])
 AC_CHECK_LIB([netcdf], [nc_inq_filter_avail], [have_par_filters=yes], [have_par_filters=no])
 AC_MSG_RESULT([${have_par_filters}])
 if test "x$have_par_filters" = xyes ; then
-   AC_DEFINE([HAVE_PAR_FILTERS], [1], [if true, netcdf-c supports filters with parallel I/O])
+   AC_DEFINE([PIO_HAS_PAR_FILTERS], [1], [if true, netcdf-c supports filters with parallel I/O])
 fi
 
 # Is this version 4.7.2, which does not work?
@@ -472,8 +472,8 @@ AC_CONFIG_HEADERS([config.h])
 
 # Create the makefiles.
 AC_CONFIG_FILES(Makefile
-	        src/Makefile
-        	src/clib/Makefile
+                src/Makefile
+                src/clib/Makefile
                 src/ncint/Makefile
                 src/flib/Makefile
                 src/gptl/Makefile

src/clib/pio_rearrange.c

@@ -1816,7 +1816,10 @@ compare_offsets(const void *a, const void *b)
     mapsort *y = (mapsort *)b;
     if (!x || !y)
         return 0;
-    return (int)(x->iomap - y->iomap);
+
+    if (x->iomap < y->iomap) { return -1; }
+    if (x->iomap > y->iomap) { return 1; }
+    return 0;
 }
 
 /**

src/flib/pio_nf.F90

@@ -400,19 +400,19 @@ module pio_nf
 #ifdef NC_HAS_QUANTIZE
   interface pio_def_var_quantize
      module procedure &
-          def_var_quantize_desc                          , &
+          def_var_quantize_desc, &
           def_var_quantize_id
   end interface pio_def_var_quantize
   interface pio_inq_var_quantize
      module procedure &
-          inq_var_quantize_desc                          , &
+          inq_var_quantize_desc, &
           inq_var_quantize_id
   end interface pio_inq_var_quantize
 #endif
 #ifdef PIO_HAS_PAR_FILTERS
   interface pio_inq_var_filter_ids
      module procedure &
-          inq_var_filter_ids_desc                          , &
+          inq_var_filter_ids_desc , &
           inq_var_filter_ids_id
   end interface pio_inq_var_filter_ids
   interface pio_inq_var_filter_info