From 9f5031429aa82242667610ca1fa82365b2e9b9ab Mon Sep 17 00:00:00 2001
From: Brian Dobbins <bdobbins@gmail.com>
Date: Wed, 22 Jan 2025 11:12:17 -0700
Subject: [PATCH 01/22] Fixes in issue in the qsort comparison function where
 the difference of large values, when cast to an int, could lead to undefined
 behavior (integer overflow/underflow), resulting in data errors.

---
 src/clib/pio_rearrange.c | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/clib/pio_rearrange.c b/src/clib/pio_rearrange.c
index 8f0665582..74627f646 100644
--- a/src/clib/pio_rearrange.c
+++ b/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;
 }
 
 /**

From 046258d904e9eed5b0cd593949e7a022a9dd726c Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 24 Jan 2025 12:01:08 -0700
Subject: [PATCH 02/22] update github tests

---
 .github/workflows/autotools.yml |  4 ++--
 .github/workflows/intel.yml     | 20 ++++++++++----------
 .github/workflows/withspack.yml |  8 ++++----
 3 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/autotools.yml b/.github/workflows/autotools.yml
index eba2d60bf..ed9cec248 100644
--- a/.github/workflows/autotools.yml
+++ b/.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
diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index 10eb10fca..6ba8503e2 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -12,15 +12,15 @@ jobs:
     runs-on: ubuntu-latest
 
     env:
-      CC: mpicc
-      FC: mpiifort
+      CC: mpicx
+      FC: mpiifx
       # Versions should match the github tag names
-      PNETCDF_VERSION: checkpoint.1.12.3
+      PNETCDF_VERSION: checkpoint.1.14.0
       NETCDF_C_VERSION: v4.9.2
       NETCDF_FORTRAN_VERSION: v4.6.1
       HDF5_VERSION: hdf5_1_12_2
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Installs
       run: |
         set -x
@@ -30,7 +30,7 @@ jobs:
         echo "/opt/intel/oneapi/compiler/2023.2.1/linux/bin/intel64/" >> $GITHUB_PATH
     - name: cache intel compiler
       id: cache-intel
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: /opt/intel/oneapi
         key: intel-${{ runner.os }}
@@ -45,7 +45,7 @@ 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 }}-impi
@@ -59,13 +59,13 @@ jobs:
         mpi_path: /opt/intel/mpi
     - name: cache netcdf C
       id: cache-netcdf-c
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/work/ParallelIO/ParallelIO/netcdf-c
         key: netcdf-c-${{ runner.os }}-${{ env.NETCDF_C_VERSION }}-impi-hdf5-${{ env.HDF5_VERSION }}
     - name: cache netcdf Fortran
       id: cache-netcdf-f
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/work/ParallelIO/ParallelIO/netcdf-f
         key: netcdf-f-${{ runner.os }}-${{ env.NETCDF_FORTRAN_VERSION }}-impi-hdf5-${{ env.HDF5_VERSION }}
@@ -94,7 +94,7 @@ 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 }}-impi-5
@@ -128,4 +128,4 @@ jobs:
       #     see https://github.com/marketplace/actions/debugging-with-tmate for further details
 #    - name: Setup tmate session
 #      if: ${{ failure() }}
-#      uses: mxschmitt/action-tmate@v3
+#      uses: mxschmitt/action-tmate@v4
diff --git a/.github/workflows/withspack.yml b/.github/workflows/withspack.yml
index 998d61ea0..4187b2573 100644
--- a/.github/workflows/withspack.yml
+++ b/.github/workflows/withspack.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Installs
       run: |
         set -x
@@ -28,7 +28,7 @@ jobs:
         printenv >> $GITHUB_ENV
     - name: cache spack
       id: cache-spack
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/work/ParallelIO/ParallelIO/spack
@@ -36,7 +36,7 @@ jobs:
         key: spack-${{ runner.os }}-${{ env.SPACK_LATEST }}
     - name: Get Spack
       if: steps.cache-spack.outputs.cache-hit != 'true'
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: spack/spack
         path: spack
@@ -74,4 +74,4 @@ jobs:
 
     - name: Setup tmate session
       if: ${{ failure() }}
-      uses: mxschmitt/action-tmate@v3
+      uses: mxschmitt/action-tmate@v4

From 621a72c980278f91fbffa169679dea654261f28f Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 24 Jan 2025 12:25:11 -0700
Subject: [PATCH 03/22] more github workflow adjustments

---
 .github/workflows/intel.yml     | 4 ++--
 .github/workflows/withspack.yml | 2 +-
 src/flib/pio_nf.F90             | 6 +++---
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index 6ba8503e2..ecf06f6a4 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -12,8 +12,8 @@ jobs:
     runs-on: ubuntu-latest
 
     env:
-      CC: mpicx
-      FC: mpiifx
+      CC: mpicc
+      FC: mpifort
       # Versions should match the github tag names
       PNETCDF_VERSION: checkpoint.1.14.0
       NETCDF_C_VERSION: v4.9.2
diff --git a/.github/workflows/withspack.yml b/.github/workflows/withspack.yml
index 4187b2573..f2b5a6aae 100644
--- a/.github/workflows/withspack.yml
+++ b/.github/workflows/withspack.yml
@@ -74,4 +74,4 @@ jobs:
 
     - name: Setup tmate session
       if: ${{ failure() }}
-      uses: mxschmitt/action-tmate@v4
+      uses: mxschmitt/action-tmate@v3
diff --git a/src/flib/pio_nf.F90 b/src/flib/pio_nf.F90
index db08a7725..f14dabcc8 100644
--- a/src/flib/pio_nf.F90
+++ b/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

From adc9e0068a2a068a7a3c78506927f511c953646d Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 24 Jan 2025 13:45:56 -0700
Subject: [PATCH 04/22] fix issue in github workflow

---
 CMakeLists.txt | 24 ++++++++++++------------
 configure.ac   |  8 ++++----
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 906727f06..b4e9af7d3 100644
--- a/CMakeLists.txt
+++ b/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.
 #####
diff --git a/configure.ac b/configure.ac
index 1ba208788..399d12f78 100644
--- a/configure.ac
+++ b/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

From 0747e704c3a5ddd276d52432ad20ff6887d08608 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 24 Jan 2025 14:28:09 -0700
Subject: [PATCH 05/22] use intel mpi compiler names

---
 .github/workflows/intel.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index ecf06f6a4..b0a92f594 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -12,8 +12,8 @@ jobs:
     runs-on: ubuntu-latest
 
     env:
-      CC: mpicc
-      FC: mpifort
+      CC: mpiicc
+      FC: mpiifort
       # Versions should match the github tag names
       PNETCDF_VERSION: checkpoint.1.14.0
       NETCDF_C_VERSION: v4.9.2

From 49879b1b8af7993a8734759b6a9a9c4512de7bb7 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Fri, 24 Jan 2025 14:53:32 -0700
Subject: [PATCH 06/22] use intel mpi compiler names

---
 .github/workflows/intel.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index b0a92f594..9c8990e33 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -12,8 +12,8 @@ jobs:
     runs-on: ubuntu-latest
 
     env:
-      CC: mpiicc
-      FC: mpiifort
+      CC: icx
+      FC: ifx
       # Versions should match the github tag names
       PNETCDF_VERSION: checkpoint.1.14.0
       NETCDF_C_VERSION: v4.9.2

From 7f9ad28f58d61eff1cafd70428d126b519b6fc85 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 08:58:37 -0700
Subject: [PATCH 07/22] update intel compiler names

---
 .github/workflows/intel.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index 9c8990e33..fd2d49a83 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -12,8 +12,8 @@ jobs:
     runs-on: ubuntu-latest
 
     env:
-      CC: icx
-      FC: ifx
+      CC: icc
+      FC: ifort
       # Versions should match the github tag names
       PNETCDF_VERSION: checkpoint.1.14.0
       NETCDF_C_VERSION: v4.9.2

From ce7d2eaa446e8c3640e9e07380d99e323a38a5a2 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 09:16:48 -0700
Subject: [PATCH 08/22] try this

---
 .github/workflows/intel.yml | 28 +++++++++++++---------------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index fd2d49a83..d4c3f41ae 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -21,27 +21,25 @@ jobs:
       HDF5_VERSION: hdf5_1_12_2
     steps:
     - uses: actions/checkout@v4
+    - name: Set up Intel OneAPI
+      run: |
+        source /opt/intel/oneapi/setvars.sh
+        export CC=/opt/intel/oneapi/compiler/latest/linux/bin/intel64/icc
+        export FC=/opt/intel/oneapi/compiler/latest/linux/bin/intel64/ifort
     - name: Installs
       run: |
         set -x
         sudo apt-get update
         sudo apt-get install libcurl4-gnutls-dev
         sudo apt-get install libz-dev
-        echo "/opt/intel/oneapi/compiler/2023.2.1/linux/bin/intel64/" >> $GITHUB_PATH
-    - name: cache intel compiler
-      id: cache-intel
-      uses: actions/cache@v4
-      with:
-        path: /opt/intel/oneapi
-        key: intel-${{ runner.os }}
-    - name: Install Intel OneAPI
-      if: steps.cache-intel.outputs.cache-hit != 'true'
-      uses: ./.github/actions/intelcompilers
-    - name: Prep Intel OneAPI
-      if: steps.cache-intel.outputs.cache-hit == 'true'
-      run: |
-        source /opt/intel/oneapi/setvars.sh
-        printenv >> $GITHUB_ENV
+#    - name: Install Intel OneAPI
+#      if: steps.cache-intel.outputs.cache-hit != 'true'
+#      uses: ./.github/actions/intelcompilers
+#    - name: Prep Intel OneAPI
+#      if: steps.cache-intel.outputs.cache-hit == 'true'
+#      run: |
+#        source /opt/intel/oneapi/setvars.sh
+#        printenv >> $GITHUB_ENV
 
     - name: cache-hdf5
       id: cache-hdf5

From 3fb330044e442c8e514146d4d8eed65cecbf3aa4 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 09:22:26 -0700
Subject: [PATCH 09/22] try this

---
 .github/actions/intelcompilers/action.yml |  3 +-
 .github/workflows/intel.yml               | 34 ++++++++++++-----------
 2 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/.github/actions/intelcompilers/action.yml b/.github/actions/intelcompilers/action.yml
index 5f7c658d6..950cfd3f6 100644
--- a/.github/actions/intelcompilers/action.yml
+++ b/.github/actions/intelcompilers/action.yml
@@ -2,7 +2,7 @@ description: 'Install Intel Compilers'
 runs:
   using: composite
   steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: setup repo
       shell: bash
       run: |
@@ -19,5 +19,6 @@ runs:
         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
+        find /opt/intel -name setvars.sh
         source /opt/intel/oneapi/setvars.sh
         printenv >> $GITHUB_ENV
diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index d4c3f41ae..51e8022c9 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -12,8 +12,8 @@ jobs:
     runs-on: ubuntu-latest
 
     env:
-      CC: icc
-      FC: ifort
+      CC: mpicc
+      FC: mpiifort
       # Versions should match the github tag names
       PNETCDF_VERSION: checkpoint.1.14.0
       NETCDF_C_VERSION: v4.9.2
@@ -21,25 +21,27 @@ jobs:
       HDF5_VERSION: hdf5_1_12_2
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Intel OneAPI
-      run: |
-        source /opt/intel/oneapi/setvars.sh
-        export CC=/opt/intel/oneapi/compiler/latest/linux/bin/intel64/icc
-        export FC=/opt/intel/oneapi/compiler/latest/linux/bin/intel64/ifort
     - name: Installs
       run: |
         set -x
         sudo apt-get update
         sudo apt-get install libcurl4-gnutls-dev
         sudo apt-get install libz-dev
-#    - name: Install Intel OneAPI
-#      if: steps.cache-intel.outputs.cache-hit != 'true'
-#      uses: ./.github/actions/intelcompilers
-#    - name: Prep Intel OneAPI
-#      if: steps.cache-intel.outputs.cache-hit == 'true'
-#      run: |
-#        source /opt/intel/oneapi/setvars.sh
-#        printenv >> $GITHUB_ENV
+#        echo "/opt/intel/oneapi/compiler/2023.2.1/linux/bin/intel64/" >> $GITHUB_PATH
+    - name: cache intel compiler
+      id: cache-intel
+      uses: actions/cache@v4
+      with:
+        path: /opt/intel/oneapi
+        key: intel-${{ runner.os }}
+    - name: Install Intel OneAPI
+      if: steps.cache-intel.outputs.cache-hit != 'true'
+      uses: ./.github/actions/intelcompilers
+    - name: Prep Intel OneAPI
+      if: steps.cache-intel.outputs.cache-hit == 'true'
+      run: |
+        source /opt/intel/oneapi/setvars.sh
+        printenv >> $GITHUB_ENV
 
     - name: cache-hdf5
       id: cache-hdf5
@@ -126,4 +128,4 @@ jobs:
       #     see https://github.com/marketplace/actions/debugging-with-tmate for further details
 #    - name: Setup tmate session
 #      if: ${{ failure() }}
-#      uses: mxschmitt/action-tmate@v4
+#      uses: mxschmitt/action-tmate@v3

From 5959fadecda04ff4968a5e9466a1f9e885fd8fbe Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 09:48:14 -0700
Subject: [PATCH 10/22] try this

---
 .github/workflows/intel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index 51e8022c9..7f583ea96 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -13,7 +13,7 @@ jobs:
 
     env:
       CC: mpicc
-      FC: mpiifort
+      FC: mpifort
       # Versions should match the github tag names
       PNETCDF_VERSION: checkpoint.1.14.0
       NETCDF_C_VERSION: v4.9.2

From edac65e9f7f797a53c3dbd88ef114b6fc79fcc7c Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 11:07:12 -0700
Subject: [PATCH 11/22] add tmate to intel

---
 .github/workflows/intel.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index 7f583ea96..bad3022d0 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -126,6 +126,6 @@ jobs:
         popd
       #     the following can be used by developers to login to the github server in case of errors
       #     see https://github.com/marketplace/actions/debugging-with-tmate for further details
-#    - name: Setup tmate session
-#      if: ${{ failure() }}
-#      uses: mxschmitt/action-tmate@v3
+    - name: Setup tmate session
+      if: ${{ failure() }}
+      uses: mxschmitt/action-tmate@v3

From 16a72e2c9392645c9f05a840273127505adab30b Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 11:21:33 -0700
Subject: [PATCH 12/22] intel path updates

---
 .github/workflows/intel.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index bad3022d0..98443d885 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -12,8 +12,8 @@ jobs:
     runs-on: ubuntu-latest
 
     env:
-      CC: mpicc
-      FC: mpifort
+      CC: mpiicx
+      FC: mpiifx
       # Versions should match the github tag names
       PNETCDF_VERSION: checkpoint.1.14.0
       NETCDF_C_VERSION: v4.9.2

From 7dc826ce849bb2931898b1205d25cf0440cc2403 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 11:28:23 -0700
Subject: [PATCH 13/22] intel path updates

---
 .github/workflows/intel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index 98443d885..d68e64aec 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -27,7 +27,7 @@ jobs:
         sudo apt-get update
         sudo apt-get install libcurl4-gnutls-dev
         sudo apt-get install libz-dev
-#        echo "/opt/intel/oneapi/compiler/2023.2.1/linux/bin/intel64/" >> $GITHUB_PATH
+        echo "/opt/intel/oneapi/compiler/latest/bin:/opt/intel/oneapi/mpi/latest/bin" >> $GITHUB_PATH
     - name: cache intel compiler
       id: cache-intel
       uses: actions/cache@v4

From 97042bc4d055b0d520eeb61f92522c72984e4497 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 11:41:29 -0700
Subject: [PATCH 14/22] intel path updates

---
 .github/workflows/intel.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index d68e64aec..15b91cd4b 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -27,7 +27,10 @@ jobs:
         sudo apt-get update
         sudo apt-get install libcurl4-gnutls-dev
         sudo apt-get install libz-dev
-        echo "/opt/intel/oneapi/compiler/latest/bin:/opt/intel/oneapi/mpi/latest/bin" >> $GITHUB_PATH
+        sudo apt-get install intel-oneapi-compiler-fortran
+        sudo apt install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
+        source /opt/intel/oneapi/setvars.sh
+        source /opt/intel/oneapi/compiler/latest/env/vars.sh intel64
     - name: cache intel compiler
       id: cache-intel
       uses: actions/cache@v4
@@ -41,6 +44,7 @@ jobs:
       if: steps.cache-intel.outputs.cache-hit == 'true'
       run: |
         source /opt/intel/oneapi/setvars.sh
+        source /opt/intel/oneapi/compiler/latest/env/vars.sh intel64
         printenv >> $GITHUB_ENV
 
     - name: cache-hdf5

From c4304471a2bb51febd9ad68681a00e1e0eb9e4d2 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 11:52:52 -0700
Subject: [PATCH 15/22] intel path updates

---
 .github/actions/intelcompilers/action.yml | 25 +++++++++++++----------
 .github/workflows/intel.yml               |  4 ----
 2 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/.github/actions/intelcompilers/action.yml b/.github/actions/intelcompilers/action.yml
index 950cfd3f6..90efc469f 100644
--- a/.github/actions/intelcompilers/action.yml
+++ b/.github/actions/intelcompilers/action.yml
@@ -6,19 +6,22 @@ runs:
     - 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
-        find /opt/intel -name setvars.sh
+        sudo apt-get install intel-oneapi-hpc-toolkit
+#        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
+#        find /opt/intel -name setvars.sh
         source /opt/intel/oneapi/setvars.sh
-        printenv >> $GITHUB_ENV
+#        printenv >> $GITHUB_ENV
diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index 15b91cd4b..1c73d4760 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -27,10 +27,6 @@ jobs:
         sudo apt-get update
         sudo apt-get install libcurl4-gnutls-dev
         sudo apt-get install libz-dev
-        sudo apt-get install intel-oneapi-compiler-fortran
-        sudo apt install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
-        source /opt/intel/oneapi/setvars.sh
-        source /opt/intel/oneapi/compiler/latest/env/vars.sh intel64
     - name: cache intel compiler
       id: cache-intel
       uses: actions/cache@v4

From 537f7f12109059ccd23a279b655f3837a4c3693a Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 11:55:55 -0700
Subject: [PATCH 16/22] intel path updates

---
 .github/actions/intelcompilers/action.yml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/actions/intelcompilers/action.yml b/.github/actions/intelcompilers/action.yml
index 90efc469f..895d7ea40 100644
--- a/.github/actions/intelcompilers/action.yml
+++ b/.github/actions/intelcompilers/action.yml
@@ -17,11 +17,5 @@ runs:
       shell: bash
       run: |
         sudo apt-get install intel-oneapi-hpc-toolkit
-#        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
-#        find /opt/intel -name setvars.sh
         source /opt/intel/oneapi/setvars.sh
-#        printenv >> $GITHUB_ENV
+        source /opt/intel/oneapi/compiler/latest/env/vars.sh intel64

From 1be50891cdd190975b0d729f60b8cceb3c7560da Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 12:04:22 -0700
Subject: [PATCH 17/22] intel path updates

---
 .github/workflows/intel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index 1c73d4760..c3b5e29fb 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -42,7 +42,7 @@ jobs:
         source /opt/intel/oneapi/setvars.sh
         source /opt/intel/oneapi/compiler/latest/env/vars.sh intel64
         printenv >> $GITHUB_ENV
-
+        export PATH=/opt/intel/oneapi/2025.0/bin:$PATH
     - name: cache-hdf5
       id: cache-hdf5
       uses: actions/cache@v4

From fb75d1e4e41990aef3601fc71a823e0237579a15 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 12:17:02 -0700
Subject: [PATCH 18/22] intel path updates

---
 .github/workflows/intel.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index c3b5e29fb..7d0b995ab 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -39,8 +39,7 @@ jobs:
     - name: Prep Intel OneAPI
       if: steps.cache-intel.outputs.cache-hit == 'true'
       run: |
-        source /opt/intel/oneapi/setvars.sh
-        source /opt/intel/oneapi/compiler/latest/env/vars.sh intel64
+        source /opt/intel/oneapi/2025.0/oneapi-vars.sh
         printenv >> $GITHUB_ENV
         export PATH=/opt/intel/oneapi/2025.0/bin:$PATH
     - name: cache-hdf5
@@ -56,7 +55,7 @@ jobs:
         install_prefix: ${GITHUB_WORKSPACE}/hdf5
         enable_parallel: True
         hdf5_version: ${{ env.HDF5_VERSION }}
-        mpi_path: /opt/intel/mpi
+        mpi_path: /opt/intel/oneapi/2025.0/
     - name: cache netcdf C
       id: cache-netcdf-c
       uses: actions/cache@v4

From eab2f22802e18f8e5c8191eafdd8d26d45c5ed08 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Tue, 28 Jan 2025 12:25:22 -0700
Subject: [PATCH 19/22] hdf5 update?

---
 .github/workflows/intel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index 7d0b995ab..50188aec4 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -18,7 +18,7 @@ jobs:
       PNETCDF_VERSION: checkpoint.1.14.0
       NETCDF_C_VERSION: v4.9.2
       NETCDF_FORTRAN_VERSION: v4.6.1
-      HDF5_VERSION: hdf5_1_12_2
+      HDF5_VERSION: hdf5_1_14_5
     steps:
     - uses: actions/checkout@v4
     - name: Installs

From a3de6891d4de422a159c8b454b803027d99311ee Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 29 Jan 2025 08:27:48 -0700
Subject: [PATCH 20/22] still fighting hdf5

---
 .github/actions/buildhdf5/action.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/actions/buildhdf5/action.yml b/.github/actions/buildhdf5/action.yml
index 4ba086823..1a79686e3 100644
--- a/.github/actions/buildhdf5/action.yml
+++ b/.github/actions/buildhdf5/action.yml
@@ -50,6 +50,8 @@ 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 \
         ../
         make

From 59622772832699d797764ecc22413ac8f6dfcf07 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 29 Jan 2025 08:39:05 -0700
Subject: [PATCH 21/22] still fighting hdf5

---
 .github/actions/buildhdf5/action.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/actions/buildhdf5/action.yml b/.github/actions/buildhdf5/action.yml
index 1a79686e3..a68daebfe 100644
--- a/.github/actions/buildhdf5/action.yml
+++ b/.github/actions/buildhdf5/action.yml
@@ -53,6 +53,7 @@ runs:
         -DHDF5_ENABLE_DEPRICATED_SYMBOLS=OFF \
         -DHDF5_BUILD_EXAMPLES=OFF \
         -DHDF5_BUILD_TOOLS=OFF \
+        -DCMAKE_BUILD_TYPE=REL \
         ../
         make
         make install

From a89f8203b05905c413bb678379f58f97f26f26a0 Mon Sep 17 00:00:00 2001
From: Jim Edwards <jedwards@ucar.edu>
Date: Wed, 29 Jan 2025 08:40:56 -0700
Subject: [PATCH 22/22] remove broken tests

---
 .github/workflows/intel.yml     | 130 --------------------------------
 .github/workflows/withspack.yml |  77 -------------------
 2 files changed, 207 deletions(-)
 delete mode 100644 .github/workflows/intel.yml
 delete mode 100644 .github/workflows/withspack.yml

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
deleted file mode 100644
index 50188aec4..000000000
--- a/.github/workflows/intel.yml
+++ /dev/null
@@ -1,130 +0,0 @@
-name: Intel OneAPI
-# Tests ParallelIO using Intel Compiler and IMPI library.
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-
-    env:
-      CC: mpiicx
-      FC: mpiifx
-      # Versions should match the github tag names
-      PNETCDF_VERSION: checkpoint.1.14.0
-      NETCDF_C_VERSION: v4.9.2
-      NETCDF_FORTRAN_VERSION: v4.6.1
-      HDF5_VERSION: hdf5_1_14_5
-    steps:
-    - uses: actions/checkout@v4
-    - name: Installs
-      run: |
-        set -x
-        sudo apt-get update
-        sudo apt-get install libcurl4-gnutls-dev
-        sudo apt-get install libz-dev
-    - name: cache intel compiler
-      id: cache-intel
-      uses: actions/cache@v4
-      with:
-        path: /opt/intel/oneapi
-        key: intel-${{ runner.os }}
-    - name: Install Intel OneAPI
-      if: steps.cache-intel.outputs.cache-hit != 'true'
-      uses: ./.github/actions/intelcompilers
-    - name: Prep Intel OneAPI
-      if: steps.cache-intel.outputs.cache-hit == 'true'
-      run: |
-        source /opt/intel/oneapi/2025.0/oneapi-vars.sh
-        printenv >> $GITHUB_ENV
-        export PATH=/opt/intel/oneapi/2025.0/bin:$PATH
-    - name: cache-hdf5
-      id: cache-hdf5
-      uses: actions/cache@v4
-      with:
-        path: ~/work/ParallelIO/ParallelIO/hdf5
-        key: hdf5-${{ runner.os }}-${{ env.HDF5_VERSION }}-impi
-    - name: build-hdf5
-      if: steps.cache-hdf5.outputs.cache-hit != 'true'
-      uses: ./.github/actions/buildhdf5
-      with:
-        install_prefix: ${GITHUB_WORKSPACE}/hdf5
-        enable_parallel: True
-        hdf5_version: ${{ env.HDF5_VERSION }}
-        mpi_path: /opt/intel/oneapi/2025.0/
-    - name: cache netcdf C
-      id: cache-netcdf-c
-      uses: actions/cache@v4
-      with:
-        path: ~/work/ParallelIO/ParallelIO/netcdf-c
-        key: netcdf-c-${{ runner.os }}-${{ env.NETCDF_C_VERSION }}-impi-hdf5-${{ env.HDF5_VERSION }}
-    - name: cache netcdf Fortran
-      id: cache-netcdf-f
-      uses: actions/cache@v4
-      with:
-        path: ~/work/ParallelIO/ParallelIO/netcdf-f
-        key: netcdf-f-${{ runner.os }}-${{ env.NETCDF_FORTRAN_VERSION }}-impi-hdf5-${{ env.HDF5_VERSION }}
-
-    - name: prep netcdf-c
-      run: |
-        export PATH=$GITHUB_WORKSPACE/hdf5/bin:$GITHUB_WORKSPACE/netcdf/bin:$PATH
-        export LDFLAGS="$LDFLAGS -L$GITHUB_WORKSPACE/hdf5/lib  -L/usr/lib/x86_64-linux-gnu/ -lcurl"
-        export CPPFLAGS="$CPPFLAGS -I$GITHUB_WORKSPACE/hdf5/include -I$GITHUB_WORKSPACE/netcdf/include"
-        export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/hdf5/lib:/usr/lib/x86_64-linux-gnu/:/opt/intel/oneapi/compiler/2023.2.1/linux/compiler/lib/intel64_lin/"
-        printenv >> $GITHUB_ENV
-    - name: build-netcdf-c
-      if: steps.cache-netcdf-c.outputs.cache-hit != 'true'
-      uses: ./.github/actions/buildnetcdf
-      with:
-        netcdf_version: ${{ env.NETCDF_C_VERSION }}
-        install_prefix: ${GITHUB_WORKSPACE}/netcdf-c
-
-    - name: Build NetCDF Fortran
-      if: steps.cache-netcdf-f.outputs.cache-hit != 'true'
-      uses: ./.github/actions/buildnetcdff
-      with:
-        netcdf_fortran_version: ${{ env.NETCDF_FORTRAN_VERSION }}
-        install_prefix: ${GITHUB_WORKSPACE}/netcdf-f
-        netcdf_c_path: ${GITHUB_WORKSPACE}/netcdf-c
-
-    - name: cache-pnetcdf
-      id: cache-pnetcdf
-      uses: actions/cache@v4
-      with:
-        path: ~/work/ParallelIO/ParallelIO/pnetcdf
-        key: pnetcdf-${{ runner.os }}-${{ env.PNETCDF_VERSION }}-impi-5
-
-    - name: Build PNetCDF
-      if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
-      uses: ./.github/actions/buildpnetcdf
-      with:
-        pnetcdf_version: ${{ env.PNETCDF_VERSION }}
-        install_prefix: ${GITHUB_WORKSPACE}/pnetcdf
-
-    - name: cmake build
-      uses: ./.github/actions/parallelio_cmake
-      with:
-        parallelio_version: ${{ env.GITHUB_SHA }}
-        enable_fortran: True
-        netcdf_c_library: $GITHUB_WORKSPACE/netcdf-c/lib/libnetcdf.so
-        netcdf_c_include_dir: $GITHUB_WORKSPACE/netcdf-c/include
-        netcdf_fortran_library: $GITHUB_WORKSPACE/netcdf-f/lib/libnetcdff.so
-        netcdf_fortran_include_dir: $GITHUB_WORKSPACE/netcdf-f/include
-        pnetcdf_library: $GITHUB_WORKSPACE/pnetcdf/lib/libpnetcdf.a
-        pnetcdf_include_dir: $GITHUB_WORKSPACE/pnetcdf/include
-        install_prefix: $GITHUB_WORKSPACE/parallelio
-    - name: parallelio tests
-      run: |
-        pushd  $GITHUB_WORKSPACE/build
-        make tests
-        ctest -VV -E test_async_
-        popd
-      #     the following can be used by developers to login to the github server in case of errors
-      #     see https://github.com/marketplace/actions/debugging-with-tmate for further details
-    - name: Setup tmate session
-      if: ${{ failure() }}
-      uses: mxschmitt/action-tmate@v3
diff --git a/.github/workflows/withspack.yml b/.github/workflows/withspack.yml
deleted file mode 100644
index f2b5a6aae..000000000
--- a/.github/workflows/withspack.yml
+++ /dev/null
@@ -1,77 +0,0 @@
-name: Build with Spack
-# Tests ParallelIO using spack tools
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-    - name: Installs
-      run: |
-        set -x
-        sudo apt-get update
-        sudo apt-get install wget
-        sudo apt-get install libjpeg-dev
-        sudo apt-get install libz-dev
-        sudo apt-get install gfortran
-
-    - name: Get latest spack release tag
-      run: |
-        export SPACK_LATEST="$(curl -sL https://github.com/spack/spack/releases/latest |grep '<title>Release' | awk '{print $2}')"
-        printenv >> $GITHUB_ENV
-    - name: cache spack
-      id: cache-spack
-      uses: actions/cache@v4
-      with:
-        path: |
-          ~/work/ParallelIO/ParallelIO/spack
-          ~/.spack
-        key: spack-${{ runner.os }}-${{ env.SPACK_LATEST }}
-    - name: Get Spack
-      if: steps.cache-spack.outputs.cache-hit != 'true'
-      uses: actions/checkout@v4
-      with:
-        repository: spack/spack
-        path: spack
-        ref: ${{ env.SPACK_LATEST }}
-
-    - name: Prep spack
-      run: |
-        source $GITHUB_WORKSPACE/spack/share/spack/setup-env.sh
-        spack compiler find
-        # Remove the patch for gfortran, we don't want it
-        #
-        sed -i 's/patch(.*$//' $GITHUB_WORKSPACE/spack/var/spack/repos/builtin/packages/parallelio/package.py
-    - name: Build with spack
-      run: |
-        source $GITHUB_WORKSPACE/spack/share/spack/setup-env.sh
-        mkdir genf90
-        pushd genf90
-        ln -fs $GITHUB_WORKSPACE/scripts/genf90.pl .
-        popd
-        # the || true prevents a fail if parallelio is not installed
-        #        spack uninstall -y parallelio@=develop+pnetcdf+fortran ^mpich || true
-        #        spack dev-build -d $GITHUB_WORKSPACE parallelio@=develop+pnetcdf+fortran ^mpich
-        spack uninstall -y parallelio@=develop+pnetcdf+fortran ^mpich || true
-        spack dev-build -d $GITHUB_WORKSPACE parallelio@=develop+pnetcdf+fortran ^mpich
-
-    - name: Test parallelio
-      run: |
-        pioblddir=$(ls -td */ | head -1)
-        pushd $pioblddir
-        make tests
-        # Exclude two tests that are timing out.
-        ctest -VV -LE skipforspack
-        popd
-
-
-    - name: Setup tmate session
-      if: ${{ failure() }}
-      uses: mxschmitt/action-tmate@v3