Updated testing and 1.14 requirements (#67)

* updated from HDF5 v1.13 to v1.14 requirements * updated testing and docs references from hpc-io and DataLib-ECP to HDFGroup
HDFGroup · Jun 12, 2024 · 0a2896a · 0a2896a
1 parent e3cb362
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diff --git a/.github/workflows/alone.yml b/.github/workflows/alone.yml
@@ -22,7 +22,6 @@ on:
 
 env:
    MPICH_VERSION: 4.1.2
-   HDF5_VERSION: 1.14.2
    ARGOBOTS_VERSION: 1.1
    ASYNC_VOL_VERSION: 1.8.1
 
@@ -31,7 +30,7 @@ jobs:
       runs-on: ubuntu-latest
       timeout-minutes: 60
       steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4.1.1
         - name: Set up dependencies
           run: |
             sudo apt-get update
@@ -67,10 +66,9 @@ jobs:
             rm -rf ${GITHUB_WORKSPACE}/HDF5
             mkdir ${GITHUB_WORKSPACE}/HDF5
             cd ${GITHUB_WORKSPACE}/HDF5
-            VER_MAJOR=${HDF5_VERSION%.*}
-            wget -cq https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${VER_MAJOR}/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz
-            tar -zxf hdf5-${HDF5_VERSION}.tar.gz
-            cd hdf5-${HDF5_VERSION}
+            wget -cq https://github.com/HDFGroup/hdf5/releases/latest/download/hdf5.tar.gz
+            tar -zxf hdf5.tar.gz
+            cd hdf5-*
             ./configure --prefix=${GITHUB_WORKSPACE}/HDF5 \
                         --silent \
                         --enable-parallel \
@@ -115,7 +113,7 @@ jobs:
             rm -rf ${ASYNC_DIR}
             mkdir ${ASYNC_DIR}
             cd ${ASYNC_DIR}
-            wget -qc https://github.com/hpc-io/vol-async/archive/refs/tags/v${ASYNC_VOL_VERSION}.tar.gz
+            wget -qc https://github.com/HDFGroup/vol-async/archive/refs/tags/v${ASYNC_VOL_VERSION}.tar.gz
             tar -xf v${ASYNC_VOL_VERSION}.tar.gz
             cd vol-async-${ASYNC_VOL_VERSION}
             mkdir build
@@ -136,7 +134,7 @@ jobs:
             rm -rf ${CAHCE_DIR}
             mkdir ${CAHCE_DIR}
             cd ${CAHCE_DIR}
-            git clone https://github.com/hpc-io/vol-cache.git
+            git clone https://github.com/HDFGroup/vol-cache.git
             cd vol-cache
             mkdir build
             cd build

diff --git a/.github/workflows/mac_mpich.yml b/.github/workflows/mac_mpich.yml
@@ -22,26 +22,24 @@ on:
 
 env:
    MPICH_VERSION: 4.1.2
-   HDF5_VERSION: 1.14.2
    NETCDF_VERSION: 4.9.2
 
 jobs:
     build:
       runs-on: macos-latest
       timeout-minutes: 60
       steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4.1.1
         - name: Set up dependencies
           run: |
             brew instal automake autoconf libtool m4 open-mpi zlib
         - name: Install HDF5
           run: |
             cd ${GITHUB_WORKSPACE}
             rm -rf HDF5 ; mkdir HDF5 ; cd HDF5
-            VER_MAJOR=${HDF5_VERSION%.*}
-            wget -cq https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${VER_MAJOR}/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz
-            tar -zxf hdf5-${HDF5_VERSION}.tar.gz
-            cd hdf5-${HDF5_VERSION}
+            wget -cq https://github.com/HDFGroup/hdf5/releases/latest/download/hdf5.tar.gz
+            tar -zxf hdf5.tar.gz
+            cd hdf5-*
             ./configure --prefix=${GITHUB_WORKSPACE}/HDF5 \
                         --silent \
                         --enable-parallel \

diff --git a/.github/workflows/ubuntu_mpich.yml b/.github/workflows/ubuntu_mpich.yml
@@ -22,15 +22,14 @@ on:
 
 env:
    MPICH_VERSION: 4.1.2
-   HDF5_VERSION: 1.14.2
    NETCDF_VERSION: 4.9.2
 
 jobs:
     build:
       runs-on: ubuntu-latest
       timeout-minutes: 60
       steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4.1.1
         - name: Set up dependencies
           run: |
             sudo apt-get update
@@ -60,10 +59,9 @@ jobs:
           run: |
             cd ${GITHUB_WORKSPACE}
             rm -rf HDF5 ; mkdir HDF5 ; cd HDF5
-            VER_MAJOR=${HDF5_VERSION%.*}
-            wget -cq https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${VER_MAJOR}/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz
-            tar -zxf hdf5-${HDF5_VERSION}.tar.gz
-            cd hdf5-${HDF5_VERSION}
+            wget -cq https://github.com/HDFGroup/hdf5/releases/latest/download/hdf5.tar.gz
+            tar -zxf hdf5.tar.gz
+            cd hdf5-*
             ./configure --prefix=${GITHUB_WORKSPACE}/HDF5 \
                         --silent \
                         --enable-parallel \

diff --git a/.github/workflows/ubuntu_openmpi.yml b/.github/workflows/ubuntu_openmpi.yml
@@ -21,15 +21,14 @@ on:
       - 'case_studies/*'
 
 env:
-   HDF5_VERSION: 1.14.2
    NETCDF_VERSION: 4.9.2
 
 jobs:
     build:
       runs-on: ubuntu-latest
       timeout-minutes: 60
       steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4.1.1
         - name: Set up dependencies
           run: |
             sudo apt-get update
@@ -45,10 +44,9 @@ jobs:
             cd ${GITHUB_WORKSPACE}
             echo "Install HDF5 on ${GITHUB_WORKSPACE}/HDF5"
             rm -rf HDF5 ; mkdir HDF5 ; cd HDF5
-            VER_MAJOR=${HDF5_VERSION%.*}
-            wget -cq https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${VER_MAJOR}/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz
-            tar -zxf hdf5-${HDF5_VERSION}.tar.gz
-            cd hdf5-${HDF5_VERSION}
+            wget -cq https://github.com/HDFGroup/hdf5/releases/latest/download/hdf5.tar.gz
+            tar -zxf hdf5.tar.gz
+            cd hdf5-*
             ./configure --prefix=${GITHUB_WORKSPACE}/HDF5 \
                         --silent \
                         --enable-parallel \

diff --git a/.github/workflows/ubuntu_stack_vols.yml b/.github/workflows/ubuntu_stack_vols.yml
@@ -22,7 +22,6 @@ on:
 
 env:
    MPICH_VERSION: 4.1.2
-   HDF5_VERSION: 1.14.2
    ARGOBOTS_VERSION: 1.1
    ASYNC_VOL_VERSION: 1.8.1
 
@@ -31,7 +30,7 @@ jobs:
       runs-on: ubuntu-latest
       timeout-minutes: 60
       steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4.1.1
         - name: Set up dependencies
           run: |
             sudo apt-get update
@@ -67,10 +66,9 @@ jobs:
             rm -rf ${GITHUB_WORKSPACE}/HDF5
             mkdir ${GITHUB_WORKSPACE}/HDF5
             cd ${GITHUB_WORKSPACE}/HDF5
-            VER_MAJOR=${HDF5_VERSION%.*}
-            wget -cq https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${VER_MAJOR}/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz
-            tar -zxf hdf5-${HDF5_VERSION}.tar.gz
-            cd hdf5-${HDF5_VERSION}
+            wget -cq https://github.com/HDFGroup/hdf5/releases/latest/download/hdf5.tar.gz
+            tar -zxf hdf5.tar.gz
+            cd hdf5-*
             ./configure --prefix=${GITHUB_WORKSPACE}/HDF5 \
                         --silent \
                         --enable-parallel \
@@ -115,7 +113,7 @@ jobs:
             rm -rf ${ASYNC_DIR}
             mkdir ${ASYNC_DIR}
             cd ${ASYNC_DIR}
-            wget -qc https://github.com/hpc-io/vol-async/archive/refs/tags/v${ASYNC_VOL_VERSION}.tar.gz
+            wget -qc https://github.com/HDFGroup/vol-async/archive/refs/tags/v${ASYNC_VOL_VERSION}.tar.gz
             tar -xf v${ASYNC_VOL_VERSION}.tar.gz
             cd vol-async-${ASYNC_VOL_VERSION}
             mkdir build
@@ -136,7 +134,7 @@ jobs:
             rm -rf ${CAHCE_DIR}
             mkdir ${CAHCE_DIR}
             cd ${CAHCE_DIR}
-            git clone https://github.com/hpc-io/vol-cache.git
+            git clone https://github.com/HDFGroup/vol-cache.git
             cd vol-cache
             mkdir build
             cd build

diff --git a/README.md b/README.md
@@ -17,9 +17,9 @@ Files created by the Log VOL conform with the HDF5 file format specification,
 but require the Log VOL to read them back.
 
 * Current build status:
-  * [![Ubuntu_mpich](https://github.com/DataLib-ECP/vol-log-based/actions/workflows/ubuntu_mpich.yml/badge.svg)](https://github.com/DataLib-ECP/vol-log-based/actions/workflows/ubuntu_mpich.yml)
-  * [![Ubuntu with OpenMPI](https://github.com/DataLib-ECP/vol-log-based/actions/workflows/ubuntu_openmpi.yml/badge.svg)](https://github.com/DataLib-ECP/vol-log-based/actions/workflows/ubuntu_openmpi.yml)
-  * [![Mac with MPICH](https://github.com/DataLib-ECP/vol-log-based/actions/workflows/mac_mpich.yml/badge.svg)](https://github.com/DataLib-ECP/vol-log-based/actions/workflows/mac_mpich.yml)
+  * [![Ubuntu_mpich](https://github.com/HDFGroup/vol-log-based/actions/workflows/ubuntu_mpich.yml/badge.svg)](https://github.com/HDFGroup/vol-log-based/actions/workflows/ubuntu_mpich.yml)
+  * [![Ubuntu with OpenMPI](https://github.com/HDFGroup/vol-log-based/actions/workflows/ubuntu_openmpi.yml/badge.svg)](https://github.com/HDFGroup/vol-log-based/actions/workflows/ubuntu_openmpi.yml)
+  * [![Mac with MPICH](https://github.com/HDFGroup/vol-log-based/actions/workflows/mac_mpich.yml/badge.svg)](https://github.com/HDFGroup/vol-log-based/actions/workflows/mac_mpich.yml)
 
 ### HDF5 VOL Connector ID
 * This Log VOL connector has been registered with the HDF group with

diff --git a/configure.ac b/configure.ac
@@ -336,31 +336,20 @@ if test "x$have_hdf5" = xno ; then
       to specify the location of HDF5 installation. Abort.
       -----------------------------------------------------------------------])
 fi
-AC_MSG_CHECKING([whether HDF5 version is 1.13.0 (develop branch) or later])
+AC_MSG_CHECKING([whether the HDF5 version is equal to or greater than 1.14.0])
 AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
 #include <hdf5.h>
-#if (H5_VERS_MAJOR*1000000 + H5_VERS_MINOR*1000 + H5_VERS_RELEASE < 1013000)
-#error HDF5 version is older than 1.13.0
+#if (H5_VERS_MAJOR*1000000 + H5_VERS_MINOR*1000 + H5_VERS_RELEASE < 1014000)
+#error HDF5 version is older than 1.14.0
 #endif
-   ]])], [hdf5_ge_1_13_0=yes], [hdf5_ge_1_13_0=no])
-AC_MSG_RESULT([$hdf5_ge_1_13_0])
-if test x$hdf5_ge_1_13_0 = xno; then
+   ]])], [hdf5_ge_1_14_0=yes], [hdf5_ge_1_14_0=no])
+AC_MSG_RESULT([$hdf5_ge_1_14_0])
+if test x$hdf5_ge_1_14_0 = xno; then
    AC_MSG_ERROR([
    -----------------------------------------------------------------------
-     H5VL_log requires HDF5 1.13.0 and later. Abort.
+     H5VL_log requires HDF5 1.14.0 and later. Abort.
    -----------------------------------------------------------------------])
 fi
-AC_MSG_CHECKING([whether HDF5 version is 1.13.3 or later])
-AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
-#include <hdf5.h>
-#if (H5_VERS_MAJOR*1000000 + H5_VERS_MINOR*1000 + H5_VERS_RELEASE < 1013003)
-#error HDF5 version is older than 1.13.3
-#endif
-   ]])], [hdf5_ge_1_13_3=yes], [hdf5_ge_1_13_3=no])
-AC_MSG_RESULT([$hdf5_ge_1_13_3])
-if test x$hdf5_ge_1_13_3 = xyes; then
-   AC_DEFINE(HDF5_GE_1133, 1, ["HDF5 version greater than 1.13.3"])
-fi
 AC_MSG_CHECKING([whether HDF5 parallel I/O is enabled])
 AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
 #include <hdf5.h>

diff --git a/doc/INSTALL.md b/doc/INSTALL.md
@@ -1,7 +1,7 @@
 ## The Log VOL connector - Build Instructions
 
 ### Software Requirements
-* [HDF5 1.13.0](https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.2/src/hdf5-1.13.2.tar.gz)
+* [Minimum HDF5 1.14](https://github.com/HDFGroup/hdf5/releases/latest/download/hdf5.tar.gz)
   + Configured with parallel I/O support (--enable-parallel)
 * MPI C and C++ compilers
   + The plugin uses the constant initializer; a C++ compiler supporting std 17 is required
@@ -12,39 +12,39 @@
   + [m4](https://www.gnu.org/software/m4/) 1.4.18
 
 ### Building HDF5 libraries
-* HDF5 1.13.0 and later (**required**)
-  + Download HDF5 official release version 1.13.0.
+* HDF5 1.14.0 and later (**required**)
+  + Download HDF5's official latest release.
     ```
-    % wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.2/src/hdf5-1.13.2.tar.gz
+    % wget https://github.com/HDFGroup/hdf5/releases/latest/download/hdf5.tar.gz
     ```
   + Configure HDF5 with parallel I/O enabled.
     ```
-    % tar -zxf hdf5-1_13_0.tar.gz
-    % cd hdf5-1_13_0.tar.gz
-    % ./configure --prefix=${HOME}/HDF5/1.13.0 --enable-parallel CC=mpicc
+    % tar -zxf hdf5.tar.gz
+    % cd hdf5-*
+    % ./configure --prefix=${HOME}/HDF5/latest --enable-parallel CC=mpicc
     % make -j4 install
     ```
   + The above example commands will install the HD5 library under the folder
-    `${HOME}/HDF5/1.13.0`.
+    `${HOME}/HDF5/latest`.
 
 ### Building the Log VOL connector
 * Obtain the source code package by either downloading the official release or
   cloning the github repository.
   + Download the latest official release version 1.1.0.
     ```
-    % wget https://github.com/DataLib-ECP/vol-log-based/archive/refs/tags/logvol.1.1.0.tar.gz
+    % wget https://github.com/HDFGroup/vol-log-based/archive/refs/tags/logvol.1.1.0.tar.gz
     % tar -zxf logvol.1.1.0.tar.gz
     % cd vol-log-based-logvol.1.1.0
     ```
   + Clone from the github repository.
     ```
-    % git clone https://github.com/DataLib-ECP/vol-log-based.git
+    % git clone https://github.com/HDFGroup/vol-log-based.git
     % cd log_io_vol
     % autoreconf -i
     ```
 * Example configure and make commands are given below.
   ```
-  % ./configure --prefix=${HOME}/Log_IO_VOL --with-hdf5=${HOME}/HDF5/1.13.0
+  % ./configure --prefix=${HOME}/Log_IO_VOL --with-hdf5=${HOME}/HDF5/latest
   % make -j 4 install
   ```
   + The above commands will install the log-vol library under the folder `${HOME}/Log_IO_VOL`.

diff --git a/doc/log_cache_async_vol.md b/doc/log_cache_async_vol.md
@@ -2,7 +2,7 @@
 * [Build Instructions](#build-instructions)
 * [Run Instructions](#run-e3sm-io)
 
-This demo uses [E3SM-IO](https://github.com/Parallel-NetCDF/E3SM-IO) to show how to run the Log VOL connector on top of the [Cache VOL connector](https://github.com/hpc-io/vol-cache) and the [Async VOL connector](https://github.com/hpc-io/vol-async).
+This demo uses [E3SM-IO](https://github.com/Parallel-NetCDF/E3SM-IO) to show how to run the Log VOL connector on top of the [Cache VOL connector](https://github.com/HDFGroup/vol-cache) and the [Async VOL connector](https://github.com/HDFGroup/vol-async).
 
 E3SM-IO is an I/O benchmark suite that measures the performance I/O kernel of
 [E3SM](https://github.com/E3SM-Project/E3SM), a state-of-the-art Earth system modeling,
@@ -30,17 +30,17 @@ The Log, Cache, and Async VOL connectors can be enabled by directly setting the
     % export HDF5_ROOT=${HDF5_DIR}
     ```
 
-+ HDF5 1.13.3: `--enable-parallel`, `--enable-threadsafe`, and `--enable-unsupported` are [required by Async VOL](https://hdf5-vol-async.readthedocs.io/en/latest/gettingstarted.html#build-async-i-o-vol) at configure time.
++ Minimum HDF5 1.14: `--enable-parallel`, `--enable-threadsafe`, and `--enable-unsupported` are [required by Async VOL](https://hdf5-vol-async.readthedocs.io/en/latest/gettingstarted.html#build-async-i-o-vol) at configure time.
 
     ```shell
     # create a new folder "HDF5" under $WORKSPACE
     % mkdir ${HDF5_DIR}
     % cd ${HDF5_DIR}
     
     # download HDF5 source codes
-    % wget -cq https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.3/src/hdf5-1.13.3.tar.gz
-    % tar -zxf hdf5-1.13.3.tar.gz
-    % cd hdf5-1.13.3
+    % wget -cq https://github.com/HDFGroup/hdf5/releases/latest/download/hdf5.tar.gz
+    % tar -zxf hdf5.tar.gz
+    % cd hdf5-*
     
     # configure, output saved to log.config
     % ./configure --prefix=${HDF5_DIR} \
@@ -98,7 +98,7 @@ The Log, Cache, and Async VOL connectors can be enabled by directly setting the
     % cd ${ASYNC_DIR}
 
     # download Async VOL source codes and create a build folder
-    % wget -qc https://github.com/hpc-io/vol-async/archive/refs/tags/v1.4.tar.gz
+    % wget -qc https://github.com/HDFGroup/vol-async/archive/refs/tags/v1.4.tar.gz
     % tar -xf v1.4.tar.gz
     % cd vol-async-1.4
     % mkdir build
@@ -127,7 +127,7 @@ The Log, Cache, and Async VOL connectors can be enabled by directly setting the
     % export LD_LIBRARY_PATH="$ABT_DIR/lib:$LD_LIBRARY_PATH"
 
     # download Cache VOL source codes and create a build folder
-    % git clone https://github.com/hpc-io/vol-cache.git
+    % git clone https://github.com/HDFGroup/vol-cache.git
     % cd vol-cache
     % mkdir build
     % cd build
@@ -151,7 +151,7 @@ The Log, Cache, and Async VOL connectors can be enabled by directly setting the
     % cd ${LOGVOL_DIR}
 
     # download Log VOL source codes
-    % git clone [email protected]:DataLib-ECP/vol-log-based.git
+    % git clone [email protected]:HDFGroup/vol-log-based.git
     % cd vol-log-based
 
     # create configure file, output saved to log.autoreconf

diff --git a/doc/userguide.md b/doc/userguide.md
@@ -24,7 +24,7 @@ applications.
 
 ## Design of the Log VOL connector
 
-The [the Log VOL connector](https://github.com/DataLib-ECP/vol-log-based) is an HDF5
+The [the Log VOL connector](https://github.com/HDFGroup/vol-log-based) is an HDF5
 Virtual Object Layer (VOL) plug-in that stores HDF5 datasets in a log-based
 storage layout, in contrast to the canonical order layout. The
 [Log-based storage layout](https://link.springer.com/chapter/10.1007/978-3-540-75416-9_34)