HDFGroup · brtnfld · Jun 12, 2024 · May 13, 2024 · May 31, 2024 · Jun 7, 2024
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/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
@@ -12,20 +12,20 @@
  + [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
@@ -44,7 +44,7 @@
  ```
 * 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/hpc-io/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

diff --git a/src/H5VL_log_dataset.cpp b/src/H5VL_log_dataset.cpp
@@ -282,7 +282,7 @@ err_out:;
  *
  *-------------------------------------------------------------------------
  */
-herr_t H5VL_log_dataset_read_1 (void *dset,
+static herr_t H5VL_log_dataset_read_1 (void *dset,
  hid_t mem_type_id,
  hid_t mem_space_id,
  hid_t file_space_id,
@@ -334,7 +334,7 @@ err_out:;
  *
  *-------------------------------------------------------------------------
  */
-herr_t H5VL_log_dataset_write_1 (void *dset,
+static herr_t H5VL_log_dataset_write_1 (void *dset,
  hid_t mem_type_id,
  hid_t mem_space_id,
  hid_t file_space_id,
@@ -378,7 +378,7 @@ err_out:;
  return err;
 } /* end H5VL_log_dataset_write() */
 
-herr_t H5VL_log_dataset_read_2 (size_t count,
+herr_t H5VL_log_dataset_read (size_t count,
  void *dset[],
  hid_t mem_type_id[],
  hid_t mem_space_id[],
@@ -387,6 +387,10 @@ herr_t H5VL_log_dataset_read_2 (size_t count,
  void *buf[],
  void **req) {
  herr_t err = 0;
+ H5VL_log_dset_t *dp = (H5VL_log_dset_t *)dset;
+ H5VL_log_dset_info_t *dip = NULL; // Dataset info
+ hid_t dsid; // Dataset space id
+ H5VL_log_selections *dsel = NULL; // Selection blocks
  size_t i;
 
  for (i = 0; i < count; i++) {
@@ -398,7 +402,7 @@ herr_t H5VL_log_dataset_read_2 (size_t count,
  return err;
 }
 
-herr_t H5VL_log_dataset_write_2 (size_t count,
+herr_t H5VL_log_dataset_write (size_t count,
  void *dset[],
  hid_t mem_type_id[],
  hid_t mem_space_id[],