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Sync develop changes March 28 - April 1 to 1 14 #4297

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merged 12 commits into from
Apr 1, 2024
Merged

Sync develop changes March 28 - April 1 to 1 14 #4297

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9ae4b3f
Relaxed behavior of H5Pset_page_buffer_size() when opening files (#4280)
derobins Mar 29, 2024
c84a902
chore: improve error message (#4287)
hyoklee Mar 29, 2024
a864a85
changed to if string contains instead (#4286)
brtnfld Mar 29, 2024
a3fab85
Fix off_t straggers (#4291)
derobins Mar 31, 2024
84a3801
Add missing foreach for VFD and Pasthrough runs (#4292)
byrnHDF Apr 1, 2024
ad5e633
Fixes for file format security issues (#4283)
jhendersonHDF Apr 1, 2024
11a1cee
Add configure options for disabling extension features (#4277)
jhendersonHDF Apr 1, 2024
0c5dbed
Add documentation (H5FD) (#4269)
bmribler Apr 1, 2024
1779d65
Use AOCC 4.2 and OpenMPI 4.1.6 (#4290)
hyoklee Apr 1, 2024
209162a
Fix problems with background buffers and array datatypes (#4218)
fortnern Apr 1, 2024
7fa7f17
Synch workflows and require apt-get update (#4294)
byrnHDF Apr 1, 2024
c680d78
Fix Figure 9. table format in HDF5 Groups User Guide (#4295)
hyoklee Apr 1, 2024
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46 changes: 23 additions & 23 deletions .github/workflows/aocc-auto.yml
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Expand Up @@ -28,43 +28,43 @@ jobs:
sudo apt install -y zlib1g-dev libcurl4-openssl-dev libjpeg-dev wget curl bzip2
sudo apt install -y m4 flex bison cmake libzip-dev openssl build-essential

- name: Install AOCC 4.1.0
- name: Install AOCC 4.2.0
shell: bash
run: |
wget https://download.amd.com/developer/eula/aocc/aocc-4-1/aocc-compiler-4.1.0.tar
tar -xvf aocc-compiler-4.1.0.tar
cd aocc-compiler-4.1.0
wget https://download.amd.com/developer/eula/aocc/aocc-4-2/aocc-compiler-4.2.0.tar
tar -xvf aocc-compiler-4.2.0.tar
cd aocc-compiler-4.2.0
bash install.sh
source /home/runner/work/hdf5/hdf5/setenv_AOCC.sh
which clang
which flang
clang -v

- name: Cache OpenMPI 4.1.5 installation
id: cache-openmpi-4_1_5
- name: Cache OpenMPI 4.1.6 installation
id: cache-openmpi-4_1_6
uses: actions/cache@v4
with:
path: /home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_5-cache
path: /home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_6-cache

- name: Install OpenMPI 4.1.5
if: ${{ steps.cache-openmpi-4_1_5.outputs.cache-hit != 'true' }}
- name: Install OpenMPI 4.1.6
if: ${{ steps.cache-openmpi-4_1_6.outputs.cache-hit != 'true' }}
run: |
export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib
wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.5.tar.gz
tar zxvf openmpi-4.1.5.tar.gz
cd openmpi-4.1.5
./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/usr/local/lib
wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.6.tar.gz
tar zxvf openmpi-4.1.6.tar.gz
cd openmpi-4.1.6
./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
make
make install

- name: Autotools Configure
env:
NPROCS: 2
run: |
export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
sh ./autogen.sh
mkdir "${{ runner.workspace }}/build"
cd "${{ runner.workspace }}/build"
Expand All @@ -73,30 +73,30 @@ jobs:
--enable-build-mode=${{ inputs.build_mode }} \
--enable-shared \
--enable-parallel \
LDFLAGS="-L/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib \
-L/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib"
LDFLAGS="-L/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib \
-L/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib"

- name: Autotools Build
shell: bash
env:
NPROCS: 2
run: |
export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
make -j3
working-directory: ${{ runner.workspace }}/build

- name: Autotools Run Tests
env:
NPROCS: 2
run: |
export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
make check -j
working-directory: ${{ runner.workspace }}/build

- name: Autotools Install
env:
NPROCS: 2
run: |
export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
make install
working-directory: ${{ runner.workspace }}/build
36 changes: 18 additions & 18 deletions .github/workflows/aocc-cmake.yml
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Expand Up @@ -28,42 +28,42 @@ jobs:
sudo apt install -y zlib1g-dev libcurl4-openssl-dev libjpeg-dev wget curl bzip2
sudo apt install -y m4 flex bison cmake libzip-dev openssl build-essential

- name: Install AOCC 4.1.0
- name: Install AOCC 4.2.0
shell: bash
run: |
wget https://download.amd.com/developer/eula/aocc/aocc-4-1/aocc-compiler-4.1.0.tar
tar -xvf aocc-compiler-4.1.0.tar
cd aocc-compiler-4.1.0
wget https://download.amd.com/developer/eula/aocc/aocc-4-2/aocc-compiler-4.2.0.tar
tar -xvf aocc-compiler-4.2.0.tar
cd aocc-compiler-4.2.0
bash install.sh
source /home/runner/work/hdf5/hdf5/setenv_AOCC.sh
which clang
which flang
clang -v

- name: Cache OpenMPI 4.1.5 installation
id: cache-openmpi-4_1_5
- name: Cache OpenMPI 4.1.6 installation
id: cache-openmpi-4_1_6
uses: actions/cache@v4
with:
path: /home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_5-cache
path: /home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_6-cache

- name: Install OpenMPI 4.1.5
if: ${{ steps.cache-openmpi-4_1_5.outputs.cache-hit != 'true' }}
- name: Install OpenMPI 4.1.6
if: ${{ steps.cache-openmpi-4_1_6.outputs.cache-hit != 'true' }}
run: |
export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib
wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.5.tar.gz
tar zxvf openmpi-4.1.5.tar.gz
cd openmpi-4.1.5
./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/usr/local/lib
wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.6.tar.gz
tar zxvf openmpi-4.1.6.tar.gz
cd openmpi-4.1.6
./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
make
make install

- name: CMake Configure
shell: bash
run: |
export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
mkdir "${{ runner.workspace }}/build"
cd "${{ runner.workspace }}/build"
CC=mpicc cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake -G Ninja \
Expand Down
4 changes: 3 additions & 1 deletion .github/workflows/cmake-bintest.yml
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Expand Up @@ -98,7 +98,9 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Install CMake Dependencies (Linux)
run: sudo apt-get install ninja-build doxygen graphviz
run: |
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz

- name: Set up JDK 19
uses: actions/setup-java@v4
Expand Down
13 changes: 9 additions & 4 deletions .github/workflows/cmake-ctest.yml
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Expand Up @@ -122,7 +122,9 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Install CMake Dependencies (Linux)
run: sudo apt-get install ninja-build graphviz
run: |
sudo apt-get update
sudo apt-get install ninja-build graphviz

- name: Install Dependencies
uses: ssciwr/doxygen-install@v1
Expand Down Expand Up @@ -330,8 +332,9 @@ jobs:
steps:
- name: Install CMake Dependencies (Linux S3)
run: |
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev

- name: Set file base name (Linux S3)
id: set-file-base
Expand Down Expand Up @@ -493,7 +496,9 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Install CMake Dependencies (Linux_intel)
run: sudo apt-get install ninja-build graphviz
run: |
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz

- name: Install Dependencies
uses: ssciwr/doxygen-install@v1
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/intel-cmake.yml
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Expand Up @@ -22,7 +22,7 @@ jobs:
- name: Install Dependencies (Linux)
shell: bash
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev

Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/julia-cmake.yml
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Expand Up @@ -22,7 +22,7 @@ jobs:
- name: Install Dependencies
shell: bash
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install -y libaec-dev zlib1g-dev wget curl bzip2 flex bison cmake libzip-dev openssl build-essential
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/main-auto-par-spc.yml
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Expand Up @@ -28,7 +28,7 @@ jobs:
# libssl, etc. are needed for the ros3 VFD
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down Expand Up @@ -86,7 +86,7 @@ jobs:
# libssl, etc. are needed for the ros3 VFD
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/main-auto-par.yml
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Expand Up @@ -36,7 +36,7 @@ jobs:
# SETUP
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down
16 changes: 8 additions & 8 deletions .github/workflows/main-auto-spc.yml
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Expand Up @@ -28,7 +28,7 @@ jobs:
# libssl, etc. are needed for the ros3 VFD
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down Expand Up @@ -89,7 +89,7 @@ jobs:
# libssl, etc. are needed for the ros3 VFD
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down Expand Up @@ -150,7 +150,7 @@ jobs:
# libssl, etc. are needed for the ros3 VFD
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down Expand Up @@ -211,7 +211,7 @@ jobs:
# libssl, etc. are needed for the ros3 VFD
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down Expand Up @@ -272,7 +272,7 @@ jobs:
# libssl, etc. are needed for the ros3 VFD
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down Expand Up @@ -333,7 +333,7 @@ jobs:
# libssl, etc. are needed for the ros3 VFD
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down Expand Up @@ -394,7 +394,7 @@ jobs:
# libssl, etc. are needed for the ros3 VFD
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down Expand Up @@ -457,7 +457,7 @@ jobs:
# libssl, etc. are needed for the ros3 VFD
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/main-auto.yml
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Expand Up @@ -37,7 +37,7 @@ jobs:
# SETUP
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/main-cmake-par.yml
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Expand Up @@ -27,7 +27,7 @@ jobs:

- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down
6 changes: 3 additions & 3 deletions .github/workflows/main-cmake-spc.yml
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Expand Up @@ -26,7 +26,7 @@ jobs:
# SETUP
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down Expand Up @@ -86,7 +86,7 @@ jobs:
# SETUP
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down Expand Up @@ -146,7 +146,7 @@ jobs:
# SETUP
- name: Install Linux Dependencies
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/main-cmake.yml
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Expand Up @@ -124,7 +124,7 @@ jobs:

- name: Install CMake Dependencies (Linux)
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install gcc-12 g++-12 gfortran-12
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/nvhpc-cmake.yml
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Expand Up @@ -22,7 +22,7 @@ jobs:
- name: Install Dependencies
shell: bash
run: |
sudo apt update
sudo apt-get update
sudo apt-get install ninja-build doxygen graphviz
sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
sudo apt install -y libaec-dev zlib1g-dev wget curl bzip2 flex bison cmake libzip-dev openssl build-essential
Expand Down
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