Installing HDF5

Procedure

Use PuTTY to log in to the server as the root user.

Set the environment variables.

export optflags="-O3"
export ldflags="-Wl,--build-id"

Create an installation directory.
```
mkdir -p /path/to/hdf5
```
Go to the installation directory.
```
cd /path/to/hdf5
```

Obtain the source code.

wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz

Decompress the HDF5 installation package.
```
tar -zxvf hdf5-1.8.12.tar.gz
```
Go to the directory generated after the decompression.
```
cd hdf5-1.8.12
```

Perform the configuration.

./configure --prefix=/path/to/hdf5 --build=aarch64-unknown-linux-gnu --enable-shared --enable-static=yes --enable-fortran CC=clang CXX=clang++ FC=flang F77=flang CFLAGS="$optflags -fPIC -Wno-incompatible-pointer-types-discards-qualifiers -Wno-non-literal-null-conversion" FCFLAGS="$optflags -fPIC" FFLAGS="$optflags -fPIC" LDFLAGS="$ldflags"

Create a libtool.patch file.

Create a libtool.patch file.
```
vi libtool.patch
```

Press i to enter the insert mode and add the following content:

diff -ruN hdf5-1.10.1/libtool hdf5-1.10.1-new/libtool
--- hdf5-1.10.1/libtool 2019-12-02 20:02:56.270676503 +0000
+++ hdf5-1.10.1-new/libtool 2019-12-02 20:03:05.062708034 +0000
@@ -11832,7 +11832,7 @@
pic_flag=""
# How to pass a linker flag through the compiler.
-wl=""
+wl="-Wl,"
# Compiler flag to prevent dynamic linking.
link_static_flag=""

Press Esc, type :wq!, and press Enter to save the file and exit.

Install the patch.
```
patch -p1 < libtool.patch
```
Perform the compilation and installation.
```
make -j 8
```
```
make install
```

Set the environment variables.

export PATH=/path/to/hdf5/bin:$PATH
export LD_LIBRARY_PATH=/path/to/hdf5/lib:$LD_LIBRARY_PATH

Parent topic: Configuring the Compilation Environment