====== HDF5 ======

Distintas suites de simulación requieren versiones levemente distintas de HDF5. En algunos casos, es conveniente 
compilar la biblioteca dentro del root de la toolchain.

Por ejemplo, [[vasp|VASP]] y [[abinit|ABINIT]] requieren distintas flags de compilación de HDF5 para funcionar, entonces tendría sentido 
estructurar estar herramientas de la siguiente forma:

<code>/data/shared/apps/vasp/libs/hdf5
/data/shared/apps/abinit/libs/hdf5
</code>

y luego mediante LMOD appendear a LD_LIBRARY_PATH los directorios respectivos a cada tool.

===== VASP =====


La versión verificada en la VASP Toolchain es la 1.14.6.

=== OpenMPI4 ===

<code>module load intel openmpi4

export CC=icx
export CXX=icpx
export FC=ifort
export CFLAGS='-O3 -xHost -ip'
export CXXFLAGS='-O3 -xHost -ip'
export FCFLAGS='-O3 -xHost -ip'

curl -LO https://github.com/HDFGroup/hdf5/releases/download/hdf5_1.14.6/hdf5-1.14.6.tar.gz
tar -zxvf hdf5-1.14.6.tar.gz
cd hdf5-1.14.6
./configure --prefix=/data/contrib/hdf5-install-autotools --enable-fortran --enable-cxx
make
make check
make install
</code>

===== ABINIT =====

Descargamos la misma versión que para vasp pero usamos otras flags de configuración.

<code>
module purge
module load intel openmpi5

curl -LO https://github.com/HDFGroup/hdf5/releases/download/hdf5_1.14.6/hdf5-1.14.6.tar.gz
tar -zxvf hdf5-1.14.6.tar.gz
mv hdf5-1.14.6 1.14.6

./configure --prefix=/data/shared/apps/abinit/10.6.3/libs  \
           CC=mpicc --enable-parallel --enable-shared
           
</code>

Al finalizar el configure deberíamos obtener el siguiente output:

<code>
        SUMMARY OF THE HDF5 CONFIGURATION
        =================================

General Information:
-------------------
                   HDF5 Version: 1.14.6
                  Configured on: Wed Feb 11 16:04:18 -03 2026
                  Configured by: bbruzzo@snmgt01
                    Host system: x86_64-pc-linux-gnu
              Uname information: Linux snmgt01 5.14.0-427.13.1.el9_4.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Apr 10 10:29:16 EDT 2024 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /data/shared/apps/abinit/10.6.3/libs

Compiling Options:
------------------
                     Build Mode: production
              Debugging Symbols: no
                        Asserts: no
                      Profiling: no
             Optimization Level: high

Linking Options:
----------------
                      Libraries: static, shared
  Statically Linked Executables: 
                        LDFLAGS: 
                     H5_LDFLAGS: 
                     AM_LDFLAGS: 
                Extra libraries: -lz -ldl -lm 
                       Archiver: ar
                       AR_FLAGS: cr
                         Ranlib: ranlib

Languages:
----------
                              C: yes
                     C Compiler: /opt/ohpc/pub/mpi/openmpi5-intel/5.0.3/bin/mpicc
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API -I/data/shared/apps/abinit/10.6.3/hdf5/1.14.6/src/H5FDsubfiling
                    AM_CPPFLAGS: 
                        C Flags: 
                     H5 C Flags:   -std=c99 -Wall   -Wl,-s   -O3
                     AM C Flags: 
               Shared C Library: yes
               Static C Library: yes


                        Fortran: no

                            C++: no

                           Java: no


Features:
---------
                     Parallel HDF5: yes
  Parallel Filtered Dataset Writes: yes
                Large Parallel I/O: yes
                High-level library: yes
Dimension scales w/ new references: no
                  Build HDF5 Tests: yes
                  Build HDF5 Tools: yes
                   Build GIF Tools: no
                      Threadsafety: no
               Default API mapping: v114
    With deprecated public symbols: yes
            I/O filters (external): deflate(zlib)
                  _Float16 support: no
                     Map (H5M) API: no
                        Direct VFD: no
                        Mirror VFD: no
                     Subfiling VFD: no
                (Read-Only) S3 VFD: no
              (Read-Only) HDFS VFD: no
    Packages w/ extra debug output: none
                       API tracing: no
              Using memory checker: no
                  Use file locking: best-effort
         Strict file format checks: no
      Optimization instrumentation: no
</code>

Procedemos a compilar:

<code>
make -j4
make check
make install
</code>