HDF5

Loading HDF5

HDF5 on Lawrencium can be loaded after loading a MPI library. For example, to load HDF5 installed under the default gcc compiler and the default Open MPI on Lawrencium:

[user@n0000 ~]$ module load gcc openmpi
[user@n0000 ~]$ module avail hdf5

------------- /global/software/rocky-8.x86_64/modfiles/openmpi/4.1.6-4xq5u5r/gcc/11.4.0 --------------
   hdf5/1.14.3

[user@n0000 ~]$ module load hdf5

Compiling programs using HDF5 library

Let's look at an example of compiling a simple C example ph5_file_create.c from hdf5-examples . The example creates a HDF5 file named SDS_row.h5.

To compile using the loaded HDF5 library, we need the appropriate CFLAGS and LDFLAGS during compilation and linking. These can be obtained in Lawrencium using

[user@n0000 ~]$ pkg-config --cflags --libs hdf5
-I/global/software/rocky-8.x86_64/gcc/linux-rocky8-x86_64/gcc-11.4.0/hdf5-1.14.3-6763puu3e5vxq4vmbaosgiv4yhzjb46s/include -L/global/software/rocky-8.x86_64/gcc/linux-rocky8-x86_64/gcc-11.4.0/hdf5-1.14.3-6763puu3e5vxq4vmbaosgiv4yhzjb46s/lib -lhdf5 

To include these directly in the compilation process, we can do the following:

mpicc -o ph5_file_create $(pkg-config --cflags --libs hdf5) ph5_file_create.c