Is sequential HDF5 supported? about h5bench

[jeanbez]

Hi! h5bench benchmark and kernels require parallel HDF5 support.

[candiceT233]

Hi! h5bench benchmark and kernels require parallel HDF5 support.

@jeanbez Thank you. I am doing a research project and I want to run the H5Bench with the Hermes VFD.
Currently, Hermes only supports sequential HDF5.
I'd like to know if it's doable, with not too many code modification on the h5bench_read.c and h5bench_write.c files, I can compile H5Bench and run it with sequential the HDF5?

[jeanbez]

It should be doable, but there will be quite some code changes I would say. You would have to drop all MPI-related functions and adapt the problem accordingly.

[sbyna]

Is there a specific pattern of h5bench you are trying to use?

Instead of trying to convert h5bench to a sequential version, it may be good to use some existing hdf5 sequential examples.
Some of them are available at https://github.com/HDFGroup/hdf5/tree/develop/examples
https://github.com/HDFGroup/hdf5/blob/develop/examples/h5_select.c may be something to define a hyperslab and read, which can be modified to mimic patterns for reading full dataset or a subset of a dataset.

[candiceT233]

Thank you for the help.
I can successfully compile and run the h5bench_read.cc and h5bench_write.cc code with sequential HDF5.
What I did is comment out all the MPI-related commands, and set the below variables:

NUM_RANKS = 1
TOTAL_PARTICLES = NUM_PARTICLES

and change H5Pset_fapl_mpio(fapl, comm, info) to H5Pset_fapl_sec2(fapl).