Hi,
I am developing an unstructured grid based CFD algorithm for
Petascale applications. I have written a program using MPI, which puts
unstructured mesh information (vertices, faces and cells) into a H5 file.
The H5 file will be read by the CFD code for solving equations. My question
is two fold.
1.) What is the best way of organizing data in the file? I am planning to
have just 3 simple datasets for vertices, faces and cells. Should the
layout be 1-dimensional or chunked? The data is contiguous and there is no
contention among different processors during the write phase. Should I
worry about queuing I/O calls upto a limit and then flush the data. Should
I also worry about alignment issues (respecting stripe boundaries)?
2.) My next question is how do I efficiently read the data in an
unstructured manner from the file? The data to be read is not contiguous
and there is contention among processors? I am, presently, using
H5S_select_elements to do this. Is there a better way to do this? Will the
HDF5 API buffer data upto a limit and then transfer to memory?
Regards
Suman Vajjala
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