Hi Roland, Ian, Everyone,
Thanks for your input. May I add a few points though to elaborate on my question. Let's assume we run a simulation with 2 MPI processes (ranks) with each process writing to it's HDF5 own file. Further assume we have output from 2 restarts on top of the first output, i.e. we have Simfactory output directories output-0000, output-0001 and output-0002. So, for a variable rho, for instance, we would then have output-0000/<parfile>/rho.file_0.h5 output-0000/<parfile>/rho.file_1.h5
output-0001/<parfile>/rho.file_0.h5 output-0001/<parfile>/rho.file_1.h5
output-0002/<parfile>/rho.file_0.h5 output-0002/<parfile>/rho.file_1.h5
Now, for purposes of visualizing the data, for instance, one would be interested in collecting all these data chunks into a single file. The question is how to bundle these into a single file. I wanted to know if any of the available Carpet tools can help with this.
I stand to be corrected, but I seem to recall that some of the non-ET tools (e.g. SimulationTools) seem to have an abstraction mechanism for transparently combining CarpetIOHDF5 output from various checkpoints. Is that the direction I may have to go?
Thank you, Dumsani
On 30/09/2016 17:56, Ian Hinder wrote:
On 30 Sep 2016, at 16:29, Roland Haas <rhaas@illinois.edu mailto:rhaas@illinois.edu> wrote:
Hello Dumsani,
there are two different things you may want to do. If you have files rho.file_0.h5 eps.file_0.h5 rho.file_1.h5 and eps.file_1.h5 and would like to combine the variables you can use:
hdf5_merge rho.file_0.h5 eps.file_0.h5 vars.file_0.h5 hdf5_merge rho.file_1.h5 eps.file_1.h5 vars.file_1.h5
ie when you want to keep the file_X structure intact. If not then you must use the hdf5 slicer:
hdf5_slicer --out3d-cube rho.file_*.h5 eps.file_*.h5 vars.h5
Also note that (as far as I know) this simply copies the datasets from one file to the other. It does not coalesce the individual rectangular components into a single one, suitable for viewing with a generic visualisation tool. This would not in general be possible for a mesh-refined grid.
-- Ian Hinder http://members.aei.mpg.de/ianhin
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