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> 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.




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