[Users] Merging CarpertIOHDF5 output from several checkpoints

[dumsani]

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 at illinois.edu 
> <mailto:rhaas at 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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