[Users] Merging CarpertIOHDF5 output from several checkpoints

dumsani g14n8326 at campus.ru.ac.za
Sat Oct 1 06:38:25 CDT 2016

Hi Roland,

I use VisIt too for the HDF5 output and sure, it does pick up the files 
all processes (var.file_*.h5) to open them as as a single (virtual) 

Your second point does answer my question anyway. Thanks.
I'll have to figure out some work-around, e.g. processing the output from
each individual checkpoint directory.


On 30/09/2016 22:54, Roland Haas wrote:
> Hello Dumsani,
>> 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.
> This depends on the visualization software you would like to use. VisIt
> will automatically use all rho files if you open the rho.file_0.h5 file
> so you typically do not have to do anything. It will however not
> combine files from the different output-???? directories. I do not know
> of any way to have VisIt read them all and present them as a single
> database.
> If you want to combine really combine the files, you can use the
> hdf5_slicer command that is part of CarpetIOHDF5 and that you can find
> in exe/sim/hdf5_slicer (it can be used to combine files if you give it
> the out3d-cube option). For your files, if you want a single file (keep
> in mind Ian's comment it will just copy the datasets, no actual merging
> of the datasets happens) you can use:
> hdf5_slicer --out3d-cube output-????/<parfile>/{rho,eps}.file_*.h5
> rho.h5
> Yours,
> Roland

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