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