[Users] Visualizing Carpet Multipatch (Llama) data

Haas, Roland rhaas at illinois.edu
Fri Jan 18 08:17:33 CST 2019

Hello Severin,

sorry for the slow response.

> for my current output
> CarpetIOHDF5::out_vars = "grid::coordinates{out_every=1000000000}
>                            HydroBase::rho"
> I receive files like
> grid-coordinates.file_0.h5
> grid-coordinates.file_1.h5
> hydrobase-rho.file_0.h5
> hydrobase-rho.file_1.h5
> Now I have basically two questions left:
> 1) How can I use both of these databases now to generate plots in
> visit, i.e., how can I use the coordinates to plot rho?
VisIt is hard-coded to expect files x.file_0.h5, y.file_0.h5,
z.file_0.h5 etc so since you had set CarpetIOHDF5::one_file_per_group
you will have to extract them afterwards. 

This command:

for i in grid-coordinates.file*.h5 ; do
  for d in x y z ; do
    h5ls $i | gawk -vd=$d '{sub(" (Dataset|Group).*","");
      if(match($0,"GRID::"d) || /Parameters/) { print }}' >dsets.txt
    hdf5_extract dsets.txt $i $d.${i#*.}

will do so when executed in the directory containing the h5 files. This
is a bit complex unfortunately. Mostly this is because hdf5_slicer
cannot be used (since it changes a hdf5 attribute that then confuses
the VisIt Reader).

> 2) If I try to plot only the grid-coordinates in VisIt (e.g. Mesh
> plot):
>      - If I plot it for the "Carpet-AMR-grid" I can see the mesh plot
> for the inner Cartesian grid.
>      - If I try to plot if for the "Carpet Multipatch", the same
> error as before occcurs:
> "The compute engine running on (...) has exited abnormally.
Yes, that is expected. Sorry, the error checking of the VisIt reader is
not very good. This happened b/c it could not find the coordinates
files and then crashed.

> Does this mean that there is something wrong with my grid setup?
There is nothing wrong with your setup. The VisIt reader is to blame.
There is a newer version of it which has error checking and some other
improvements here: 

git clone git at bitbucket.org:rhaas80/carpethdf5.git

though you would have to compile it yourself. I have
to go talk to the VisIt devs to have the new version included in VisIt.


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