Hello,

I have a set of 3D output files from CarpetIOHDF5 (rho.xyz_file<n>.h5), each containing many iterations, and I want to create a set of new CarpetIOHDF5 files containing the data related to the last iteration. I have tried something, but I couldn't get anything to work, so I am asking for help here.

For each file rho.xyz_file<n>.h5, I used the hdf5_extract utility to create a new file containing the dataset related to the last iteration ("HYDROBASE::rho it=1067600 tl=0 rl=0 c=<n>") and the group "Parameters and Global Attributes". However, when I try to open the set of new files with VisIt I get the following error:

VisIt could not read from the file "/home/lorenzo/CBD_prod_WZ9_400_140_280_output-0014/Output/rho.xyz_it1067600_tl0_rl0_c* database".

The generated error message was:

There was an error opening /home/lorenzo/CBD_prod_WZ9_400_140_280_output-0014/Output/rho.xyz_it1067600_tl0_rl0_c* database. It may be an invalid file. VisIt tried using the following file format readers to open the file: CarpetHDF5

The following error(s) may be helpful in identifying the problem:
Tried to access an invalid index 1 (Maximum = 0).

I thought that maybe some metadata in the new files are telling VisIt that there are multiple iterations available, which is not true; I'm not completely sure this is really the issue, though.

In the new files, the attributes "GH$iteration" and "carpet_global_time" from the group "Parameters and Global Attributes" are still respectively set to the first iteration (992800) and the first time (148920) available in the original files, while I am extracting the last iteration (1067600, time 160140). Also, in the new files, the dataset "Grid Structure v5" (a string) still contains "grid_times:[[[148920,148919.85000000001,148919.69999999998]]]", which also looks wrong. Therefore, I used h5py to generate new files in which I fixed "GH$iteration", "carpet_global_time" and "Grid Structure v5", but I still get the same error from VisIt.

I have also thought about re-running the simulation that produced the original files from the last checkpoint and just dump the last iteration, but that simulation was run some time ago and the code I am using has evolved quite a bit in the meantime, to the point that some parameters are not even defined anymore.

Is there any other attribute/dataset I should edit in order to fix the new files? Are there smarter ways to extract an iteration from a set of 3D CarpetHDF5 output files? Please let me know if you need additional information from my end.

Thank you very much,

Lorenzo Ennoggi