[Users] CarpetIOHDF5 to S5 converter for yt

Jonah Miller jonah.maxwell.miller at gmail.com
Wed Oct 5 17:44:33 CDT 2016

Hi Roland,

I think this could be caused by an incompatibility with Llama. Erik can 
confirm for the development version, but at least for the release 
version, SimulationIO does not correctly slurp up Llama data. We would 
like SimulationIO to know the coordinate system, but this hasn't been 
implemented for arbitrary coordinate maps.



On 16-10-05 06:38 PM, Roland Haas wrote:
> Hello Erik, Jonah,
> this failed for me when calculating the active regions with:
> Calculating active regions...
>    discretization: iteration.0000350208-timelevel.0-map.000-level.00
>      region: {([0,0,0]:[89,89,50])}
> terminate called after throwing an instance of 'std::out_of_range'
>    what():  vector::_M_range_check: __n (which is 0) >= this->size() (which is 0)
> Aborted (core dumped)
> The code that generated the HDF5 is the 2016_05 CarpetIOHDF5 3d output code for vertex centering and with mesh refinement and Llama.
> Is any of those (not master code, Llama?) likely to cause this?
> Yours,
> Roland
>> Roland
>> Yes, such a converter exists; it is part of the SimulationIO package <
>> https://github.com/eschnett/SimulationIO>, and is called
>> "sio-convert-carpet-output". It should be built by the default makefile
>> target.
>> You call it as "./sio-convert-carpet-output [--copy|--extlink]? <output
>> file name> {<input file name>}*". There is one output file, and there can
>> be multiple input files (e.g. one for each process). The "copy" option
>> copies datasets, the "extlink" option creates external links to the
>> original HDF5 files. The latter is faster and creates smaller files, but
>> you obviously need to keep the originals around, and need to preserve their
>> path (either their relative or absolute path, depending on what you
>> specified on the command line).
>> I believe one of these two options is currently broken in the development
>> version, sorry about this. I don't recall which.
>> -erik
>> On Fri, Sep 30, 2016 at 5:01 PM, Roland Haas <rhaas at illinois.edu> wrote:
>>> Hello Jonah, Einstein Toolkit users,
>>> I think you were working on a plugin to read S5 files into yt, right?
>>> Do you also have a converter tool to convert CarpetIOHDF5 3d output
>>> files (vertex centered, mesh refined) to S5 files? If only cell
>>> centering is supported this is also fine as or this project a slight
>>> inaccuracy does not matter.
>>> I would be working with Nathan Goldbaum locally to read them into yt so
>>> once I have them in that format I will hopefully be home free.
>>> Yours,
>>> Roland
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