[Users] CarpetIOHDF5 to S5 converter for yt

[Jonah Miller]

Hi Roland,


Here are build and use instructions for SimulationIO and the 
SimulationIO converter. You can find much of the same information in the 
slides for my presentation at the ET workshop:

https://github.com/Yurlungur/simulationio-and-yt


Let me know if you have any trouble.


Best,

Jonah


To build the release version of SimulationIO, use my fork of Erik's repo:

https://github.com/Yurlungur/SimulationIO/tree/release-0.1

And the instructions are here:

https://github.com/Yurlungur/SimulationIO/blob/release-0.1/README.md

This installs the SimulationIO reader and the python API. It also adds 
the utilities sio-convert-carpet-output and sio-list, which you can use 
to generate and look at SimulationIO files.


The version of yt with a working SimulationIO frontend is:

https://bitbucket.org/Yurlungur/yt-simulationio

To use it:

hg clone ssh://hg@bitbucket.org/Yurlungur/yt-simulationio

cd yt-simulationio

hg update simulationio

python setup.py install

(add --user or --prefix=path or whatever you prefer)

Then you can load simulationio files by

import yt

ds = yt.load(filename,configuration=configuration)

where configuration is a name for the time level and timestep in the 
SimulationIO file. You may also need to specify that there are no ghost 
zones, etc.


On 16-10-05 06:46 PM, Roland Haas wrote:
> Hello Erik, Jonah,
>
> yes, Llama seems involved. If I use only the data for the Cartesian
> grid it aborts with a different error:
>
>    opening dataset WEYLSCAL4::Psi4r it=357120 tl=0 m=0 rl=5 c=6...
>      field name: WEYLSCAL4::Psi4r
>      tensor rank: 0
>      tensor type: Scalar3D
>      tensor indices: []
>      iteration: 357120
>      time level: 0
>      map: 0
>      refinement level: 5
>      component: 6
> sio-convert-carpet-output: convert-carpet-output.cpp:612: main(int, char**)::<lambda(const H5::Group&, const string&, const H5L_info_t*)>: Assertion `loc == val' failed.
> Aborted (core dumped)
>
>
> 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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>>>
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>>
>
>
>
>
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