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<p>Hi Roland,</p>
<br>
<p>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:</p>
<p><a class="moz-txt-link-freetext" href="https://github.com/Yurlungur/simulationio-and-yt">https://github.com/Yurlungur/simulationio-and-yt</a></p>
<p><br>
</p>
<p>Let me know if you have any trouble.<br>
</p>
<p><br>
</p>
<p>Best,</p>
<p>Jonah<br>
</p>
<p><br>
</p>
<p>To build the release version of SimulationIO, use my fork of
Erik's repo:</p>
<p><a class="moz-txt-link-freetext" href="https://github.com/Yurlungur/SimulationIO/tree/release-0.1">https://github.com/Yurlungur/SimulationIO/tree/release-0.1</a></p>
<p>And the instructions are here:</p>
<p><a class="moz-txt-link-freetext" href="https://github.com/Yurlungur/SimulationIO/blob/release-0.1/README.md">https://github.com/Yurlungur/SimulationIO/blob/release-0.1/README.md</a></p>
<p>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.<br>
</p>
<p><br>
</p>
<p>The version of yt with a working SimulationIO frontend is:</p>
<p><a class="moz-txt-link-freetext" href="https://bitbucket.org/Yurlungur/yt-simulationio">https://bitbucket.org/Yurlungur/yt-simulationio</a></p>
<p>To use it:</p>
<p>hg clone <a class="moz-txt-link-freetext" href="ssh://hg@bitbucket.org/Yurlungur/yt-simulationio">ssh://hg@bitbucket.org/Yurlungur/yt-simulationio</a></p>
<p>cd yt-simulationio</p>
<p>hg update simulationio</p>
<p>python setup.py install <br>
</p>
<p>(add --user or --prefix=path or whatever you prefer)</p>
<p>Then you can load simulationio files by <br>
</p>
<p>import yt</p>
<p>ds = yt.load(filename,configuration=configuration)</p>
<p>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.</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 16-10-05 06:46 PM, Roland Haas
wrote:<br>
</div>
<blockquote
cite="mid:20161005174612.72fe71ea@8992d193.ncsa.illinois.edu"
type="cite">
<pre wrap="">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
</pre>
<blockquote type="cite">
<pre wrap="">Roland
Yes, such a converter exists; it is part of the SimulationIO package <a class="moz-txt-link-rfc2396E" href="https://github.com/eschnett/SimulationIO"><
https://github.com/eschnett/SimulationIO></a>, 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 <a class="moz-txt-link-rfc2396E" href="mailto:rhaas@illinois.edu"><rhaas@illinois.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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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</blockquote>
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