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<p>Hi Roland,
<br>
<br>
<br>
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.
<br>
<br>
<br>
Best,
<br>
<br>
Jonah
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<div class="moz-cite-prefix">On 16-10-05 06:38 PM, Roland Haas
wrote:<br>
</div>
<blockquote
cite="mid:20161005173808.0a2bb9f4@8992d193.ncsa.illinois.edu"
type="cite">
<pre wrap="">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
</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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