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<p>The Tutorial server has the full current release of the ETK,
including SILO and OpenPMD.</p>
<p>--Steve<br>
</p>
<div class="moz-cite-prefix">On 6/30/2025 11:53 AM, Erik Schnetter
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:40E50047-069B-4E89-B913-37D46EB9711D@gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
Javiera
<div><br>
</div>
<div>Unfortunately I don't recall what software is installed on
the ETK tutorial server... I'm sure someone else can help us out
here?</div>
<div><br>
</div>
<div>-erik<br id="lineBreakAtBeginningOfMessage">
<div><br>
<blockquote type="cite">
<div>On Jun 30, 2025, at 12:17, Javiera Hernández Morales
<a class="moz-txt-link-rfc2396E" href="mailto:javihernandezm@posteo.net"><javihernandezm@posteo.net></a> wrote:</div>
<br class="Apple-interchange-newline">
<div>
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content="text/html; charset=UTF-8">
<div
style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi
Erik,
<div><br>
</div>
<div>Thanks for your answer. Maybe for more context I
should mention that I am starting to learn how to use
the ETK, and for that I am using the notebooks
provided in the tutorial server (<a
href="http://etk.cct.lsu.edu/"
moz-do-not-send="true">etk.cct.lsu.edu</a>),
together with some of the ones used for the last ETK
workshop.</div>
<div><br>
</div>
<div>To answer your last question, I am not doing
anything specific with the output, I wanted to get 3D
data to see if that could help me visualise the output
of the examples I did with the WaveToyX thorn.</div>
<div><br>
</div>
<div>Unfortunately I am not familiar with SILO, so I
tried to use the 1D .tsv files, but they only provide
the values in a slice (for example the wave as a
function of x, for y=z=0), but I wanted to create a 3D
plot similar to the one found in the
CreatingANewThorn-WaveEqn notebook from the tutorial
server (I leave a screenshot attached), that is why I
thought of outputting 3D.</div>
<div><br>
</div>
<div>To use SILO files I understand that one has to have
VisIt installed, however when I wanted to install it
in the tutorial server via terminal, I got the error
that I am not allowed to install software, which I
suppose makes sense.</div>
<div><br>
</div>
<div>In principle all I want to do is experiment with
the WaveToyX thorn (and the other examples, like <span
style="caret-color: rgb(0, 0, 0);">SpacetimeWaveToyX
or Flux</span><span
style="caret-color: rgb(0, 0, 0);">WaveToyX</span>),
changing parameters and see how things behave, but I
am struggling a lot with the visualisation part. Do
you have any recommendations that I could implement in
the environment of the ETK Tutorial server? </div>
<div><br>
</div>
<div>Thanks in advance.</div>
<div><br>
</div>
<div>Best regards,</div>
<div><br>
</div>
<div>Javiera H.M.</div>
<div><br>
</div>
<div><span id="cid:0AD95A8F-4914-48B6-ADF0-8B0919BB8DFD"><Screen
Shot 2025-06-30 at 17.12.42 p.m..png></span></div>
<div><br>
<blockquote type="cite">
<div>El 30.06.2025, a las 16:45, Erik Schnetter
<a class="moz-txt-link-rfc2396E" href="mailto:schnetter@gmail.com"><schnetter@gmail.com></a> escribió:</div>
<br class="Apple-interchange-newline">
<div>
<meta http-equiv="content-type"
content="text/html; charset=UTF-8">
<div
style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Javiera
<div><br>
</div>
<div>I recommend using 3D output in the way
others are. CarpetX supports many parameters,
but not all parameter combinations are well
tested, or are intended for production runs.</div>
<div><br>
</div>
<div>(1, 2) Yes, there are two ways of 3D ASCII
(tsv) output. This is very slow and is thus
only intended for debugging. Therefore it
doesn't have all the features needed for
comfortable output in production runs.</div>
<div><br>
</div>
<div>(3) Either OpenPMD or Silo output are the
preferred ways for production runs. These
formats are also supported by post-processing
and visualization tools. These are not file
formats, but they only describe how the
metadata are arranged (i.e. what names the
attributes have) in the output files. The
actual file formats are ADIOS2 (preferred,
faster) or HDF5. OpenPMD uses ADIOS2 by
default, Silo uses HDF5 by default.</div>
<div><br>
</div>
<div>I do not know why the OpenPMD/HDF5 output
is not working. The error message doesn't show
enough detail.</div>
<div><br>
</div>
<div>If you want HDF5 output then I recommend
using Silo. This will produce an HDF5 file.
I'm not sure that's what you want because,
whatever you are going to do with the file,
you will need to understand the metadata in
the file, and thus that tool or script will
need to understand either the OpenMPD or Silo
layout. Otherwise your HDF5 will look like a
bag of 3D arrays, each array describing a
Fortran array, and it will be very difficult
to find out which component of which variable
and which time step on which refinement level
is stored in what array: That's what the
metadata describes.</div>
<div><br>
</div>
<div>On the other hand, if you want to have an
easy way to read the file, then you could use
e.g. the Julia or Python of C++ bindings of
the OpenMPD library, and you then wouldn't
need to care whether the low-level file format
is ADIOS2 or HDF5.</div>
<div><br>
</div>
<div>What do you want to do with the 3D output?</div>
<div><br>
</div>
<div>-erik<br id="lineBreakAtBeginningOfMessage">
<div><br>
<blockquote type="cite">
<div>On Jun 27, 2025, at 12:54, Javiera
Hernández Morales
<a class="moz-txt-link-rfc2396E" href="mailto:javihernandezm@posteo.net"><javihernandezm@posteo.net></a> wrote:</div>
<br class="Apple-interchange-newline">
<div>
<meta http-equiv="content-type"
content="text/html; charset=UTF-8">
<div
style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi
all,
<div><br>
</div>
<div>I am starting to learn the use of
CarpetX and for this I started using
the WaveToyX thorn. I wanted to ask
for guidance for three problems that
I have encountered so far, all of
them related to the output data:</div>
<div><br>
</div>
<div>1) I wanted to get 3D data, for
example in .tsv format. Here I
realised that there is an ambiguous
definition in the documentation for
the parameter “out_tsv”, which in
section 12.1 it says to control TSV
output and have default value “yes”,
but in section 14 it says to control
the 3D output in TSV and have
default value “no”. This last
behaviour is the one that I
encounter when running the
parfiles. </div>
<div><br>
</div>
<div>2) When I set up “<font>out_tsv"
to “yes” and “out_tsv_every” to a
number, for example = 16, I get 1D
output every 16 iterations, but 3D
output in every iteration,
therefore I suspect
that “out_tsv_every” is only
controlling the frequency of the
1D output, and I cannot find a way
to control the frequency of 3D
output.</font></div>
<div><font><br>
</font></div>
<div><font>3) I attempted to output
data in HDF5 format but I did not
succeed. I first set the parameter
“openpmd_format” to “HDF5” and
also set “out_openpmd_vars” to the
variables that I wanted, but I got
an error in the first iteration:</font></div>
<div><font><br>
</font></div>
<div>
<pre class="code highlight" lang="c"
style="caret-color: rgb(0, 0, 0);"><span
class="n">INFO</span> <span
class="p">(</span><span class="n">CarpetX</span><span
class="p">)</span><span class="o">:</span> <span
class="n">OutputGH</span><span
class="o">:</span> <span class="n">iteration</span> <span
class="mi">0</span><span class="p">,</span> <span
class="n">time</span> <span
class="mi">0</span><span class="p">.</span><span
class="mo">000000</span><span
class="p">,</span> <span class="n">run</span> <span
class="n">time</span> <span
class="mi">1</span> <span class="n">s</span>
<span class="n">INFO</span> <span class="p">(</span><span class="n">CarpetX</span><span
class="p">)</span><span class="o">:</span> <span
class="n">OutputOpenPMD</span><span
class="p">...</span>
<span class="n">INFO</span> <span class="p">(</span><span class="n">CarpetX</span><span
class="p">)</span><span class="o">:</span> <span
class="n">Creating</span> <span
class="n">openPMD</span> <span
class="n">object</span><span
class="p">...</span>
<span class="n">INFO</span> <span class="p">(</span><span class="n">CarpetX</span><span
class="p">)</span><span class="o">:</span> <span
class="n">options</span><span
class="o">:</span>
<span class="p">{</span>
<span class="s">"adios2"</span><span class="o">:</span> <span
class="p">{</span>
<span class="s">"dataset"</span><span class="o">:</span> <span
class="p">{</span>
<span class="s">"operators"</span><span class="o">:</span> <span
class="p">[</span>
<span class="p">]</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="p">[</span><span class="n">et</span><span class="o">-</span><span
class="n">juphub</span><span
class="o">:</span><span class="mi">699479</span><span
class="p">]</span> <span class="o">***</span> <span
class="n">An</span> <span class="n">error</span> <span
class="n">occurred</span> <span
class="n">in</span> <span class="n">MPI_Comm_create_keyval</span>
<span class="p">[</span><span class="n">et</span><span class="o">-</span><span
class="n">juphub</span><span
class="o">:</span><span class="mi">699479</span><span
class="p">]</span> <span class="o">***</span> <span
class="n">reported</span> <span
class="n">by</span> <span class="n">process</span> <span
class="p">[</span><span class="mi">211877889</span><span
class="p">,</span><span class="mi">2</span><span
class="p">]</span>
<span class="p">[</span><span class="n">et</span><span class="o">-</span><span
class="n">juphub</span><span
class="o">:</span><span class="mi">699479</span><span
class="p">]</span> <span class="o">***</span> <span
class="n">on</span> <span class="n">communicator</span> <span
class="n">MPI_COMM_WORLD</span>
<span class="p">[</span><span class="n">et</span><span class="o">-</span><span
class="n">juphub</span><span
class="o">:</span><span class="mi">699479</span><span
class="p">]</span> <span class="o">***</span> <span
class="n">MPI_ERR_ARG</span><span
class="o">:</span> <span class="n">invalid</span> <span
class="n">argument</span> <span
class="n">of</span> <span class="n">some</span> <span
class="n">other</span> <span
class="n">kind</span>
<span class="p">[</span><span class="n">et</span><span class="o">-</span><span
class="n">juphub</span><span
class="o">:</span><span class="mi">699479</span><span
class="p">]</span> <span class="o">***</span> <span
class="n">MPI_ERRORS_ARE_FATAL</span> <span
class="p">(</span><span class="n">processes</span> <span
class="n">in</span> <span class="n">this</span> <span
class="n">communicator</span> <span
class="n">will</span> <span
class="n">now</span> <span class="n">abort</span><span
class="p">,</span>
<span class="p">[</span><span class="n">et</span><span class="o">-</span><span
class="n">juphub</span><span
class="o">:</span><span class="mi">699479</span><span
class="p">]</span> <span class="o">***</span> <span
class="n">and</span> <span class="n">potentially</span> <span
class="n">your</span> <span
class="n">MPI</span> <span class="n">job</span><span
class="p">)</span>
<span class="p">[</span><span class="n">et</span><span class="o">-</span><span
class="n">juphub</span><span
class="o">:</span><span class="mi">699473</span><span
class="p">]</span> <span class="n">PMIX</span> <span
class="n">ERROR</span><span
class="o">:</span> <span class="n">UNREACHABLE</span> <span
class="n">in</span> <span class="n">file</span> <span
class="p">..</span><span class="o">/</span><span
class="p">..</span><span class="o">/</span><span
class="p">..</span><span class="o">/</span><span
class="n">src</span><span class="o">/</span><span
class="n">server</span><span
class="o">/</span><span class="n">pmix_server</span><span
class="p">.</span><span class="n">c</span> <span
class="n">at</span> <span class="n">line</span> <span
class="mi">2193</span>
<span class="p">[</span><span class="n">et</span><span class="o">-</span><span
class="n">juphub</span><span
class="o">:</span><span class="mi">699473</span><span
class="p">]</span> <span class="mi">3</span> <span
class="n">more</span> <span
class="n">processes</span> <span
class="n">have</span> <span
class="n">sent</span> <span
class="n">help</span> <span
class="n">message</span> <span
class="n">help</span><span class="o">-</span><span
class="n">mpi</span><span class="o">-</span><span
class="n">errors</span><span
class="p">.</span><span class="n">txt</span> <span
class="o">/</span> <span class="n">mpi_errors_are_fatal</span>
<span class="p">[</span><span class="n">et</span><span class="o">-</span><span
class="n">juphub</span><span
class="o">:</span><span class="mi">699473</span><span
class="p">]</span> <span class="n">Set</span> <span
class="n">MCA</span> <span class="n">parameter</span> <span
class="s">"orte_base_help_aggregate"</span> <span
class="n">to</span> <span class="mi">0</span> <span
class="n">to</span> <span class="n">see</span> <span
class="n">all</span> <span class="n">help</span> <span
class="o">/</span> <span class="n">error</span> <span
class="n">messages</span>
<span class="n">Simfactory</span> <span class="n">Done</span> <span
class="n">at</span> <span class="n">date</span><span
class="o">:</span> <span class="n">Thu</span> <span
class="mi">26</span> <span class="n">Jun</span> <span
class="mi">2025</span> <span
class="mi">09</span><span class="o">:</span><span
class="mi">19</span><span class="o">:</span><span
class="mi">08</span> <span class="n">AM</span> <span
class="n">UTC</span></pre>
<pre class="code highlight" lang="c"><font
face="Helvetica"><span
style="white-space: normal;">And I did not know how to move on from there.</span></font></pre>
<pre class="code highlight" lang="c"><font
face="Helvetica"><span
style="caret-color: rgb(0, 0, 0); white-space: normal;">I am working on the ETK Tutorial server, in case that is important.</span></font></pre>
<pre class="code highlight" lang="c"><font
face="Helvetica"><span
style="white-space: normal;">Thanks in advance to anyone who took the time to read until here, I will be looking forward to any piece of advice :)</span></font></pre>
<pre class="code highlight" lang="c"><font
face="Helvetica"><span
style="caret-color: rgb(0, 0, 0); white-space: normal;">Best,</span></font></pre>
<pre class="code highlight" lang="c"><font
face="Helvetica"><span
style="caret-color: rgb(0, 0, 0); white-space: normal;">Javiera H.M. </span></font></pre>
</div>
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