The Tutorial server has the full current release of the ETK, including
SILO and OpenPMD.
--Steve
On 6/30/2025 11:53 AM, Erik Schnetter wrote:
Javiera
Unfortunately I don't recall what software is installed on the ETK
tutorial server... I'm sure someone else can help us out here?
-erik
On Jun 30, 2025, at 12:17, Javiera Hernández Morales
<javihernand...@posteo.net> wrote:
Hi Erik,
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 (etk.cct.lsu.edu
<http://etk.cct.lsu.edu/>), together with some of the ones used for
the last ETK workshop.
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.
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.
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.
In principle all I want to do is experiment with the WaveToyX thorn
(and the other examples, like SpacetimeWaveToyX or FluxWaveToyX),
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?
Thanks in advance.
Best regards,
Javiera H.M.
<Screen Shot 2025-06-30 at 17.12.42 p.m..png>
El 30.06.2025, a las 16:45, Erik Schnetter <schnet...@gmail.com>
escribió:
Javiera
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.
(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.
(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.
I do not know why the OpenPMD/HDF5 output is not working. The error
message doesn't show enough detail.
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.
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.
What do you want to do with the 3D output?
-erik
On Jun 27, 2025, at 12:54, Javiera Hernández Morales
<javihernand...@posteo.net> wrote:
Hi all,
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:
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.
2) When I set up “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.
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:
INFO (CarpetX): OutputGH: iteration 0, time 0.000000, run time 1 s
INFO (CarpetX): OutputOpenPMD...
INFO (CarpetX): Creating openPMD object...
INFO (CarpetX): options:
{
"adios2": {
"dataset": {
"operators": [
]
}
}
}
[et-juphub:699479] *** An error occurred in MPI_Comm_create_keyval
[et-juphub:699479] *** reported by process [211877889,2]
[et-juphub:699479] *** on communicator MPI_COMM_WORLD
[et-juphub:699479] *** MPI_ERR_ARG: invalid argument of some other kind
[et-juphub:699479] *** MPI_ERRORS_ARE_FATAL (processes in this communicator
will now abort,
[et-juphub:699479] *** and potentially your MPI job)
[et-juphub:699473] PMIX ERROR: UNREACHABLE in file
../../../src/server/pmix_server.c at line 2193
[et-juphub:699473] 3 more processes have sent help message help-mpi-errors.txt
/ mpi_errors_are_fatal
[et-juphub:699473] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages
Simfactory Done at date: Thu 26 Jun 2025 09:19:08 AM UTC
And I did not know how to move on from there.
I am working on the ETK Tutorial server, in case that is important.
Thanks in advance to anyone who took the time to read until here, I
will be looking forward to any piece of advice :)
Best,
Javiera H.M.
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