[Users] Problems with output in CarpetX

Wed Jul 2 09:41:56 CDT 2025

Hi Javiera (and all),

Last year, we added experimental support
<https://github.com/Sbozzolo/kuibit/commit/49c86debf1b6edbf052ba9fbdc409a0c2f7efc8e>
to reading OpenPMD files to kuibit <https://github.com/Sbozzolo/kuibit>.

I haven't tried it for anything more than toy data, but the example we were
working with is precisely the output generated with WaveToyX, as seen here
<https://github.com/Sbozzolo/kuibit/tree/master/tests/grid_functions/batman.it00000000.bp4>
.

You could give it a try. kuibit will read the data and represent it with
its HierarchicalGridData data structure, which can be sampled to a uniform
grid and visualized with matplotlib (or you can slice it a given dimension
to get a 1D/2D cut and visualize those).

Best,
Gabriele

On Tue, Jul 1, 2025 at 8:49 AM Steven Brandt <sbrandt at cct.lsu.edu> wrote:

> I could add Visit. I included it on etk1 for the workshop. The only
> catch is it has to run headless.
>
> --Steve
>
> On 6/30/2025 12:20 PM, Roland Haas wrote:
> > Hello all,
> >
> > There's no VisIt instance installed on the tutorial server (it only
> > provides an interface using jupyter notebooks, no X11 server access).
> >
> > I believe Steve has written some Python code to visualize CarpetX data.
> >
> > Yours,
> > Roland
> >
> >> [CAUTION: Non-UBC Email]
> >>
> >> 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 <
> javihernandezm at 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 <schnetter at 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 <
> javihernandezm at 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.
> >>>>> _______________________________________________
> >>>>> Users mailing list
> >>>>> Users at einsteintoolkit.org
> >>>>> http://lists.einsteintoolkit.org/mailman/listinfo/users
> >>>>
> >>>
> >
> > Yours,
> > Roland
> >
> _______________________________________________
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> Users at einsteintoolkit.org
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>
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