[Users] Problems with output in CarpetX
Steven Brandt
sbrandt at cct.lsu.edu
Wed Jul 2 13:50:11 CDT 2025
Some of the tutorials on ETK1 use Kuibit to plot data from CarpetX runs,
including the basic one on building and running with the ET.
--Steve
On 7/2/2025 9:41 AM, Gabriele Bozzola wrote:
> 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>
> <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
> >
> _______________________________________________
> Users mailing list
> Users at einsteintoolkit.org
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>
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