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 <[email protected]> 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 < > [email protected]> 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 <[email protected]> > 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 < > [email protected]> 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 > >>>>> [email protected] > >>>>> http://lists.einsteintoolkit.org/mailman/listinfo/users > >>>> > >>> > > > > Yours, > > Roland > > > _______________________________________________ > Users mailing list > [email protected] > http://lists.einsteintoolkit.org/mailman/listinfo/users >
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