Hi all, I used the code from the tutorials from the last workshop that use kuibit and now I can indeed visualise the results.
Thanks a lot for all the help! :) Best, Javiera > El 02.07.2025, a las 20:50, Steven Brandt <[email protected]> escribió: > > 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 <[email protected] >> <mailto:[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] <mailto:[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/> <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] >>> >>>> <mailto:[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] <mailto:[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] <mailto:[email protected]> >>> >>>>> http://lists.einsteintoolkit.org/mailman/listinfo/users >>> >>>> >>> >>> >>> > >>> > Yours, >>> > Roland >>> > >>> _______________________________________________ >>> Users mailing list >>> [email protected] <mailto:[email protected]> >>> http://lists.einsteintoolkit.org/mailman/listinfo/users
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