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