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 -- My email is as private as my paper mail. 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