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 >> >
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