[Users] Problems with output in CarpetX

Tue Jul 1 10:48:46 CDT 2025

The Tutorial server has the full current release of the ETK, including 
SILO and OpenPMD.

--Steve

On 6/30/2025 11:53 AM, Erik Schnetter wrote:
> 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 
>> <javihernandezm at posteo.net> 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 <schnetter at gmail.com> 
>>> 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 
>>>> <javihernandezm at posteo.net> 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.
>>>> _______________________________________________
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>>>> Users at einsteintoolkit.org
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>>>
>>
>
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