[Users] Problems with output in CarpetX

Steven Brandt sbrandt at cct.lsu.edu
Wed Jul 2 13:50:11 CDT 2025


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 <sbrandt at cct.lsu.edu> 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
>     <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>
>     <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.
>     >>>>> _______________________________________________
>     >>>>> Users mailing list
>     >>>>> Users at einsteintoolkit.org
>     >>>>> http://lists.einsteintoolkit.org/mailman/listinfo/users
>     >>>>
>     >>>
>     >
>     > Yours,
>     > Roland
>     >
>     _______________________________________________
>     Users mailing list
>     Users at einsteintoolkit.org
>     http://lists.einsteintoolkit.org/mailman/listinfo/users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.einsteintoolkit.org/pipermail/users/attachments/20250702/f6523d24/attachment.htm>


More information about the Users mailing list