[petsc-users] VecView DMDA and HDF5 - Unable to write out files properly

Thu Oct 14 10:58:00 CDT 2021

Thanks, Matthew for the clarification/ suggestion.
Thanks, Matteo for the scripts, I'll give this a try and get back with an
update

On Thu, 14 Oct 2021 at 19:57, Matthew Knepley <knepley at gmail.com> wrote:

> On Thu, Oct 14, 2021 at 9:21 AM Matteo Semplice <
> matteo.semplice at uninsubria.it> wrote:
>
>>
>> Il 14/10/21 14:37, Matthew Knepley ha scritto:
>>
>> On Wed, Oct 13, 2021 at 6:30 PM Abhishek G.S. <gsabhishek1ags at gmail.com>
>> wrote:
>>
>>> Hi,
>>> I need some help with getting the file output working right.
>>>
>>> I am using a DMDACreate3D to initialize my DM. This is my write function
>>>
>>> void write(){
>>> PetscViewer viewer;
>>>
>>> PetscViewerHDF5Open(PETSC_COMM_WORLD,filename.c_str(),FILE_MODE_WRITE,&viewer);
>>> DMDAVecRestoreArray(dm,global_vector,global_array)
>>> VecView(global_vec, viewer);
>>> DMDAVecGetArray(dm,global_vector,global_array);
>>> PetscViewerDestroy(&viewer);
>>> }
>>>
>>> 1) I have 2 PDE's to solve. Still, I went ahead creating a single DM
>>> with dof=1 and creating two vectors using the DMCreateGlobalVector(). I
>>> want to write the file out periodically.  Should I perform
>>> DMDAVecRestoreArray and DMDAVecGetArray every time is write out the
>>> global_vector? (I know that it is just indexing the pointers and there is
>>> no copying of values. But I am not sure)
>>>
>>
>> I don't think you need the Get/RestoreArray() calls here.
>>
>>
>>> 2) I am writing out to HDF5 format. I see that the vecview is supposed
>>> to reorder the global_vector based on the DM. However, when I read the H5
>>> files, I get an error on ViSIT and my output image becomes a 1D image
>>> rather than a 2D/3D. What might be the reason for this ?.
>>> Error Msg : "In domain 0, your zonal variable "avtGhostZones" has 25600
>>> values, but it should have 160.  Some values were removed to ensure VisIt
>>> runs smoothly"
>>> I was using a 160x160x1 DM
>>>
>>
>> I do not believe we support HDF5 <--> Visit/Paraview for DMDA. The
>> VecView() is just writing out the vector as a linear array without mesh
>> details. For
>> interfacing with the visualization, I think we use .vtu files. You should
>> be able to get this effect using
>>
>>   VecViewFromOptions(global_vec, NULL, "-vec_view");
>>
>> in your code, and then
>>
>>   -vec_view vtk:sol.vtu
>>
>> on the command line.
>>
>> Hi.
>>
>> If you want to stick with HDF5, you can also write a XDMF file with the
>> grid information and open that in Paraview.
>>
>> I am attaching some routines that I have written to do that in a solver
>> that deals with a time dependent PDE system with 2 variables; with them I
>> end up with a single XDMF file that Paraview can load and which contains
>> references to all timesteps in my simulations, with each timestep being
>> contained in an HDF5 file on its own. The idea is to call writeDomain at
>> the beginning of the simulation, writeHDF5 for each timestep that I want to
>> save and writeSimulationXDMF at the end. (Warning: 3D is in use, while 2D
>> ia almost untested...)
>>
>> It's not the optimal solution since (1) all timesteps could be in the
>> same HDF5 and (2) in each HDF5 i write the vectors separately and it would
>> be better to dump the entire data in one go and interpret them as a
>> Nx*Ny*Nz*Nvariables data from the XDMF. Nevertheless they might be a
>> starting point for you if you wan to try this approach.
>>
>> You can have HDF5 put the vectors in a single array with a time dimension
> now. Then you just alter the xdmf to point into that array. I do this
> with the unstructured code.
>
>   Thanks,
>
>      Matt
>
>> Matteo
>>
>>
>>
>>> 3) I tried using the "petsc_gen_xdmf.py" to generate the xdmf files for
>>> use in Paraview. Here the key ["viz/geometry"] is missing. The keys present
>>> in the output H5 file are just the two vectors I am writing and has no info
>>> about mesh. Isn't this supposed to come automatically since the vector is
>>> attached to the DM? How do I sort this out?
>>>
>>
>> This support is for unstructured grids, DMPlex and DMForest.
>>
>>
>>> 4) Can I have multiple vectors attached to the DM by
>>> DMCreateGlobalVector() even though I created the DMDA using dof=1.
>>>
>>
>> Yes.
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> thanks,
>>> Abhishek
>>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=04%7C01%7Cmatteo.semplice%40uninsubria.it%7Cf27a34f639784d0231c708d98f0f7279%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637698118789688898%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Xb8nyv7BIl6zSBbbLFkQzluIF8s%2BOLwUQeVfjtr3q4k%3D&reserved=0>
>>
>> --
>> ---
>> Professore Associato in Analisi Numerica
>> Dipartimento di Scienza e Alta Tecnologia
>> Università degli Studi dell'Insubria
>> Via Valleggio, 11 - Como
>>
>>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
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