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

[Abhishek G.S.]

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)

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

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?

4) Can I have multiple vectors attached to the DM by DMCreateGlobalVector()
even though I created the DMDA using dof=1.

thanks,
Abhishek
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