[petsc-users] Load Vec from 1D HDF5 dataset MATT READ THIS EMAIL!

[Barry Smith]

  Hakon,

    I have pushed to the branch barry/feature-hdf5-flexible-initial-dimension and next the change so that Vecs and Vecs obtained from DMCreateGlobalVector() with a DMDA will NOT have the extra dimension if BS == 1. To add that extra dimension even when bs == 1 with VecView() or to handle a file with that extra dimension with VecLoad() one must call PetscViewerHDF5SetBaseDimension2() or -viewer_hdf5_base_dimension2 true

   Please try it out and let me know if you have any trouble

   Thanks

  Barry

  Matt,

   Scream as much as you want but adding that extra dimension automatically is not intuitive so it cannot be the default. 

> On Mar 25, 2015, at 10:36 AM, Håkon Strandenes <haakon at hakostra.net> wrote:
> 
> Did you come to any conclusion on this issue?
> 
> Regards,
> Håkon
> 
> On 20. mars 2015 22:02, Håkon Strandenes wrote:
>> On 20. mars 2015 20:48, Barry Smith wrote:
>>> Why is 1 dimension a special case that is not worthy of its own
>>> format? The same thing would hold for 2d and 3d. One could then argue
>>> that we should have a single six dimensional format for the files for
>>> all vectors that PETSc produces. Then a 1d problem has five of the
>>> dimensions being 1.
>> 
>> This is a very good point, and support my view.
>> 
>> Let me come with two very simple example cases:
>> 
>> 
>> Case 1:
>> Create a list of grid points in an external preprocessor for the purpose
>> of loading this into a Vec later:
>> 
>>   x = np.linspace(0.0, 1.0, num=21)
>>   f.create_dataset('/MESH/nodes/x', data=x)
>> 
>> vs.
>> 
>>   x = np.linspace(0.0, 1.0, num=21)
>>   x = x.reshape((21,1))
>>   f.create_dataset('/MESH/nodes/x', data=x)
>> 
>> 
>> Case 2:
>> Read three Vecs written to disk by PETSc, and calculate total "bounding
>> box volume" of the grid:
>> 
>>   g = h5py.File('grid.h5', 'r')
>>   x = g['/MESH/nodes/x']
>>   y = g['/MESH/nodes/y']
>>   z = g['/MESH/nodes/z']
>>   Vol = (xp[-1] - xp[0])*(yp[-1] - yp[0])*(zp[-1] - zp[0])
>> 
>> vs.
>> 
>>   g = h5py.File('grid.h5', 'r')
>>   x = g['/MESH/nodes/x'][:,0]
>>   y = g['/MESH/nodes/y'][:,0]
>>   z = g['/MESH/nodes/z'][:,0]
>>   Vol = (x[-1] - x[0])*(y[-1] - y[0])*(z[-1] - z[0])
>> 
>> 
>> In both cases I think handling this extra, unnecessary dimension makes
>> the code less attractive. It's not that either way is difficult,
>> problematic or impossible, but it's just that 1D Vecs should intuitively
>> be 1D datasets, and not 2D, 3D or 6D. This seriously confused me for
>> quite a while until I figured this out, even after having written an
>> entire Navier-Stokes DNS solver using the PETSc library for everything
>> except time integration and filling these simple 1D coordinate arrays!
>> 
>> Regards,
>> Håkon