dolfin team mailing list archive

[Johan Hake <hake.dev@xxxxxxxxx>]

On 10/08/2012 10:49 AM, Garth N. Wells wrote:
> On Mon, Oct 8, 2012 at 9:21 AM, Johan Hake <hake.dev@xxxxxxxxx> wrote:
>> On 10/07/2012 02:44 PM, Garth N. Wells wrote:
>>> Thanks to good work by Chris Richardson, support for the XDMF output
>>> format with HDF5 data storage is available in the development version
>>> of DOLFIN. HDF5 must be installed ('apt-get install
>>> libhdf5-openmpi-dev' or 'apt-get install libhdf5-mpich-dev' for
>>> Debian/Ubuntu users) to use it. To write to an XDMF file, just do
>>>
>>>    file = File("foo.xdmf")
>>>    file << u
>>>
>>> XDMF files can be read by ParaView, and have the following advantages
>>> over the VTK format:
>>>
>>> - All output data is stored in a single file (even in parallel),
>>> rather than the (#num_time_steps x #num_processes) files for VTK XML
>>> files
>>>
>>> - For Functions, the Mesh is not stored at every time step. At present
>>> the Mesh data structure is hashed to detect changes, with a new Mesh
>>> written to file only when a change is detected. This may change in the
>>> future.
>>
>> Nice! How did you hash the mesh data? Just num_vertices/num_cells or a
>> more detailed one. Would be nice with a robust and fast routine for such
>> a computation.
>>
> 
> We're using to Boost to hash two a big data structures: (1) a vector
> holding all the coords and (2) a vectors holding all the connectivity.
> We need to check how expensive this is. There is also scope for
> optimisations of what we have.

Ok. I see that keeping data in standard libraries comes with some
benefits ;)

>>> - Output files are much small than uncompressed VTK files
>>>
>>> - Writing output files is faster (about 5x for meshes, at present)
>>>
>>> Please try it out and report any issues. Since HDF5 is an optional
>>> dependency, no demos have been set to use XDMF yet. Some options for
>>> adding XDMF output to the demos are
>>>
>>> 1) Fall-back to VTK/PVD format if XDMF is not available; or
>>> 2) Add support for writing ASCII data in the XDMF file if HDF5 is not available.
>>
>> I also see that there are no File::Type corresponding to HDF5 or xdmf.
>> Is this intentionally? Even if dolfin has not been compiled with HDF5
>> support we could include the enum and then issue an error?
>>
> 
> Thanks - I've made a fix and will push it shortly.

Great!

Johan

> Garth
> 
>> Johan
>>
>>> Garth
>>>
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>>