dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

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.

>> - 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.

Garth

> Johan
>
>> Garth
>>
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>