On Thu, Jul 15, 2021 at 6:39 AM Matteo Semplice < [email protected]> wrote:
> > Il 12/07/21 17:51, Matthew Knepley ha scritto: > > On Mon, Jul 12, 2021 at 11:40 AM Matteo Semplice < > [email protected]> wrote: > >> Dear all, >> >> I am experimenting with hdf5+xdmf output. At >> https://www.xdmf.org/index.php/XDMF_Model_and_Format >> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.xdmf.org%2Findex.php%2FXDMF_Model_and_Format&data=04%7C01%7Cmatteo.semplice%40uninsubria.it%7Cb7db50b8974544e2f5ed08d9454ce429%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637617019536687302%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=gBEr%2BY1%2BD4Tw8u8oUdEiqJQgMmsHhqXAKr2Z9xBH8Do%3D&reserved=0> >> I read that "XDMF uses XML to store Light data and to describe the data >> Model. Either HDF5[3] >> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.hdfgroup.org%2FHDF5&data=04%7C01%7Cmatteo.semplice%40uninsubria.it%7Cb7db50b8974544e2f5ed08d9454ce429%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637617019536697248%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=8evP7yBnpwcrxdFeGdAo7PFNIDS7Xn1Q05pVMrHidH4%3D&reserved=0> >> or binary files can be used to store Heavy data. The data Format is stored >> redundantly in both XML and HDF5." >> >> However, if I call DMView(dmda,hdf5viewer) and then I run h5ls or h5stat >> on the resulting h5 file, I see no "geometry" section in the file. How >> should I write the geometry to the HDF5 file? >> >> Here below is what I have tried. >> > The HDF5 stuff is only implemented for DMPlex since unstructured grids > need to be explicitly stored. You can usually just define the structured > grid in the XML > without putting anything in the HDF5. We could write metadata so that the > XML could be autogenerated, but we have not done that. > > Thanks for the clarification. It shouldn't be hard to produce the XML from > my code. > > Just another related question: if I call VecView in parallel with the HDF5 > viewer, I get a single output file. Does this mean that data are gathered > by one process and written or it handles it smartly by coordinating the > output of all processes to a single file? > This is slightly more complicated than you would expect. We have two implementations, one which uses MPI-IO, and one which sends data from each process to 0, which writes it out. It turns out that MPI-IO is sometimes poorly supported or badly implemented, so you need the fallback. Thanks, Matt > Matteo > -- 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/>
