On Thu, Jul 15, 2021 at 8:20 AM Matteo Semplice < [email protected]> wrote:
> > Il 15/07/21 14:15, Matthew Knepley ha scritto: > > 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%7Cfb0d540c87a64e4ea51d08d9478a4e9b%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637619481622608977%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=sOQskFoMTHdOwjOec0d9npdw%2BiAVbar1SXBuU%2BH8xKc%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%7Cfb0d540c87a64e4ea51d08d9478a4e9b%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637619481622618934%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=akFyfHE4BULSscevnO0MxjMhEByT3USoJFQKsikJSzg%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! > > On my machine I am compiling from the git repo with --download-hdf5, so I > have some control, but on clusters I prefer to use the available petsc. > Is there a simple way to check which implementation is begin used in a run? > You have to check the configure output. We never gather everything to one process, so you should not have to worry about it. 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/>
