On Mon, Sep 1, 2014 at 9:02 AM, Åsmund Ervik <[email protected]> wrote:
> On 01. sep. 2014 14:02, Matthew Knepley wrote: > > On Mon, Sep 1, 2014 at 6:57 AM, Åsmund Ervik <[email protected]> > wrote: > > > >> > >> No, I am not able to, that is why I switched to "--with-hdf5-dir=". Like > >> I said in the first email, the version of HDF5 (1.8.10) that ships with > >> PETSc 3.5.1 does not compile on my machine. This is apparently a known > >> bug that was fixed upstream, cf. > >> > >> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=711777 > >> > >> This is the reason why I asked whether I can somehow tell > >> "--download-hdf5" to download a more recent version. 1.8.11 should do > it. > > > > > > People who leave commented out code in there should be tarred, feathered, > > and run out of town on a rail. You can just go in and delete that line, > and > > then > > reconfigure. It will use the source that is already downloaded. > > Okay, I also had to do the same for two lines in > h5dump/h5dump_ddl.c:1344 and then I was able to configure with > "--download-hdf5". I am now able to run vec/ex10.c using HDF5 with success! > > Thanks a lot :) (and double on the tar and feathers for people who use > C++ comments in C code). > > After some tinkering I am now able to produce 3D plots of scalar fields > from my code, and this looks good in Visit and in Tec360 Ex. However, it > only works for scalars where only a single DOF is associated to a DMDA. > Vector valued fields don't work either. But I am able to save two > separate scalar fields to the same HDF5 file, as long as both are the > single DOF associated to a DMDA. > It seems like these programs expect a different organization than we use for multiple DOF. Do you know what they want? > Also, if I call PetscViewerHDF5IncrementTimestep() the resulting HDF5 > files can no longer be visualized even for the scalars, both Tec360 and > Visit give error messages. > HDF5 is a generic format, and programs like Visit and Tec360 assume some organization inside. For time we just add an array dimension, but they might do something else. I recommend looking at bin/pythonscripts/petsc_ge_xdmf.py, which creates .xdmf to describe our HDF5 organization. Thanks, Matt Any hints on how to get full-fledged HDF5 files with timestep and > vector/multiple scalar support? > > Thanks again, > Åsmund > > -- 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
