[petsc-users] Configure/make with "--download-hdf5" or "--with-hdf5-dir=" crashes

[Matthew Knepley]

On Mon, Sep 1, 2014 at 9:02 AM, Åsmund Ervik <asmund.ervik at ntnu.no> wrote:

> On 01. sep. 2014 14:02, Matthew Knepley wrote:
> > On Mon, Sep 1, 2014 at 6:57 AM, Åsmund Ervik <asmund.ervik at ntnu.no>
> 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
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