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

[Åsmund Ervik]

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.

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.

Any hints on how to get full-fledged HDF5 files with timestep and
vector/multiple scalar support?

Thanks again,
Åsmund

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