[petsc-users] HDF5 corruption

[Matthew Knepley]

On Wed, Oct 6, 2021 at 11:05 PM Adrian Croucher <a.croucher at auckland.ac.nz>
wrote:

> hi,
>
> One of the users of my PETSc-based code has reported that HDF5 output
> files can be corrupted and unusable if e.g. the run is killed. I've just
> done a bit of reading about this and it appears to be a known issue with
> HDF5.
>
> Some people suggest flushing the HDF5 file periodically to help prevent
> data loss. I had a look at PetscViewerFlush() but it doesn't seem to be
> implemented for the HDF5 viewer- is that correct?
>
> I am currently calling PetscViewerHDF5Open() once at the start of the
> run and closing it at the end. Some other people suggest doing this
> before and after each write instead. Is there likely to be a significant
> performance penalty in doing that?
>

I don't think so. This is what I did on another project to guard against the
HDF5 issue.


> I gather HDF5 journaling has been promised for a while to get around
> this problem but as far as I can see it hasn't materialised yet...
>

Don't worry. It will happen right after fusion power and world peace :)

  Thanks,

      Matt


> Regards, Adrian
>
> --
> Dr Adrian Croucher
> Senior Research Fellow
> Department of Engineering Science
> University of Auckland, New Zealand
> email: a.croucher at auckland.ac.nz
> tel: +64 (0)9 923 4611
>
>

-- 
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/>
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