[petsc-users] HDF5 corruption

[Adrian Croucher]

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 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...

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