On Thu, Jan 19, 2012 at 2:50 AM, Mohamad M. Nasr-Azadani <mmnasr at gmail.com>wrote:
> Hi guys, > > I have compiled petsc to use HDF5 package. > > I like to store the data from a parallel vector(s) (obtained from > structured DA in 3 dimensions) to file using VecView() in conjunction with > PetscViewerHDF5Open(). > > I followed the example here > http://www.mcs.anl.gov/petsc/petsc-current/src/dm/examples/tutorials/ex10.c.html > and everything looks fine. > > However, I had a couple questions: > > 1- When I am done writing the parallel vector obtained from the DA (and > PETSC_COMM_WORLD), > > // Create the HDF5 viewer > PetscViewerHDF5Open<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerHDF5Open.html#PetscViewerHDF5Open> > (PETSC_COMM_WORLD<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PETSC_COMM_WORLD.html#PETSC_COMM_WORLD> > ,"gauss.h5",FILE_MODE_WRITE,&H5viewer); > // Write the H5 file > > VecView<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecView.html#VecView> > (gauss,H5viewer); > // Cleaning stage > PetscViewerDestroy<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerDestroy.html#PetscViewerDestroy> > (&H5viewer); > > how can I add data that are just simple 1-D numbers stored on local > arrays. > Easier said, I would like to add the structured grid coordinates (first > all x's, then all y's, and then all z's) at the end (or to the beginning) > of each data (*.h5) file. But the grid coordinates are stored locally on > each machine and not derived from any parallel vectors or DA. I was > thinking about creating vectors and viewers using PETSC_COMM_SELF but i am > not sure if that is the right approach since that vector is created on all > processors locally. > Use the DA coordinate mechanism and you can get the coordinates as a parallel Vec. > 2- When using VecView() and HDF5 writer, what is the status of data > compression? > The reason that I am asking is that, I used the same example above and > comparing two files saved via two different PetscViewers, i.e. (just) > Binary and HDF5 (Binary) the size is not reduced in the (*.h5) case. > In fact, it is slightly bigger than pure binary file!! > Is there any command we have to set in Petsc to tell HDF5 viewer to use > data compression? > We do not support it. We are happy to take patches that enable this. Thanks, Matt > Thanks for your patience, > Best, > Mohamad > > > > > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120119/186d4d8f/attachment-0001.htm>
