On Thu, Jan 19, 2012 at 5:19 PM, Mohamad M. Nasr-Azadani <mmnasr at gmail.com>wrote:
> Thanks Mat, > Use the DA coordinate mechanism and you can get the coordinates as a > parallel Vec. > > well, that won't be working for me since although I use one DA and the > parallel vectors derived from same DA, yet I am using staggered grid > formulation. So, there the coordinates could be different for different > vectors. > Is there any other way around this ? > I do not understand what you mean, be more specific. Matt > On Thu, Jan 19, 2012 at 6:59 AM, Matthew Knepley <knepley at gmail.com>wrote: > >> 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 >> > > -- 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/20120119/06f4388f/attachment.htm>
