[petsc-users] storing many petsc objects in a single file

[Storm Weiner]

Thanks for the advice.

Barry,  did you mean to add more information after that ":"?

HDF5 sounds like a great option for my application,  but I don't see much
information about how it interfaces with PETSc.   All I can find are the
doc pages for a few viewer routines.  Do you have a link to a more detailed
description?

Specifically,  I'd like to know if PETSc has automatically configured HDF5
datatypes and how to access them.  And if there is a standard way to make
compound data types derived from PETSc datatypes.   In short,  how much do
I need to muck around in HDF5 myself,  and how much can I let PETSc take
care of?

-Storm

On Nov 26, 2017 5:49 AM, "Smith, Barry F." <bsmith at mcs.anl.gov> wrote:

>
>   Storm,
>
>    Specifically for TS there is an abstract object called TSTrajectory
> which is a way to store histories of simulations (it is used by TSAdjoint
> but also useable for other purposes). It has several ways to store
> histories and more can be added.
>
>    One draw back to saving everything in PETSc binary in one file is that
> we don't have simple support for random access of a particular vector.
>
>    You can also store to HDF5 format and some others that may be useful
> for you:
>
>
>    Barry
>
>
> > On Nov 26, 2017, at 2:27 AM, Jose E. Roman <jroman at dsic.upv.es> wrote:
> >
> >
> >
> >> El 26 nov 2017, a las 2:25, Storm Weiner <stormweiner at berkeley.edu>
> escribió:
> >>
> >> Hey there,
> >>
> >> For simulations, its useful to store the history as a series of state
> vectors.  For simulations with many time-steps it can get annoying to store
> each state vector as a separate file.  It would be useful if there were
> some way to manage a database of petsc vectors.  To save the current
> time-step, append the state vector to the database. To restart a
> simulation, load the corresponding state vector out of the database.
> >>
> >> Is there a standard way to do this in PETSc?
> >>
> >> Thanks,
> >> Storm
> >
> > In the command line, you can use the “append” option for the viewer. For
> instance in the MFN solver in SLEPc you can do this:
> >   $ ./ex23 -mfn_view_solution binary:vectors.bin::append
> > It will save one vector in each call to MFNSolve(), and all vectors will
> be stored in the same file ‘vectors.bin’.
> >
> > Alternatively, in the source code you can use PetscViewerBinaryOpen() to
> open the viewer, then save as many vectors as you want with VecView(), and
> finally close the file with PetscViewerDestroy(). Use VecLoad() to load the
> vectors.
> >
> > Jose
> >
>
>
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