[petsc-users] Output portability, binary, HDF5, ascii

Arturo Fountain art.fountain at gmail.com
Thu Feb 18 15:58:56 CST 2010

Aha. Thanks for the head's up; I was unaware the Matlab could read
PETSc matrices; they certainly do not advertise this fact (at least
for our semi-ancient version 7.5.0) which is a shame!

For a 'real' application I would never want to use such an
intermediate step, but I only want to do so to create pictures for use
in papers.

Thanks again for the help,


On Thu, Feb 18, 2010 at 2:10 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> On Feb 18, 2010, at 2:35 PM, Arturo Fountain wrote:
>> Greetings:
>> I've been using the PETSc libraries for a few weeks now and am very
>> impressed with the software. Great work folks!
>> I'm writing with an issue I've been unable to work around. I'd like to
>> save output and import it into an external program (hdfview or matlab,
>> for example). Vectors are no problem to output but as mentioned at
>> https://lists.mcs.anl.gov/mailman/htdig/petsc-users/2010-January/005796.html,
>> this is not possible in PETSc for matrices.
>    This is an indirect way of doing but since PETSc can dump vectors and
> sparse matrices in PETSc format rapidly and they can be read into Matlab
> rapidly, could you then use Matlab's HDF5 capability to write then into any
> HDF5 format you like? I realize this is not ideal, but it is just a single
> extra postprocessing step.
>    You could also write your own PETSc object viewers that wrote to HDF5,
> for sparse matrices, but I think it is easy just to dump to Matlab and have
> it save it in the format you want.
>    ASCII is just SO slow for large data sets I think it is impractical.
>   Barry
>> Furthermore: "It won't buy
>> you any speed, disk space, or portability."
>> Certainly the PETSc binary format works fine for PETSc I/O but I am
>> unable to find anything to convert between this format and any other.
>> I'm most concerned with portability; I would like to utilize external
>> visualization packages. Is it standard practice to simply use ASCII
>> output? I can certainly do that but for larger problems size will
>> certainly become an impending issue....
>> Thanks in advance for any help you can offer,
>> Arturo

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