[petsc-users] Vec, Mat and binaryfiles.

[Matthew Knepley]

On Thu, Nov 8, 2018 at 4:56 AM Sal Am via petsc-users <
petsc-users at mcs.anl.gov> wrote:

> Thanks, I missed that,
>
> I do care about scalability, the long term plan is to make it fully
> compatible on a cluster so I guess I would need to convert it to PETSc
> binary format before reading it in.
>
> Is this the file you were referring to
> https://github.com/erdc/petsc-dev/blob/master/bin/pythonscripts/PetscBinaryIO.py
>
> Cannot seem to find docs on how to use it, do you happen to have any
> examples?
>

The documentation is at the top of the file. You can see it by clicking the
link.

   Matt


> All the best,
> S
>
>
>
>
> On Wed, Nov 7, 2018 at 4:07 PM Jed Brown <jed at jedbrown.org> wrote:
>
>> Please always use "reply-all" so that your messages go to the list.
>> This is standard mailing list etiquette.  It is important to preserve
>> threading for people who find this discussion later and so that we do
>> not waste our time re-answering the same questions that have already
>> been answered in private side-conversations.  You'll likely get an
>> answer faster that way too.
>>
>> Sal Am <tempohoper at gmail.com> writes:
>>
>> > Thank you Jed for the quick response!
>> >
>> >>
>> >> Yes, of course the formats would have to match.  I would recommend
>> >> writing the files in an existing format such as PETSc's binary format.
>> >>
>> >
>> > Unfortunately I do not think I can change the source code to output
>> those
>> > two files in PETSc format and it would probably take a very long time
>> > converting everything into PETSc (it is not even my code).
>>
>> File-based workflows are very often bottlenecks.  You can also use any
>> convenient software (e.g., Python or Matlab/Octave) to convert your
>> custom binary formats to PETSc binary format (see PetscBinaryIO provided
>> with PETSc), at which point you'll be able to read in parallel.  If you
>> don't care about scalability or only need to read once, then you can
>> write code of the type you propose.
>>
>> > Do you have any other suggestions on how to read in those two complex
>> > binary files? Also why would it be more difficult to parallelise as
>> > I thought getting the two files in PETSc vector format would allow me to
>> > use the rest of PETSc library the usual way?
>> >
>> > Kind regards,
>> > S
>> >
>> >
>> > On Mon, Nov 5, 2018 at 4:49 PM Jed Brown <jed at jedbrown.org> wrote:
>> >
>> >> Sal Am via petsc-users <petsc-users at mcs.anl.gov> writes:
>> >>
>> >> > Hi,
>> >> >
>> >> > I am trying to solve a Ax=b complex system. the vector b and
>> "matrix" A
>> >> are
>> >> > both binary and NOT created by PETSc. So I keep getting error
>> messages
>> >> that
>> >> > they are not correct format when I read the files with
>> >> PetscViewBinaryOpen,
>> >> > after some digging it seems that one cannot just read a binary file
>> that
>> >> > was created by another software.
>> >>
>> >> Yes, of course the formats would have to match.  I would recommend
>> >> writing the files in an existing format such as PETSc's binary format.
>> >> While the method you describe can be made to work, it will be more work
>> >> to make it parallel.
>> >>
>> >> > How would I go on to solve this problem?
>> >> >
>> >> > More info and trials:
>> >> >
>> >> > "matrix" A consists of two files, one that contains row column index
>> >> > numbers and one that contains the non-zero values. So what I would
>> have
>> >> to
>> >> > do is multiply the last term in a+b with PETSC_i to get a real +
>> >> imaginary
>> >> > vector A.
>> >> >
>> >> > vector b is in binary, so what I have done so far (not sure if it
>> works)
>> >> is:
>> >> >
>> >> > std::ifstream input("Vector_b.bin", std::ios::binary );
>> >> > while (input.read(reinterpret_cast<char*>(&v), sizeof(float)))
>> >> >      ierr    =
>> VecSetValues(u,1,&iglobal,&v,INSERT_VALUES);CHKERRQ(ierr);
>> >> >
>> >> > where v is a PetscScalar.
>> >> >
>> >> > Once I am able to read both matrices I think I can figure out the
>> solvers
>> >> > to solve the system.
>> >> >
>> >> > All the best,
>> >> > S
>> >>
>>
>

-- 
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

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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