[petsc-users] Vec, Mat and binaryfiles.

[Sal Am]

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?

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
> >>
>
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