[petsc-users] Vec, Mat and binaryfiles.

[Jed Brown]

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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
>>