PETSc developers and users,
I apologize for my rude and unfair message to PETSc developers.
I have removed myself from the PETSc mailing lists and removed my access
to the PETSc repository and will no longer be involved in PETSc.
Barry
> On Feb 18, 2020, at 9:10 PM, Smith, Barry F. <bsm...@mcs.anl.gov> wrote:
>
>
> In the past you needed a brain to get a Stanford email account
>
>
>> Begin forwarded message:
>>
>> From: Yuyun Yang <yyan...@stanford.edu>
>> Subject: Re: [petsc-users] Matrix-free method in PETSc
>> Date: February 18, 2020 at 8:26:11 AM CST
>> To: Matthew Knepley <knep...@gmail.com>
>> Cc: "Smith, Barry F." <bsm...@mcs.anl.gov>, "petsc-us...@mcs.anl.gov"
>> <petsc-us...@mcs.anl.gov>
>>
>> Thanks. Also, when using KSP, would the syntax be KSPSetOperators(ksp,A,A)?
>> Since you mentioned preconditioners are not generally used for matrix-free
>> operators, I wasn’t sure whether I should still put “A” in the Pmat field.
>>
>> Is it still possible to use TS in conjunction with the matrix-free operator?
>> I’d like to create a simple test case that solves the 1d heat equation
>> implicitly with variable coefficients, but didn’t know how the time stepping
>> can be set up.
>>
>> Thanks,
>> Yuyun
>>
>> From: Matthew Knepley <knep...@gmail.com>
>> Date: Tuesday, February 18, 2020 at 9:23 PM
>> To: Yuyun Yang <yyan...@stanford.edu>
>> Cc: "Smith, Barry F." <bsm...@mcs.anl.gov>, "petsc-us...@mcs.anl.gov"
>> <petsc-us...@mcs.anl.gov>
>> Subject: Re: [petsc-users] Matrix-free method in PETSc
>>
>> On Tue, Feb 18, 2020 at 8:20 AM Yuyun Yang <yyan...@stanford.edu> wrote:
>> Thanks for the clarification.
>>
>> Got one more question: if I have variable coefficients, my stencil will be
>> updated at every time step, so will the coefficients in myMatMult. In that
>> case, is it necessary to destroy the shell matrix and create it all over
>> again, or can I use it as it is, only calling the stencil update function,
>> assuming the result will be passed into the matrix operation automatically?
>>
>> You update the information in the context associated with the shell matrix.
>> No need to destroy it.
>>
>> Thanks,
>>
>> Matt
>>
>> Thanks,
>> Yuyun
>>
>> On 2/18/20, 7:34 AM, "Smith, Barry F." <bsm...@mcs.anl.gov> wrote:
>>
>>
>>
>> > On Feb 17, 2020, at 7:56 AM, Yuyun Yang <yyan...@stanford.edu> wrote:
>> >
>> > Hello,
>> >
>> > I actually have a question about the usage of DMDA since I'm quite new
>> to this. I wonder if the DMDA suite of functions can be directly called on
>> vectors created from VecCreate?
>>
>> Yes, but you have to make sure the ones you create have the same
>> sizes and parallel layouts. Generally best to get them from the DMDA or
>> VecDuplicate() than the hassle of figuring out sizes.
>>
>> > Or the vectors have to be formed by DMDACreateGlobalVector? I'm also
>> not sure about what the dof and stencil width arguments do.
>> >
>> > I'm still unsure about the usage of MatCreateShell and
>> MatShellSetOperation, since it seems that MyMatMult should still have 3
>> inputs just like MatMult (the matrix and two vectors). Since I'm not forming
>> the matrix, does that mean the matrix input is meaningless but still needs
>> to exist for the sake of this format?
>>
>> Well the matrix input is your shell matrix so it likely has
>> information you need to do your multiply routine. MatShellGetContext() (No
>> you do not want to put your information about the matrix stencil inside
>> global variables!)
>>
>>
>> >
>> > After I create such a shell matrix, can I use it like a regular matrix
>> in KSP and utilize preconditioners?
>> >
>> > Thanks!
>> > Yuyun
>> > From: petsc-users <petsc-users-boun...@mcs.anl.gov> on behalf of Yuyun
>> Yang <yyan...@stanford.edu>
>> > Sent: Sunday, February 16, 2020 3:12 AM
>> > To: Smith, Barry F. <bsm...@mcs.anl.gov>
>> > Cc: petsc-us...@mcs.anl.gov <petsc-us...@mcs.anl.gov>
>> > Subject: Re: [petsc-users] Matrix-free method in PETSc
>> >
>> > Thank you, that is very helpful information indeed! I will try it and
>> send you my code when it works.
>> >
>> > Best regards,
>> > Yuyun
>> > From: Smith, Barry F. <bsm...@mcs.anl.gov>
>> > Sent: Saturday, February 15, 2020 10:02 PM
>> > To: Yuyun Yang <yyan...@stanford.edu>
>> > Cc: petsc-us...@mcs.anl.gov <petsc-us...@mcs.anl.gov>
>> > Subject: Re: [petsc-users] Matrix-free method in PETSc
>> >
>> > Yuyun,
>> >
>> > If you are speaking about using a finite difference stencil on a
>> structured grid where you provide the Jacobian vector products yourself by
>> looping over the grid doing the stencil operation we unfortunately do not
>> have exactly that kind of example.
>> >
>> > But it is actually not difficult. I suggest starting with
>> src/ts/examples/tests/ex22.c It computes the sparse matrix explicitly with
>> FormIJacobian()
>> >
>> > What you need to do is instead in main() use MatCreateShell() and
>> MatShellSetOperation(,MATOP_MULT,(void (*)(void))MyMatMult) then provide the
>> routine MyMatMult() to do your stencil based matrix free product; note that
>> you can create this new routine by taking the structure of IFunction() and
>> reorganizing it to do the Jacobian product instead. You will need to get the
>> information about the shell matrix size on each process by calling
>> DMDAGetCorners().
>> >
>> > You will then remove the explicit computation of the Jacobian, and
>> also remove the Event stuff since you don't need it.
>> >
>> > Extending to 2 and 3d is straight forward.
>> >
>> > Any questions let us know.
>> >
>> > Barry
>> >
>> > If you like this would make a great merge request with your code to
>> improve our examples.
>> >
>> >
>> > > On Feb 15, 2020, at 9:42 PM, Yuyun Yang <yyan...@stanford.edu> wrote:
>> > >
>> > > Hello team,
>> > >
>> > > I wanted to apply the Krylov subspace method to a matrix-free
>> implementation of a stencil, such that the iterative method acts on the
>> operation without ever constructing the matrix explicitly (for example, when
>> doing backward Euler).
>> > >
>> > > I'm not sure whether there is already an example for that somewhere.
>> If so, could you point me to a relevant example?
>> > >
>> > > Thank you!
>> > >
>> > > Best regards,
>> > > Yuyun
>>
>>
>>
>>
>>
>> --
>> 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/
>
