[petsc-users] convergence problem- 3D Cahn Hillard

[Barry Smith]

> On Jan 10, 2021, at 3:25 PM, Sepideh Kavousi <skavou1 at lsu.edu> wrote:
> 
> Yes, the entire code is finite difference. 
> Is it possible that the large Laplacian term makes the equation stiff, such that the time step is reduced to solve the problem?

   Yes, a bit, but no way near to this degree. 

   What are your boundary conditions? Is it possible there is a null space lurking around, unlikely since the direct solver has no issues but if so it could cause difficulties.

   Barry

> Best,
> Sepideh
> From: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> Sent: Thursday, January 7, 2021 1:38 PM
> To: Sepideh Kavousi <skavou1 at lsu.edu <mailto:skavou1 at lsu.edu>>
> Cc: petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] convergence problem- 3D Cahn Hillard
>  
> 
>   It looks like valgrind is being run on bash, not on your program, so these leaks are not relevant.  by 0x41C482: main (in /usr/bin/bash)
> 
>   So the entire code is finite difference based?
> 
>   Barry
> 
> 
>> On Jan 7, 2021, at 12:48 PM, Sepideh Kavousi <skavou1 at lsu.edu <mailto:skavou1 at lsu.edu>> wrote:
>> 
>> I use finite difference and, as an example,  the discretization of Pxx is:
>>  Pxx=((aY[k][j][i+1].p+aY[k][j][i-1].p-2.0*aY[k][j][i].p)/hx2);
>> 
>> I ran the code with valgrind and it seems there is a memory leak problem. 
>> I am trying to figure out what is causing the memory error. 
>> Best,
>> Sepideh
>> 
>> From: Jed Brown <jed at jedbrown.org <mailto:jed at jedbrown.org>>
>> Sent: Tuesday, January 5, 2021 10:31 PM
>> To: Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>>; Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
>> Cc: petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>; Sepideh Kavousi <skavou1 at lsu.edu <mailto:skavou1 at lsu.edu>>
>> Subject: Re: [petsc-users] convergence problem- 3D Cahn Hillard
>>  
>> Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>> writes:
>> 
>> > On Tue, Jan 5, 2021 at 9:52 PM Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>> wrote:
>> >
>> >>
>> >> Ah, -snes_fd_color so it was already using finite differencing with
>> >> coloring to compute the Jacobian which explains why the differences below
>> >> are exactly zero.
>> >>
>> >> Implicit time-step schemes essentially add terms like I/dt  to the
>> >> Jacobian evaluation (and the function defining the ODE) so for tiny
>> >> time-steps the nonlinear system gets easier and easier to solve (the
>> >> nonlinear function becomes linear) But we didn't see that with your earlier
>> >> run where  dt 3.72529e-13 (which is absurdly small).  for tiny time-steps
>> >> SNES still made no progress. It is hard to understand how this is possible,
>> >> regardless of the problem you are solving.
>> >>
>> >> I would next run the code with valgrind to insure there are no issues of
>> >> memory corruption or un-initialized data.
>> >>
>> >> How are you computing
>> >>
>> >> (dp/dt)*(Pxx+Pyy+Pzz)
>> >>
>> >>
>> >> That is, how are you computing Pxx etc?
>> >>
>> >> Are you using finite elements for the U and P model? Exactly what elements?
>> >>
>> >
>> > I agree with Barry. This does not seem to make sense, so I would expect
>> > some kind of inconsistent discretization, or other
>> > mathematical problem which makes your system unsolvable.
>> 
>> Try -mat_fd_type ds before ruling out sensitivity to differencing parameter. 
>> <valgrind-out.txt>
> 
> <valgrind-5.txt>

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