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

[Sepideh Kavousi]

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?
Best,
Sepideh
________________________________
From: Barry Smith <bsmith at petsc.dev>
Sent: Thursday, January 7, 2021 1:38 PM
To: Sepideh Kavousi <skavou1 at lsu.edu>
Cc: petsc-users at mcs.anl.gov <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>

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