> On Oct 30, 2017, at 12:39 PM, Mark Lohry <[email protected]> wrote: > > > > > > 3) Are there any hooks analogous to KSPSetPreSolve/PostSolve for the FD > > computation of the jacobians, or for the computation of the preconditioner? > > I'd like to get a handle on the relative costs of these. > > No, do you just want the time? You can get that from the logging; for > example -log_view > > Yes, was just thinking in regards to your suggestion of recomputing when the > number of linear iterations gets too high; I assume it's the ratio of > preconditioner cost vs linear solver cost at runtime that's the metric of > interest, and not the absolute value of either. But I'll cross that bridge > when I come to it. > > When I had asked, I was looking to see where a long pause was happening > thinking it was the FD jacobian; turned out to be before that in > MatColoringApply which seems surprisingly expensive. MATCOLORINGJP took ~15 > minutes on 32 cores on a small 153,000^2 system, with MATCOLORINGGREEDY > taking 30 seconds. Any guidance there, or is this expected? I'm not using DM, > just manually entering the sparsity resulting from a metis decomposition of a > tetrahedral mesh.
Hmm, metis doesn't really have anything to do with the sparsity of the Jacobian does it? Matt, These times are huge. What is going on? Barry > > > Thanks for the info on the lag logic, I'll play with the TS pre/post calls > for the time-accurate problems and only use LagJacobian. > > On Mon, Oct 30, 2017 at 11:29 AM, Smith, Barry F. <[email protected]> wrote: > > > On Oct 29, 2017, at 11:50 AM, Mark Lohry <[email protected]> wrote: > > > > Thanks again Barry, I've got the preconditioners hooked up with > > -snes_mf_operator and at least AMG looks to be working great on a high > > order unstructured DG problem. > > > > Couple questions on the SNESSetLagJacobian + SNESSetLagPreconditioner code > > flow: > > > > 1) With -snes_mf_operator, and given SNESSetLagJacobian(snes, 1) (default) > > and SNESSetLagPreconditioner(snes, 2), after the first KSP solve in a > > newton iteration, will it do the finite different jacobian calculation? Or > > will the Jacobian only be computed when the preconditioner lag setting > > demands it on the 3rd newton step? I suspect it's the latter based on where > > I see the code pause. > > SNES with -snes_mf_operator will ALWAYS use the matrix-free finite > difference f(x+h) - f(x) to apply the matrix vector product. > > The LagJacobian and LagPreconditioner are not coordinated. The first > determines how often the Jacobian used for preconditioning is recomputed and > the second determines how often the preconditioner is recomputed. > > If you are using -snes_mf_operator then it never makes sense to have > lagJacobian < lagPreconditioner since it would recompute the Jacobian but not > actually use it. It also makes no sense for lagPreconditioner < lagJacobian > because you'd be recomputing the preconditioner on the same Jacobian. > > But actually if you don't change the Jacobian used in building the > preconditioner then when it tries to recompute the preconditioner it > determines the matrix has not changed so skips rebuilding the preconditioner. > So when using -snes_mf_operator there is really no reason generally to set > the preconditioner lag. > > > > 2) How do implicit TS and SNESSetLagPreconditioner/Persists interact? Does > > the counter since-last-preconditioner-compute reset with time steps, or > > does that lag counter just increment with every SNES solve regardless of > > how many nonlinear solves might have happened in a given timestep? Say lag > > preconditioner is 2, and a time stepper uses 3, 2, and 3 nonlinear solves > > on 3 steps, is the flow > > > > (time step 1)->(update preconditioner)->(snes solve)->(snes solve)->(update > > preconditioner)->(snes solve) > > (time step 2)->(snes solve)->(update preconditioner)->(snes solve) > > (time step 3)->(snes solve)->(update preconditioner)->(snes solve)->(snes > > solve) > > > > or > > > > (time step 1)->(update preconditioner)->(snes solve)->(snes solve)->(update > > preconditioner)->(snes solve) > > (time step 2)->(update preconditioner)->(snes solve)->(snes solve) > > (time step 3)->(update preconditioner)->(snes solve)->(snes solve)->(update > > preconditioner)->(snes solve) > > > > ? > > > > I think for implicit time stepping I'd probably want the preconditioner to > > be recomputed just once at the beginning of each time step, or some > > multiple of that. Does that sound reasonable? > > Yes, what you want to do is completely reasonable. > > You can use SNESSetLagJacobian() and SNESSetLagJacobianPersists() in > combination to have the Jacobian recomputed ever fixed number of times; if > you set the persists flag and set LagJacobian to 10 it will recompute the > Jacobian used in the preconditioner every 10th time a new Jacobian is needed. > > If you want to compute the new Jacobian used to build the preconditioner > once at the beginning of each new TS stage you can set SNESSetLagJacobian() > to negative -2 in the TS prestage call. There are possibly other tricks you > can do by setting the two flags at different locations. > > An alternative to hardwiring how often the Jacobian used to build the > preconditioner is rebuilt is to rebuild based on when the preconditioner > starts "working less well". Here you could put an additional KSPMonitor or > SNESMonitor that detects if the number of linear iterations is above a > certain amount and then sets the recompute Jacobian flag to -2 so that for > the next solve it recreates the Jacobian used in building the preconditioner. > > > > > > 3) Are there any hooks analogous to KSPSetPreSolve/PostSolve for the FD > > computation of the jacobians, or for the computation of the preconditioner? > > I'd like to get a handle on the relative costs of these. > > No, do you just want the time? You can get that from the logging; for > example -log_view > > > > > > > Best, > > Mark > > > > On Sat, Sep 23, 2017 at 3:28 PM, Mark Lohry <[email protected]> wrote: > > Great, thanks Barry. > > > > On Sat, Sep 23, 2017 at 3:12 PM, Barry Smith <[email protected]> wrote: > > > > > On Sep 23, 2017, at 12:48 PM, Mark W. Lohry <[email protected]> wrote: > > > > > > I'm currently using JFNK in an application where I don't have a > > > hand-coded jacobian, and it's working well enough but as expected the > > > scaling isn't great. > > > > > > What is the general process for using PC with MatMFFDComputeJacobian? > > > Does it make sense to occasionally have petsc re-compute the jacobian via > > > finite differences, and then recompute the preconditioner? Any that just > > > need the sparsity structure? > > > > Mark > > > > Yes, this is a common approach. SNESSetLagJacobian -snes_lag_jacobian > > > > The normal approach in SNES to use matrix-free for the operator and use > > finite differences to compute an approximate Jacobian used to construct > > preconditioners is to to create a sparse matrix with the sparsity of the > > approximate Jacobian (yes you need a way to figure out the sparsity, if you > > use DMDA it will figure out the sparsity for you). Then you use > > > > SNESSetJacobian(snes,J,J, SNESComputeJacobianDefaultColor, NULL); > > > > and use the options database option -snes_mf_operator > > > > > > > Are there any PCs that don't work in the matrix-free context? > > > > If you do the above you can use almost all the PC since you are providing > > an explicit matrix from which to build the preconditioner > > > > > Are there any example codes I overlooked? > > > > > > Last but not least... can the Boomer-AMG preconditioner work with JFNK? > > > To really show my ignorance of AMG, can it actually be written as a > > > matrix P^-1(Ax-b)=0, , or is it just a linear operator? > > > > Again, if you provide an approximate Jacobian like above you can use it > > with BoomerAMG, if you provide NO explicit matrix you cannot use BoomerAMG > > or almost any other preconditioner. > > > > Barry > > > > > > > > Thanks, > > > Mark > > > > > > > >
