On Jul 10, 2014, at 10:07 PM, Sun, Hui <[email protected]> wrote: > I have also noticed those unnecessary zeros, in both cases DMDA_STENTIL_BOX > and DMDA_STENTIL_STAR there are many unnecessary zeros. Do you have any idea > how to get rid of those entries?
These zeros are for all the locations allowed by the stencil (assuming a full stencil for every variable). The only way to get rid of them is to use a custom matrix allocation. The box stencil will have many extra of these zeros since it includes a lot of “coupling” in the matrix that doesn’t exist. Barry > > > ________________________________________ > From: Barry Smith [[email protected]] > Sent: Thursday, July 10, 2014 7:46 PM > To: Sun, Hui > Cc: [email protected] > Subject: Re: [petsc-users] a strange bug on using DMDA_STENCIL_BOX > > Hmm. Because the box stencil puts extra zeros in the original matrix (due > to the “extra” stencil locations) ilu(0) will converge differently with the > box stencil than the star stencil with the linear solver. Thus one will > actually get a different convergence history. With Jacobi (which doesn’t > depend on the non-zero structure of the matrix) the convergence won’t change. > I checked with Jacobi and -da_refine 1 and they converge the same. Are you > sure there is an issue with box stencil? You wrote originally > >>>> However, if I change it to DMDA_STENTIL_BOX, it does not converge, the >>>> residue \|Ax-b\|_2 remains large. > > can you explain to me how to reproduce this “does not converge, the residue > \|Ax-b\|_2 remains large.” business. > > Barry > > On Jul 10, 2014, at 8:46 PM, Sun, Hui <[email protected]> wrote: > >> Thanks for the hint. That is a possible bug. However, I still haven't caught >> the bug after rethinking about it. I've got three degrees of freedom on each >> node, MAC grid, and std 5 points laplacian, central differencing for >> derivatives. Here I've also attached my code. >> >> >> ________________________________________ >> From: Barry Smith [[email protected]] >> Sent: Thursday, July 10, 2014 6:14 PM >> To: Sun, Hui >> Cc: [email protected] >> Subject: Re: [petsc-users] a strange bug on using DMDA_STENCIL_BOX >> >> Perhaps the code is not correct for the star stencil? That is perhaps you >> are actually setting values in the “corner” locations that are not being >> communicated with stencil but are communicated with star? If your finite >> difference stencil involves the “corner” locations then you need to always >> use the box stencil type. >> >> What is exactly your finite difference stencil? How many degrees of freedom >> per point? >> >> >> Barry >> >> On Jul 10, 2014, at 8:07 PM, Sun, Hui <[email protected]> wrote: >> >>> If I run: >>> ./test_29 -da_grid_x 6 -da_grid_y 6 -ksp_type bcgs -ksp_monitor_short >>> -ksp_converged_reason >>> >>> For DMDA_STENCIL_BOX, I get: >>> >>> 0 KSP Residual norm 17.5431 >>> 1 KSP Residual norm 3.23193 >>> 2 KSP Residual norm 0.399307 >>> 3 KSP Residual norm 0.0103842 >>> 4 KSP Residual norm 0.000124391 >>> Linear solve converged due to CONVERGED_RTOL iterations 4 >>> >>> For DMDA_STENCIL_STAR, I get: >>> >>> 0 KSP Residual norm 60.7996 >>> 1 KSP Residual norm 13.7279 >>> 2 KSP Residual norm 4.15583 >>> 3 KSP Residual norm 0.430568 >>> 4 KSP Residual norm 0.0999957 >>> 5 KSP Residual norm 0.00260724 >>> 6 KSP Residual norm 0.00191392 >>> 7 KSP Residual norm 5.4681e-05 >>> Linear solve converged due to CONVERGED_RTOL iterations 7 >>> >>> The history seems different. >>> >>> >>> ________________________________________ >>> From: Barry Smith [[email protected]] >>> Sent: Thursday, July 10, 2014 5:54 PM >>> To: Sun, Hui >>> Cc: [email protected] >>> Subject: Re: [petsc-users] a strange bug on using DMDA_STENCIL_BOX >>> >>> Your interpretation is correct. If DMDA_STENTIL_STAR works then one >>> absolutely expects that DMDA_STENTIL_BOX would produce the same answer. If >>> you are running with linux could you run with valgrind to see if there is >>> some strange memory corruption or lack of initialization >>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>> >>> What happens with -ksp_monitor on both cases? Same convergence history or >>> different? >>> >>> Barry >>> >>> >>> >>> On Jul 10, 2014, at 7:49 PM, Sun, Hui <[email protected]> wrote: >>> >>>> I'm using KSP for 2D Navier Stokes, finite difference. I have DM object >>>> created with DMDA_STENTIL_STAR. I'm only using one single process to run >>>> the code. It works fine, the linear system converges to the correct >>>> solution with correct order, as expected. However, if I change it to >>>> DMDA_STENTIL_BOX, it does not converge, the residue \|Ax-b\|_2 remains >>>> large. >>>> >>>> I have checked that the rhs for both cases are exactly the same, and the >>>> matrices also seem to be the same because I have checked the output of >>>> A*y, where y is the analytic solution, and both cases give exactly the >>>> same answer. If the linear system is exactly the same, then it seems very >>>> strange to me that DMDA_STENTIL_STAR works while DMDA_STENTIL_BOX does not >>>> work, for I use the same solver, there shouldn't be any difference. >>>> >>>> If you happen to encounter this kind of bug before and have some idea >>>> what's going on, please let me know. Thank you very much! If you want to >>>> look at the code I've written, feel free to ask. >>> >> >> <test_29_cp.c> >
