Hi Barry, Sorry, I had no idea that Newton TR would have anything to do with the linear solver. I was using TR because it is trustworthy and converges every time. I tried LS just now with GAMG+GMRES and it converges, so I don't have the CONVERGED_STEP_LENGTH problem anymore.
Thanks for you help! Harshad On Wed, Sep 14, 2016 at 2:51 PM, Barry Smith <[email protected]> wrote: > > Oh, you are using SNESSolve_NEWTONTR ! > > Now it all makes sense! The trust region methods impose other > conditions on the linear solution so it needs to have their own special > convergence test. In particular it requires that the solution from the > linear solve be inside the trust region (i.e. not too big) > > So, any particular reason you use SNESSolve_NEWTONTR instead of the > default line search NEWTONLS? In general unless you have a good reason I > recommend just using the NEWTONLS. > > If you really want to use the TR then the "early" return from the > linear solve is expected, it is controlled by the trust region size and is > not under user control. > > I'm sorry I was so brain dead and did not realize you had be using TR > or we could have resolved this much sooner. > > Barry > > > > > On Sep 14, 2016, at 1:31 PM, Harshad Sahasrabudhe <[email protected]> > wrote: > > > > Thanks. I now put a watchpoint on > > > > watch *( (PetscErrorCode (**)(KSP, PetscInt, PetscReal, > KSPConvergedReason *, void *)) &(ksp->converged) ) > > > > The function pointer changes in the first iteration of SNES. It changed > at the following place: > > > > Old value = > > (PetscErrorCode (*)(KSP, PetscInt, PetscReal, KSPConvergedReason *, > void *)) 0x2b54acdd00aa <KSPConvergedDefault(KSP, PetscInt, PetscReal, > KSPConvergedReason*, void*)> > > New value = > > (PetscErrorCode (*)(KSP, PetscInt, PetscReal, KSPConvergedReason *, > void *)) 0x2b54ad436ce8 <.SNES_TR_KSPConverged_ > Private.SNES_TR_KSPConverged_Private.SNES_TR_KSPConverged_Private(_p_KSP*, > int, double, KSPConvergedReason*, void*)> > > KSPSetConvergenceTest (ksp=0x22bf090, converge=0x2b54ad436ce8 > <SNES_TR_KSPConverged_Private(_p_KSP*, int, double, KSPConvergedReason*, > void*)>, cctx=0x1c8b3e0, > > destroy=0x2b54ad437210 <SNES_TR_KSPConverged_Destroy(void*)>) > > at /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/ksp/ksp/interface/itfunc.c:1768 > > 1767 ksp->converged = converge; > > > > Here's the backtrace: > > > > #0 KSPSetConvergenceTest (ksp=0x22bf090, converge=0x2b54ad436ce8 > <SNES_TR_KSPConverged_Private(_p_KSP*, int, double, KSPConvergedReason*, > void*)>, cctx=0x1c8b3e0, > > destroy=0x2b54ad437210 <SNES_TR_KSPConverged_Destroy(void*)>) > > at /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/ksp/ksp/interface/itfunc.c:1768 > > #1 0x00002b54ad43865a in SNESSolve_NEWTONTR (snes=0x1d9e490) at > /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/snes/impls/tr/tr.c:146 > > #2 0x00002b54acedab57 in SNESSolve (snes=0x1d9e490, b=0x0, x=0x1923420) > > at /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/snes/interface/snes.c:3743 > > #3 0x00002b54abe8b780 in libMesh::PetscNonlinearSolver<double>::solve > (this=0x19198c0, jac_in=..., x_in=..., r_in=...) at > src/solvers/petsc_nonlinear_solver.C:714 > > #4 0x00002b54abefa61d in libMesh::NonlinearImplicitSystem::solve > (this=0x1910fe0) at src/systems/nonlinear_implicit_system.C:183 > > #5 0x00002b54a5dcdceb in NonlinearPoisson::execute_solver > (this=0x100c500) at NonlinearPoisson.cpp:1191 > > #6 0x00002b54a5da733c in NonlinearPoisson::do_solve (this=0x100c500) at > NonlinearPoisson.cpp:948 > > #7 0x00002b54a6423785 in Simulation::solve (this=0x100c500) at > Simulation.cpp:781 > > #8 0x00002b54a634826e in Nemo::run_simulations (this=0x63b020) at > Nemo.cpp:1313 > > #9 0x0000000000426d0d in main (argc=6, argv=0x7ffcdb910768) at > main.cpp:447 > > > > Thanks, > > Harshad > > > > > > On Wed, Sep 14, 2016 at 2:07 PM, Barry Smith <[email protected]> wrote: > > > > Super strange, it should never have switched to the function > SNES_TR_KSPConverged_Private > > > > Fortunately you can use the same technique to track down where the > function pointer changes. Just watch ksp->converged to see when the > function pointer gets changed and send back the new stack trace. > > > > Barry > > > > > > > > > > > On Sep 14, 2016, at 12:39 PM, Harshad Sahasrabudhe < > [email protected]> wrote: > > > > > > Hi Barry, > > > > > > I put a watchpoint on *((KSP_CONVERGED_REASON*) &( > ((_p_KSP*)ksp)->reason )) in gdb. The ksp->reason switched between: > > > > > > Old value = KSP_CONVERGED_ITERATING > > > New value = KSP_CONVERGED_RTOL > > > 0x00002b143054bef2 in KSPConvergedDefault (ksp=0x23c3090, n=12, > rnorm=5.3617149831259514e-08, reason=0x23c3310, ctx=0x2446210) > > > at /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/ksp/ksp/interface/iterativ.c:764 > > > 764 *reason = KSP_CONVERGED_RTOL; > > > > > > and > > > > > > Old value = KSP_CONVERGED_RTOL > > > New value = KSP_CONVERGED_ITERATING > > > KSPSetUp (ksp=0x23c3090) at /depot/ncn/apps/conte/conte- > gcc-petsc35-dbg/libs/petsc/build-real/src/ksp/ksp/interface/itfunc.c:226 > > > 226 if (!((PetscObject)ksp)->type_name) { > > > > > > However, after iteration 6, it changed to KSP_CONVERGED_STEP_LENGTH > > > > > > Old value = KSP_CONVERGED_ITERATING > > > New value = KSP_CONVERGED_STEP_LENGTH > > > SNES_TR_KSPConverged_Private (ksp=0x23c3090, n=1, > rnorm=0.097733468578376406, reason=0x23c3310, cctx=0x1d8f3e0) > > > at /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/snes/impls/tr/tr.c:36 > > > 36 PetscFunctionReturn(0); > > > > > > Any ideas why that function was executed? Backtrace when the program > stopped here: > > > > > > #0 SNES_TR_KSPConverged_Private (ksp=0x23c3090, n=1, > rnorm=0.097733468578376406, reason=0x23c3310, cctx=0x1d8f3e0) > > > at /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/snes/impls/tr/tr.c:36 > > > #1 0x00002b14305d3fda in KSPGMRESCycle (itcount=0x7ffdcf2d4ffc, > ksp=0x23c3090) > > > at /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/ksp/ksp/impls/gmres/gmres.c:182 > > > #2 0x00002b14305d4711 in KSPSolve_GMRES (ksp=0x23c3090) at > /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/ksp/ksp/impls/gmres/gmres.c:235 > > > #3 0x00002b1430526a8a in KSPSolve (ksp=0x23c3090, b=0x1a916c0, > x=0x1d89dc0) > > > at /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/ksp/ksp/interface/itfunc.c:460 > > > #4 0x00002b1430bb3905 in SNESSolve_NEWTONTR (snes=0x1ea2490) at > /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/snes/impls/tr/tr.c:160 > > > #5 0x00002b1430655b57 in SNESSolve (snes=0x1ea2490, b=0x0, > x=0x1a27420) > > > at /depot/ncn/apps/conte/conte-gcc-petsc35-dbg/libs/petsc/ > build-real/src/snes/interface/snes.c:3743 > > > #6 0x00002b142f606780 in libMesh::PetscNonlinearSolver<double>::solve > (this=0x1a1d8c0, jac_in=..., x_in=..., r_in=...) at > src/solvers/petsc_nonlinear_solver.C:714 > > > #7 0x00002b142f67561d in libMesh::NonlinearImplicitSystem::solve > (this=0x1a14fe0) at src/systems/nonlinear_implicit_system.C:183 > > > #8 0x00002b1429548ceb in NonlinearPoisson::execute_solver > (this=0x1110500) at NonlinearPoisson.cpp:1191 > > > #9 0x00002b142952233c in NonlinearPoisson::do_solve (this=0x1110500) > at NonlinearPoisson.cpp:948 > > > #10 0x00002b1429b9e785 in Simulation::solve (this=0x1110500) at > Simulation.cpp:781 > > > #11 0x00002b1429ac326e in Nemo::run_simulations (this=0x63b020) at > Nemo.cpp:1313 > > > #12 0x0000000000426d0d in main (argc=6, argv=0x7ffdcf2d7908) at > main.cpp:447 > > > > > > > > > Thanks! > > > Harshad > > > > > > On Wed, Sep 14, 2016 at 10:10 AM, Harshad Sahasrabudhe < > [email protected]> wrote: > > > I think I found the problem. I configured PETSc with COPTFLAGS=-O3. > I'll remove that option and try again. > > > > > > Thanks! > > > Harshad > > > > > > On Wed, Sep 14, 2016 at 10:06 AM, Harshad Sahasrabudhe < > [email protected]> wrote: > > > Hi Barry, > > > > > > Thanks for your inputs. I tried to set a watchpoint on > ((_p_KSP*)ksp)->reason, but gdb says no symbol _p_KSP in context. > Basically, GDB isn't able to find the PETSc source code. I built PETSc with > --with-debugging=1 statically and -fPIC, but it seems the libpetsc.a I get > doesn't contain debugging symbols (checked using objdump -g). How do I get > PETSc library to have debugging info? > > > > > > Thanks, > > > Harshad > > > > > > On Tue, Sep 13, 2016 at 2:47 PM, Barry Smith <[email protected]> > wrote: > > > > > > > On Sep 13, 2016, at 1:01 PM, Harshad Sahasrabudhe < > [email protected]> wrote: > > > > > > > > Hi Barry, > > > > > > > > I compiled with mpich configured using --enable-g=meminit to get rid > of MPI errors in Valgrind. Doing this reduced the number of errors to 2. I > have attached the Valgrind output. > > > > > > This isn't helpful but it seems not to be a memory corruption issue > :-( > > > > > > > > I'm using GAMG+GMRES for in each linear iteration of SNES. The > linear solver converges with CONVERGED_RTOL for the first 6 iterations and > with CONVERGED_STEP_LENGTH after that. I'm still very confused about why > this is happening. Any thoughts/ideas? > > > > > > Does this happen on one process? If so I would run in the debugger > and track the variable to see everyplace the variable is changed, this > would point to exactly what piece of code is changing the variable to this > unexpected value. > > > > > > For example with lldb one can use watch > http://lldb.llvm.org/tutorial.html to see each time a variable gets > changed. Similar thing with gdb. > > > > > > The variable to watch is ksp->reason Once you get the hang of this > it can take just a few minutes to track down the code that is making this > unexpected value, though I understand if you haven't done it before it can > be intimidating. > > > > > > Barry > > > > > > You can do the same thing in parallel (like on two processes) if you > need to but it is more cumbersome since you need run multiple debuggers. > You can have PETSc start up multiple debuggers with mpiexec -n 2 ./ex > -start_in_debugger > > > > > > > > > > > > > > > > > > > > Thanks, > > > > Harshad > > > > > > > > On Thu, Sep 8, 2016 at 11:26 PM, Barry Smith <[email protected]> > wrote: > > > > > > > > Install your MPI with --download-mpich as a PETSc ./configure > option, this will eliminate all the MPICH valgrind errors. Then send as an > attachment the resulting valgrind file. > > > > > > > > I do not 100 % trust any code that produces such valgrind errors. > > > > > > > > Barry > > > > > > > > > > > > > > > > > On Sep 8, 2016, at 10:12 PM, Harshad Sahasrabudhe < > [email protected]> wrote: > > > > > > > > > > Hi Barry, > > > > > > > > > > Thanks for the reply. My code is in C. I ran with Valgrind and > found many "Conditional jump or move depends on uninitialized value(s)", > "Invalid read" and "Use of uninitialized value" errors. I think all of them > are from the libraries I'm using (LibMesh, Boost, MPI, etc.). I'm not > really sure what I'm looking for in the Valgrind output. At the end of the > file, I get: > > > > > > > > > > ==40223== More than 10000000 total errors detected. I'm not > reporting any more. > > > > > ==40223== Final error counts will be inaccurate. Go fix your > program! > > > > > ==40223== Rerun with --error-limit=no to disable this cutoff. Note > > > > > ==40223== that errors may occur in your program without prior > warning from > > > > > ==40223== Valgrind, because errors are no longer being displayed. > > > > > > > > > > Can you give some suggestions on how I should proceed? > > > > > > > > > > Thanks, > > > > > Harshad > > > > > > > > > > On Thu, Sep 8, 2016 at 1:59 PM, Barry Smith <[email protected]> > wrote: > > > > > > > > > > This is very odd. CONVERGED_STEP_LENGTH for KSP is very > specialized and should never occur with GMRES. > > > > > > > > > > Can you run with valgrind to make sure there is no memory > corruption? http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > > > > > > > > > > Is your code fortran or C? > > > > > > > > > > Barry > > > > > > > > > > > On Sep 8, 2016, at 10:38 AM, Harshad Sahasrabudhe < > [email protected]> wrote: > > > > > > > > > > > > Hi, > > > > > > > > > > > > I'm using GAMG + GMRES for my Poisson problem. The solver > converges with KSP_CONVERGED_STEP_LENGTH at a residual of > 9.773346857844e-02, which is much higher than what I need (I need a > tolerance of at least 1E-8). I am not able to figure out which tolerance I > need to set to avoid convergence due to CONVERGED_STEP_LENGTH. > > > > > > > > > > > > Any help is appreciated! Output of -ksp_view and -ksp_monitor: > > > > > > > > > > > > 0 KSP Residual norm 3.121347818142e+00 > > > > > > 1 KSP Residual norm 9.773346857844e-02 > > > > > > Linear solve converged due to CONVERGED_STEP_LENGTH iterations > 1 > > > > > > KSP Object: 1 MPI processes > > > > > > type: gmres > > > > > > GMRES: restart=30, using Classical (unmodified) Gram-Schmidt > Orthogonalization with no iterative refinement > > > > > > GMRES: happy breakdown tolerance 1e-30 > > > > > > maximum iterations=10000, initial guess is zero > > > > > > tolerances: relative=1e-08, absolute=1e-50, divergence=10000 > > > > > > left preconditioning > > > > > > using PRECONDITIONED norm type for convergence test > > > > > > PC Object: 1 MPI processes > > > > > > type: gamg > > > > > > MG: type is MULTIPLICATIVE, levels=2 cycles=v > > > > > > Cycles per PCApply=1 > > > > > > Using Galerkin computed coarse grid matrices > > > > > > Coarse grid solver -- level ------------------------------- > > > > > > KSP Object: (mg_coarse_) 1 MPI processes > > > > > > type: preonly > > > > > > maximum iterations=1, initial guess is zero > > > > > > tolerances: relative=1e-05, absolute=1e-50, > divergence=10000 > > > > > > left preconditioning > > > > > > using NONE norm type for convergence test > > > > > > PC Object: (mg_coarse_) 1 MPI processes > > > > > > type: bjacobi > > > > > > block Jacobi: number of blocks = 1 > > > > > > Local solve is same for all blocks, in the following KSP > and PC objects: > > > > > > KSP Object: (mg_coarse_sub_) 1 MPI > processes > > > > > > type: preonly > > > > > > maximum iterations=1, initial guess is zero > > > > > > tolerances: relative=1e-05, absolute=1e-50, > divergence=10000 > > > > > > left preconditioning > > > > > > using NONE norm type for convergence test > > > > > > PC Object: (mg_coarse_sub_) 1 MPI > processes > > > > > > type: lu > > > > > > LU: out-of-place factorization > > > > > > tolerance for zero pivot 2.22045e-14 > > > > > > using diagonal shift on blocks to prevent zero pivot > [INBLOCKS] > > > > > > matrix ordering: nd > > > > > > factor fill ratio given 5, needed 1.91048 > > > > > > Factored matrix follows: > > > > > > Mat Object: 1 MPI processes > > > > > > type: seqaij > > > > > > rows=284, cols=284 > > > > > > package used to perform factorization: petsc > > > > > > total: nonzeros=7726, allocated nonzeros=7726 > > > > > > total number of mallocs used during > MatSetValues calls =0 > > > > > > using I-node routines: found 133 nodes, > limit used is 5 > > > > > > linear system matrix = precond matrix: > > > > > > Mat Object: 1 MPI processes > > > > > > type: seqaij > > > > > > rows=284, cols=284 > > > > > > total: nonzeros=4044, allocated nonzeros=4044 > > > > > > total number of mallocs used during MatSetValues > calls =0 > > > > > > not using I-node routines > > > > > > linear system matrix = precond matrix: > > > > > > Mat Object: 1 MPI processes > > > > > > type: seqaij > > > > > > rows=284, cols=284 > > > > > > total: nonzeros=4044, allocated nonzeros=4044 > > > > > > total number of mallocs used during MatSetValues calls =0 > > > > > > not using I-node routines > > > > > > Down solver (pre-smoother) on level 1 > ------------------------------- > > > > > > KSP Object: (mg_levels_1_) 1 MPI processes > > > > > > type: chebyshev > > > > > > Chebyshev: eigenvalue estimates: min = 0.195339, max = > 4.10212 > > > > > > maximum iterations=2 > > > > > > tolerances: relative=1e-05, absolute=1e-50, > divergence=10000 > > > > > > left preconditioning > > > > > > using nonzero initial guess > > > > > > using NONE norm type for convergence test > > > > > > PC Object: (mg_levels_1_) 1 MPI processes > > > > > > type: sor > > > > > > SOR: type = local_symmetric, iterations = 1, local > iterations = 1, omega = 1 > > > > > > linear system matrix = precond matrix: > > > > > > Mat Object: () 1 MPI processes > > > > > > type: seqaij > > > > > > rows=9036, cols=9036 > > > > > > total: nonzeros=192256, allocated nonzeros=192256 > > > > > > total number of mallocs used during MatSetValues calls =0 > > > > > > not using I-node routines > > > > > > Up solver (post-smoother) same as down solver (pre-smoother) > > > > > > linear system matrix = precond matrix: > > > > > > Mat Object: () 1 MPI processes > > > > > > type: seqaij > > > > > > rows=9036, cols=9036 > > > > > > total: nonzeros=192256, allocated nonzeros=192256 > > > > > > total number of mallocs used during MatSetValues calls =0 > > > > > > not using I-node routines > > > > > > > > > > > > Thanks, > > > > > > Harshad > > > > > > > > > > > > > > > > > > > > > > <valgrind.log.33199> > > > > > > > > > > > > > > > > > >
