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> > >
