On Jul 26, 2010, at 3:53 PM, Barry Smith wrote: > > ./configure an optimized version of PETSc (that is with the ./ > configure flag of --with-debugging=0)
./configure --with -debugging=0 it says I should config/configure.py --with-mpi=0 --with-debugging=no --download-f-blas-lapack=1 so I did this. When I compile my code again, I got: gcc -Wall -Wwrite-strings -Wno-strict-aliasing -O -o pihm pihm.o f.o read_alloc.o initialize.o is_sm_et.o update.o print.o -Wl,-rpath,/gpfs/ home/xxy113/soft/petsc-3.1-p2/linux-gnu-c-opt/lib -L/gpfs/home/xxy113/ soft/petsc-3.1-p2/linux-gnu-c-opt/lib -lpetsc -lX11 -Wl,-rpath,/ gpfs/home/xxy113/soft/petsc-3.1-p2/linux-gnu-c-opt/lib -L/gpfs/home/ xxy113/soft/petsc-3.1-p2/linux-gnu-c-opt/lib -lflapack -lfblas -lm -L/ usr/lib/gcc/x86_64-redhat-linux/4.1.2 -ldl -lgcc_s -lgfortran -lm -lm - ldl -lgcc_s -ldl /usr/bin/ld: cannot find -lpetsc collect2: ld returned 1 exit status > and run with -log_summary to get a summary of where it is spending > the time. > This will give you a better idea of why it is taking so long. > > Barry > > On Jul 26, 2010, at 2:49 PM, Xuan YU wrote: > >> Hi, >> >> I am using TS solving a nonlinear problem. I created an approximate >> data structure for Jacobian matrix to be used with matcoloring, my >> MatFDColoringView is like this: >> <Picture 1.png> >> >> But the speed of code is too slow than what I expected. Only 10 >> time step costs 11seconds! >> >> What's wrong with my code? How can I speed up? >> >> Thanks! >> >> This is the ts_view result. >> >> TS Object: >> type: beuler >> maximum steps=100 >> maximum time=10 >> total number of nonlinear solver iterations=186 >> total number of linear solver iterations=423 >> SNES Object: >> type: ls >> line search variant: SNESLineSearchCubic >> alpha=0.0001, maxstep=1e+08, minlambda=1e-12 >> maximum iterations=50, maximum function evaluations=10000 >> tolerances: relative=1e-08, absolute=1e-50, solution=1e-08 >> total number of linear solver iterations=1 >> total number of function evaluations=19 >> KSP Object: >> 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-05, absolute=1e-50, divergence=10000 >> left preconditioning >> using PRECONDITIONED norm type for convergence test >> PC Object: >> type: ilu >> ILU: out-of-place factorization >> 0 levels of fill >> tolerance for zero pivot 1e-12 >> using diagonal shift to prevent zero pivot >> matrix ordering: natural >> factor fill ratio given 1, needed 1 >> Factored matrix follows: >> Matrix Object: >> type=seqaij, rows=1838, cols=1838 >> package used to perform factorization: petsc >> total: nonzeros=8464, allocated nonzeros=8464 >> total number of mallocs used during MatSetValues calls =0 >> not using I-node routines >> linear system matrix = precond matrix: >> Matrix Object: >> type=seqaij, rows=1838, cols=1838 >> total: nonzeros=8464, allocated nonzeros=9745 >> total number of mallocs used during MatSetValues calls =37 >> not using I-node routines >> >> >> Xuan YU >> xxy113 at psu.edu >> >> >> >> > > Xuan YU (??) xxy113 at psu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20100726/513a6d18/attachment-0001.htm>