Perhaps you missed a step here. After 'configure' you shoud do 'make all' to rebuild the PETSc libraries.
Then you should try 'make test' to verify the build. After that - attempt to build your code. satish On Mon, 26 Jul 2010, Xuan YU wrote: > > 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 > > > >
