[petsc-users] about speed

[Satish Balay]

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 (俞烜)
> xxy113 at psu.edu
> 
> 
> 
>