[petsc-users] about speed

[Xuan YU]

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




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