[petsc-users] my code runs too slow

Wed Jul 7 13:33:24 CDT 2010

Sorry, this is the complete one:

[0]PETSC ERROR: --------------------- Error Message  
------------------------------------
[0]PETSC ERROR: Object is in wrong state!
[0]PETSC ERROR: Not for unassembled matrix!
[0]PETSC ERROR:  
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development HG revision:  
fdc7be12de37b8a400b6e561de9850bcc7e79f4f  HG Date: Fri Jul 02 21:17:36  
2010 -0500
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:  
------------------------------------------------------------------------
[0]PETSC ERROR: ./pihm on a arch-linu named lionxi.rcc.psu.edu by  
xxy113 Wed Jul  7 14:32:11 2010
[0]PETSC ERROR: Libraries linked from /gpfs/home/xxy113/soft/petsc-dev/ 
arch-linux-gnu-c-debug/lib
[0]PETSC ERROR: Configure run at Sun Jul  4 14:09:16 2010
[0]PETSC ERROR: Configure options --download-f-blas-lapack=1 -- 
download-mpich=1
[0]PETSC ERROR:  
------------------------------------------------------------------------
[0]PETSC ERROR: MatGetColoring() line 491 in src/mat/color/color.c
[0]PETSC ERROR: VecRestoreArrayPrivate3() line 201 in /work/petsc/pihm.c

On Jul 7, 2010, at 2:28 PM, Satish Balay wrote:

>>> ierr = SNESComputeJacobian(ts_snes,CV_Y,&J,&J,&flag);CHKERRQ(ierr);
>
> Perhaps there is a function thats set to compute jacobinan thats not
> assembling the matrix properly?
>
> Also - please dont' truncate error messages - when you send
> them. Incomplete info is not useful.
>
> Satish
>
> On Wed, 7 Jul 2010, Matthew Knepley wrote:
>
>> You have to assemble
>>
>>  a) after setting values
>>
>>  b) before using the matrix
>>
>> Please consult the user examples where this is done correctly and  
>> the manual
>> section which explains the assembly process.
>>
>>    Matt
>>
>> On Wed, Jul 7, 2010 at 8:13 PM, Xuan YU <xxy113 at psu.edu> wrote:
>>
>>>
>>> On Jul 7, 2010, at 2:06 PM, Satish Balay wrote:
>>>
>>> On Wed, 7 Jul 2010, Xuan YU wrote:
>>>
>>> ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N, 
>>> 10,PETSC_NULL,&J);CHKERRQ(ierr);
>>>
>>>
>>> ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>>>
>>> ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>>>
>>>
>>> This assembly removes the unused space here. Since no values are
>>> inserted - it squezes out all of the allocated space. Perhaps you  
>>> just
>>> need to remove these 2 calls as the actual matrix is assembled  
>>> further
>>> down the code.
>>>
>>>
>>> I removed these 2
>>> But got Error Message
>>>
>>> [0]PETSC ERROR: Object is in wrong state!
>>> [0]PETSC ERROR: Not for unassembled matrix!
>>>
>>>
>>>
>>>
>>>
>>> Satish
>>>
>>> ierr = SNESComputeJacobian(ts_snes,CV_Y,&J,&J,&flag);CHKERRQ(ierr);
>>>
>>> ierr = MatGetColoring(J,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr);
>>>
>>> ierr =  
>>> MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr);
>>>
>>> ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode
>>>
>>> (*)(void))f,(void*)&appctx);CHKERRQ(ierr);
>>>
>>> ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
>>>
>>> ierr =
>>> TSSetRHSJacobian 
>>> (ts,J,J,TSDefaultComputeJacobianColor,matfdcoloring);
>>>
>>>
>>> These are the Jacobian related codes.
>>>
>>>
>>>
>>>
>>>
>>> On Jul 7, 2010, at 1:51 PM, Satish Balay wrote:
>>>
>>>
>>> total: nonzeros=1830
>>>
>>> mallocs used during MatSetValues calls =1830
>>>
>>>
>>> Looks like you are zero-ing out the non-zero structure - before
>>>
>>> assembling the matrix.
>>>
>>>
>>> Are you calling MatZeroRows() or MatZeroEntries() or something  
>>> else -
>>>
>>> before assembling the matrix?
>>>
>>>
>>> Satish
>>>
>>>
>>> On Wed, 7 Jul 2010, Xuan YU wrote:
>>>
>>>
>>> I made a change: ierr =
>>>
>>> MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,5,PETSC_NULL,&J);CHKERRQ(ierr);
>>>
>>>
>>> Time of the code did not change much, and got the info:
>>>
>>> Matrix Object:
>>>
>>>    type=seqaij, rows=1830, cols=1830
>>>
>>>    total: nonzeros=1830, allocated nonzeros=36600
>>>
>>>    total number of mallocs used during MatSetValues calls =1830
>>>
>>>      not using I-node routines
>>>
>>>
>>>
>>>
>>> On Jul 7, 2010, at 12:51 PM, Satish Balay wrote:
>>>
>>>
>>>  total: nonzeros=1830, allocated nonzeros=29280
>>>
>>>  total number of mallocs used during MatSetValues calls =1830
>>>
>>>
>>> There is something wrong with your preallocation or matrix
>>>
>>> assembly. You should see zero mallocs for efficient assembly.
>>>
>>>
>>>
>>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#efficient-assembly
>>>
>>>
>>> satish
>>>
>>>
>>>
>>> On Wed, 7 Jul 2010, Xuan YU wrote:
>>>
>>>
>>> Hi,
>>>
>>>
>>> I finite difference Jacobian approximation for my TS model. The size
>>>
>>> of
>>>
>>> the
>>>
>>> vector is 1830. I got the following info with(-ts_view):
>>>
>>>
>>> type: beuler
>>>
>>> maximum steps=50
>>>
>>> maximum time=50
>>>
>>> total number of nonlinear solver iterations=647
>>>
>>> total number of linear solver iterations=647
>>>
>>> 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=50
>>>
>>> total number of function evaluations=51
>>>
>>> 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=1830, cols=1830
>>>
>>>        package used to perform factorization: petsc
>>>
>>>        total: nonzeros=1830, allocated nonzeros=1830
>>>
>>>        total number of mallocs used during MatSetValues calls =0
>>>
>>>          not using I-node routines
>>>
>>> linear system matrix = precond matrix:
>>>
>>> Matrix Object:
>>>
>>>  type=seqaij, rows=1830, cols=1830
>>>
>>>  total: nonzeros=1830, allocated nonzeros=29280
>>>
>>>  total number of mallocs used during MatSetValues calls =1830
>>>
>>>    not using I-node routines
>>>
>>>
>>>
>>> 50 output time step takes me 11.877s. So I guess there is something
>>>
>>> not
>>>
>>> appropriate with my Jacobian Matrix. Could you please tell me how to
>>>
>>> speed
>>>
>>> up
>>>
>>> my code?
>>>
>>>
>>> Thanks!
>>>
>>>
>>> Xuan YU
>>>
>>> xxy113 at psu.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Xuan YU (俞烜)
>>>
>>> xxy113 at psu.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>> Xuan YU (俞烜)
>>>
>>> xxy113 at psu.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>> Xuan YU (俞烜)
>>> xxy113 at psu.edu
>>>
>>>
>>>
>>>
>>>
>>
>>
>>

Xuan YU (俞烜)
xxy113 at psu.edu

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