[petsc-users] Slepc: Computing first 4 smallest eigenvalues and eigenvectors of a large graph Laplacian
Hong
hzhang at mcs.anl.gov
Sun Mar 26 16:06:57 CDT 2017
For icc and cholesky factorizations, MatSolve_SeqSBAIJ() is used for
both aij and sbaij. Why it gives different flops?
Hong
On Sun, Mar 26, 2017 at 2:44 PM, Bodhisatta Pramanik <bodhi91 at iastate.edu>
wrote:
> *The flop rate for the MatMult and MatSolve are much lower than I would
> expect. Try using the AIJ matrix instead of SBAIJ.*
> SeqAIJ:
> MatMult = 213 Mflop/s
> MatSolve = 204 Mflop/s
> AIJ:
> MatMult = 211 Mflop/s
> MatSolve = 198 Mflop/s
> SBAIJ:
> MatMult = 179 Mflop/s
> MatSolve = 167 Mflop/s
>
> Shouldn't the SBAIJ provide the best performance since it only works with
> the upper triangular part of the whole large sparse symmetric matrix?
>
> Thanks,
> Bodhi
>
> On Sun, Mar 26, 2017 at 12:30 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>>
>> The flop rate for the MatMult and MatSolve are much lower than I would
>> expect. Try using the AIJ matrix instead of SBAIJ.
>>
>>
>> > On Mar 26, 2017, at 6:25 AM, Bodhisatta Pramanik <bodhi91 at iastate.edu>
>> wrote:
>> >
>> > *First set a new PETSC_ARCH say arch-opt and ./configure with the
>> additional argument --with-debugging=0 then recompile PETSc with the new
>> PETSC_ARCH and recompile your code then send the new -log_view output.*
>> > I have attached the new log summary with this file. The computation
>> time is a lot faster now. It takes around 23 seconds to compute the first 3
>> eigenvectors of a 200K sized matrix.
>> >
>> > Thanks,
>> > Bodhi
>> >
>> > On Sun, Mar 26, 2017 at 3:14 AM, Bodhisatta Pramanik <
>> bodhi91 at iastate.edu> wrote:
>> > *The error is in EPSComputeError(), not in EPSSolve(). Did you modify
>> the state of the EPS object between EPSSolve() and EPSComputeError()?*
>> >
>> > I am not modifying the eps object. I have copied a part of the code
>> where I am computing the eigenvectors.
>> >
>> > EPSCreate(PETSC_COMM_WORLD,&eps);
>> > EPSSetOperators(eps,m.Lpl,NULL);
>> > EPSSetProblemType(eps,EPS_HEP);
>> > EPSSetFromOptions(eps);
>> >
>> > EPSSolve(eps); //Solving for the eigenvalues
>> >
>> > EPSGetIterationNumber(eps,&its);
>> > PetscPrintf(PETSC_COMM_WORLD,"Number of iterations of the
>> method: %D\n",its);
>> > EPSGetType(eps,&type);
>> > PetscPrintf(PETSC_COMM_WORLD,"Solution Method: %s\n\n",type);
>> > EPSGetTolerances(eps,&get_tol,&maxit);
>> > PetscPrintf(PETSC_COMM_WORLD,"Stopping condition: tol=%.4g,
>> maxit=%D\n",(double)get_tol,maxit);
>> > EPSGetConverged(eps,&nconv);
>> > PetscPrintf(PETSC_COMM_WORLD, "Number of converged eigenpairs:
>> %D\n\n",nconv);
>> > if(nconv>0)
>> > {
>> > PetscPrintf(PETSC_COMM_WORLD,
>> > " k ||Ax-kx||/||kx||\n"
>> > "-------------- ----------------\n");
>> > for(i=0;i<nconv;i++)
>> > {
>> > EPSGetEigenpair(eps,i,&kr,&ki,xr,xi);
>> > EPSComputeError(eps,i,EPS_ERR
>> OR_RELATIVE,&error);
>> > re = PetscRealPart(kr);
>> > im = PetscImaginaryPart(kr);
>> >
>> > re = kr;
>> > im = ki;
>> > if(im!=0.0) {
>> > PetscPrintf(PETSC_COMM_WORLD,"
>> %9f%+9fi %12g\n",(double)re,(double)im,(double)error);
>> > }
>> > else {
>> > PetscPrintf(PETSC_COMM_WORLD,"
>> %12f %12g\n",(double)re,(double)error);
>> > }
>> > }
>> > PetscPrintf(PETSC_COMM_WORLD,"\n");
>> > }
>> >
>> > EPSDestroy(&eps);
>> > VecDestroy(&xr);
>> > VecDestroy(&xi);
>> > }
>> >
>> > This is what I pass through my command line:
>> > ./RunPart -eps_type jd -eps_nev 3 -st_ksp_type cg -st_ksp_rtol 0.001
>> -eps_tol 0.001 -st_pc_type bjacobi -eps_smallest_real
>> >
>> >
>> > *In graph partitioning, I would strongly recommend deflating the
>> eigenvector corresponding to the zero eigenvalue, as is done in ex11.c:*
>> > I have tried doing this but for some reason the eigenvalues
>> fail to converge.
>> >
>> >
>> >
>> > On Sun, Mar 26, 2017 at 2:41 AM, Jose E. Roman <jroman at dsic.upv.es>
>> wrote:
>> >
>> > > El 26 mar 2017, a las 6:08, Bodhisatta Pramanik <bodhi91 at iastate.edu>
>> escribió:
>> > >
>> > > Send all the output in the error message:
>> > >
>> > > [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> > > [0]PETSC ERROR: Object is in wrong state
>> > > [0]PETSC ERROR: Must call EPSSolve() first: Parameter #1
>> > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html for trouble shooting.
>> > > [0]PETSC ERROR: Petsc Release Version 3.7.5, Jan, 01, 2017
>> > > [0]PETSC ERROR: ./RunPart on a arch-linux2-c-debug named
>> research-5.ece.iastate.edu by bodhi91 Sat Mar 25 22:33:56 2017
>> > > [0]PETSC ERROR: Configure options --with-cc=gcc --with-css=g++
>> -with-fc=gfortran --download-fblaslapack --download-mpich
>> > > [0]PETSC ERROR: #10468 EPSComputeError() line 643 in
>> /tmp/Bodhi/slepc-3.7.3/src/eps/interface/epssolve.c
>> > > 0.000000 2.0795e-317
>> > >
>> >
>> > The error is in EPSComputeError(), not in EPSSolve(). Did you modify
>> the state of the EPS object between EPSSolve() and EPSComputeError()?
>> >
>> > In graph partitioning, I would strongly recommend deflating the
>> eigenvector corresponding to the zero eigenvalue, as is done in ex11.c:
>> > http://slepc.upv.es/documentation/current/src/eps/examples/
>> tutorials/ex11.c.html
>> >
>> > Jose
>> >
>> >
>> >
>> >
>> > --
>> > Bodhisatta Pramanik,
>> > Graduate Student,
>> > Department of Electrical and Computer Engineering,
>> > 301 Durham,
>> > Iowa State University,
>> > Ames,Iowa 50011,
>> > bodhi91 at iastate.edu
>> > 515-735-6300
>> >
>> >
>> >
>> > --
>> > Bodhisatta Pramanik,
>> > Graduate Student,
>> > Department of Electrical and Computer Engineering,
>> > 301 Durham,
>> > Iowa State University,
>> > Ames,Iowa 50011,
>> > bodhi91 at iastate.edu
>> > 515-735-6300
>> > <New Log Summary>
>>
>>
>
>
> --
> *Bodhisatta Pramanik,*
> *Graduate Student,*
> *Department of Electrical and Computer Engineering,*
> *301 Durham,*
> *Iowa State University,*
> *Ames,Iowa 50011,*
> bodhi91 at iastate.edu
> *515-735-6300 <(515)%20735-6300>*
>
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