[petsc-users] Slepc: Computing first 4 smallest eigenvalues and eigenvectors of a large graph Laplacian
Barry Smith
bsmith at mcs.anl.gov
Sat Mar 25 23:15:27 CDT 2017
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.
Barry
##########################################################
# #
# WARNING!!! #
# #
# This code was compiled with a debugging option, #
# To get timing results run ./configure #
# using --with-debugging=no, the performance will #
# be generally two or three times faster. #
# #
##########################################################
> On Mar 25, 2017, at 11:08 PM, Bodhisatta Pramanik <bodhi91 at iastate.edu> wrote:
>
>
> 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/documentation/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
>
>
> Send the output from -log_view:
> I have attached the .txt file: "Log Summary".txt
>
>
> Ok. Since it only stores half the matrix it requires less memory and because of the way it does the MatMult and MatSolve it can be a tiny bit faster.
> I do get a little improvement in speed, but nothing significant.
>
> Thanks,
> Bodhi
>
>
> On Sat, Mar 25, 2017 at 10:56 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> > On Mar 25, 2017, at 10:48 PM, Bodhisatta Pramanik <bodhi91 at iastate.edu> wrote:
> >
> > Try -st_pc_type gamg:
> >
> > Doing this with the existing eigensolver,linear solver : ./RunPart -eps_type jd -eps_nev 3 -st_ksp_type cg -st_ksp_rtol 0.001 -eps_tol 0.001 -st_pc_type gamg -eps_smallest_real results in the following issues:-
> > PETSC ERROR: Object is in wrong state
> > PETSC ERROR: Must call EPSSolve() first: Parameter #1
>
> I cannot explain this. A different preconditioner with nothing else changed shouldn't cause any problem like this. Send all the output in the error message.
> >
> > Try -st_pc_type sor
> >
> > Doing this again with the existing eigensolver,linear solver returns me the eigenvalues but it takes more time. (106 seconds) for a Laplacian matrix of 200K size. The bjacobi was giving me the same eigenvalues but in 60 seconds.
>
> Ok, this is reasonable.
>
> >
> >
> > Run with -log_view to see where the computation is taking the most time:
>
> Send the output from -log_view
> >
> > EPSSolve and KSPSolve take the most time to finish computation.
> >
> > Since the matrix is symmetric are you using the sbaij format instead of AIJ?
> >
> > I am using the sbaij format but with block size 1. I guess that is equivalent to the AIJ format itself.
>
> Ok. Since it only stores half the matrix it requires less memory and because of the way it does the MatMult and MatSolve it can be a tiny bit faster.
>
> Barry
>
> >
> >
> > Thanks,
> > Bodhi
> >
> >
> >
> >
> > On Sat, Mar 25, 2017 at 10:22 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> > > On Mar 25, 2017, at 8:52 PM, Bodhisatta Pramanik <bodhi91 at iastate.edu> wrote:
> > >
> > > Hi,
> > >
> > > I apologize for the slepc question. I could not find any user lists so I'm hoping someone on here might be able to offer some guidance.
> > >
> > > Problem Definition:
> > > I am working on a graph partitioning problem. I have the laplacian of a large graph(500,000 nodes) and am interested in extracting its global information in order to find good partitioning. An approach is to compute the first few(4-5) eigenvalues and use that information to formulate the partition algorithm.
> > >
> > > I am leveraging the EPS solvers of the Slepc library. It appears that the Jacobi-davidson eigen solver gives me the eigenvalues in the shortest period of time compared to others (Krylov-Schur, Rayleigh quotient, Lanczos, etc). I use this eigensolver with the conjugate gradient linear solver and the block-jacobi preconditioner. So this is what I am basically passing through the command line:
> > >
> > > ./RunPart -eps_type jd -eps_nev 4 -st_ksp_type cg -st_ksp_rtol 0.001 -eps_tol 0.001 -st_pc_type bjacobi -eps_smallest_real
> >
> > Try -st_pc_type gamg
> >
> > One one process default bjacobi results in ILU which is not a great preconditioner.
> >
> > Also try -st_pc_type sor
> >
> > >
> > > Question:
> > > The time it takes to compute the first 4-5 eigenvectors of a matrix of size (200k) is near about 60 seconds. CPU config: Intel Xeon 2GHz. I am using a single processor to run my code. Is there any way I can gain major speedup than what I am getting?
> >
> > Run with -log_view to see where the computation is taking the most time.
> >
> > >
> > > Is it possible to obtain the eigenvalues inside 10-15 seconds of such huge matrices even if I do not use multiple processor??
> > >
> > > Can someone provide me with some valuable guidance??
> >
> > Since the matrix is symmetric are you using the sbaij format instead of AIJ?
> >
> > >
> > > Thanks,
> > > Bodhi
> >
> >
> >
> >
> > --
> > 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
> <Log Summary>
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