[petsc-users] Re-configuring PETSc

[Najeeb Ahmad]

On Mon, May 28, 2018 at 9:32 PM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:

>
>
> > On May 28, 2018, at 10:32 AM, Najeeb Ahmad <nahmad16 at ku.edu.tr> wrote:
> >
> > Thanks a lot Satish for your prompt reply.
> >
> > I just checked that SuperLU_dist package works only for matrices of type
> aij. and uses lu preconditioner. I am currently working with baij matrix.
> What is the best preconditioner choice for baij matrices on parallel
> machines?
>
>     The best preconditioner is always problem specific. Where does your
> problem come from? CFD? Structural mechanics? other apps?
>

        I am interested in writing solver for reservoir simulation
employing FVM and unstructured grids. My main objective is to study
performance of the code with different data structures/data layouts and
architecture specific optimizations, specifically targeting the multicore
architectures like KNL for instance. Later the study may be extended to
include GPUs. The options for switching between AIJ and BAIJ etc. are
therefore very useful for my study.

        The purpose why I wanted to change the preconditioner is that the
default preconditioner is giving me different iterations count for
different number of processesors. I would rather like a preconditioner that
would give me same iteration count for any processor count so that I can
better compare the performance results.

        Your suggestions in this regard are highly appreciated,
specifically with reference to the following points:

         - Is it possible to explicitly use high bandwidth memory in PETSc
for selected object placement (e.g. using memkind library for instance)?
         - What would it take to take advantage of architecture specific
compiler flags to achieve good performance on a given platform (e.g.
-xMIC-AVX512 for AVX512 on KNL, #pragma SIMD etc.).

       Sorry for some very basic questions as I am a novice PETSc user.

     Thanks for your time :)

>
>      Anyways you probably want to make your code be able to switch between
> AIJ and BAIJ at run time since the different formats support somewhat
> different solvers. If your code alls MatSetFromOptions then you can switch
> via the command line option -mat_type aij or baij
>
>    Barry
>
> >
> > Thanks
> >
> > On Mon, May 28, 2018 at 8:23 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> > On Mon, 28 May 2018, Najeeb Ahmad wrote:
> >
> > > Hi All,
> > >
> > > I have Petsc release version 3.9.2 configured with the following
> options:
> > >
> > > Configure options --with-cc=mpiicc --with-cxx=mpiicpc
> --with-fc=mpiifort
> > > --download-fblaslapack=1
> > >
> > > Now I want to use PCILU in my code and when I set the PC type to PCILU
> in
> > > the code, I get the following error:
> > >
> > > [0]PETSC ERROR: --------------------- Error Message
> > > --------------------------------------------------------------
> > > [0]PETSC ERROR: See
> > > http://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html for
> > > possible LU and Cholesky solvers
> > > [0]PETSC ERROR: Could not locate a solver package. Perhaps you must
> > > ./configure with --download-<package>
> > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for
> > > trouble shooting.
> > > [0]PETSC ERROR: Petsc Release Version 3.9.2, unknown
> > > [0]PETSC ERROR: ./main on a arch-linux2-c-debug named Karachi by
> nahmad Mon
> > > May 28 17:52:41 2018
> > > [0]PETSC ERROR: Configure options --with-cc=mpiicc --with-cxx=mpiicpc
> > > --with-fc=mpiifort --download-fblaslapack=1
> > > [0]PETSC ERROR: #1 MatGetFactor() line 4318 in
> > > /home/nahmad/PETSc/petsc/src/mat/interface/matrix.c
> > > [0]PETSC ERROR: #2 PCSetUp_ILU() line 142 in
> > > /home/nahmad/PETSc/petsc/src/ksp/pc/impls/factor/ilu/ilu.c
> > > [0]PETSC ERROR: #3 PCSetUp() line 923 in
> > > /home/nahmad/PETSc/petsc/src/ksp/pc/interface/precon.c
> > > [0]PETSC ERROR: #4 KSPSetUp() line 381 in
> > > /home/nahmad/PETSc/petsc/src/ksp/ksp/interface/itfunc.c
> > > [0]PETSC ERROR: #5 KSPSolve() line 612 in
> > > /home/nahmad/PETSc/petsc/src/ksp/ksp/interface/itfunc.c
> > > [0]PETSC ERROR: #6 SolveSystem() line 60 in
> > > /home/nahmad/Aramco/petsc/petsc/BlockSolveTest/src/main.c
> > >
> > >
> > > I assume that I am missing LU package like SuperLU_dist for instance
> and I
> > > need to download and configure it with Petsc.
> >
> > yes - petsc has sequential LU - but you need superlu_dist/mumps for
> parallel lu.
> >
> > >
> > > I am wondering what is the best way to reconfigure Petsc to download
> and
> > > use the appropriate package to support PCILU?
> >
> > Rerun configure with the additional option --download-superlu_dist=1.
> >
> > You can do this with current PETSC_ARCH you are using [i.e reinstall
> > over the current build] - or use a different PETSC_ARCH - so both
> > builds exist and useable.
> >
> > Satish
> >
> > >
> > > You advice is highly appreciated.
> > >
> > >
> >
> >
> >
> >
> > --
> > Najeeb Ahmad
> >
> > Research and Teaching Assistant
> > PARallel and MultiCORE Computing Laboratory (ParCoreLab)
> > Computer Science and Engineering
> > Koç University, Istanbul, Turkey
> >
>
>


-- 
*Najeeb Ahmad*


*Research and Teaching Assistant*
*PARallel and MultiCORE Computing Laboratory (ParCoreLab) *

*Computer Science and Engineering*
*Koç University, Istanbul, Turkey*
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