[petsc-users] Strange Partition in PETSc 3.11 version on some computers

[Matthew Knepley]

On Sun, Sep 15, 2019 at 5:19 PM Danyang Su via petsc-users <
petsc-users at mcs.anl.gov> wrote:

> Dear All,
>
> I have a question regarding strange partition problem in PETSc 3.11
> version. The problem does not exist on my local workstation. However, on a
> cluster with different PETSc versions, the partition seems quite different,
> as you can find in the figure below, which is tested with 160 processors.
> The color means the processor owns that subdomain. In this layered prism
> mesh, there are 40 layers from bottom to top and each layer has around 20k
> nodes. The natural order of nodes is also layered from bottom to top.
>
> The left partition (PETSc 3.10 and earlier) looks good with minimum number
> of ghost nodes while the right one (PETSc 3.11) looks weired with huge
> number of ghost nodes. Looks like the right one uses partition layer by
> layer. This problem exists on a a cluster but not on my local workstation
> for the same PETSc version (with different compiler and MPI). Other than
> the difference in partition and efficiency, the simulation results are the
> same.
>
> [image: partition difference]
>
> Below is PETSc configuration on three machine:
>
> Local workstation (works fine):  ./configure --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-mpich --download-scalapack
> --download-parmetis --download-metis --download-ptscotch
> --download-fblaslapack --download-hypre --download-superlu_dist
> --download-hdf5=yes --download-ctetgen --with-debugging=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --with-cxx-dialect=C++11
>
> Cluster with PETSc 3.9.3 (works fine):
> --prefix=/scinet/niagara/software/2018a/opt/intel-2018.2-intelmpi-2018.2/petsc/3.9.3
> CC=mpicc CXX=mpicxx F77=mpif77 F90=mpif90 FC=mpifc COPTFLAGS="-march=native
> -O2" CXXOPTFLAGS="-march=native -O2" FOPTFLAGS="-march=native -O2"
> --download-chaco=1 --download-hypre=1 --download-metis=1 --download-ml=1
> --download-mumps=1 --download-parmetis=1 --download-plapack=1
> --download-prometheus=1 --download-ptscotch=1 --download-scotch=1
> --download-sprng=1 --download-superlu=1 --download-superlu_dist=1
> --download-triangle=1 --with-avx512-kernels=1
> --with-blaslapack-dir=/scinet/niagara/intel/2018.2/compilers_and_libraries_2018.2.199/linux/mkl
> --with-debugging=0 --with-hdf5=1
> --with-mkl_pardiso-dir=/scinet/niagara/intel/2018.2/compilers_and_libraries_2018.2.199/linux/mkl
> --with-scalapack=1
> --with-scalapack-lib="[/scinet/niagara/intel/2018.2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so,/scinet/niagara/intel/2018.2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so]"
> --with-x=0
>
> Cluster with PETSc 3.11.3 (looks weired):
> --prefix=/scinet/niagara/software/2019b/opt/intel-2019u4-intelmpi-2019u4/petsc/3.11.3
> CC=mpicc CXX=mpicxx F77=mpif77 F90=mpif90 FC=mpifc COPTFLAGS="-march=native
> -O2" CXXOPTFLAGS="-march=native -O2" FOPTFLAGS="-march=native -O2"
> --download-chaco=1 --download-hdf5=1 --download-hypre=1 --download-metis=1
> --download-ml=1 --download-mumps=1 --download-parmetis=1
> --download-plapack=1 --download-prometheus=1 --download-ptscotch=1
> --download-scotch=1 --download-sprng=1 --download-superlu=1
> --download-superlu_dist=1 --download-triangle=1 --with-avx512-kernels=1
> --with-blaslapack-dir=/scinet/intel/2019u4/compilers_and_libraries_2019.4.243/linux/mkl
> --with-cxx-dialect=C++11 --with-debugging=0
> --with-mkl_pardiso-dir=/scinet/intel/2019u4/compilers_and_libraries_2019.4.243/linux/mkl
> --with-scalapack=1
> --with-scalapack-lib="[/scinet/intel/2019u4/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so,/scinet/intel/2019u4/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so]"
> --with-x=0
>
> And the partition is used by default dmplex distribution.
>
>       !c distribute mesh over processes
>       call DMPlexDistribute(dmda_flow%da,stencil_width,                &
>                             PETSC_NULL_SF,                             &
>                             PETSC_NULL_OBJECT,                         &
>                             distributedMesh,ierr)
>       CHKERRQ(ierr)
>
> Any idea on this strange problem?
>
> I just looked at the code. Your mesh should be partitioned by k-way
partitioning using Metis since its on 1 proc for partitioning. This code
is the same for 3.9 and 3.11, and you get the same result on your machine.
I cannot understand what might be happening on your cluster
(MPI plays no role). Is it possible that you changed the adjacency
specification in that version?

  Thanks,

     Matt

> Thanks,
>
> Danyang
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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