[petsc-users] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: Strange Partition in PETSc 3.11 version on some computers

Sun Sep 15 23:26:15 CDT 2019

On 2019-09-15 4:43 p.m., Smith, Barry F. wrote:
>    Send the configure.log and make.log for the two system configurations that produce very different results as well as the output running with -dm_view -info for both runs. The cause is likely not subtle, one is likely using metis and the other is likely just not using any partitioner.

Hi Barry,

Attached is the output information with -dm_view -info for both runs. 
The configure.log and make.log will be mailed to you once I get it from 
the SCINET staff who installed PETSc on this cluster.

Thanks,

Danyang

>
>
>
>> On Sep 15, 2019, at 6:07 PM, Matthew Knepley via petsc-users <petsc-users at mcs.anl.gov> wrote:
>>
>> On Sun, Sep 15, 2019 at 6:59 PM Danyang Su <danyang.su at gmail.com> wrote:
>> Hi Matt,
>>
>> Thanks for the quick reply. I have no change in the adjacency. The source code and the simulation input files are all the same. I also tried to use GNU compiler and mpich with petsc 3.11.3 and it works fine.
>>
>> It looks like the problem is caused by the difference in configuration. However, the configuration is pretty the same as petsc 3.9.3 except the compiler and mpi used. I will contact scinet staff to check if they have any idea on this.
>>
>> Very very strange since the partition is handled completely by Metis, and does not use MPI.
>>
>>    Thanks,
>>
>>      Matt
>>   
>> Thanks,
>>
>> Danyang
>>
>> On September 15, 2019 3:20:18 p.m. PDT, Matthew Knepley <knepley at gmail.com> wrote:
>> 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.
>>
>>
>>
>>
>> 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/
>>
>> -- 
>> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>>
>>
>> -- 
>> 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/
-------------- next part --------------
A non-text attachment was scrubbed...
Name: basin-3d-petsc3.3.9.log.tar.gz
Type: application/gzip
Size: 226582 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20190915/5ecc2209/attachment-0002.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: basin-3d-petsc3.11.3.log.tar.gz
Type: application/gzip
Size: 751782 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20190915/5ecc2209/attachment-0003.bin>