[petsc-users] Sporadic MPI_Allreduce() called in different locations on larger core counts
Mark Lohry
mlohry at gmail.com
Sun Aug 11 14:47:31 CDT 2019
Sorry, forgot to reply to the mailing list.
where does your matrix come from? A mesh? Structured, unstructured, a
> graph, something else? What type of discretization?
Unstructured tetrahedral mesh (CGNS, I can give links to the files if
that's of interest), the discretization is arbitrary order discontinuous
galerkin for compressible navier-stokes. 5 coupled equations x 10 nodes per
element for this 2nd order case to give the 50x50 blocks. Each tet cell
dependent on neighbors, so for tets 4 extra off-diagonal blocks per cell.
I would expect one could exploit the large block size here in computing the
coloring -- the underlying mesh is 2M nodes with the same connectivity as a
standard cell-centered finite volume method.
On Sun, Aug 11, 2019 at 2:12 PM Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>
> These are due to attempting to copy the entire matrix to one process and
> do the sequential coloring there. Definitely won't work for larger
> problems, we'll
>
> need to focus on
>
> 1) having useful parallel coloring and
> 2) maybe using an alternative way to determine the coloring:
>
> where does your matrix come from? A mesh? Structured, unstructured, a
> graph, something else? What type of discretization?
>
> Barry
>
>
> > On Aug 11, 2019, at 10:21 AM, Mark Lohry <mlohry at gmail.com> wrote:
> >
> > On the very large case, there does appear to be some kind of overflow
> ending up with an attempt to allocate too much memory in MatFDColorCreate,
> even with --with-64-bit-indices. Full terminal output here:
> >
> https://raw.githubusercontent.com/mlohry/petsc_miscellany/master/slurm-3451378.out
> >
> > In particular:
> > PETSC ERROR: Memory requested 1036713571771129344
> >
> > Log filename here:
> > https://github.com/mlohry/petsc_miscellany/blob/master/petsclogfile.0
> >
> > On Sun, Aug 11, 2019 at 9:49 AM Mark Lohry <mlohry at gmail.com> wrote:
> > Hi Barry, I made a minimum example comparing the colorings on a very
> small case. You'll need to unzip the jacobian_sparsity.tgz to run it.
> >
> > https://github.com/mlohry/petsc_miscellany
> >
> > This is sparse block system with 50x50 block sizes, ~7,680 blocks.
> Comparing the coloring types sl, lf, jp, id, greedy, I get these timings
> wallclock, running with -np 16:
> >
> > SL: 1.5s
> > LF: 1.3s
> > JP: 29s !
> > ID: 1.4s
> > greedy: 2s
> >
> > As far as I'm aware, JP is the only parallel coloring implemented? It is
> looking as though I'm simply running out of memory with the sequential
> methods (I should apologize to my cluster admin for chewing up 10TB and
> crashing...).
> >
> > On this small problem JP is taking 30 seconds wallclock, but that time
> grows exponentially with larger problems (last I tried it, I killed the job
> after 24 hours of spinning.)
> >
> > Also as I mentioned, the "greedy" method appears to be producing an
> invalid coloring for me unless I also specify weights "lexical". But
> "-mat_coloring_test" doesn't complain. I'll have to make a different
> example to actually show it's an invalid coloring.
> >
> > Thanks,
> > Mark
> >
> >
> >
> > On Sat, Aug 10, 2019 at 4:38 PM Smith, Barry F. <bsmith at mcs.anl.gov>
> wrote:
> >
> > Mark,
> >
> > Would you be able to cook up an example (or examples) that
> demonstrate the problem (or problems) and how to run it? If you send it to
> us and we can reproduce the problem then we'll fix it. If need be you can
> send large matrices to petsc-maint at mcs.anl.gov don't send them to
> petsc-users since it will reject large files.
> >
> > Barry
> >
> >
> > > On Aug 10, 2019, at 1:56 PM, Mark Lohry <mlohry at gmail.com> wrote:
> > >
> > > Thanks Barry, been trying all of the above. I think I've homed in on
> it to an out-of-memory and/or integer overflow inside MatColoringApply.
> Which makes some sense since I only have a sequential coloring algorithm
> working...
> > >
> > > Is anyone out there using coloring in parallel? I still have the same
> previously mentioned issues with MATCOLORINGJP (on small problems takes
> upwards of 30 minutes to run) which as far as I can see is the only
> "parallel" implementation. MATCOLORINGSL and MATCOLORINGID both work on
> less large problems, MATCOLORINGGREEDY works on less large problems if and
> only if I set weight type to MAT_COLORING_WEIGHT_LEXICAL, and all 3 are
> failing on larger problems.
> > >
> > > On Tue, Aug 6, 2019 at 9:36 AM Smith, Barry F. <bsmith at mcs.anl.gov>
> wrote:
> > >
> > > There is also
> > >
> > > $ ./configure --help | grep color
> > > --with-is-color-value-type=<char,short>
> > > char, short can store 256, 65536 colors current: short
> > >
> > > I can't imagine you have over 65 k colors but something to check
> > >
> > >
> > > > On Aug 6, 2019, at 8:19 AM, Mark Lohry <mlohry at gmail.com> wrote:
> > > >
> > > > My first guess is that the code is getting integer overflow
> somewhere. 25 billion is well over the 2 billion that 32 bit integers can
> hold.
> > > >
> > > > Mine as well -- though in later tests I have the same issue when
> using --with-64-bit-indices. Ironically I had removed that flag at some
> point because the coloring / index set was using a serious chunk of total
> memory on medium sized problems.
> > >
> > > Understood
> > >
> > > >
> > > > Questions on the petsc internals there though: Are matrices indexed
> with two integers (i,j) so the max matrix dimension is (int limit) x (int
> limit) or a single integer so the max dimension is sqrt(int limit)?
> > > > Also I was operating under the assumption the 32 bit limit should
> only constrain per-process problem sizes (25B over 400 processes giving 62M
> non-zeros per process), is that not right?
> > >
> > > It is mostly right but may not be right for everything in PETSc.
> For example I don't know about the MatFD code
> > >
> > > Since using a debugger is not practical for large code counts to
> find the point the two processes diverge you can try
> > >
> > > -log_trace
> > >
> > > or
> > >
> > > -log_trace filename
> > >
> > > in the second case it will generate one file per core called
> filename.%d note it will produce a lot of output
> > >
> > > Good luck
> > >
> > >
> > >
> > > >
> > > > We are adding more tests to nicely handle integer overflow but it
> is not easy since it can occur in so many places
> > > >
> > > > Totally understood. I know the pain of only finding an overflow bug
> after days of waiting in a cluster queue for a big job.
> > > >
> > > > We urge you to upgrade.
> > > >
> > > > I'll do that today and hope for the best. On first tests on 3.11.3,
> I still have a couple issues with the coloring code:
> > > >
> > > > * I am still getting the nasty hangs with MATCOLORINGJP mentioned
> here:
> https://lists.mcs.anl.gov/mailman/htdig/petsc-users/2017-October/033746.html
> > > > * MatColoringSetType(coloring, MATCOLORINGGREEDY); this produces a
> wrong jacobian unless I also set MatColoringSetWeightType(coloring,
> MAT_COLORING_WEIGHT_LEXICAL);
> > > > * MATCOLORINGMIS mentioned in the documentation doesn't seem to
> exist.
> > > >
> > > > Thanks,
> > > > Mark
> > > >
> > > > On Tue, Aug 6, 2019 at 8:56 AM Smith, Barry F. <bsmith at mcs.anl.gov>
> wrote:
> > > >
> > > > My first guess is that the code is getting integer overflow
> somewhere. 25 billion is well over the 2 billion that 32 bit integers can
> hold.
> > > >
> > > > We urge you to upgrade.
> > > >
> > > > Regardless for problems this large you likely need the
> ./configure option --with-64-bit-indices
> > > >
> > > > We are adding more tests to nicely handle integer overflow but it
> is not easy since it can occur in so many places
> > > >
> > > > Hopefully this will resolve your problem with large process counts
> > > >
> > > > Barry
> > > >
> > > >
> > > > > On Aug 6, 2019, at 7:43 AM, Mark Lohry via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
> > > > >
> > > > > I'm running some larger cases than I have previously with a
> working code, and I'm running into failures I don't see on smaller cases.
> Failures are on 400 cores, ~100M unknowns, 25B non-zero jacobian entries.
> Runs successfully on half size case on 200 cores.
> > > > >
> > > > > 1) The first error output from petsc is "MPI_Allreduce() called in
> different locations". Is this a red herring, suggesting some process failed
> prior to this and processes have diverged?
> > > > >
> > > > > 2) I don't think I'm running out of memory -- globally at least.
> Slurm output shows e.g.
> > > > > Memory Utilized: 459.15 GB (estimated maximum)
> > > > > Memory Efficiency: 26.12% of 1.72 TB (175.78 GB/node)
> > > > > I did try with and without --64-bit-indices.
> > > > >
> > > > > 3) The debug traces seem to vary, see below. I *think* the failure
> might be happening in the vicinity of a Coloring call. I'm using
> MatFDColoring like so:
> > > > >
> > > > > ISColoring iscoloring;
> > > > > MatFDColoring fdcoloring;
> > > > > MatColoring coloring;
> > > > >
> > > > > MatColoringCreate(ctx.JPre, &coloring);
> > > > > MatColoringSetType(coloring, MATCOLORINGGREEDY);
> > > > >
> > > > > // converges stalls badly without this on small cases, don't
> know why
> > > > > MatColoringSetWeightType(coloring,
> MAT_COLORING_WEIGHT_LEXICAL);
> > > > >
> > > > > // none of these worked.
> > > > > // MatColoringSetType(coloring, MATCOLORINGJP);
> > > > > // MatColoringSetType(coloring, MATCOLORINGSL);
> > > > > // MatColoringSetType(coloring, MATCOLORINGID);
> > > > > MatColoringSetFromOptions(coloring);
> > > > >
> > > > > MatColoringApply(coloring, &iscoloring);
> > > > > MatColoringDestroy(&coloring);
> > > > > MatFDColoringCreate(ctx.JPre, iscoloring, &fdcoloring);
> > > > >
> > > > > I have had issues in the past with getting a functional coloring
> setup for finite difference jacobians, and the above is the only
> configuration I've managed to get working successfully. Have there been any
> significant development changes to that area of code since v3.8.3? I'll try
> upgrading in the mean time and hope for the best.
> > > > >
> > > > >
> > > > >
> > > > > Any ideas?
> > > > >
> > > > >
> > > > > Thanks,
> > > > > Mark
> > > > >
> > > > >
> > > > > *************************************
> > > > >
> > > > > mlohry at lancer:/ssd/dev_ssd/cmake-build$ grep "\[0\]"
> slurm-3429773.out
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Petsc has generated inconsistent data
> > > > > [0]PETSC ERROR: MPI_Allreduce() called in different locations
> (functions) on different processors
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h19c1n19
> by mlohry Tue Aug 6 06:05:02 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun --with-64-bit-indices
> > > > > [0]PETSC ERROR: #1 TSSetMaxSteps() line 2944 in
> /home/mlohry/build/external/petsc/src/ts/interface/ts.c
> > > > > [0]PETSC ERROR: #2 TSSetMaxSteps() line 2944 in
> /home/mlohry/build/external/petsc/src/ts/interface/ts.c
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Invalid argument
> > > > > [0]PETSC ERROR: Enum value must be same on all processes, argument
> # 2
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h19c1n19
> by mlohry Tue Aug 6 06:05:02 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun --with-64-bit-indices
> > > > > [0]PETSC ERROR: #3 TSSetExactFinalTime() line 2250 in
> /home/mlohry/build/external/petsc/src/ts/interface/ts.c
> > > > > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > > > > [0]PETSC ERROR: Caught signal number 15 Terminate: Some process
> (or the batch system) has told this process to end
> > > > > [0]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> > > > > [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> > > > > [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
> Mac OS X to find memory corruption errors
> > > > > [0]PETSC ERROR: likely location of problem given in stack below
> > > > > [0]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> > > > > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> > > > > [0]PETSC ERROR: INSTEAD the line number of the start of the
> function
> > > > > [0]PETSC ERROR: is given.
> > > > > [0]PETSC ERROR: [0] PetscCommDuplicate line 130
> /home/mlohry/build/external/petsc/src/sys/objects/tagm.c
> > > > > [0]PETSC ERROR: [0] PetscHeaderCreate_Private line 34
> /home/mlohry/build/external/petsc/src/sys/objects/inherit.c
> > > > > [0]PETSC ERROR: [0] DMCreate line 36
> /home/mlohry/build/external/petsc/src/dm/interface/dm.c
> > > > > [0]PETSC ERROR: [0] DMShellCreate line 983
> /home/mlohry/build/external/petsc/src/dm/impls/shell/dmshell.c
> > > > > [0]PETSC ERROR: [0] TSGetDM line 5287
> /home/mlohry/build/external/petsc/src/ts/interface/ts.c
> > > > > [0]PETSC ERROR: [0] TSSetIFunction line 1310
> /home/mlohry/build/external/petsc/src/ts/interface/ts.c
> > > > > [0]PETSC ERROR: [0] TSSetExactFinalTime line 2248
> /home/mlohry/build/external/petsc/src/ts/interface/ts.c
> > > > > [0]PETSC ERROR: [0] TSSetMaxSteps line 2942
> /home/mlohry/build/external/petsc/src/ts/interface/ts.c
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Signal received
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h19c1n19
> by mlohry Tue Aug 6 06:05:02 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun --with-64-bit-indices
> > > > > [0]PETSC ERROR: #4 User provided function() line 0 in unknown file
> > > > >
> > > > >
> > > > > *************************************
> > > > >
> > > > >
> > > > > mlohry at lancer:/ssd/dev_ssd/cmake-build$ grep "\[0\]"
> slurm-3429158.out
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Petsc has generated inconsistent data
> > > > > [0]PETSC ERROR: MPI_Allreduce() called in different locations
> (code lines) on different processors
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h21c2n1 by
> mlohry Mon Aug 5 23:58:19 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun
> > > > > [0]PETSC ERROR: #1 MatSetBlockSizes() line 7206 in
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: #2 MatSetBlockSizes() line 7206 in
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: #3 MatSetBlockSize() line 7170 in
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Petsc has generated inconsistent data
> > > > > [0]PETSC ERROR: MPI_Allreduce() called in different locations
> (code lines) on different processors
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h21c2n1 by
> mlohry Mon Aug 5 23:58:19 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun
> > > > > [0]PETSC ERROR: #4 VecSetSizes() line 1310 in
> /home/mlohry/build/external/petsc/src/vec/vec/interface/vector.c
> > > > > [0]PETSC ERROR: #5 VecSetSizes() line 1310 in
> /home/mlohry/build/external/petsc/src/vec/vec/interface/vector.c
> > > > > [0]PETSC ERROR: #6 VecCreateMPIWithArray() line 609 in
> /home/mlohry/build/external/petsc/src/vec/vec/impls/mpi/pbvec.c
> > > > > [0]PETSC ERROR: #7 MatSetUpMultiply_MPIAIJ() line 111 in
> /home/mlohry/build/external/petsc/src/mat/impls/aij/mpi/mmaij.c
> > > > > [0]PETSC ERROR: #8 MatAssemblyEnd_MPIAIJ() line 735 in
> /home/mlohry/build/external/petsc/src/mat/impls/aij/mpi/mpiaij.c
> > > > > [0]PETSC ERROR: #9 MatAssemblyEnd() line 5243 in
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
> Violation, probably memory access out of range
> > > > > [0]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> > > > > [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> > > > > [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
> Mac OS X to find memory corruption errors
> > > > > [0]PETSC ERROR: likely location of problem given in stack below
> > > > > [0]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> > > > > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> > > > > [0]PETSC ERROR: INSTEAD the line number of the start of the
> function
> > > > > [0]PETSC ERROR: is given.
> > > > > [0]PETSC ERROR: [0] PetscSFSetGraphLayout line 497
> /home/mlohry/build/external/petsc/src/vec/is/utils/pmap.c
> > > > > [0]PETSC ERROR: [0] GreedyColoringLocalDistanceTwo_Private line
> 208 /home/mlohry/build/external/petsc/src/mat/color/impls/greedy/greedy.c
> > > > > [0]PETSC ERROR: [0] MatColoringApply_Greedy line 559
> /home/mlohry/build/external/petsc/src/mat/color/impls/greedy/greedy.c
> > > > > [0]PETSC ERROR: [0] MatColoringApply line 357
> /home/mlohry/build/external/petsc/src/mat/color/interface/matcoloring.c
> > > > > [0]PETSC ERROR: [0] VecSetSizes line 1308
> /home/mlohry/build/external/petsc/src/vec/vec/interface/vector.c
> > > > > [0]PETSC ERROR: [0] VecCreateMPIWithArray line 605
> /home/mlohry/build/external/petsc/src/vec/vec/impls/mpi/pbvec.c
> > > > > [0]PETSC ERROR: [0] MatSetUpMultiply_MPIAIJ line 24
> /home/mlohry/build/external/petsc/src/mat/impls/aij/mpi/mmaij.c
> > > > > [0]PETSC ERROR: [0] MatAssemblyEnd_MPIAIJ line 698
> /home/mlohry/build/external/petsc/src/mat/impls/aij/mpi/mpiaij.c
> > > > > [0]PETSC ERROR: [0] MatAssemblyEnd line 5234
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: [0] MatSetBlockSizes line 7204
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: [0] MatSetBlockSize line 7167
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Signal received
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h21c2n1 by
> mlohry Mon Aug 5 23:58:19 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun
> > > > > [0]PETSC ERROR: #10 User provided function() line 0 in unknown
> file
> > > > >
> > > > >
> > > > >
> > > > > *************************
> > > > >
> > > > >
> > > > > mlohry at lancer:/ssd/dev_ssd/cmake-build$ grep "\[0\]"
> slurm-3429134.out
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Petsc has generated inconsistent data
> > > > > [0]PETSC ERROR: MPI_Allreduce() called in different locations
> (code lines) on different processors
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h20c2n1 by
> mlohry Mon Aug 5 23:24:23 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun
> > > > > [0]PETSC ERROR: #1 PetscSplitOwnership() line 88 in
> /home/mlohry/build/external/petsc/src/sys/utils/psplit.c
> > > > > [0]PETSC ERROR: #2 PetscSplitOwnership() line 88 in
> /home/mlohry/build/external/petsc/src/sys/utils/psplit.c
> > > > > [0]PETSC ERROR: #3 PetscLayoutSetUp() line 137 in
> /home/mlohry/build/external/petsc/src/vec/is/utils/pmap.c
> > > > > [0]PETSC ERROR: #4 VecCreate_MPI_Private() line 489 in
> /home/mlohry/build/external/petsc/src/vec/vec/impls/mpi/pbvec.c
> > > > > [0]PETSC ERROR: #5 VecCreate_MPI() line 537 in
> /home/mlohry/build/external/petsc/src/vec/vec/impls/mpi/pbvec.c
> > > > > [0]PETSC ERROR: #6 VecSetType() line 51 in
> /home/mlohry/build/external/petsc/src/vec/vec/interface/vecreg.c
> > > > > [0]PETSC ERROR: #7 VecCreateMPI() line 40 in
> /home/mlohry/build/external/petsc/src/vec/vec/impls/mpi/vmpicr.c
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Object is in wrong state
> > > > > [0]PETSC ERROR: Vec object's type is not set: Argument # 1
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h20c2n1 by
> mlohry Mon Aug 5 23:24:23 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun
> > > > > [0]PETSC ERROR: #8 VecGetLocalSize() line 665 in
> /home/mlohry/build/external/petsc/src/vec/vec/interface/vector.c
> > > > >
> > > > >
> > > > >
> > > > > **************************************
> > > > >
> > > > >
> > > > >
> > > > > mlohry at lancer:/ssd/dev_ssd/cmake-build$ grep "\[0\]"
> slurm-3429102.out
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Petsc has generated inconsistent data
> > > > > [0]PETSC ERROR: MPI_Allreduce() called in different locations
> (code lines) on different processors
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h19c1n16
> by mlohry Mon Aug 5 22:50:12 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun
> > > > > [0]PETSC ERROR: #1 TSSetExactFinalTime() line 2250 in
> /home/mlohry/build/external/petsc/src/ts/interface/ts.c
> > > > > [0]PETSC ERROR: #2 TSSetExactFinalTime() line 2250 in
> /home/mlohry/build/external/petsc/src/ts/interface/ts.c
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Petsc has generated inconsistent data
> > > > > [0]PETSC ERROR: MPI_Allreduce() called in different locations
> (code lines) on different processors
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h19c1n16
> by mlohry Mon Aug 5 22:50:12 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun
> > > > > [0]PETSC ERROR: #3 MatSetBlockSizes() line 7206 in
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: #4 MatSetBlockSizes() line 7206 in
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: #5 MatSetBlockSize() line 7170 in
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Petsc has generated inconsistent data
> > > > > [0]PETSC ERROR: MPI_Allreduce() called in different locations
> (code lines) on different processors
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h19c1n16
> by mlohry Mon Aug 5 22:50:12 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun
> > > > > [0]PETSC ERROR: #6 MatStashScatterBegin_Ref() line 476 in
> /home/mlohry/build/external/petsc/src/mat/utils/matstash.c
> > > > > [0]PETSC ERROR: #7 MatStashScatterBegin_Ref() line 476 in
> /home/mlohry/build/external/petsc/src/mat/utils/matstash.c
> > > > > [0]PETSC ERROR: #8 MatStashScatterBegin_Private() line 455 in
> /home/mlohry/build/external/petsc/src/mat/utils/matstash.c
> > > > > [0]PETSC ERROR: #9 MatAssemblyBegin_MPIAIJ() line 679 in
> /home/mlohry/build/external/petsc/src/mat/impls/aij/mpi/mpiaij.c
> > > > > [0]PETSC ERROR: #10 MatAssemblyBegin() line 5154 in
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
> Violation, probably memory access out of range
> > > > > [0]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> > > > > [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> > > > > [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
> Mac OS X to find memory corruption errors
> > > > > [0]PETSC ERROR: likely location of problem given in stack below
> > > > > [0]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> > > > > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> > > > > [0]PETSC ERROR: INSTEAD the line number of the start of the
> function
> > > > > [0]PETSC ERROR: is given.
> > > > > [0]PETSC ERROR: [0] MatStashScatterEnd_Ref line 137
> /home/mlohry/build/external/petsc/src/mat/utils/matstash.c
> > > > > [0]PETSC ERROR: [0] MatStashScatterEnd_Private line 126
> /home/mlohry/build/external/petsc/src/mat/utils/matstash.c
> > > > > [0]PETSC ERROR: [0] MatAssemblyEnd_MPIAIJ line 698
> /home/mlohry/build/external/petsc/src/mat/impls/aij/mpi/mpiaij.c
> > > > > [0]PETSC ERROR: [0] MatAssemblyEnd line 5234
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: [0] MatStashScatterBegin_Ref line 473
> /home/mlohry/build/external/petsc/src/mat/utils/matstash.c
> > > > > [0]PETSC ERROR: [0] MatStashScatterBegin_Private line 454
> /home/mlohry/build/external/petsc/src/mat/utils/matstash.c
> > > > > [0]PETSC ERROR: [0] MatAssemblyBegin_MPIAIJ line 676
> /home/mlohry/build/external/petsc/src/mat/impls/aij/mpi/mpiaij.c
> > > > > [0]PETSC ERROR: [0] MatAssemblyBegin line 5143
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: [0] MatSetBlockSizes line 7204
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: [0] MatSetBlockSize line 7167
> /home/mlohry/build/external/petsc/src/mat/interface/matrix.c
> > > > > [0]PETSC ERROR: [0] TSSetExactFinalTime line 2248
> /home/mlohry/build/external/petsc/src/ts/interface/ts.c
> > > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > [0]PETSC ERROR: Signal received
> > > > > [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> > > > > [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> > > > > [0]PETSC ERROR: maDG on a arch-linux2-c-opt named tiger-h19c1n16
> by mlohry Mon Aug 5 22:50:12 2019
> > > > > [0]PETSC ERROR: Configure options
> PETSC_DIR=/home/mlohry/build/external/petsc PETSC_ARCH=arch-linux2-c-opt
> --with-cc=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigcc
> --with-cxx=/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpigxx
> --with-fc=0 --with-clanguage=C++ --with-pic=1 --with-debugging=yes
> COPTFLAGS='-O3' CXXOPTFLAGS='-O3' --with-shared-libraries=1
> --download-parmetis --download-metis MAKEFLAGS=$MAKEFLAGS
> --with-mpiexec=/usr/bin/srun
> > > > > [0]PETSC ERROR: #11 User provided function() line 0 in unknown
> file
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
>
>
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