[petsc-users] MPI Iterative solver crash on HPC
Matthew Knepley
knepley at gmail.com
Thu Jan 17 10:24:09 CST 2019
On Thu, Jan 17, 2019 at 9:18 AM Sal Am <tempohoper at gmail.com> wrote:
> 1) Running out of memory
>>
>> 2) You passed an invalid array
>>
> I have select=4:ncpus=32:mpiprocs=32:mem=300GB in the job script, i.e.
> using 300GB/node, a total of 1200GB memory, using 4 nodes and 32 processors
> per node (128 processors in total).
> I am not sure what would constitute an invalid array or how I can check
> that. I am using the same procedure as when dealing with the smaller
> matrix. i.e. Generate matrix A and vector b using FEM software then convert
> the matrix and vector using a python script ready for petsc. read in petsc
> and calculate.
>
> Are you running with 64-bit ints here?
>>
> Yes I have it configured petsc with --with-64-bit-indices and debugging
> mode, which this was run on.
>
It sounds like you have enough memory, but the fact that is runs for
smaller problems makes me suspicious. It
could still be a memory overwrite. Can you either
a) Run under valgrind
or
b) Run under the debugger and get a stack trace
?
Thanks,
Matt
> On Thu, Jan 17, 2019 at 1:59 PM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Thu, Jan 17, 2019 at 8:16 AM Sal Am <tempohoper at gmail.com> wrote:
>>
>>> SuperLU_dist supports 64-bit ints. Are you not running in parallel?
>>>>
>>> I will try that, although I think solving the real problem (later on if
>>> I can get this to work) with 30 million finite elements might be a problem
>>> for SuperLU_dist. so it is better to get an iterative solver to work with
>>> first.
>>>
>>> 1) Try using -build_twosided allreduce on this run
>>>>
>>> How I ran it: mpiexec valgrind --tool=memcheck -q --num-callers=20
>>> --log-file=valgrind.log-osaii.%p ./solveCSys -malloc off -ksp_type bcgs
>>> -pc_type gamg -mattransposematmult_via scalable -build_twosided allreduce
>>> -ksp_monitor -log_view
>>> I have attached the full error output.
>>>
>>
>> You are getting an SEGV on MatSetValues(), so its either
>>
>> 1) Running out of memory
>>
>> 2) You passed an invalid array
>>
>>
>>> 2) Is it possible to get something that fails here but we can run. None
>>>> of our tests show this problem.
>>>>
>>> I am not how I can do that, but i have added my code which is quite
>>> short and should only read and solve the system, the problem arises at
>>> larger matrices for example current test case has 6 million finite elements
>>> (~2B non-zero numbers and 25M x 25M matrix).
>>>
>>
>> Are you running with 64-bit ints here?
>>
>> Matt
>>
>>
>>> On Wed, Jan 16, 2019 at 1:12 PM Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> On Wed, Jan 16, 2019 at 3:52 AM Sal Am via petsc-users <
>>>> petsc-users at mcs.anl.gov> wrote:
>>>>
>>>>> The memory requested is an insane number. You may need to use 64 bit
>>>>>> integers.
>>>>>
>>>>> Thanks Mark, I reconfigured it to use 64bit, however in the process it
>>>>> says I can no longer use MUMPS and SuperLU as they are not supported (I see
>>>>> on MUMPS webpage it supports 64int). However it does not exactly solve the
>>>>> problem.
>>>>>
>>>>
>>>> SuperLU_dist supports 64-bit ints. Are you not running in parallel?
>>>>
>>>>
>>>>> This time, it crashes at
>>>>>> [6]PETSC ERROR: #1 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ() line
>>>>>> 1989 in /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c
>>>>>> ierr = PetscMalloc1(bi[pn]+1,&bj);
>>>>>> which allocates local portion of B^T*A.
>>>>>> You may also try to increase number of cores to reduce local matrix
>>>>>> size.
>>>>>>
>>>>>
>>>>> So I increased the number of cores to 16 on one node and ran it by :
>>>>> mpiexec valgrind --tool=memcheck -q --num-callers=20
>>>>> --log-file=valgrind.log-osa.%p ./solveCSys -malloc off -ksp_type bcgs
>>>>> -pc_type gamg -mattransposematmult_via scalable -ksp_monitor -log_view
>>>>> It crashed after reading in the matrix and before starting to solve.
>>>>> The error:
>>>>>
>>>>> [15]PETSC ERROR: [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: [1]PETSC ERROR:
>>>>> ------------------------------------------------------------------------
>>>>> [2]PETSC ERROR:
>>>>> ------------------------------------------------------------------------
>>>>> [2]PETSC ERROR: Caught signal number 15 Terminate: Some process (or
>>>>> the batch system) has told this process to end
>>>>> [3]PETSC ERROR:
>>>>> ------------------------------------------------------------------------
>>>>> [4]PETSC ERROR:
>>>>> ------------------------------------------------------------------------
>>>>> [4]PETSC ERROR: [5]PETSC ERROR: [6]PETSC ERROR:
>>>>> ------------------------------------------------------------------------
>>>>> [8]PETSC ERROR:
>>>>> ------------------------------------------------------------------------
>>>>> [12]PETSC ERROR:
>>>>> ------------------------------------------------------------------------
>>>>> [12]PETSC ERROR: [14]PETSC ERROR:
>>>>> ------------------------------------------------------------------------
>>>>> [14]PETSC ERROR: Caught signal number 15 Terminate: Some process (or
>>>>> the batch system) has told this process to end
>>>>>
>>>>> --------------------------------------------------------------------------
>>>>> mpiexec noticed that process rank 10 with PID 0 on node r03n01 exited
>>>>> on signal 9 (Killed).
>>>>>
>>>>> Now I was running this with valgrind as someone had previously
>>>>> suggested and the 16 files created all contain the same type of error:
>>>>>
>>>>
>>>> Okay, its possible that there are bugs in the MPI implementation. So
>>>>
>>>> 1) Try using -build_twosided allreduce on this run
>>>>
>>>> 2) Is it possible to get something that fails here but we can run. None
>>>> of our tests show this problem.
>>>>
>>>> Thanks,
>>>>
>>>> Matt
>>>>
>>>>
>>>>> ==25940== Invalid read of size 8
>>>>> ==25940== at 0x5103326: PetscCheckPointer (checkptr.c:81)
>>>>> ==25940== by 0x4F42058: PetscCommGetNewTag (tagm.c:77)
>>>>> ==25940== by 0x4FC952D: PetscCommBuildTwoSidedFReq_Ibarrier
>>>>> (mpits.c:373)
>>>>> ==25940== by 0x4FCB29B: PetscCommBuildTwoSidedFReq (mpits.c:572)
>>>>> ==25940== by 0x52BBFF4: VecAssemblyBegin_MPI_BTS (pbvec.c:251)
>>>>> ==25940== by 0x52D6B42: VecAssemblyBegin (vector.c:140)
>>>>> ==25940== by 0x5328C97: VecLoad_Binary (vecio.c:141)
>>>>> ==25940== by 0x5329051: VecLoad_Default (vecio.c:516)
>>>>> ==25940== by 0x52E0BAB: VecLoad (vector.c:933)
>>>>> ==25940== by 0x4013D5: main (solveCmplxLinearSys.cpp:31)
>>>>> ==25940== Address 0x19f807fc is 12 bytes inside a block of size 16
>>>>> alloc'd
>>>>> ==25940== at 0x4C2A603: memalign (vg_replace_malloc.c:899)
>>>>> ==25940== by 0x4FD0B0E: PetscMallocAlign (mal.c:41)
>>>>> ==25940== by 0x4FD23E7: PetscMallocA (mal.c:397)
>>>>> ==25940== by 0x4FC948E: PetscCommBuildTwoSidedFReq_Ibarrier
>>>>> (mpits.c:371)
>>>>> ==25940== by 0x4FCB29B: PetscCommBuildTwoSidedFReq (mpits.c:572)
>>>>> ==25940== by 0x52BBFF4: VecAssemblyBegin_MPI_BTS (pbvec.c:251)
>>>>> ==25940== by 0x52D6B42: VecAssemblyBegin (vector.c:140)
>>>>> ==25940== by 0x5328C97: VecLoad_Binary (vecio.c:141)
>>>>> ==25940== by 0x5329051: VecLoad_Default (vecio.c:516)
>>>>> ==25940== by 0x52E0BAB: VecLoad (vector.c:933)
>>>>> ==25940== by 0x4013D5: main (solveCmplxLinearSys.cpp:31)
>>>>> ==25940==
>>>>>
>>>>>
>>>>> On Mon, Jan 14, 2019 at 7:29 PM Zhang, Hong <hzhang at mcs.anl.gov>
>>>>> wrote:
>>>>>
>>>>>> Fande:
>>>>>>
>>>>>>> According to this PR
>>>>>>> https://bitbucket.org/petsc/petsc/pull-requests/1061/a_selinger-feature-faster-scalable/diff
>>>>>>>
>>>>>>> Should we set the scalable algorithm as default?
>>>>>>>
>>>>>> Sure, we can. But I feel we need do more tests to compare scalable
>>>>>> and non-scalable algorithms.
>>>>>> On theory, for small to medium matrices, non-scalable matmatmult()
>>>>>> algorithm enables more efficient
>>>>>> data accessing. Andreas optimized scalable implementation. Our
>>>>>> non-scalable implementation might have room to be further optimized.
>>>>>> Hong
>>>>>>
>>>>>>>
>>>>>>> On Fri, Jan 11, 2019 at 10:34 AM Zhang, Hong via petsc-users <
>>>>>>> petsc-users at mcs.anl.gov> wrote:
>>>>>>>
>>>>>>>> Add option '-mattransposematmult_via scalable'
>>>>>>>> Hong
>>>>>>>>
>>>>>>>> On Fri, Jan 11, 2019 at 9:52 AM Zhang, Junchao via petsc-users <
>>>>>>>> petsc-users at mcs.anl.gov> wrote:
>>>>>>>>
>>>>>>>>> I saw the following error message in your first email.
>>>>>>>>>
>>>>>>>>> [0]PETSC ERROR: Out of memory. This could be due to allocating
>>>>>>>>> [0]PETSC ERROR: too large an object or bleeding by not properly
>>>>>>>>> [0]PETSC ERROR: destroying unneeded objects.
>>>>>>>>>
>>>>>>>>> Probably the matrix is too large. You can try with more compute
>>>>>>>>> nodes, for example, use 8 nodes instead of 2, and see what happens.
>>>>>>>>>
>>>>>>>>> --Junchao Zhang
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Fri, Jan 11, 2019 at 7:45 AM Sal Am via petsc-users <
>>>>>>>>> petsc-users at mcs.anl.gov> wrote:
>>>>>>>>>
>>>>>>>>>> Using a larger problem set with 2B non-zero elements and a matrix
>>>>>>>>>> of 25M x 25M I get the following error:
>>>>>>>>>> [4]PETSC ERROR:
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> [4]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>>>>>>>>>> Violation, probably memory access out of range
>>>>>>>>>> [4]PETSC ERROR: Try option -start_in_debugger or
>>>>>>>>>> -on_error_attach_debugger
>>>>>>>>>> [4]PETSC ERROR: or see
>>>>>>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>>>>>>>>>> [4]PETSC ERROR: or try http://valgrind.org on GNU/linux and
>>>>>>>>>> Apple Mac OS X to find memory corruption errors
>>>>>>>>>> [4]PETSC ERROR: likely location of problem given in stack below
>>>>>>>>>> [4]PETSC ERROR: --------------------- Stack Frames
>>>>>>>>>> ------------------------------------
>>>>>>>>>> [4]PETSC ERROR: Note: The EXACT line numbers in the stack are not
>>>>>>>>>> available,
>>>>>>>>>> [4]PETSC ERROR: INSTEAD the line number of the start of the
>>>>>>>>>> function
>>>>>>>>>> [4]PETSC ERROR: is given.
>>>>>>>>>> [4]PETSC ERROR: [4] MatCreateSeqAIJWithArrays line 4422
>>>>>>>>>> /lustre/home/vef002/petsc/src/mat/impls/aij/seq/aij.c
>>>>>>>>>> [4]PETSC ERROR: [4] MatMatMultSymbolic_SeqAIJ_SeqAIJ line 747
>>>>>>>>>> /lustre/home/vef002/petsc/src/mat/impls/aij/seq/matmatmult.c
>>>>>>>>>> [4]PETSC ERROR: [4]
>>>>>>>>>> MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable line 1256
>>>>>>>>>> /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c
>>>>>>>>>> [4]PETSC ERROR: [4] MatTransposeMatMult_MPIAIJ_MPIAIJ line 1156
>>>>>>>>>> /lustre/home/vef002/petsc/src/mat/impls/aij/mpi/mpimatmatmult.c
>>>>>>>>>> [4]PETSC ERROR: [4] MatTransposeMatMult line 9950
>>>>>>>>>> /lustre/home/vef002/petsc/src/mat/interface/matrix.c
>>>>>>>>>> [4]PETSC ERROR: [4] PCGAMGCoarsen_AGG line 871
>>>>>>>>>> /lustre/home/vef002/petsc/src/ksp/pc/impls/gamg/agg.c
>>>>>>>>>> [4]PETSC ERROR: [4] PCSetUp_GAMG line 428
>>>>>>>>>> /lustre/home/vef002/petsc/src/ksp/pc/impls/gamg/gamg.c
>>>>>>>>>> [4]PETSC ERROR: [4] PCSetUp line 894
>>>>>>>>>> /lustre/home/vef002/petsc/src/ksp/pc/interface/precon.c
>>>>>>>>>> [4]PETSC ERROR: [4] KSPSetUp line 304
>>>>>>>>>> /lustre/home/vef002/petsc/src/ksp/ksp/interface/itfunc.c
>>>>>>>>>> [4]PETSC ERROR: --------------------- Error Message
>>>>>>>>>> --------------------------------------------------------------
>>>>>>>>>> [4]PETSC ERROR: Signal received
>>>>>>>>>> [4]PETSC ERROR: See
>>>>>>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>>>>>>>>> shooting.
>>>>>>>>>> [4]PETSC ERROR: Petsc Release Version 3.10.2, unknown
>>>>>>>>>> [4]PETSC ERROR: ./solveCSys on a linux-cumulus-debug named r02g03
>>>>>>>>>> by vef002 Fri Jan 11 09:13:23 2019
>>>>>>>>>> [4]PETSC ERROR: Configure options PETSC_ARCH=linux-cumulus-debug
>>>>>>>>>> --with-cc=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpicc
>>>>>>>>>> --with-fc=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpifort
>>>>>>>>>> --with-cxx=/usr/local/depot/openmpi-3.1.1-gcc-7.3.0/bin/mpicxx
>>>>>>>>>> --download-parmetis --download-metis --download-ptscotch
>>>>>>>>>> --download-superlu_dist --download-mumps --with-scalar-type=complex
>>>>>>>>>> --with-debugging=yes --download-scalapack --download-superlu
>>>>>>>>>> --download-fblaslapack=1 --download-cmake
>>>>>>>>>> [4]PETSC ERROR: #1 User provided function() line 0 in unknown
>>>>>>>>>> file
>>>>>>>>>>
>>>>>>>>>> --------------------------------------------------------------------------
>>>>>>>>>> MPI_ABORT was invoked on rank 4 in communicator MPI_COMM_WORLD
>>>>>>>>>> with errorcode 59.
>>>>>>>>>>
>>>>>>>>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
>>>>>>>>>> processes.
>>>>>>>>>> You may or may not see output from other processes, depending on
>>>>>>>>>> exactly when Open MPI kills them.
>>>>>>>>>>
>>>>>>>>>> --------------------------------------------------------------------------
>>>>>>>>>> [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
>>>>>>>>>>
>>>>>>>>>> Using Valgrind on only one of the valgrind files the following
>>>>>>>>>> error was written:
>>>>>>>>>>
>>>>>>>>>> ==9053== Invalid read of size 4
>>>>>>>>>> ==9053== at 0x5B8067E: MatCreateSeqAIJWithArrays (aij.c:4445)
>>>>>>>>>> ==9053== by 0x5BC2608: MatMatMultSymbolic_SeqAIJ_SeqAIJ
>>>>>>>>>> (matmatmult.c:790)
>>>>>>>>>> ==9053== by 0x5D106F8:
>>>>>>>>>> MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable (mpimatmatmult.c:1337)
>>>>>>>>>> ==9053== by 0x5D0E84E: MatTransposeMatMult_MPIAIJ_MPIAIJ
>>>>>>>>>> (mpimatmatmult.c:1186)
>>>>>>>>>> ==9053== by 0x5457C57: MatTransposeMatMult (matrix.c:9984)
>>>>>>>>>> ==9053== by 0x64DD99D: PCGAMGCoarsen_AGG (agg.c:882)
>>>>>>>>>> ==9053== by 0x64C7527: PCSetUp_GAMG (gamg.c:522)
>>>>>>>>>> ==9053== by 0x6592AA0: PCSetUp (precon.c:932)
>>>>>>>>>> ==9053== by 0x66B1267: KSPSetUp (itfunc.c:391)
>>>>>>>>>> ==9053== by 0x4019A2: main (solveCmplxLinearSys.cpp:68)
>>>>>>>>>> ==9053== Address 0x8386997f4 is not stack'd, malloc'd or
>>>>>>>>>> (recently) free'd
>>>>>>>>>> ==9053==
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Fri, Jan 11, 2019 at 8:41 AM Sal Am <tempohoper at gmail.com>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> Thank you Dave,
>>>>>>>>>>>
>>>>>>>>>>> I reconfigured PETSc with valgrind and debugging mode, I ran the
>>>>>>>>>>> code again with the following options:
>>>>>>>>>>> mpiexec -n 8 valgrind --tool=memcheck -q --num-callers=20
>>>>>>>>>>> --log-file=valgrind.log.%p ./solveCSys -malloc off -ksp_type bcgs -pc_type
>>>>>>>>>>> gamg -log_view
>>>>>>>>>>> (as on the petsc website you linked)
>>>>>>>>>>>
>>>>>>>>>>> It finished solving using the iterative solver, but the
>>>>>>>>>>> resulting valgrind.log.%p files (all 8 corresponding to each processor) are
>>>>>>>>>>> all empty. And it took a whooping ~15hours, for what used to take
>>>>>>>>>>> ~10-20min. Maybe this is because of valgrind? I am not sure. Attached is
>>>>>>>>>>> the log_view.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Thu, Jan 10, 2019 at 8:59 AM Dave May <
>>>>>>>>>>> dave.mayhem23 at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Thu, 10 Jan 2019 at 08:55, Sal Am via petsc-users <
>>>>>>>>>>>> petsc-users at mcs.anl.gov> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> I am not sure what is exactly is wrong as the error changes
>>>>>>>>>>>>> slightly every time I run it (without changing the parameters).
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> This likely implies that you have a memory error in your code
>>>>>>>>>>>> (a memory leak would not cause this behaviour).
>>>>>>>>>>>> I strongly suggest you make sure your code is free of memory
>>>>>>>>>>>> errors.
>>>>>>>>>>>> You can do this using valgrind. See here
>>>>>>>>>>>>
>>>>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>>>>>>>>>>>>
>>>>>>>>>>>> for an explanation of how to use valgrind.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> I have attached the first two run's errors and my code.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Is there a memory leak somewhere? I have tried running it with
>>>>>>>>>>>>> -malloc_dump, but not getting anything printed out, however, when run with
>>>>>>>>>>>>> -log_view I see that Viewer is created 4 times, but destroyed 3 times. The
>>>>>>>>>>>>> way I see it, I have destroyed it where I see I no longer have use for it
>>>>>>>>>>>>> so not sure if I am wrong. Could this be the reason why it keeps crashing?
>>>>>>>>>>>>> It crashes as soon as it reads the matrix, before entering the solving mode
>>>>>>>>>>>>> (I have a print statement before solving starts that never prints).
>>>>>>>>>>>>>
>>>>>>>>>>>>> how I run it in the job script on 2 node with 32 processors
>>>>>>>>>>>>> using the clusters OpenMPI.
>>>>>>>>>>>>>
>>>>>>>>>>>>> mpiexec ./solveCSys -ksp_type bcgs -pc_type gamg
>>>>>>>>>>>>> -ksp_converged_reason -ksp_monitor_true_residual -log_view
>>>>>>>>>>>>> -ksp_error_if_not_converged -ksp_monitor -malloc_log -ksp_view
>>>>>>>>>>>>>
>>>>>>>>>>>>> the matrix:
>>>>>>>>>>>>> 2 122 821 366 (non-zero elements)
>>>>>>>>>>>>> 25 947 279 x 25 947 279
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks and all the best
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>
>>>> --
>>>> 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/>
>>>>
>>>
>>
>> --
>> 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/>
>>
>
--
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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