[petsc-users] MPI Iterative solver crash on HPC
Fande Kong
fdkong.jd at gmail.com
Mon Jan 14 11:26:59 CST 2019
Hi Hong,
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?
Thanks,
Fande Kong,
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
>>>>>>
>>>>>
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