[petsc-users] MPI Iterative solver crash on HPC

Sal Am tempohoper at gmail.com
Thu Jan 17 08:18:30 CST 2019 

>
> 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.

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/>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20190117/07bf2421/attachment-0001.html>

More information about the petsc-users mailing list