[petsc-users] Error - Out of memory. This could be due to allocating too large an object or bleeding by not properly destroying unneeded objects.
Tsung-Hsing Chen
barrydog505 at gmail.com
Sun Feb 23 02:52:44 CST 2020
This error came with a matrix approximate 300,000*300,000, and I was
solving a 3D model.
" the memory requirements for LU are N log(N) in 2D and N^4/3 in 3D. " What
unit is it? Byte?
Stefano Zampini <stefano.zampini at gmail.com> 於 2020年2月23日 週日 下午4:33寫道：
> This seems integer overflow when computing the factors.
>
> How large is the matrix when you encounter the error?
> Note that LU is not memory optimal and you can easily encounter
> out-of-memory issues with large matrices.
> Assuming sparsity, the memory requirements for LU are N log(N) in 2D and
> N^4/3 in 3D.
>
>
> Il giorno dom 23 feb 2020 alle ore 11:01 Tsung-Hsing Chen <
> barrydog505 at gmail.com> ha scritto:
>
>> Hi all,
>>
>> I have written a simple code to solve the FEM problem, and I want to use
>> LU to solve the Ax=b.
>> My problem(error) won't happen at the beginning until M & N in A_matrix
>> is getting larger. (Can also be understood as mesh vertex increase.)
>> All the error output seems to relate to LU, but I don't know what should
>> be done.
>> The followings are the code I wrote(section) and the error output.
>>
>> Here's the code (section) :
>> /*
>> code ...
>> */
>> ierr = MatCreate(PETSC_COMM_WORLD, &A_matrix);CHKERRQ(ierr);
>> ierr = MatSetSizes(A_matrix, PETSC_DECIDE, PETSC_DECIDE, M,
>> N);CHKERRQ(ierr);
>> ierr = MatSetType(A_matrix, MATSEQAIJ);CHKERRQ(ierr);
>> // setting nnz ...
>> ierr = MatSeqAIJSetPreallocation(A_matrix, 0, nnz);CHKERRQ(ierr);
>> /*
>> MatSetValues(); ...
>> MatAssemblyBegin();
>> MatAssemblyEnd();
>> */
>> ierr = KSPCreate(PETSC_COMM_WORLD, &ksp);CHKERRQ(ierr);
>> ierr = KSPSetOperators(ksp, A_matrix, A_matrix);CHKERRQ(ierr);
>> ierr = KSPSetType(ksp, KSPPREONLY);CHKERRQ(ierr);
>> ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr);
>> ierr = PCSetType(pc, PCLU);CHKERRQ(ierr);
>> ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
>> ierr = KSPSetUp(ksp);CHKERRQ(ierr);
>> /*
>> code ...
>> */
>>
>> Here's the error (run with valgrind --tool=memcheck --leak-check=full) :
>> ==6371== Warning: set address range perms: large range [0x7c84a040,
>> 0xb4e9a598) (undefined)
>> ==6371== Warning: set address range perms: large range [0xb4e9b040,
>> 0x2b4e9aeac) (undefined)
>> ==6371== Warning: set address range perms: large range [0x2b4e9b040,
>> 0x4b4e9aeac) (undefined)
>> ==6371== Argument 'size' of function memalign has a fishy (possibly
>> negative) value: -5187484888
>> ==6371== at 0x4C320A6: memalign (in
>> /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
>> ==6371== by 0x501B4B0: PetscMallocAlign (mal.c:49)
>> ==6371== by 0x501CE37: PetscMallocA (mal.c:422)
>> ==6371== by 0x5ACFF0C: MatLUFactorSymbolic_SeqAIJ (aijfact.c:366)
>> ==6371== by 0x561D8B3: MatLUFactorSymbolic (matrix.c:3005)
>> ==6371== by 0x644ED9C: PCSetUp_LU (lu.c:90)
>> ==6371== by 0x65A2C32: PCSetUp (precon.c:894)
>> ==6371== by 0x6707E71: KSPSetUp (itfunc.c:376)
>> ==6371== by 0x13AB09: Calculate (taylor_hood.c:1780)
>> ==6371== by 0x10CB85: main (taylor_hood.c:228)
>> ==6371==
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [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.
>> [0]PETSC ERROR: Memory allocated 0 Memory used by process 15258234880
>> [0]PETSC ERROR: Try running with -malloc_dump or -malloc_view for info.
>> [0]PETSC ERROR: Memory requested 18446744068522065920
>> [0]PETSC ERROR: See
>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>> shooting.
>> [0]PETSC ERROR: Petsc Release Version 3.12.4, unknown
>> [0]PETSC ERROR: ./taylor_hood on a arch-linux2-c-debug named e2-120 by
>> barry Sun Feb 23 14:18:46 2020
>> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
>> --with-fc=gfortran --download-mpich --download-fblaslapack
>> --download-triangle
>> [0]PETSC ERROR: #1 MatLUFactorSymbolic_SeqAIJ() line 366 in
>> /home/barry/petsc/src/mat/impls/aij/seq/aijfact.c
>> [0]PETSC ERROR: #2 PetscMallocA() line 422 in
>> /home/barry/petsc/src/sys/memory/mal.c
>> [0]PETSC ERROR: #3 MatLUFactorSymbolic_SeqAIJ() line 366 in
>> /home/barry/petsc/src/mat/impls/aij/seq/aijfact.c
>> [0]PETSC ERROR: #4 MatLUFactorSymbolic() line 3005 in
>> /home/barry/petsc/src/mat/interface/matrix.c
>> [0]PETSC ERROR: #5 PCSetUp_LU() line 90 in
>> /home/barry/petsc/src/ksp/pc/impls/factor/lu/lu.c
>> [0]PETSC ERROR: #6 PCSetUp() line 894 in
>> /home/barry/petsc/src/ksp/pc/interface/precon.c
>> [0]PETSC ERROR: #7 KSPSetUp() line 376 in
>> /home/barry/petsc/src/ksp/ksp/interface/itfunc.c
>> [0]PETSC ERROR: #8 Calculate() line 1780 in
>> /home/barry/brain/brain/3D/taylor_hood.c
>> [0]PETSC ERROR: #9 main() line 230 in
>> /home/barry/brain/brain/3D/taylor_hood.c
>> [0]PETSC ERROR: PETSc Option Table entries:
>> [0]PETSC ERROR: -dm_view
>> [0]PETSC ERROR: -f mesh/ellipsoid.msh
>> [0]PETSC ERROR: -matload_block_size 1
>> [0]PETSC ERROR: ----------------End of Error Message -------send entire
>> error message to petsc-maint at mcs.anl.gov----------
>>
>> Is there any setting that should be done but I ignore?
>>
>> Thanks in advance,
>>
>> Tsung-Hsing Chen
>>
>
>
> --
> Stefano
>
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