[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 04:22:44 CST 2020
A problem related to elasticity.
I think I will try those external packages.
Thanks for your assistance.
Stefano Zampini <stefano.zampini at gmail.com> 於 2020年2月23日 週日 下午5:35寫道：
>
>
> Il giorno dom 23 feb 2020 alle ore 11:53 Tsung-Hsing Chen <
> barrydog505 at gmail.com> ha scritto:
>
>> 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?
>>
>
> Number of floating-point entries.
>
> Assuming an optimal nested dissection ordering can be found (i.e. no
> "dense" rows), the largest front is asymptotically as large as N^(2/3) (N
> the size of the matrix)
> Storing it in memory requires (N^(2/3))^2 entries, thus N^4/3 entries.
> What problem are you solving?
> If you plan to use direct methods, you may want to experiment with
> parallel factorization packages like MUMPS or SUPERLU_DIST
>
>
>>
>> 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
>>>
>>
>
> --
> Stefano
>
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