[petsc-users] Error - Out of memory. This could be due to allocating too large an object or bleeding by not properly destroying unneeded objects.

[Stefano Zampini]

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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