Il giorno dom 23 feb 2020 alle ore 11:53 Tsung-Hsing Chen < [email protected]> 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 <[email protected]> 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 < >> [email protected]> 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 [email protected] >>> >>> Is there any setting that should be done but I ignore? >>> >>> Thanks in advance, >>> >>> Tsung-Hsing Chen >>> >> >> >> -- >> Stefano >> > -- Stefano
