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 <[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 >
