A problem related to elasticity. I think I will try those external packages.
Thanks for your assistance. Stefano Zampini <[email protected]> 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 < > [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 >
