Dear all, I reconfigured petsc with "--with-debugging=1". It throws more messages which I attached below.
Best, Changqing ________________________________________ 发件人: Ye Changqing <ye_changq...@outlook.com> 发送时间: 2025年3月24日 16:33 收件人: petsc-users@mcs.anl.gov 主题: Floating point exception when save complex vector into a hdf5 file Dear PETSc developers, I encountered a strange problem when I tried to save a DMDA vector into an hdf5 file, a floating point error was thrown. I can repeat the problem on the cluster. However, the same codes run fine on my local computer. Below the .cxx file is the minimal working example, the .txt is the runtime error obtained from SLURM, and the .py file should tell the configure options that I used to build the library. Any suggestions? Best, Changqing
[8]PETSC ERROR: ------------------------------------------------------------------------ [8]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [8]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [8]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [8]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [8]PETSC ERROR: The line numbers in the error traceback are not always exact. [8]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [8]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [8]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [8]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [20]PETSC ERROR: ------------------------------------------------------------------------ [20]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [20]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [20]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [20]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [20]PETSC ERROR: The line numbers in the error traceback are not always exact. [20]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [20]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [20]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [20]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [24]PETSC ERROR: ------------------------------------------------------------------------ [24]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [24]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [24]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [24]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [24]PETSC ERROR: The line numbers in the error traceback are not always exact. [24]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [24]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [24]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [24]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [28]PETSC ERROR: ------------------------------------------------------------------------ [28]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [28]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [28]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [28]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [28]PETSC ERROR: The line numbers in the error traceback are not always exact. [28]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [28]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [28]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [28]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [40]PETSC ERROR: ------------------------------------------------------------------------ [40]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [40]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [40]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [40]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [40]PETSC ERROR: The line numbers in the error traceback are not always exact. [40]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [40]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [40]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [40]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [48]PETSC ERROR: ------------------------------------------------------------------------ [48]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [48]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [48]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [48]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [48]PETSC ERROR: The line numbers in the error traceback are not always exact. [48]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [48]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [48]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [48]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [52]PETSC ERROR: ------------------------------------------------------------------------ [52]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [52]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [52]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [52]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [52]PETSC ERROR: The line numbers in the error traceback are not always exact. [52]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [52]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [52]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [52]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [0]PETSC ERROR: The line numbers in the error traceback are not always exact. [0]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [0]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [0]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [0]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [4]PETSC ERROR: ------------------------------------------------------------------------ [4]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [4]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [4]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [4]PETSC ERROR: The line numbers in the error traceback are not always exact. [4]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [4]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [4]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [4]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [12]PETSC ERROR: ------------------------------------------------------------------------ [12]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [12]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [12]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [12]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [12]PETSC ERROR: The line numbers in the error traceback are not always exact. [12]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [12]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [12]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [12]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [16]PETSC ERROR: ------------------------------------------------------------------------ [16]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [16]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [16]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [16]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [16]PETSC ERROR: The line numbers in the error traceback are not always exact. [16]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [16]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [16]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [16]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [32]PETSC ERROR: ------------------------------------------------------------------------ [32]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [32]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [32]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [32]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [32]PETSC ERROR: The line numbers in the error traceback are not always exact. [32]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [32]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [32]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [32]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [36]PETSC ERROR: ------------------------------------------------------------------------ [36]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [36]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [36]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [36]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [36]PETSC ERROR: The line numbers in the error traceback are not always exact. [36]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [36]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [36]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [36]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 [44]PETSC ERROR: ------------------------------------------------------------------------ [44]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [44]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [44]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [44]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [44]PETSC ERROR: The line numbers in the error traceback are not always exact. [44]PETSC ERROR: #1 VecGetHDF5ChunkSize() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:328 [44]PETSC ERROR: #2 VecView_MPI_HDF5_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:489 [44]PETSC ERROR: #3 VecView_MPI_DA() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/dm/impls/da/gr2.c:685 [44]PETSC ERROR: #4 VecView() at /sh3/ysuanbase/home/yeesuan14477/petsc-3.22.4/src/vec/vec/interface/vector.c:805 Abort(59) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Abort(59) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 4 Abort(59) on node 8 (rank 8 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 8 Abort(59) on node 12 (rank 12 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 12 Abort(59) on node 16 (rank 16 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 16 Abort(59) on node 20 (rank 20 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 20 Abort(59) on node 24 (rank 24 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 24 Abort(59) on node 28 (rank 28 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 28 Abort(59) on node 32 (rank 32 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 32 Abort(59) on node 36 (rank 36 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 36 Abort(59) on node 40 (rank 40 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 40 Abort(59) on node 44 (rank 44 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 44 Abort(59) on node 48 (rank 48 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 48 Abort(59) on node 52 (rank 52 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 52
