Invalid memory operation in delete_object in HDF5

0samuraiE
Sun, 22 Dec 2024 13:57:54 +0000
General Usage

Hi. As title suggests, my application crashes occasionally when call delete_object.
Every time I try, the error message changes. Sometimes

free(): invalid pointer
malloc(): unaligned tcache chunk detected
Aborted (core dumped)

or sometimes

double free or corruption (!prev)

[3916181] signal 6 (-6): Aborted

I suspect GC might be doing something bad.

MWE

        h5open(file, "cw") do h
        if haskey(h, key)
           delete_object(h, key)
        end
        write(h, key, data)
        end

versioninfo

Julia Version 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 384 × AMD EPYC 9654 96-Core Processor
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, znver4)
Threads: 16 default, 0 interactive, 8 GC (on 384 virtual cores)

LocalPreference

[CUDA_Runtime_jll]
local = "true"
version = "12.3"

[HDF5]
libhdf5 = ".../free/hdf5-parallel/1.14.3/nvhpc24.1/openmpi5.0.2/lib/libhdf5.so"
libhdf5_hl = ".../free/hdf5-parallel/1.14.3/nvhpc24.1/openmpi5.0.2/lib/libhdf5_hl.so"

[HDF5_jll]
libhdf5_hl_path = ".../free/hdf5-parallel/1.14.3/nvhpc24.1/openmpi5.0.2/lib/libhdf5_hl.so"
libhdf5_path = ".../free/hdf5-parallel/1.14.3/nvhpc24.1/openmpi5.0.2/lib/libhdf5.so"

[MPIPreferences]
__clear__ = ["preloads_env_switch"]
_format = "1.0"
abi = "OpenMPI"
binary = "system"
cclibs = []
libmpi = "libmpi"
mpiexec = "mpiexec"
preloads = []

5 posts - 2 participants