Segmentation fault when opening already open dataset #1444
Description
Environment
OS: Ubuntu 24.04 (Docker 28.5.1)
Python: 3.12.3
netcdf4-python: 1.7.3 (1.6.5 also tested)
Steps to reproduce (docker)
docker run --rm -it ubuntu:24.04 bashIn the docker container:
apt-get update DEBIAN_FRONTEND=noninteractive apt-get install -y python3 python3-pip python3-venv netcdf-bin python3 -m venv venv source ./venv/bin/activate pip3 install netCDF4==1.7.3 cat <<EOF > example.cdl netcdf example { variables: string example; } EOF ncgen -4 -b example.cdl cat <<EOF > main.py from netCDF4 import Dataset for i in range(50): file = Dataset("example.nc", "r") print("Success") file.close() EOFRun:
python3 main.pyOutput:
Segmentation fault (core dumped)Description
Although the code in the example is definitely not recommended, I do not believe that the segmentation error should be the result of its execution.
Some observations:
- No segmentation fault when type
float(instead ofstring) is used in theexample.cdl - I could not reproduce in netcdf-c
- Segmentation fault also for netCDF4-python==1.6.5
- Valgrind log:
==5042== Invalid read of size 1 ==5042== at 0x5779194: H5F_addr_decode (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x59A4E16: H5VL__native_blob_specific (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x599D95E: H5VL_blob_specific (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x598C59B: H5T__vlen_disk_isnull (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x597D009: H5T__conv_vlen (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x58D3490: H5T_convert_with_ctx (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x58D3669: H5T_convert (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x5740732: H5D_get_create_plist (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x59A5EF4: H5VL__native_dataset_get (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x59934A3: H5VL_dataset_get (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x5714242: H5Dget_create_plist (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x5429E4C: nc4_get_var_meta (in /venv/lib/python3.12/site-packages/netcdf4.libs/libnetcdf-306d3f1b.so.22) ==5042== Address 0x40 is not stack'd, malloc'd or (recently) free'd ==5042== ==5042== ==5042== Process terminating with default action of signal 11 (SIGSEGV): dumping core ==5042== Access not within mapped region at address 0x40 ==5042== at 0x5779194: H5F_addr_decode (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x59A4E16: H5VL__native_blob_specific (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x599D95E: H5VL_blob_specific (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x598C59B: H5T__vlen_disk_isnull (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x597D009: H5T__conv_vlen (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x58D3490: H5T_convert_with_ctx (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x58D3669: H5T_convert (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x5740732: H5D_get_create_plist (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x59A5EF4: H5VL__native_dataset_get (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x59934A3: H5VL_dataset_get (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x5714242: H5Dget_create_plist (in /venv/lib/python3.12/site-packages/netcdf4.libs/libhdf5-49234e76.so.310.5.1) ==5042== by 0x5429E4C: nc4_get_var_meta (in /venv/lib/python3.12/site-packages/netcdf4.libs/libnetcdf-306d3f1b.so.22) ==5042== If you believe this happened as a result of a stack ==5042== overflow in your program's main thread (unlikely but ==5042== possible), you can try to increase the size of the ==5042== main thread stack using the --main-stacksize= flag. ==5042== The main thread stack size used in this run was 8388608. ==5042== ==5042== HEAP SUMMARY: ==5042== in use at exit: 8,131,126 bytes in 11,506 blocks ==5042== total heap usage: 19,922 allocs, 8,416 frees, 48,204,805 bytes allocated Sorry if duplicated.