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conda-forge / gdal-feedstock

A conda-smithy repository for gdal.
BSD 3-Clause "New" or "Revised" License
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Segmentation Fault when reading ZARR for GDAL=3.8.3 #884

Closed mccarthyryanc closed 7 months ago

mccarthyryanc commented 7 months ago

Solution to issue cannot be found in the documentation.

Issue

Running gdalinfo on any of the gdal testing zarr files results in a Segmentation Fault:

gdalinfo array_attrs.zarr
Segmentation fault (core dumped)

Installed packages

# packages in environment at /home/rcm/miniconda3/envs/gdal-383:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
azure-core-cpp            1.11.0               h91d86a7_1    conda-forge
azure-storage-blobs-cpp   12.10.0              h00ab1b0_0    conda-forge
azure-storage-common-cpp  12.5.0               hb858b4b_2    conda-forge
blosc                     1.21.5               h0f2a231_0    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.26.0               hd590300_0    conda-forge
ca-certificates           2023.11.17           hbcca054_0    conda-forge
cairo                     1.18.0               h3faef2a_0    conda-forge
cfitsio                   4.3.1                hbdc6101_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_1    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
freexl                    2.0.0                h743c826_0    conda-forge
gdal                      3.8.3           py312ha82c271_0    conda-forge
geos                      3.12.1               h59595ed_0    conda-forge
geotiff                   1.7.1               h6b2125f_15    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
giflib                    5.2.1                h0b41bf4_3    conda-forge
hdf4                      4.2.15               h2a13503_7    conda-forge
hdf5                      1.14.3          nompi_h4f84152_100    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
json-c                    0.17                 h7ab15ed_0    conda-forge
kealib                    1.5.3                h2f55d51_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
lcms2                     2.16                 hb7c19ff_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libabseil                 20230802.1      cxx17_h59595ed_0    conda-forge
libaec                    1.1.2                h59595ed_1    conda-forge
libarchive                3.7.2                h2aa1ff5_1    conda-forge
libblas                   3.9.0           21_linux64_openblas    conda-forge
libboost-headers          1.84.0               ha770c72_0    conda-forge
libcblas                  3.9.0           21_linux64_openblas    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcurl                   8.5.0                hca28451_0    conda-forge
libdeflate                1.19                 hd590300_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_4    conda-forge
libgdal                   3.8.3                hcd1fc54_0    conda-forge
libgfortran-ng            13.2.0               h69a702a_4    conda-forge
libgfortran5              13.2.0               ha4646dd_4    conda-forge
libglib                   2.78.3               h783c2da_0    conda-forge
libgomp                   13.2.0               h807b86a_4    conda-forge
libgoogle-cloud           2.12.0               hef10d8f_5    conda-forge
libgrpc                   1.60.0               h74775cd_1    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
libkml                    1.3.0             h01aab08_1018    conda-forge
liblapack                 3.9.0           21_linux64_openblas    conda-forge
libnetcdf                 4.9.2           nompi_h9612171_113    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.26          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libpq                     16.1                 h33b98f1_7    conda-forge
libprotobuf               4.25.1               hf27288f_0    conda-forge
libre2-11                 2023.06.02           h7a70373_0    conda-forge
librttopo                 1.1.0               h8917695_15    conda-forge
libspatialite             5.1.0                h7bd4643_4    conda-forge
libsqlite                 3.44.2               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_4    conda-forge
libtiff                   4.6.0                ha9c0a0a_2    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.3.2                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.4               h232c23b_1    conda-forge
libzip                    1.10.1               h2629f0a_3    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
minizip                   4.0.4                h0ab5242_0    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
nspr                      4.35                 h27087fc_0    conda-forge
nss                       3.97                 h1d7d5a4_0    conda-forge
numpy                     1.26.3          py312heda63a1_0    conda-forge
openjpeg                  2.5.0                h488ebb8_3    conda-forge
openssl                   3.2.1                hd590300_0    conda-forge
pcre2                     10.42                hcad00b1_0    conda-forge
pip                       23.3.2             pyhd8ed1ab_0    conda-forge
pixman                    0.43.2               h59595ed_0    conda-forge
poppler                   23.12.0              h590f24d_0    conda-forge
poppler-data              0.4.12               hd8ed1ab_0    conda-forge
postgresql                16.1                 h7387d8b_7    conda-forge
proj                      9.3.1                h1d62c97_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
python                    3.12.1          hab00c5b_1_cpython    conda-forge
python_abi                3.12                    4_cp312    conda-forge
re2                       2023.06.02           h2873b5e_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
setuptools                69.0.3             pyhd8ed1ab_0    conda-forge
snappy                    1.1.10               h9fff704_0    conda-forge
sqlite                    3.44.2               h2c6b66d_0    conda-forge
tiledb                    2.19.1               h4386cac_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tzcode                    2023d                h3f72095_0    conda-forge
tzdata                    2023d                h0c530f3_0    conda-forge
uriparser                 0.9.7                hcb278e6_1    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
xerces-c                  3.2.5                hac6953d_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.7                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Environment info

active environment : gdal-383
    active env location : /home/rcm/miniconda3/envs/gdal-383
            shell level : 2
       user config file : /home/rcm/.condarc
 populated config files : 
          conda version : 23.3.1
    conda-build version : not installed
         python version : 3.9.16.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.35=0
                          __linux=6.5.0=0
                          __unix=0=0
       base environment : /home/rcm/miniconda3  (writable)
      conda av data dir : /home/rcm/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/rcm/miniconda3/pkgs
                          /home/rcm/.conda/pkgs
       envs directories : /home/rcm/miniconda3/envs
                          /home/rcm/.conda/envs
               platform : linux-64
             user-agent : conda/23.3.1 requests/2.31.0 CPython/3.9.16 Linux/6.5.0-14-generic ubuntu/22.04.3 glibc/2.35
                UID:GID : 1000:1000
             netrc file : /home/rcm/.netrc
           offline mode : False
akrherz commented 7 months ago

my guess is you are hitting conda-forge/tiledb-feedstock#228

mccarthyryanc commented 7 months ago

Thanks @akrherz ! If I install azure-core-cpp=1.10.3 I am able to read ZARR again. I'll close this issue!