QGIS 3.28.1 + scikit-learn causes QH6259 qhull internal error on Linux #284
Comments
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Also when importing running I know scipy has internal version which maybe now conflicts? |
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Sounds like this might be more an issue between gdal and scipy. Scikit-learn depends on scipy, so probably, it also runs |
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Maybe @rouault have some idea? |
ah, if scipy has an internal version of qhull, and it doesn't rename symbols, then yes, that's likely the cause of the issue.
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This reverts commit b3bd22d because of an issue when using gdal and scipy.spatial.Delaunay, the later apparently bundling qhull. See conda-forge/qgis-feedstock#284 (comment) for details
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Revert of qhull dependency for GDAL proposed in conda-forge/gdal-feedstock#705 |
Thanks, @rouault, I guess this should fix it as soon as qgis is compatible with gdal 3.6.1. Currently, I get this when attempting to update gdal to 3.6.1: |
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I guess that many other dependencies need to be rebuilt to use gdal 3.6.1 before we can build qgis itself |
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The fastest solution would be to backport conda-forge/gdal-feedstock#705 to gdal 3.6.0, right? Not sure if this is possible. |
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On the other hand, 3.6.0 has a nasty bug with geopackages, so would be better to really bump gdal to 3.6.1 in qgis |
Thanks for looking at this @rouault . I guess ATM anything that links to |
yes, most likely. There is nothing GDAL specific in that crash. The fact that it happens in a QGIS context and not in simpler scenarios is typically of symbol clashes where the order of symbol loading is somewhat "random", and sometimes you're lucky, sometimes not. |
Right, but at the moment, any QGIS plugin, that directly or indirectly depends on scipy, will crash QGIS. So far as I understand from the release notes of gdal 3.6.1, setting OGR_GPKG_ALLOW_THREADED_RTREE=NO would fix the issue there. |
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I am ok rebuilding qgis with a gdal 3.6.0 patched version, but since 3.6.1 is already out, I will make sure to rebuild it for that version as well as soon as possible. Geopackage is QGIS default format, which means it will impact most of our user. Although there's a workaround, most folks won't know about it, so better fix it as soon as possible. |
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looks like this issue could be closed |
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Indeed. FYI did submit this to the scipy-dev mailing list (https://mail.python.org/archives/list/scipy-dev@python.org/thread/I535LGRTWUXJIP2VM7VQGF3HELHQJ4B2/). I'll post back here with how it got resolved. |
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Just FYI, turns out that scipy does implement symbol hiding for these symbols (and those from other vendored libs) on Linux when built using Meson. However, conda-forge still uses distutils for reasons detailed here: conda-forge/scipy-feedstock#213 and distutils builds don't implement symbol hiding. So, turns out it is hard to get a consistent software stack! @rouault scipy (with Meson) uses the |
Switching to Meson for anything but Windows is quite straightforward by now though, and can be done either now or for SciPy |
I've tried to avoid linker specific solutions for symbol hiding. What I do is that using objdump I establish the list of symbols of the vendored library and then generate a header file with a list of "#define symbol_in_the_vendored_lib gdal_symbol_in_the_vendored_lib". Fully cross platform.
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Solution to issue cannot be found in the documentation.
Issue
I just installed QGIS 3.28.1 (py311h7bb8ebf_2) together with scikit-learn 1.2.0 (py311h67c5ca5_0) into the same environment on Linux (Ubuntu 20.04). QGIS starts, but as soon as scikit-learn is imported, QGIS crashes and prints the the following message on the command line:
This happens with all Python>=3.9 environments on Linux but works properly in the same setup on Windows or also on Linux with QGIS 3.22.11 (py310heaafcf0_0).
It can be reproduced with
mamba create -n qgis_sklearn "qgis=3.28.1" scikit-learn.Installed packages
# Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge alsa-lib 1.2.8 h166bdaf_0 conda-forge attr 2.5.1 h166bdaf_1 conda-forge blosc 1.21.3 hafa529b_0 conda-forge boost-cpp 1.78.0 h75c5d50_1 conda-forge brotlipy 0.7.0 py311hd4cff14_1005 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2022.12.7 ha878542_0 conda-forge cairo 1.16.0 ha61ee94_1014 conda-forge certifi 2022.12.7 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py311h409f033_3 conda-forge cfitsio 4.2.0 hd9d235c_0 conda-forge charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge coverage 6.5.0 py311hd4cff14_1 conda-forge cryptography 38.0.4 py311hb3c386c_0 conda-forge curl 7.86.0 h7bff187_1 conda-forge dbus 1.13.6 h5008d03_3 conda-forge draco 1.5.5 h924138e_0 conda-forge eigen 3.4.0 h4bd325d_0 conda-forge exiv2 0.27.5 h848de5d_0 conda-forge expat 2.5.0 h27087fc_0 conda-forge fftw 3.3.10 nompi_hf0379b8_106 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 hab24e00_0 conda-forge fontconfig 2.14.1 hc2a2eb6_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge freexl 1.0.6 h166bdaf_1 conda-forge future 0.18.2 pyhd8ed1ab_6 conda-forge gdal 3.6.0 py311hf6158c2_7 conda-forge geos 3.11.1 h27087fc_0 conda-forge geotiff 1.7.1 ha76d385_4 conda-forge gettext 0.21.1 h27087fc_0 conda-forge giflib 5.2.1 h36c2ea0_2 conda-forge glib 2.74.1 h6239696_1 conda-forge glib-tools 2.74.1 h6239696_1 conda-forge gsl 2.7 he838d99_0 conda-forge gst-plugins-base 1.21.2 h3e40eee_0 conda-forge gstreamer 1.21.2 hd4edc92_0 conda-forge gstreamer-orc 0.4.33 h166bdaf_0 conda-forge hdf4 4.2.15 h9772cbc_5 conda-forge hdf5 1.12.2 nompi_h2386368_100 conda-forge httplib2 0.21.0 pyhd8ed1ab_0 conda-forge icu 70.1 h27087fc_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge jack 1.9.21 h583fa2b_2 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge joblib 1.2.0 pyhd8ed1ab_0 conda-forge jpeg 9e h166bdaf_2 conda-forge json-c 0.16 hc379101_0 conda-forge kealib 1.4.15 ha7026e8_1 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.19.3 h3790be6_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge laz-perf 3.0.0 h4bd325d_0 conda-forge lcms2 2.14 h6ed2654_0 conda-forge ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libcap 2.66 ha37c62d_0 conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libclang 15.0.6 default_h2e3cab8_0 conda-forge libclang13 15.0.6 default_h3a83d3e_0 conda-forge libcups 2.3.3 h3e49a29_2 conda-forge libcurl 7.86.0 h7bff187_1 conda-forge libdb 6.2.32 h9c3ff4c_0 conda-forge libdeflate 1.14 h166bdaf_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.10 h9b69904_4 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libflac 1.4.2 h27087fc_0 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgcrypt 1.10.1 h166bdaf_0 conda-forge libgdal 3.6.0 ha189470_7 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libglib 2.74.1 h606061b_1 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libgpg-error 1.45 hc0c96e0_0 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libkml 1.3.0 h37653c0_1015 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge libllvm15 15.0.6 h63197d8_0 conda-forge libnetcdf 4.8.1 nompi_h261ec11_106 conda-forge libnghttp2 1.47.0 hdcd2b5c_1 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpng 1.6.39 h753d276_0 conda-forge libpq 14.5 h72a31a5_3 conda-forge libprotobuf 3.21.12 h3eb15da_0 conda-forge librttopo 1.1.0 ha49c73b_12 conda-forge libsecret 0.18.8 h329b89f_2 conda-forge libsndfile 1.1.0 hcb278e6_1 conda-forge libspatialindex 1.9.3 h9c3ff4c_4 conda-forge libspatialite 5.0.1 h7c8129e_22 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libsystemd0 252 h2a991cd_0 conda-forge libtiff 4.4.0 h55922b4_4 conda-forge libtool 2.4.6 h9c3ff4c_1008 conda-forge libudev1 252 h166bdaf_0 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp 1.2.4 h522a892_0 conda-forge libwebp-base 1.2.4 h166bdaf_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxkbcommon 1.0.3 he3ba5ed_0 conda-forge libxml2 2.10.3 h7463322_0 conda-forge libxslt 1.1.37 h873f0b0_0 conda-forge libzip 1.9.2 hc869a4a_1 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge markupsafe 2.1.1 py311hd4cff14_2 conda-forge mock 4.0.3 pyhd8ed1ab_4 conda-forge mpg123 1.31.1 h27087fc_0 conda-forge mysql-common 8.0.31 haf5c9bc_0 conda-forge mysql-libs 8.0.31 h28c427c_0 conda-forge ncurses 6.3 h27087fc_1 conda-forge nitro 2.7.dev6 h27087fc_5 conda-forge nose2 0.9.2 py_0 conda-forge nspr 4.35 h27087fc_0 conda-forge nss 3.82 he02c5a1_0 conda-forge numpy 1.23.5 py311h7d28db0_0 conda-forge openjpeg 2.5.0 h7d73246_1 conda-forge openssl 1.1.1s h0b41bf4_1 conda-forge owslib 0.27.2 pyhd8ed1ab_1 conda-forge packaging 22.0 pyhd8ed1ab_0 conda-forge pcre2 10.40 hc3806b6_0 conda-forge pdal 2.4.3 hbf2fe72_3 conda-forge pip 22.3.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge plotly 5.11.0 pyhd8ed1ab_1 conda-forge ply 3.11 py_1 conda-forge poppler 22.11.0 h92391eb_0 conda-forge poppler-data 0.4.11 hd8ed1ab_0 conda-forge postgresql 14.5 h5bbe9e2_3 conda-forge proj 9.1.0 h93bde94_0 conda-forge psycopg2 2.9.3 py311hd4cff14_1 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pulseaudio 16.1 h4a94279_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygments 2.13.0 pyhd8ed1ab_0 conda-forge pyopenssl 22.1.0 pyhd8ed1ab_0 conda-forge pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge pyproj 3.4.1 py311h7c961c7_0 conda-forge pyqt 5.15.7 py311h3408d8f_2 conda-forge pyqt5-sip 12.11.0 py311ha362b79_2 conda-forge pyqtwebkit 5.15.7 py311h3408d8f_3 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge python 3.11.0 h582c2e5_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python_abi 3.11 3_cp311 conda-forge pytz 2022.6 pyhd8ed1ab_0 conda-forge pyyaml 6.0 py311hd4cff14_5 conda-forge qca 2.3.5 h51e5271_0 conda-forge qgis 3.28.1 py311h7bb8ebf_2 conda-forge qhull 2020.2 h4bd325d_2 conda-forge qjson 0.9.0 h51e5271_1007 conda-forge qscintilla2 2.13.3 py311h3408d8f_4 conda-forge qt-main 5.15.6 h7acdfc8_2 conda-forge qtkeychain 0.13.2 h1601faa_0 conda-forge qtwebkit 5.212 h3383a02_6 conda-forge qwt 6.2.0 h1d9fb53_4 conda-forge readline 8.1.2 h0f457ee_0 conda-forge requests 2.28.1 pyhd8ed1ab_1 conda-forge scikit-learn 1.2.0 py311h67c5ca5_0 conda-forge scipy 1.9.3 py311h69910c8_2 conda-forge setuptools 65.5.1 pyhd8ed1ab_0 conda-forge sip 6.7.5 py311ha362b79_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.9 hbd366e4_2 conda-forge sqlite 3.40.0 h4ff8645_0 conda-forge tenacity 8.1.0 pyhd8ed1ab_0 conda-forge threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge tiledb 2.11.3 h1e4a385_1 conda-forge tk 8.6.12 h27826a3_0 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tzcode 2022g h166bdaf_0 conda-forge tzdata 2022g h191b570_0 conda-forge urllib3 1.26.13 pyhd8ed1ab_0 conda-forge wheel 0.38.4 pyhd8ed1ab_0 conda-forge xcb-util 0.4.0 h516909a_0 conda-forge xcb-util-image 0.4.0 h166bdaf_0 conda-forge xcb-util-keysyms 0.4.0 h516909a_0 conda-forge xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge xcb-util-wm 0.4.1 h516909a_0 conda-forge xerces-c 3.2.4 h55805fa_1 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.7.2 h7f98852_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h7f98852_1 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zstd 1.5.2 h6239696_4 conda-forgeEnvironment info
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