Comments (4)
johnlees
commented on August 26, 2024
This may be an interaction between our use of libgomp and sklearn's.
See scikit-learn/scikit-learn#14485 and pytorch/pytorch#2575 (comment)
Can you please confirm how you installed the package, include the output of conda list, and the version of pp-sketchlib (from running sketchlib).
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johnlees
commented on August 26, 2024
Also whether you are running on OS X (and whether intel or M1) or linux
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davidtong28
commented on August 26, 2024
Hi,
Thanks for reaching back.
I am using a linux system.
I installed everything via conda create -y -n poppunk_2.6 poppunk=2.6.0
here is the output of conda list
# packages in environment at /home/davidtong28/.conda/envs/poppunk_2.6:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aom 3.5.0 h27087fc_0 conda-forge
at-spi2-atk 2.38.0 h0630a04_3 conda-forge
at-spi2-core 2.40.3 h0630a04_0 conda-forge
atk-1.0 2.38.0 hd4edc92_1 conda-forge
biopython 1.81 pypi_0 pypi
boost 1.78.0 py310hc4a4660_4 conda-forge
boost-cpp 1.78.0 h6582d0a_3 conda-forge
brotli 1.0.9 pypi_0 pypi
brotli-bin 1.0.9 h166bdaf_9 conda-forge
brotli-python 1.0.9 py310hd8f1fbe_9 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.19.1 hd590300_0 conda-forge
ca-certificates 2023.05.30 h06a4308_0
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 hbbf8b49_1016 conda-forge
cairomm-1.16 1.16.2 h7e731d7_1 conda-forge
certifi 2023.5.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 pypi_0 pypi
charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
contourpy 1.1.0 pypi_0 pypi
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 3.0.0 pypi_0 pypi
dav1d 1.2.1 hd590300_0 conda-forge
dbus 1.13.18 hb2f20db_0
dendropy 4.6.1 pyhdfd78af_0 bioconda
docopt 0.6.2 py_1 conda-forge
epoxy 1.5.10 h166bdaf_1 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
ffmpeg 6.0.0 gpl_hdbbbd96_103 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 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.41.0 pypi_0 pypi
freetype 2.12.1 hca18f0e_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gdk-pixbuf 2.42.10 h6b639ba_2 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
glib 2.76.4 hfc55251_0 conda-forge
glib-tools 2.76.4 hfc55251_0 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
gnutls 3.7.8 hf3e180e_0 conda-forge
graph-tool 2.57 py310haee70ea_0 conda-forge
graph-tool-base 2.57 py310h9dc9c16_0 conda-forge
graphite2 1.3.14 h295c915_1
gtk3 3.24.38 hf583ffa_0 conda-forge
h5py 3.8.0 pypi_0 pypi
harfbuzz 7.3.0 hdb3a94d_0 conda-forge
hdbscan 0.8.33 pypi_0 pypi
hdf5 1.12.2 nompi_h4df4325_101 conda-forge
hicolor-icon-theme 0.17 ha770c72_2 conda-forge
icu 72.1 hcb278e6_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
joblib 1.3.0 pyhd8ed1ab_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 pypi_0 pypi
krb5 1.21.1 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.15 haa2dc70_1 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.0.6 hcb278e6_1 conda-forge
libass 0.17.1 hc9aadba_0 conda-forge
libblas 3.9.0 17_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_9 conda-forge
libbrotlidec 1.0.9 h166bdaf_9 conda-forge
libbrotlienc 1.0.9 h166bdaf_9 conda-forge
libcblas 3.9.0 17_linux64_openblas conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.2.0 hca28451_0 conda-forge
libdeflate 1.18 h0b41bf4_0 conda-forge
libdrm 2.4.114 h166bdaf_0 conda-forge
libedit 3.1.20221030 h5eee18b_0
libev 4.33 h516909a_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.4 h6a678d5_0
libgcc-ng 13.1.0 he5830b7_0 conda-forge
libgfortran-ng 13.1.0 h69a702a_0 conda-forge
libgfortran5 13.1.0 h15d22d2_0 conda-forge
libgirepository 1.76.1 h8bf6c18_0 conda-forge
libglib 2.76.4 hebfc3b9_0 conda-forge
libgomp 13.1.0 he5830b7_0 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libidn2 2.3.4 h166bdaf_0 conda-forge
libjpeg-turbo 2.1.5.1 h0b41bf4_0 conda-forge
liblapack 3.9.0 17_linux64_openblas conda-forge
libnghttp2 1.52.0 h61bc06f_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.23 pthreads_h80387f5_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpciaccess 0.17 h166bdaf_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
librsvg 2.56.1 h98fae49_0 conda-forge
libsqlite 3.42.0 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge
libtasn1 4.19.0 h166bdaf_0 conda-forge
libtiff 4.5.1 h8b53f26_0 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libva 2.19.0 hd590300_0 conda-forge
libvpx 1.13.0 hcb278e6_0 conda-forge
libwebp-base 1.3.1 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxkbcommon 1.5.0 h5d7e998_3 conda-forge
libxml2 2.11.4 h0d562d8_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
mandrake 1.2.2 pypi_0 pypi
matplotlib 3.7.1 pypi_0 pypi
matplotlib-base 3.7.1 py310he60537e_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
ncurses 6.4 hcb278e6_0 conda-forge
nettle 3.8.1 hc379101_1 conda-forge
networkx 3.1 pyhd8ed1ab_0 conda-forge
numpy 1.25.1 pypi_0 pypi
openblas 0.3.23 pthreads_h855a84d_0 conda-forge
openh264 2.3.1 hcb278e6_2 conda-forge
openjpeg 2.5.0 hfec8fc6_2 conda-forge
openssl 3.1.1 hd590300_1 conda-forge
p11-kit 0.24.1 hc5aa10d_0 conda-forge
packaging 23.1 pyhd8ed1ab_0 conda-forge
pandas 2.0.3 pypi_0 pypi
pango 1.50.14 heaa33ce_1 conda-forge
pcre2 10.40 hc3806b6_0 conda-forge
pillow 10.0.0 pypi_0 pypi
pip 23.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
platformdirs 3.9.1 pyhd8ed1ab_0 conda-forge
plotly 5.15.0 pyhd8ed1ab_0 conda-forge
pooch 1.7.0 pyha770c72_3 conda-forge
poppunk 2.6.0 pypi_0 pypi
pp-sketchlib 2.1.1 pypi_0 pypi
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pycairo 1.24.0 pypi_0 pypi
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygobject 3.44.1 pypi_0 pypi
pyparsing 3.1.0 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pypi_0 pypi
python 3.10.12 hd12c33a_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.10 3_cp310 conda-forge
pytz 2023.3 pyhd8ed1ab_0 conda-forge
rapidnj 2.3.2 h4ac6f70_4 bioconda
readline 8.2 h8228510_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
scikit-learn 1.3.0 pypi_0 pypi
scipy 1.11.1 pypi_0 pypi
setuptools 68.0.0 pyhd8ed1ab_0 conda-forge
sigcpp-3.0 3.4.0 hcb278e6_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sparsehash 2.0.4 hcb278e6_1 conda-forge
svt-av1 1.6.0 h59595ed_0 conda-forge
tenacity 8.2.2 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.2.0 pyha21a80b_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tqdm 4.65.0 pyhd8ed1ab_1 conda-forge
treeswift 1.1.37 pyh7cba7a3_0 bioconda
typing-extensions 4.7.1 hd8ed1ab_0 conda-forge
typing_extensions 4.7.1 pyha770c72_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
unicodedata2 15.0.0 pypi_0 pypi
urllib3 2.0.4 pyhd8ed1ab_0 conda-forge
wayland 1.22.0 h8c25dac_1 conda-forge
wheel 0.40.0 pyhd8ed1ab_1 conda-forge
x264 1!164.3095 h166bdaf_2 conda-forge
x265 3.5 h924138e_3 conda-forge
xkeyboard-config 2.39 hd590300_0 conda-forge
xorg-compositeproto 0.4.2 h7f98852_1001 conda-forge
xorg-damageproto 1.2.1 h7f98852_1002 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 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 1.8.6 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxaw 1.0.14 h7f98852_1 conda-forge
xorg-libxcomposite 0.4.6 h0b41bf4_1 conda-forge
xorg-libxcursor 1.2.0 h0b41bf4_1 conda-forge
xorg-libxdamage 1.1.5 h7f98852_1 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxinerama 1.1.5 h27087fc_0 conda-forge
xorg-libxmu 1.1.3 h7f98852_0 conda-forge
xorg-libxpm 3.5.16 hd590300_0 conda-forge
xorg-libxrandr 1.5.2 h7f98852_1 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_0 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-randrproto 1.5.0 h7f98852_1001 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-util-macros 1.19.3 h7f98852_0 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.4.2 h5eee18b_0
zlib 1.2.13 hd590300_5 conda-forge
zstandard 0.19.0 pypi_0 pypi
zstd 1.5.5 hc292b87_0
Sincerely,
David
from poppunk.
johnlees
commented on August 26, 2024
The solution from the linked issues seem to be to update your glibc, see scikit-learn/scikit-learn#14485 (comment)
from poppunk.
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