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The multiprocessing pool does not work expectively when importing some modules from pymatgen #3402

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TsumiNa opened this issue Oct 11, 2023 · 1 comment
Open

The multiprocessing pool does not work expectively when importing some modules from pymatgen #3402

TsumiNa opened this issue Oct 11, 2023 · 1 comment
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bug needs investigation Needs further research to pinpoint cause of issue performance Some functionality is too slow or regressed pkg Package health and distribution related stuff

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@TsumiNa
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TsumiNa commented Oct 11, 2023 •
edited by janosh
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HI! I was trying to use CrystalNN with a multiprocessing pool and found that the CPU usage was unexpected. I have given some small tests to figure out where the problems are and then found that when I import some modules from pymatgen, such as from pymatgen.analysis.local_env import CrystalNN, from pymatgen.core import Structure, the issue will occur.

The following codes show minimal implementation to reproduce this issue.

The normal case.

from multiprocessing import Pool
import math

def task(arg):
    return sum([math.sqrt(i) for i in range(1, arg)])
 

with Pool(16) as pool:
    # perform calculations
    results = pool.map(task, range(1,50000))

171697055957_ pic

The bugged case. Whatever change the number of processes, the total CPU usage is 200% (In the follow case, is 12.5 x 16 = 200%),

from multiprocessing import Pool
import math

import pymatgen.core.periodic_table  # <- this cause error

def task(arg):
    return sum([math.sqrt(i) for i in range(1, arg)])
 

with Pool(16) as pool:
    # perform calculations
    results = pool.map(task, range(1,50000))

161697055940_ pic

OS: Ubuntu 22.04.3 LTS

My Python(3.8.17) env:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
aiofiles 22.1.0 pypi_0 pypi
aiohttp 3.8.6 py38h01eb140_1 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
aiosqlite 0.19.0 pypi_0 pypi
alsa-lib 1.2.8 h166bdaf_0 conda-forge
annotated-types 0.6.0 pyhd8ed1ab_0 conda-forge
ansi2html 1.8.0 pypi_0 pypi
anyio 4.0.0 pyhd8ed1ab_0 conda-forge
aom 3.5.0 h27087fc_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py38h01eb140_4 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
ase 3.22.1 pyhd8ed1ab_1 conda-forge
asttokens 2.4.0 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
aws-c-auth 0.7.0 hf8751d9_2 conda-forge
aws-c-cal 0.6.0 h93469e0_0 conda-forge
aws-c-common 0.8.23 hd590300_0 conda-forge
aws-c-compression 0.2.17 h862ab75_1 conda-forge
aws-c-event-stream 0.3.1 h9599702_1 conda-forge
aws-c-http 0.7.11 hbe98c3e_0 conda-forge
aws-c-io 0.13.28 h3870b5a_0 conda-forge
aws-c-mqtt 0.8.14 h2e270ba_2 conda-forge
aws-c-s3 0.3.13 heb0bb06_2 conda-forge
aws-c-sdkutils 0.1.11 h862ab75_1 conda-forge
aws-checksums 0.1.16 h862ab75_1 conda-forge
aws-crt-cpp 0.20.3 he9c0e7f_4 conda-forge
aws-sdk-cpp 1.10.57 hbc2ea52_17 conda-forge
babel 2.13.0 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
blas 1 mkl conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
blinker 1.6.3 pyhd8ed1ab_0 conda-forge
boost 1.78.0 py38hae673b5_5 conda-forge
boost-cpp 1.78.0 h5adbc97_2 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py38h17151c0_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.20.1 hd590300_0 conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachelib 0.9.0 pypi_0 pypi
cairo 1.16.0 ha61ee94_1014 conda-forge
certifi 2023.7.22 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py38h6d47a40_0 conda-forge
cftime 1.6.2 py38h7f0c24c_2 conda-forge
charset-normalizer 3.3.0 pyhd8ed1ab_0 conda-forge
chgnet 0.2.0 pypi_0 pypi
chronic 0.3.4 pyhd3deb0d_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.1.4 pyhd8ed1ab_0 conda-forge
contourpy 1.1.1 py38h7f3f72f_1 conda-forge
cryptography 41.0.4 py38hcdda232_0 conda-forge
crystal-toolkit 2023.8.9 pypi_0 pypi
crystallus 0.3.1_rc1 pypi_0 pypi
crystaltoolkit-extension 0.6.0 pypi_0 pypi
cuda-cudart 11.8.89 0 nvidia
cuda-cupti 11.8.87 0 nvidia
cuda-libraries 11.8.0 0 nvidia
cuda-nvrtc 11.8.89 0 nvidia
cuda-nvtx 11.8.86 0 nvidia
cuda-runtime 11.8.0 0 nvidia
cuda-version 12 hffde075_2 conda-forge
curl 8.1.2 h409715c_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
cython 3.0.0 pypi_0 pypi
dash 2.12.0 pypi_0 pypi
dash-core-components 2.0.0 pypi_0 pypi
dash-html-components 2.0.0 pypi_0 pypi
dash-mp-components 0.4.37 pypi_0 pypi
dash-table 5.0.0 pypi_0 pypi
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.8.0 py38h17151c0_1 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.14 pypi_0 pypi
dgl 1.1.2.cu118 py38_0 dglteam/label/cu118
dnspython 2.4.2 pyhd8ed1ab_0 conda-forge
docker-pycreds 0.4.0 py_0 conda-forge
double-conversion 3.2.0 h27087fc_1 conda-forge
eigen 3.4.0 h00ab1b0_0 conda-forge
emmet-core 0.69.5 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
et_xmlfile 1.1.0 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.1.3 pyhd8ed1ab_0 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fastcluster 1.2.6 py38h53bb729_3 conda-forge
ffmpeg 5.1.2 gpl_h8dda1f0_106 conda-forge
fftw 3.3.10 nompi_hc118613_108 conda-forge
filelock 3.12.4 pyhd8ed1ab_0 conda-forge
flask 2.2.5 pypi_0 pypi
flask-caching 2.0.2 pypi_0 pypi
flit-core 3.9.0 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3 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 4.43.1 py38h01eb140_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
frozendict 2.3.8 py38h01eb140_1 conda-forge
frozenlist 1.4.0 py38h01eb140_1 conda-forge
fsspec 2023.6.0 pypi_0 pypi
future 0.18.3 pyhd8ed1ab_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gitdb 4.0.10 pyhd8ed1ab_0 conda-forge
gitpython 3.1.37 pyhd8ed1ab_0 conda-forge
gl2ps 1.4.2 h0708190_0 conda-forge
glew 2.1.0 h9c3ff4c_2 conda-forge
glib 2.78.0 hfc55251_0 conda-forge
glib-tools 2.78.0 hfc55251_0 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
gmpy2 2.1.2 py38h793c122_1 conda-forge
gnutls 3.7.8 hf3e180e_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
greenlet 3.0.0 py38h17151c0_1 conda-forge
gst-plugins-base 1.22.0 h4243ec0_2 conda-forge
gstreamer 1.22.0 h25f0c4b_2 conda-forge
gstreamer-orc 0.4.34 hd590300_0 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
h5py 3.8.0 nompi_py38hd5fa8ee_100 conda-forge
harfbuzz 6.0.0 h8e241bc_0 conda-forge
hdf4 4.2.15 h9772cbc_5 conda-forge
hdf5 1.12.2 nompi_h4df4325_101 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 1.0.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
imageio 2.31.1 pypi_0 pypi
importlib-metadata 6.8.0 pyha770c72_0 conda-forge
importlib-resources 6.1.0 pyhd8ed1ab_0 conda-forge
importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge
importlib_resources 6.1.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.25.2 pyh2140261_0 conda-forge
ipython 8.12.2 pyh41d4057_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 8.1.1 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
itsdangerous 2.1.2 pyhd8ed1ab_0 conda-forge
jack 1.9.22 h11f4161_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
json5 0.9.14 pyhd8ed1ab_0 conda-forge
jsoncpp 1.9.5 h4bd325d_1 conda-forge
jsonpointer 2.4 py38h578d9bd_3 conda-forge
jsonschema 4.19.1 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.19.1 pyhd8ed1ab_0 conda-forge
jupyter 1.0.0 pyhd8ed1ab_10 conda-forge
jupyter-client 7.4.9 pypi_0 pypi
jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge
jupyter-server-fileid 0.9.0 pypi_0 pypi
jupyter-server-ydoc 0.8.0 pypi_0 pypi
jupyter-ydoc 0.2.5 pypi_0 pypi
jupyter_client 8.4.0 pyhd8ed1ab_0 conda-forge
jupyter_console 6.6.3 pyhd8ed1ab_0 conda-forge
jupyter_core 5.4.0 py38h578d9bd_0 conda-forge
jupyter_events 0.7.0 pyhd8ed1ab_2 conda-forge
jupyter_server 2.7.3 pyhd8ed1ab_1 conda-forge
jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge
jupyterlab 3.6.5 pypi_0 pypi
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.25.0 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.9 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py38h7f3f72f_1 conda-forge
krb5 1.20.1 h81ceb04_0 conda-forge
lame 3.1 h166bdaf_1003 conda-forge
latexcodec 2.0.1 pyh9f0ad1d_0 conda-forge
lazy-loader 0.3 pypi_0 pypi
lcms2 2.15 hfd0df8a_0 conda-forge
ld_impl_linux-64 2.4 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
libblas 3.9.0 16_linux64_mkl conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.67 he9d0100_0 conda-forge
libcblas 3.9.0 16_linux64_mkl conda-forge
libclang 15.0.7 default_h7634d5b_3 conda-forge
libclang13 15.0.7 default_h9986a30_3 conda-forge
libcublas 11.11.3.6 0 nvidia
libcufft 10.9.0.58 0 nvidia
libcufile 1.5.0.59 hcb278e6_0 conda-forge
libcups 2.3.3 h36d4200_3 conda-forge
libcurand 10.3.1.50 hcb278e6_0 conda-forge
libcurl 8.1.2 h409715c_0 conda-forge
libcusolver 11.4.1.48 0 nvidia
libcusparse 11.7.5.86 0 nvidia
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.17 h0b41bf4_0 conda-forge
libdrm 2.4.114 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h28343ad_4 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-ng 13.2.0 h807b86a_2 conda-forge
libgcrypt 1.10.1 h166bdaf_0 conda-forge
libgfortran-ng 13.2.0 h69a702a_2 conda-forge
libgfortran5 13.2.0 ha4646dd_2 conda-forge
libglib 2.78.0 hebfc3b9_0 conda-forge
libglu 9.0.0 he1b5a44_1001 conda-forge
libgomp 13.2.0 h807b86a_2 conda-forge
libgpg-error 1.47 h71f35ed_0 conda-forge
libhwloc 2.9.1 hd6dc26d_0 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libidn2 2.3.4 h166bdaf_0 conda-forge
liblapack 3.9.0 16_linux64_mkl conda-forge
libllvm15 15.0.7 hadd5161_1 conda-forge
libnetcdf 4.9.1 nompi_h34a3ff0_101 conda-forge
libnghttp2 1.52.0 h61bc06f_0 conda-forge
libnpp 11.8.0.86 0 nvidia
libnsl 2.0.0 hd590300_1 conda-forge
libnvjpeg 11.9.0.86 0 nvidia
libogg 1.3.4 h7f98852_1 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
libpq 15.3 hbcd7760_1 conda-forge
libprotobuf 4.24.4 hf27288f_0 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.43.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_2 conda-forge
libsystemd0 253 h8c4010b_1 conda-forge
libtasn1 4.19.0 h166bdaf_0 conda-forge
libtheora 1.1.1 h7f98852_1005 conda-forge
libtiff 4.5.0 h6adf6a1_2 conda-forge
libtool 2.4.7 h27087fc_0 conda-forge
libudev1 253 h0b41bf4_1 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libva 2.18.0 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libvpx 1.11.0 h9c3ff4c_3 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.5.0 h79f4944_1 conda-forge
libxml2 2.10.3 hca2bb57_4 conda-forge
libzip 1.10.1 h2629f0a_3 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lightning-utilities 0.9.0 pypi_0 pypi
llvm-openmp 17.0.2 h4dfa4b3_0 conda-forge
loguru 0.7.2 py38h578d9bd_1 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
markupsafe 2.1.3 py38h01eb140_1 conda-forge
matgl 0.8.2 pypi_0 pypi
matid 0.6.3 pyhd8ed1ab_0 conda-forge
matminer 0.8.0 pyhd8ed1ab_0 conda-forge
matplotlib-base 3.7.3 py38h58ed7fa_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mistune 3.0.1 pyhd8ed1ab_0 conda-forge
mkl 2022.2.1 h84fe81f_16997 conda-forge
monty 2023.9.25 pyhd8ed1ab_0 conda-forge
mordred 1.2.0 py_1 conda-forge
mp-api 0.33.3 pyhd8ed1ab_0 conda-forge
mpc 1.3.1 hfe3b2da_0 conda-forge
mpfr 4.2.0 hb012696_0 conda-forge
mpg123 1.32.3 h59595ed_0 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.6 py38h7f3f72f_0 conda-forge
multidict 6.0.4 py38h01eb140_1 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.33 hf1915f5_5 conda-forge
mysql-libs 8.0.33 hca2cd23_5 conda-forge
nbclassic 1.0.0 pypi_0 pypi
nbclient 0.8.0 pyhd8ed1ab_0 conda-forge
nbconvert 7.9.2 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.9.2 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.9.2 pyhd8ed1ab_0 conda-forge
nbformat 5.9.2 pyhd8ed1ab_0 conda-forge
ncurses 6.4 hcb278e6_0 conda-forge
nest-asyncio 1.5.7 pyhd8ed1ab_0 conda-forge
netcdf4 1.6.3 nompi_py38h08fe49f_100 conda-forge
nettle 3.8.1 hc379101_1 conda-forge
networkx 2.8.8 pypi_0 pypi
nglview 3.0.8 pyh1da8cd4_0 conda-forge
nlohmann_json 3.11.2 h27087fc_0 conda-forge
notebook 6.5.5 pypi_0 pypi
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.94 h1d7d5a4_0 conda-forge
numpy 1.24.4 py38h59b608b_0 conda-forge
openai 0.28.1 pyhd8ed1ab_0 conda-forge
openh264 2.3.1 hcb278e6_2 conda-forge
openjpeg 2.5.0 hfec8fc6_2 conda-forge
openpyxl 3.1.2 py38h01eb140_1 conda-forge
openssl 3.1.3 hd590300_0 conda-forge
overrides 7.4.0 pyhd8ed1ab_0 conda-forge
p11-kit 0.24.1 hc5aa10d_0 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
palettable 3.3.3 pyhd8ed1ab_0 conda-forge
pandas 2.0.3 py38h01efb38_1 conda-forge
pandas-stubs 2.1.1.230928 pyhd8ed1ab_0 conda-forge
pandoc 3.1.3 h32600fe_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pathtools 0.1.2 py_1 conda-forge
patsy 0.5.3 pyhd8ed1ab_0 conda-forge
pcre2 10.4 hc3806b6_0 conda-forge
peewee 3.16.3 py38h39d08e6_1 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
phonopy 2.20.0 py38h31356c5_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.4.0 py38hde6dc18_1 conda-forge
pint 0.21 pyhd8ed1ab_0 conda-forge
pip 23.2.1 pyhd8ed1ab_0 conda-forge
pixman 0.42.2 h59595ed_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 3.11.0 pyhd8ed1ab_0 conda-forge
plotly 5.17.0 pyhd8ed1ab_0 conda-forge
ply 3.11 py_1 conda-forge
pooch 1.7.0 pyhd8ed1ab_4 conda-forge
proj 9.1.1 h8ffa02c_2 conda-forge
prometheus_client 0.17.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.39 pyha770c72_0 conda-forge
prompt_toolkit 3.0.39 hd8ed1ab_0 conda-forge
protobuf 4.24.4 py38hf14ab21_0 conda-forge
psutil 5.9.5 py38h01eb140_1 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pugixml 1.11.4 h59595ed_1 conda-forge
pulseaudio 16.1 hcb278e6_3 conda-forge
pulseaudio-client 16.1 h5195f5e_3 conda-forge
pulseaudio-daemon 16.1 ha8d29e2_3 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pybtex 0.24.0 pyhd8ed1ab_2 conda-forge
pycairo 1.25.0 py38h1a1917b_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydantic 2.4.2 pyhd8ed1ab_0 conda-forge
pydantic-core 2.10.1 py38h0cc4f7c_0 conda-forge
pydantic-settings 2.0.3 pyhd8ed1ab_0 conda-forge
pygments 2.16.1 pyhd8ed1ab_0 conda-forge
pymatgen 2023.8.10 py38h905acbe_0 conda-forge
pymongo 4.5.0 py38h17151c0_1 conda-forge
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py38hffdaa6c_5 conda-forge
pyqt5-sip 12.12.2 py38h17151c0_5 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.8.18 hd12c33a_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-dotenv 1.0.0 pyhd8ed1ab_1 conda-forge
python-fastjsonschema 2.18.1 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.8 4_cp38 conda-forge
pytorch 2.0.1 py3.8_cuda11.8_cudnn8.7.0_0 pytorch
pytorch-cuda 11.8 h7e8668a_5 pytorch
pytorch-lightning 2.0.6 pypi_0 pypi
pytorch-mutex 1 cuda pytorch
pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge
pywavelets 1.4.1 pypi_0 pypi
pyyaml 6.0.1 py38h01eb140_1 conda-forge
pyzmq 24.0.1 pypi_0 pypi
qt-main 5.15.8 h5d23da1_6 conda-forge
qtconsole 5.4.4 pyhd8ed1ab_0 conda-forge
qtconsole-base 5.4.4 pyha770c72_0 conda-forge
qtpy 2.4.0 pyhd8ed1ab_0 conda-forge
rdkit 2023.03.3 py38h36d2b2f_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.30.2 pyhd8ed1ab_0 conda-forge
reportlab 4.0.6 py38h01eb140_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
retrying 1.3.4 pypi_0 pypi
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.10.4 py38h0cc4f7c_0 conda-forge
ruamel.yaml 0.17.35 py38h01eb140_0 conda-forge
ruamel.yaml.clib 0.2.7 py38h01eb140_2 conda-forge
s2n 1.3.46 h06160fa_0 conda-forge
scikit-image 0.21.0 pypi_0 pypi
scikit-learn 1.3.1 py38ha25d942_1 conda-forge
scipy 1.10.1 py38h59b608b_3 conda-forge
seaborn 0.13.0 hd8ed1ab_0 conda-forge
seaborn-base 0.13.0 pyhd8ed1ab_0 conda-forge
send2trash 1.8.2 pyh41d4057_0 conda-forge
sentry-sdk 1.32.0 pyhd8ed1ab_0 conda-forge
setproctitle 1.3.3 py38h01eb140_0 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
shapely 2.0.1 pypi_0 pypi
sip 6.7.11 py38h17151c0_1 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smmap 3.0.5 pyh44b312d_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
spglib 2.1.0 py38hb851694_0 conda-forge
sqlalchemy 2.0.21 py38h01eb140_1 conda-forge
sqlite 3.43.2 h2c6b66d_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
statsmodels 0.14.0 py38h7f0c24c_2 conda-forge
svt-av1 1.4.1 hcb278e6_0 conda-forge
sympy 1.12 pypyh9d50eac_103 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
tbb 2021.9.0 hf52228f_0 conda-forge
tbb-devel 2021.9.0 hf52228f_0 conda-forge
tenacity 8.2.3 pyhd8ed1ab_0 conda-forge
terminado 0.17.1 pyh41d4057_0 conda-forge
threadpoolctl 3.2.0 pyha21a80b_0 conda-forge
tifffile 2023.7.10 pypi_0 pypi
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.13 h2797004_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
torchdata 0.6.1 py38h6972470_0 conda-forge
torchmetrics 1.0.3 pypi_0 pypi
torchtext 0.15.2 py38 pytorch
torchtriton 2.0.0 py38 pytorch
torchvision 0.15.2 py38_cu118 pytorch
tornado 6.3.3 py38h01eb140_1 conda-forge
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
traitlets 5.11.2 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.8.19.14 pyhd8ed1ab_0 conda-forge
types-pytz 2023.3.1.1 pyhd8ed1ab_0 conda-forge
typing-extensions 4.8.0 hd8ed1ab_0 conda-forge
typing_extensions 4.8.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
uncertainties 3.1.7 pyhd8ed1ab_0 conda-forge
unicodedata2 15.1.0 py38h01eb140_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.0.6 pyhd8ed1ab_0 conda-forge
utfcpp 3.2.5 ha770c72_0 conda-forge
vtk 9.2.6 qt_py38h6b1c7ce_200 conda-forge
wandb 0.15.12 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.8 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.6.4 pyhd8ed1ab_0 conda-forge
werkzeug 2.2.3 pypi_0 pypi
wheel 0.41.2 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.9 pyhd8ed1ab_0 conda-forge
wrapt 1.15.0 pypi_0 pypi
wslink 1.12.3 pyhd8ed1ab_0 conda-forge
x264 1!164.3095 h166bdaf_2 conda-forge
x265 3.5 h924138e_3 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
xenonpy 0.6.7 pypi_0 pypi
xkeyboard-config 2.38 h0b41bf4_0 conda-forge
xorg-fixesproto 5 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 1.8.4 h0b41bf4_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-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.3.0 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
y-py 0.6.0 pypi_0 pypi
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.2 py38h01eb140_1 conda-forge
ypy-websocket 0.8.4 pypi_0 pypi
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
@janosh janosh added bug performance Some functionality is too slow or regressed pkg Package health and distribution related stuff needs investigation Needs further research to pinpoint cause of issue labels Oct 12, 2023
@TsumiNa
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TsumiNa commented Oct 12, 2023

Update. Everything worked well When I created a new environment with only pymatgen, matminer, and minimal necessary dependence.

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bug needs investigation Needs further research to pinpoint cause of issue performance Some functionality is too slow or regressed pkg Package health and distribution related stuff
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