pymatgen
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Published
20 hours ago •
materialsproject
materialsproject
The multiprocessing pool does not work expectively when importing some modules from pymatgen
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))
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))
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 |
Update. Everything worked well When I created a new environment with only pymatgen, matminer, and minimal necessary dependence.