Open Lumen97 opened 2 months ago
Below is a Conda environment that can run PMDM correctly:
name: pmdm channels: - nvidia - conda-forge - pytorch - defaults dependencies: - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=2_gnu - acpype=2022.7.21=pyhd8ed1ab_1 - ambertools=22.4=py39h804d063_0 - arpack=3.7.0=hdefa2d7_2 - blas=1.0=mkl - boost=1.78.0=py39hda80f44_5 - boost-cpp=1.78.0=h2c5509c_4 - bottleneck=1.3.7=py39ha9d4c09_0 - brotli=1.0.9=h5eee18b_7 - brotli-bin=1.0.9=h5eee18b_7 - brotli-python=1.0.9=py39h6a678d5_7 - bzip2=1.0.8=hd590300_5 - c-ares=1.19.1=h5eee18b_0 - ca-certificates=2024.3.11=h06a4308_0 - cairo=1.18.0=h3faef2a_0 - certifi=2024.2.2=py39h06a4308_0 - charset-normalizer=2.0.4=pyhd3eb1b0_0 - contourpy=1.2.0=py39hdb19cb5_0 - cuda-cudart=11.8.89=0 - cuda-cupti=11.8.87=0 - cuda-libraries=11.8.0=0 - cuda-nvrtc=11.8.89=0 - cuda-nvtx=11.8.86=0 - cuda-runtime=11.8.0=0 - cuda-version=11.8=h70ddcb2_3 - cudatoolkit=11.8.0=h4ba93d1_13 - cudatoolkit-dev=11.7.0=h1de0b5d_6 - cudnn=8.9.7.29=hbc23b4c_3 - curl=8.5.0=hdbd6064_0 - cycler=0.11.0=pyhd3eb1b0_0 - cython=3.0.10=py39h5eee18b_0 - expat=2.5.0=h6a678d5_0 - ffmpeg=4.3=hf484d3e_0 - fftw=3.3.10=nompi_hc118613_108 - filelock=3.13.1=py39h06a4308_0 - font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0 - font-ttf-inconsolata=2.001=hcb22688_0 - font-ttf-source-code-pro=2.030=hd3eb1b0_0 - font-ttf-ubuntu=0.83=h8b1ccd4_0 - fontconfig=2.14.2=h14ed4e7_0 - fonts-anaconda=1=h8fa9717_0 - fonts-conda-ecosystem=1=hd3eb1b0_0 - freetype=2.12.1=h4a9f257_0 - gdbm=1.18=hd4cb3f1_4 - glib=2.78.4=h6a678d5_0 - glib-tools=2.78.4=h6a678d5_0 - gmp=6.2.1=h295c915_3 - gmpy2=2.1.2=py39heeb90bb_0 - gnutls=3.6.15=he1e5248_0 - greenlet=3.0.1=py39h6a678d5_0 - hdf4=4.2.15=h9772cbc_5 - hdf5=1.12.2=nompi_h4df4325_101 - icu=73.2=h59595ed_0 - idna=3.4=py39h06a4308_0 - importlib_resources=6.1.1=py39h06a4308_1 - intel-openmp=2023.1.0=hdb19cb5_46306 - jinja2=3.1.3=py39h06a4308_0 - jpeg=9e=h5eee18b_1 - kiwisolver=1.4.4=py39h6a678d5_0 - krb5=1.20.1=h143b758_1 - lame=3.100=h7b6447c_0 - lcms2=2.12=h3be6417_0 - ld_impl_linux-64=2.38=h1181459_1 - lerc=3.0=h295c915_0 - libaec=1.1.3=h59595ed_0 - libblas=3.9.0=1_h86c2bf4_netlib - libbrotlicommon=1.0.9=h5eee18b_7 - libbrotlidec=1.0.9=h5eee18b_7 - libbrotlienc=1.0.9=h5eee18b_7 - libcublas=11.11.3.6=0 - libcufft=10.9.0.58=0 - libcufile=1.9.1.3=0 - libcurand=10.3.5.147=0 - libcurl=8.5.0=h251f7ec_0 - libcusolver=11.4.1.48=0 - libcusparse=11.7.5.86=0 - libdeflate=1.17=h5eee18b_1 - libedit=3.1.20230828=h5eee18b_0 - libev=4.33=h7f8727e_1 - libffi=3.4.4=h6a678d5_0 - libgcc-ng=13.2.0=h807b86a_5 - libgfortran-ng=13.2.0=h69a702a_5 - libgfortran5=13.2.0=ha4646dd_5 - libglib=2.78.4=hdc74915_0 - libgomp=13.2.0=h807b86a_5 - libiconv=1.17=hd590300_2 - libidn2=2.3.4=h5eee18b_0 - libjpeg-turbo=2.0.0=h9bf148f_0 - liblapack=3.9.0=5_h92ddd45_netlib - libnetcdf=4.9.1=nompi_h34a3ff0_101 - libnghttp2=1.57.0=h2d74bed_0 - libnpp=11.8.0.86=0 - libnsl=2.0.1=hd590300_0 - libnvjpeg=11.9.0.86=0 - libpng=1.6.39=h5eee18b_0 - libsqlite=3.45.2=h2797004_0 - libssh2=1.10.0=hdbd6064_2 - libstdcxx-ng=13.2.0=h7e041cc_5 - libtasn1=4.19.0=h5eee18b_0 - libtiff=4.5.1=h6a678d5_0 - libunistring=0.9.10=h27cfd23_0 - libuuid=2.38.1=h0b41bf4_0 - libwebp-base=1.3.2=h5eee18b_0 - libxcb=1.15=h7f8727e_0 - libxcrypt=4.4.36=hd590300_1 - libxml2=2.12.6=h232c23b_1 - libzip=1.10.1=h2629f0a_3 - libzlib=1.2.13=hd590300_5 - llvm-openmp=14.0.6=h9e868ea_0 - lz4-c=1.9.4=h6a678d5_0 - markupsafe=2.1.3=py39h5eee18b_0 - mkl=2023.1.0=h213fc3f_46344 - mkl-service=2.4.0=py39h5eee18b_1 - mkl_fft=1.3.8=py39h5eee18b_0 - mkl_random=1.2.4=py39hdb19cb5_0 - mpc=1.1.0=h10f8cd9_1 - mpfr=4.0.2=hb69a4c5_1 - mpmath=1.3.0=py39h06a4308_0 - munkres=1.1.4=py_0 - ncurses=6.4=h6a678d5_0 - netcdf-fortran=4.6.0=nompi_heb5813c_103 - nettle=3.7.3=hbbd107a_1 - networkx=3.1=py39h06a4308_0 - numexpr=2.8.7=py39h85018f9_0 - numpy=1.23.5=py39hf6e8229_1 - numpy-base=1.23.5=py39h060ed82_1 - openbabel=3.1.1=py39h2d01fe1_9 - openh264=2.1.1=h4ff587b_0 - openjpeg=2.4.0=h3ad879b_0 - openssl=3.2.1=hd590300_1 - packaging=23.2=py39h06a4308_0 - packmol=20.010=h86c2bf4_0 - pandas=2.1.3=py39hddac248_0 - parmed=3.4.4=py39h227be39_0 - pcre2=10.42=hebb0a14_0 - perl=5.34.0=h5eee18b_2 - pillow=10.2.0=py39h5eee18b_0 - pip=23.3.1=py39h06a4308_0 - pixman=0.43.2=h59595ed_0 - pycairo=1.23.0=py39hd1222b9_0 - pyparsing=3.0.9=py39h06a4308_0 - pysocks=1.7.1=py39h06a4308_0 - python=3.9.18=h0755675_1_cpython - python-dateutil=2.8.2=pyhd3eb1b0_0 - python-tzdata=2023.3=pyhd3eb1b0_0 - python_abi=3.9=4_cp39 - pytorch=2.1.1=py3.9_cuda11.8_cudnn8.7.0_0 - pytorch-cuda=11.8=h7e8668a_5 - pytorch-mutex=1.0=cuda - pytz=2023.3.post1=py39h06a4308_0 - pyyaml=6.0.1=py39h5eee18b_0 - rdkit=2022.09.1=py39hb00a813_2 - readline=8.2=h5eee18b_0 - reportlab=3.5.67=py39hfdd840d_1 - requests=2.31.0=py39h06a4308_1 - scipy=1.12.0=py39h5f9d8c6_0 - setuptools=68.2.2=py39h06a4308_0 - six=1.16.0=pyhd3eb1b0_1 - sqlalchemy=2.0.25=py39h5eee18b_0 - sqlite=3.41.2=h5eee18b_0 - sympy=1.12=py39h06a4308_0 - tbb=2021.8.0=hdb19cb5_0 - tk=8.6.13=noxft_h4845f30_101 - torchaudio=2.1.1=py39_cu118 - torchtriton=2.1.0=py39 - torchvision=0.16.1=py39_cu118 - typing-extensions=4.9.0=py39h06a4308_1 - typing_extensions=4.9.0=py39h06a4308_1 - tzdata=2024a=h04d1e81_0 - urllib3=2.1.0=py39h06a4308_1 - wheel=0.41.2=py39h06a4308_0 - xorg-kbproto=1.0.7=h7f98852_1002 - xorg-libice=1.1.1=hd590300_0 - xorg-libsm=1.2.4=h7391055_0 - xorg-libx11=1.8.9=h8ee46fc_0 - xorg-libxext=1.3.4=h0b41bf4_2 - xorg-libxrender=0.9.11=hd590300_0 - xorg-libxt=1.3.0=hd590300_1 - xorg-renderproto=0.11.1=h7f98852_1002 - xorg-xextproto=7.3.0=h0b41bf4_1003 - xorg-xproto=7.0.31=h27cfd23_1007 - xz=5.4.6=h5eee18b_0 - yaml=0.2.5=h7b6447c_0 - zipp=3.17.0=py39h06a4308_0 - zlib=1.2.13=hd590300_5 - zstd=1.5.5=hc292b87_0 - pip: - aiohttp==3.9.4 - aiosignal==1.3.1 - amberlite==22.0 - amberutils==21.0 - async-timeout==4.0.3 - attrs==23.2.0 - biopython==1.83 - easydict==1.13 - einops==0.7.0 - fonttools==4.45.0 - frozenlist==1.4.1 - fsspec==2024.3.1 - joblib==1.4.0 - lmdb==1.4.1 - matplotlib==3.8.2 - mmpbsa-py==16.0 - multidict==6.0.5 - packmol-memgen==1.2.3rc0 - pdb4amber==22.0 - psutil==5.9.8 - pytraj==2.0.6 - sander==22.0 - scikit-learn==1.4.2 - threadpoolctl==3.4.0 - torch-cluster==1.6.3+pt21cu118 - torch-geometric==2.4.0 - torch-scatter==2.1.2+pt21cu118 - torch-sparse==0.6.18+pt21cu118 - torch-spline-conv==1.2.2+pt21cu118 - tqdm==4.66.2 - yarl==1.9.4 prefix: /home/user/miniconda3/envs/pmdm
Great thanks for this useful information. Yes, PMDM could work on this env. I will update the env file.
Below is a Conda environment that can run PMDM correctly: