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Created August 25, 2025 21:40
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  1. t-nissie created this gist Aug 25, 2025.
    108 changes: 108 additions & 0 deletions !deepmdkit.md
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    DeePMD-kiy Memo
    ===============
    On going!

    $ sudo apt install mpich libmpich-dev
    $ sudo apt install mpich libxc-dev
    $ sudo apt install mpich libfftw3-dev
    $ sudo apt install python3.12-venv

    $ tar xf qe-7.4.1-ReleasePack.tar.gz
    $ cd qe-7.4.1
    $ ./configure F90=gfortran F77=gfortran CC=gcc MPIF90=mpif90 --enable-openmp --enable-parallel --with-libxc
    $ make all -j11

    $ mkdir deepmdvenv
    $ python3 -m venv deepmdvenv
    $ source deepmdvenv/bin/activate
    (deepmdvenv) takeshi@shinobi:~$ which python3 --version
    /home/takeshi/deepmdvenv/bin/python3
    (deepmdvenv) takeshi@shinobi:~$ python3 --version
    Python 3.12.3
    (deepmdvenv) pip install torch --index-url https://download.pytorch.org/whl/cpu
    (deepmdvenv) pip install deepmd-kit
    (deepmdvenv) pip install lammps
    (deepmdvenv) pip install ase
    (deepmdvenv) pip install mpi4py
    (deepmdvenv) takeshi@shinobi:~$ pip list
    Package Version
    ----------------- -------------
    annotated-types 0.7.0
    array-api-compat 1.12.0
    ase 3.26.0
    bracex 2.6
    colorama 0.4.6
    contourpy 1.3.3
    cycler 0.12.1
    dargs 0.4.10
    deepmd-kit 3.1.0
    Deprecated 1.2.18
    filelock 3.13.1
    fonttools 4.59.1
    fsspec 2024.6.1
    greenlet 3.2.4
    h5py 3.14.0
    Jinja2 3.1.4
    kiwisolver 1.4.9
    lammps 2025.7.22.0.2
    MarkupSafe 2.1.5
    matplotlib 3.10.5
    mendeleev 1.1.0
    ml_dtypes 0.5.3
    mpi4py 4.1.0
    mpmath 1.3.0
    networkx 3.3
    numpy 2.3.2
    packaging 25.0
    pandas 2.3.2
    pillow 11.3.0
    pip 24.0
    pydantic 2.11.7
    pydantic_core 2.33.2
    pyfiglet 0.8.post1
    Pygments 2.19.2
    pyparsing 3.2.3
    python-dateutil 2.9.0.post0
    pytz 2025.2
    PyYAML 6.0.2
    scipy 1.16.1
    setuptools 70.2.0
    six 1.17.0
    SQLAlchemy 2.0.43
    sympy 1.13.3
    torch 2.8.0+cpu
    typeguard 4.4.4
    typing_extensions 4.14.1
    typing-inspection 0.4.1
    tzdata 2025.2
    wcmatch 10.1
    wrapt 1.17.3
    (deepmdvenv)



    ## On Ubuntu, pip install gives an error
    Use venv.

    ``` txt
    error: externally-managed-environment
    × This environment is externally managed
    ╰─> To install Python packages system-wide, try apt install
    python3-xyz, where xyz is the package you are trying to
    install.
    If you wish to install a non-Debian-packaged Python package,
    create a virtual environment using python3 -m venv path/to/venv.
    Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make
    sure you have python3-full installed.
    If you wish to install a non-Debian packaged Python application,
    it may be easiest to use pipx install xyz, which will manage a
    virtual environment for you. Make sure you have pipx installed.
    See /usr/share/doc/python3.12/README.venv for more information.
    note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
    hint: See PEP 668 for the detailed specification.
    ```