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.

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.