Issue: Your installed Caffe2 version uses protobuf but the protobuf library cannot be found.

[zhoufy20]

Dear developers of deepmd-gnn:
I get some trouble when execute export CMAKE_PREFIX_PATH=$(python -c "import torch;print(torch.utils.cmake_prefix_path)") and pip install . Below are callback error:

---

      Call Stack (most recent call first):
        /home/feiyu/miniconda3/envs/deepmd/lib/python3.10/site-packages/torch/share/cmake/Caffe2/Caffe2Config.cmake:53 (include)
        /home/feiyu/miniconda3/envs/deepmd/lib/python3.10/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:68 (find_package)
        CMakeLists.txt:46 (find_package)


      CMake Error at /home/feiyu/miniconda3/envs/deepmd/lib/python3.10/site-packages/torch/share/cmake/Caffe2/Caffe2Config.cmake:55 (message):
        Your installed Caffe2 version uses protobuf but the protobuf library cannot
        be found.  Did you accidentally remove it, or have you set the right
        CMAKE_PREFIX_PATH? If you do not have protobuf, you will need to install
        protobuf and set the library path accordingly.
      Call Stack (most recent call first):
        /home/feiyu/miniconda3/envs/deepmd/lib/python3.10/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:68 (find_package)
        CMakeLists.txt:46 (find_package)


      -- Configuring incomplete, errors occurred!

      *** CMake configuration failed
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for deepmd-gnn
Failed to build deepmd-gnn
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (deepmd-gnn)

deepmd-kit
I install the deepmd-kit from off-line packages.

All packages

Package                   Version          Editable project location
------------------------- ---------------- ----------------------------------------------------------
absl-py                   2.1.0
aiohappyeyeballs          2.4.0
aiohttp                   3.10.6
aiosignal                 1.3.1
anyio                     4.6.2
archspec                  0.2.3
argon2-cffi               21.3.0
argon2-cffi-bindings      21.2.0
array_api_compat          1.8
ase                       3.23.0
asttokens                 2.0.5
astunparse                1.6.3
async-lru                 2.0.4
async-timeout             4.0.3
attrs                     24.2.0
Babel                     2.11.0
beautifulsoup4            4.12.3
bleach                    4.1.0
blinker                   1.8.2
boltons                   24.0.0
bracex                    2.2.1
Brotli                    1.1.0
cached-property           1.5.2
cachetools                5.5.0
certifi                   2024.8.30
cffi                      1.17.1
charset-normalizer        3.3.2
click                     8.1.7
cloudpickle               3.0.0
cmake                     3.30.5
colorama                  0.4.6
comm                      0.2.1
conda                     24.7.1
conda-libmamba-solver     24.7.0
conda-package-handling    2.3.0
conda_package_streaming   0.10.0
ConfigArgParse            1.7
contourpy                 1.3.0
cryptography              43.0.1
cycler                    0.12.1
dargs                     0.4.8
debugpy                   1.6.7
decorator                 5.1.1
deepmd-kit                3.0.0b4
defusedxml                0.7.1
distro                    1.9.0
dpdata                    0.2.21
e3nn                      0.4.4
exceptiongroup            1.2.0
executing                 0.8.3
f90wrap                   0.2.15
fastjsonschema            2.16.2
filelock                  3.16.1
Flask                     3.0.3
flatbuffers               24.3.25
fonttools                 4.54.1
frozendict                2.4.4
frozenlist                1.4.1
gast                      0.5.5
gitdb                     4.0.11
GitPython                 3.1.43
gmpy2                     2.1.5
google-auth               2.35.0
google-auth-oauthlib      1.0.0
google-pasta              0.2.0
greenlet                  3.1.1
grpcio                    1.54.3
h11                       0.14.0
h2                        4.1.0
h5py                      3.11.0
horovod                   0.28.1
hpack                     4.0.0
httpcore                  1.0.2
httpx                     0.27.0
hyperframe                6.0.1
idna                      3.10
importlib_metadata        8.5.0
ipykernel                 6.29.5
ipython                   8.27.0
ipywidgets                8.1.2
itsdangerous              2.2.0
jedi                      0.19.1
Jinja2                    3.1.4
json5                     0.9.6
jsonpatch                 1.33
jsonpointer               3.0.0
jsonschema                4.23.0
jsonschema-specifications 2023.7.1
jupyter                   1.0.0
jupyter_client            8.6.0
jupyter-console           6.6.3
jupyter_core              5.7.2
jupyter-events            0.10.0
jupyter-lsp               2.2.0
jupyter_server            2.14.1
jupyter_server_terminals  0.4.4
jupyterlab                4.2.5
jupyterlab-pygments       0.1.2
jupyterlab_server         2.27.3
jupyterlab-widgets        3.0.10
keras                     2.14.0
kiwisolver                1.4.7
lammps                    2024.8.29
libmambapy                1.5.10
lightning-utilities       0.11.8
mace-torch                0.3.7            /mnt/e/ComPhys/GitDemo/work/deepmd/env/mace-main/mace-main
Markdown                  3.6
MarkupSafe                2.1.5
matplotlib                3.9.2
matplotlib-inline         0.1.6
matscipy                  1.1.1
mendeleev                 0.17.0
menuinst                  2.1.2
mistune                   2.0.4
ml-dtypes                 0.2.0
monty                     2024.7.30
mpi4py                    4.0.0
mpmath                    1.3.0
multidict                 6.1.0
munkres                   1.1.4
nbclient                  0.8.0
nbconvert                 7.16.4
nbformat                  5.10.4
nest-asyncio              1.6.0
networkx                  3.3
notebook                  7.2.2
notebook_shim             0.2.3
numpy                     1.26.4
oauthlib                  3.2.2
opt-einsum                3.3.0
opt-einsum-fx             0.1.4
overrides                 7.4.0
packaging                 24.1
pandas                    2.2.3
pandocfilters             1.5.0
parso                     0.8.3
pexpect                   4.8.0
pillow                    10.4.0
pip                       24.2
platformdirs              4.3.6
pluggy                    1.5.0
ply                       3.11
prettytable               3.11.0
prometheus-client         0.14.1
prompt-toolkit            3.0.43
protobuf                  4.21.12
psutil                    6.0.0
ptyprocess                0.7.0
pure-eval                 0.2.2
pyasn1                    0.6.1
pyasn1_modules            0.4.1
pycosat                   0.6.6
pycparser                 2.22
pyfiglet                  0.8.post1
Pygments                  2.18.0
PyJWT                     2.9.0
pyOpenSSL                 24.2.1
pyparsing                 3.1.4
PyQt5                     5.15.10
PyQt5-sip                 12.13.0
PySocks                   1.7.1
python-dateutil           2.9.0
python-hostlist           2.0.0
python-json-logger        2.0.7
pytz                      2024.1
pyu2f                     0.1.5
PyYAML                    6.0.2
pyzmq                     25.1.2
qtconsole                 5.6.0
QtPy                      2.4.1
quippy-ase                0.9+gitnone
referencing               0.30.2
requests                  2.32.3
requests-oauthlib         2.0.0
rfc3339-validator         0.1.4
rfc3986-validator         0.1.1
rpds-py                   0.10.6
rsa                       4.9
ruamel.yaml               0.18.6
ruamel.yaml.clib          0.2.8
scipy                     1.14.1
Send2Trash                1.8.2
setuptools                75.1.0
sip                       6.7.12
six                       1.16.0
smmap                     5.0.1
sniffio                   1.3.0
soupsieve                 2.5
SQLAlchemy                2.0.35
stack-data                0.2.0
sympy                     1.13.2
tensorboard               2.14.1
tensorboard-data-server   0.7.0
tensorflow                2.14.0
tensorflow-estimator      2.14.0
termcolor                 2.4.0
terminado                 0.17.1
tinycss2                  1.2.1
tomli                     2.0.1
torch                     2.0.0.post200
torch-ema                 0.3
torchaudio                2.0.0
torchmetrics              1.5.1
torchvision               0.15.2a0+ab7b3e6
tornado                   6.4.1
tqdm                      4.66.5
traitlets                 5.14.3
truststore                0.9.2
typeguard                 4.3.0
typing_extensions         4.12.2
tzdata                    2024.2
unicodedata2              15.1.0
urllib3                   2.2.3
wcmatch                   9.0
wcwidth                   0.2.5
webencodings              0.5.1
websocket-client          1.8.0
Werkzeug                  3.0.4
wheel                     0.44.0
widgetsnbextension        4.0.10
wrapt                     1.14.1
xtb                       22.1
yarl                      1.12.1
zipp                      3.20.2
zstandard                 0.23.0

Thank you for your assistance!

[njzjz]

        Your installed Caffe2 version uses protobuf but the protobuf library cannot
        be found.  Did you accidentally remove it, or have you set the right
        CMAKE_PREFIX_PATH?

According to the error message, appending the prefix of protobuf (it should be in CONDA_PREFIX) to CMAKE_PREFIX_PATH may resolve the problem.

[njzjz]

Indeed, I cannot reproduce the error.

[caolz]

I use 'Easy install' to install dpmd-kit= 3.0.1 then execute export CMAKE_PREFIX_PATH=$(python -c "import torch;print(torch.utils.cmake_prefix_path)")

ImportError: libomp.so: cannot open shared object file: No such file or directory

I dnf install libomp
and pip install .

Below are callback error:
`Building wheels for collected packages: deepmd-gnn
Building wheel for deepmd-gnn (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building wheel for deepmd-gnn (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [43 lines of output]
*** scikit-build-core 0.10.7 using CMake 3.26.5 (wheel)
*** Configuring CMake...
2025-01-23 22:49:01,084 - scikit_build_core - WARNING - Unsupported CMAKE_ARGS ignored: -DCMAKE_BUILD_TYPE=Release
2025-01-23 22:49:01,101 - scikit_build_core - WARNING - Unsupported CMAKE_ARGS ignored: -DCMAKE_BUILD_TYPE=Release
loading initial cache file /tmp/tmpxiag_0y2/build/CMakeInit.txt
-- The CXX compiler identification is GNU 11.4.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/ustb-clz/software/intelpython3/envs/deepmd/bin/x86_64-conda-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Caffe2: Found protobuf with new-style protobuf targets.
-- Caffe2: Protobuf version 27.5.0
-- Could NOT find CUDA (missing: CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (found version "12.6")
CMake Warning at /home/ustb-clz/software/intelpython3/envs/deepmd/lib/python3.12/site-packages/torch/share/cmake/Caffe2/public/cuda.cmake:31 (message):
Caffe2: CUDA cannot be found. Depending on whether you are building Caffe2
or a Caffe2 dependent library, the next warning / error will give you more
info.
Call Stack (most recent call first):
/home/ustb-clz/software/intelpython3/envs/deepmd/lib/python3.12/site-packages/torch/share/cmake/Caffe2/Caffe2Config.cmake:86 (include)
/home/ustb-clz/software/intelpython3/envs/deepmd/lib/python3.12/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:68 (find_package)
CMakeLists.txt:47 (find_package)

  CMake Error at /home/ustb-clz/software/intelpython3/envs/deepmd/lib/python3.12/site-packages/torch/share/cmake/Caffe2/Caffe2Config.cmake:90 (message):
    Your installed Caffe2 version uses CUDA but I cannot find the CUDA
    libraries.  Please set the proper CUDA prefixes and / or install CUDA.
  Call Stack (most recent call first):
    /home/ustb-clz/software/intelpython3/envs/deepmd/lib/python3.12/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:68 (find_package)
    CMakeLists.txt:47 (find_package)


  -- Configuring incomplete, errors occurred!

  *** CMake configuration failed
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for deepmd-gnn
Failed to build deepmd-gnn
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (deepmd-gnn)`