unable to setup
AndrewHo1998 opened this issue · comments
on running pip install -e . I got:
Obtaining file:///users/andrewho/Documents/ferminet-main
Collecting kfac_jax@ git+https://github.com/deepmind/kfac-jax
Cloning https://github.com/deepmind/kfac-jax to /tmp/pip-install-qnrbw3gg/kfac-jax_f460d57ceba14857a5582fea1fed6cc3
Running command git clone -q https://github.com/deepmind/kfac-jax /tmp/pip-install-qnrbw3gg/kfac-jax_f460d57ceba14857a5582fea1fed6cc3
Resolved https://github.com/deepmind/kfac-jax to commit f8b6405a9da0fbb4b9dc957d1997e8eb24a96c18
Requirement already satisfied: absl-py in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from ferminet==0.2) (1.0.0)
Collecting attrs
Using cached attrs-21.4.0-py2.py3-none-any.whl (60 kB)
Requirement already satisfied: chex in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from ferminet==0.2) (0.1.3)
Requirement already satisfied: h5py in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from ferminet==0.2) (3.6.0)
Requirement already satisfied: jax in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from ferminet==0.2) (0.3.8)
Requirement already satisfied: jaxlib in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from ferminet==0.2) (0.3.7)
Collecting ml-collections
Using cached ml_collections-0.1.1-py3-none-any.whl
Collecting optax
Using cached optax-0.1.2-py3-none-any.whl (140 kB)
Requirement already satisfied: numpy in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from ferminet==0.2) (1.22.3)
Collecting pandas
Using cached pandas-1.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB)
Collecting pyscf
Using cached pyscf-2.0.1.tar.gz (7.7 MB)
Collecting pyblock
Using cached pyblock-0.6-py3-none-any.whl
Requirement already satisfied: scipy in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from ferminet==0.2) (1.8.0)
Requirement already satisfied: tables in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from ferminet==0.2) (3.7.0)
Requirement already satisfied: typing_extensions in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from ferminet==0.2) (4.2.0)
Requirement already satisfied: six in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from absl-py->ferminet==0.2) (1.16.0)
Requirement already satisfied: dm-tree>=0.1.5 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from chex->ferminet==0.2) (0.1.7)
Requirement already satisfied: toolz>=0.9.0 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from chex->ferminet==0.2) (0.11.2)
Requirement already satisfied: opt-einsum in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from jax->ferminet==0.2) (3.3.0)
Requirement already satisfied: flatbuffers<3.0,>=1.12 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from jaxlib->ferminet==0.2) (2.0)
Requirement already satisfied: immutabledict>=2.2.1 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from kfac_jax@ git+https://github.com/deepmind/kfac-jax->ferminet==0.2) (2.2.1)
Requirement already satisfied: distrax>=0.1.1 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from kfac_jax@ git+https://github.com/deepmind/kfac-jax->ferminet==0.2) (0.1.2)
Requirement already satisfied: tensorflow-probability>=0.15.0 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from distrax>=0.1.1->kfac_jax@ git+https://github.com/deepmind/kfac-jax->ferminet==0.2) (0.16.0)
Requirement already satisfied: decorator in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from tensorflow-probability>=0.15.0->distrax>=0.1.1->kfac_jax@ git+https://github.com/deepmind/kfac-jax->ferminet==0.2) (5.1.1)
Requirement already satisfied: gast>=0.3.2 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from tensorflow-probability>=0.15.0->distrax>=0.1.1->kfac_jax@ git+https://github.com/deepmind/kfac-jax->ferminet==0.2) (0.5.3)
Requirement already satisfied: cloudpickle>=1.3 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from tensorflow-probability>=0.15.0->distrax>=0.1.1->kfac_jax@ git+https://github.com/deepmind/kfac-jax->ferminet==0.2) (2.0.0)
Requirement already satisfied: PyYAML in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from ml-collections->ferminet==0.2) (6.0)
Requirement already satisfied: contextlib2 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from ml-collections->ferminet==0.2) (21.6.0)
Requirement already satisfied: python-dateutil>=2.8.1 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from pandas->ferminet==0.2) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from pandas->ferminet==0.2) (2022.1)
Requirement already satisfied: packaging in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from tables->ferminet==0.2) (21.3)
Requirement already satisfied: numexpr>=2.6.2 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from tables->ferminet==0.2) (2.8.1)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages (from packaging->tables->ferminet==0.2) (3.0.8)
Building wheels for collected packages: kfac-jax, pyscf
Building wheel for kfac-jax (setup.py) ... done
Created wheel for kfac-jax: filename=kfac_jax-0.0.1-py3-none-any.whl size=118136 sha256=3d01eb1af325d295ba97b5d7e623a649182882d556ec4d9da5c53f8db833fd60
Stored in directory: /tmp/pip-ephem-wheel-cache-7s0_5zoa/wheels/d3/a2/bf/79a38a03091a1a334020b9eff654f78c3d51f59e588f897163
Building wheel for pyscf (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /users/andrewho/.conda/envs/fmnet/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-qnrbw3gg/pyscf_591825adafd5410e9a5da0cf1a9e00ab/setup.py'"'"'; __file__='"'"'/tmp/pip-install-qnrbw3gg/pyscf_591825adafd5410e9a5da0cf1a9e00ab/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-a180qok7
cwd: /tmp/pip-install-qnrbw3gg/pyscf_591825adafd5410e9a5da0cf1a9e00ab/
Complete output (8 lines):
running bdist_wheel
running build
running build_ext
Configuring extensions
cmake -S/tmp/pip-install-qnrbw3gg/pyscf_591825adafd5410e9a5da0cf1a9e00ab/pyscf/lib -Bbuild/temp.linux-x86_64-3.10
CMake Error: The source directory "" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
error: command '/bin/cmake' failed with exit code 1
----------------------------------------
ERROR: Failed building wheel for pyscf
Running setup.py clean for pyscf
Successfully built kfac-jax
Failed to build pyscf
Installing collected packages: pyscf, pyblock, pandas, optax, ml-collections, kfac-jax, attrs, ferminet
Running setup.py install for pyscf ... error
ERROR: Command errored out with exit status 1:
command: /users/andrewho/.conda/envs/fmnet/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-qnrbw3gg/pyscf_591825adafd5410e9a5da0cf1a9e00ab/setup.py'"'"'; __file__='"'"'/tmp/pip-install-qnrbw3gg/pyscf_591825adafd5410e9a5da0cf1a9e00ab/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-edw8qsmk/install-record.txt --single-version-externally-managed --compile --install-headers /users/andrewho/.conda/envs/fmnet/include/python3.10/pyscf
cwd: /tmp/pip-install-qnrbw3gg/pyscf_591825adafd5410e9a5da0cf1a9e00ab/
Complete output (10 lines):
running install
/users/andrewho/.conda/envs/fmnet/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_ext
Configuring extensions
cmake -S/tmp/pip-install-qnrbw3gg/pyscf_591825adafd5410e9a5da0cf1a9e00ab/pyscf/lib -Bbuild/temp.linux-x86_64-3.10
CMake Error: The source directory "" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
error: command '/bin/cmake' failed with exit code 1
----------------------------------------
ERROR: Command errored out with exit status 1: /users/andrewho/.conda/envs/fmnet/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-qnrbw3gg/pyscf_591825adafd5410e9a5da0cf1a9e00ab/setup.py'"'"'; __file__='"'"'/tmp/pip-install-qnrbw3gg/pyscf_591825adafd5410e9a5da0cf1a9e00ab/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-edw8qsmk/install-record.txt --single-version-externally-managed --compile --install-headers /users/andrewho/.conda/envs/fmnet/include/python3.10/pyscf Check the logs for full command output.
It seems to be conflict of packages' versions
I think that this is not because of a conflict in package versions but rather that pyscf does not yet have pre-built wheels for python 3.10 (pyscf/pyscf#1231). You can verify this by attempting pip install pyscf in a fresh python 3.10 environment, which for me gives the same cmake error (also pyscf/pyscf#1112). You can either install pyscf manually from source before installing ferminet or use python 3.8 or 3.9.
Please note that we do not test with conda, only with normal virtual environments.