Create Conda Environment with YAML File
1
Hello,
I'm trying to follow these instructions to create a conda environment with this YAML file but the environment keeps getting stuck on solving.
name: p2b1
dependencies:
- python= 3.7.5
- scipy= 1.5.3
- keras= 2.4.3
- h5py= 2.10.0
- numpy= 1.19.5
- tensorflow-gpu= 2.2.0
- pandas= 1.2.0
- scikit-learn= 0.24.0
- tqdm= 4.56.0
- matplotlib= 3.3.3
- numba= 0.52.0
- astropy= 4.2
- patsy= 0.5.1
- statsmodels= 0.12.1.
It works when I only include numpy in the list of packages and add conda forge and defaults into the YAML file. I am using conda version 23.3.1 Any way to resolve this?
Python
• 1.5k views
It worked for me. It may just take a long time because there are a lot of dependencies to resolve. Try micromamba instead for a faster solve.
And once you have the environment, export it completely into a yaml file. This should also help to speed the solving up the next time you install it.
Here is the solved environment:
name: p2b1
channels:
- conda-forge
- pkgs/main
dependencies:
- _libgcc_mutex= 0.1= conda_forge
- _openmp_mutex= 4.5= 2_gnu
- _tflow_select= 2.1.0= gpu
- absl-py= 2.1.0= pyhd8ed1ab_0
- aiohttp= 3.7.4.post0= py37h5e8e339_1
- astor= 0.8.1= pyh9f0ad1d_0
- astropy= 4.2.1= py37h5e8e339_0
- astunparse= 1.6.3= pyhd8ed1ab_0
- async-timeout= 3.0.1= py_1000
- attrs= 23.2.0= pyh71513ae_0
- blinker= 1.6.3= pyhd8ed1ab_0
- brotli-python= 1.0.9= py37hd23a5d3_7
- c-ares= 1.27.0= hd590300_0
- ca-certificates= 2024.2.2= hbcca054_0
- cachetools= 5.3.3= pyhd8ed1ab_0
- certifi= 2024.2.2= pyhd8ed1ab_0
- cffi= 1.14.6= py37hc58025e_0
- chardet= 4.0.0= py37h89c1867_3
- charset-normalizer= 3.3.2= pyhd8ed1ab_0
- click= 8.1.3= py37h89c1867_0
- cryptography= 39.0.1= py37h9ce1e76_0
- cudatoolkit= 10.1.243= h6d9799a_13
- cudnn= 7.6.5.32= hc0a50b0_1
- cupti= 10.1.168= 0
- cycler= 0.11.0= pyhd8ed1ab_0
- dbus= 1.13.18= hb2f20db_0
- expat= 2.6.2= h59595ed_0
- fontconfig= 2.14.2= h14ed4e7_0
- freetype= 2.12.1= h267a509_2
- gast= 0.3.3= py_0
- glib= 2.69.1= h4ff587b_1
- google-auth= 2.28.2= pyhca7485f_0
- google-auth-oauthlib= 0.4.6= pyhd8ed1ab_0
- google-pasta= 0.2.0= pyh8c360ce_0
- grpc-cpp= 1.48.1= h05bd8bd_1
- grpcio= 1.48.1= py37h3fae8ff_1
- gst-plugins-base= 1.14.1= h6a678d5_1
- gstreamer= 1.14.1= h5eee18b_1
- h5py= 2.10.0= nompi_py37ha3df211_106
- hdf5= 1.10.6= nompi_h6a2412b_1114
- icu= 73.2= h59595ed_0
- idna= 3.6= pyhd8ed1ab_0
- importlib-metadata= 4.11.4= py37h89c1867_0
- joblib= 1.3.2= pyhd8ed1ab_0
- jpeg= 9e= h0b41bf4_3
- keras= 2.4.3= pyhd8ed1ab_0
- keras-preprocessing= 1.1.2= pyhd8ed1ab_0
- keyutils= 1.6.1= h166bdaf_0
- kiwisolver= 1.4.4= py37h7cecad7_0
- krb5= 1.20.1= hf9c8cef_0
- lcms2= 2.12= hddcbb42_0
- ld_impl_linux-64= 2.40= h41732ed_0
- lerc= 3.0= h9c3ff4c_0
- libabseil= 20220623.0= cxx17_h05df665_6
- libblas= 3.9.0= 20_linux64_openblas
- libcblas= 3.9.0= 20_linux64_openblas
- libclang= 14.0.6= default_h7634d5b_1
- libclang13= 14.0.6= default_h9986a30_1
- libcups= 2.3.3= h36d4200_3
- libcurl= 7.87.0= h6312ad2_0
- libdeflate= 1.10= h7f98852_0
- libedit= 3.1.20191231= he28a2e2_2
- libev= 4.33= hd590300_2
- libexpat= 2.6.2= h59595ed_0
- libffi= 3.3= h58526e2_2
- libgcc-ng= 13.2.0= h807b86a_5
- libgfortran-ng= 13.2.0= h69a702a_5
- libgfortran5= 13.2.0= ha4646dd_5
- libgomp= 13.2.0= h807b86a_5
- libiconv= 1.17= hd590300_2
- liblapack= 3.9.0= 20_linux64_openblas
- libllvm10= 10.0.1= he513fc3_3
- libllvm14= 14.0.6= hcd5def8_4
- libnghttp2= 1.51.0= hdcd2b5c_0
- libopenblas= 0.3.25= pthreads_h413a1c8_0
- libpng= 1.6.43= h2797004_0
- libpq= 12.15= h37d81fd_1
- libprotobuf= 3.21.8= h6239696_0
- libsqlite= 3.45.2= h2797004_0
- libssh2= 1.10.0= haa6b8db_3
- libstdcxx-ng= 13.2.0= h7e041cc_5
- libtiff= 4.3.0= h0fcbabc_4
- libuuid= 2.38.1= h0b41bf4_0
- libwebp-base= 1.3.2= hd590300_0
- libxcb= 1.15= h0b41bf4_0
- libxkbcommon= 1.6.0= hd429924_1
- libxml2= 2.12.5= h232c23b_0
- libzlib= 1.2.13= hd590300_5
- llvmlite= 0.35.0= py37h9d7f4d0_1
- markdown= 3.5.2= pyhd8ed1ab_0
- markupsafe= 2.1.1= py37h540881e_1
- matplotlib= 3.3.3= py37h89c1867_0
- matplotlib-base= 3.3.3= py37h0c9df89_0
- multidict= 6.0.2= py37h540881e_1
- mysql= 5.7.20= hf484d3e_1001
- ncurses= 6.4= h59595ed_2
- numba= 0.52.0= py37hdc94413_0
- numpy= 1.19.5= py37h3e96413_3
- oauthlib= 3.2.2= pyhd8ed1ab_0
- olefile= 0.47= pyhd8ed1ab_0
- openjpeg= 2.5.0= h7d73246_0
- openssl= 1.1.1w= hd590300_0
- opt_einsum= 3.3.0= pyhc1e730c_2
- packaging= 23.2= pyhd8ed1ab_0
- pandas= 1.2.0= py37hdc94413_1
- patsy= 0.5.1= py_0
- pcre= 8.45= h9c3ff4c_0
- pillow= 8.4.0= py37h0f21c89_0
- pip= 24.0= pyhd8ed1ab_0
- protobuf= 4.21.8= py37hd23a5d3_0
- pthread-stubs= 0.4= h36c2ea0_1001
- pyasn1= 0.5.1= pyhd8ed1ab_0
- pyasn1-modules= 0.3.0= pyhd8ed1ab_0
- pycparser= 2.21= pyhd8ed1ab_0
- pyerfa= 2.0.0.1= py37hda87dfa_2
- pyjwt= 2.8.0= pyhd8ed1ab_1
- pyopenssl= 23.2.0= pyhd8ed1ab_1
- pyparsing= 3.1.2= pyhd8ed1ab_0
- pyqt= 5.15.4= py37hd23a5d3_0
- pyqt5-sip= 12.9.0= py37hd23a5d3_0
- pysocks= 1.7.1= py37h89c1867_5
- python= 3.7.5= hffdb5ce_0_cpython
- python-dateutil= 2.9.0= pyhd8ed1ab_0
- python_abi= 3.7= 4_cp37m
- pytz= 2024.1= pyhd8ed1ab_0
- pyu2f= 0.1.5= pyhd8ed1ab_0
- pyyaml= 6.0= py37h540881e_4
- qt-main= 5.15.2= h110a718_10
- re2= 2022.06.01= h27087fc_1
- readline= 8.2= h8228510_1
- requests= 2.31.0= pyhd8ed1ab_0
- requests-oauthlib= 1.4.0= pyhd8ed1ab_0
- rsa= 4.9= pyhd8ed1ab_0
- scikit-learn= 0.24.0= py37h69acf81_0
- scipy= 1.5.3= py37h14a347d_0
- setuptools= 59.8.0= py37h89c1867_1
- sip= 6.5.1= py37hcd2ae1e_2
- six= 1.16.0= pyh6c4a22f_0
- sqlite= 3.45.2= h2c6b66d_0
- statsmodels= 0.12.1= py37h902c9e0_2
- tensorboard= 2.11.2= pyhd8ed1ab_0
- tensorboard-data-server= 0.6.0= py37h38fbfac_2
- tensorboard-plugin-wit= 1.8.1= pyhd8ed1ab_0
- tensorflow= 2.2.0= gpu_py37h1a511ff_0
- tensorflow-base= 2.2.0= gpu_py37h8a81be8_0
- tensorflow-estimator= 2.6.0= py37hcd2ae1e_0
- tensorflow-gpu= 2.2.0= h0d30ee6_0
- termcolor= 2.3.0= pyhd8ed1ab_0
- threadpoolctl= 3.1.0= pyh8a188c0_0
- tk= 8.6.13= noxft_h4845f30_101
- toml= 0.10.2= pyhd8ed1ab_0
- tornado= 6.2= py37h540881e_0
- tqdm= 4.56.0= pyhd8ed1ab_0
- typing-extensions= 4.7.1= hd8ed1ab_0
- typing_extensions= 4.7.1= pyha770c72_0
- urllib3= 2.2.1= pyhd8ed1ab_0
- werkzeug= 2.2.3= pyhd8ed1ab_0
- wheel= 0.42.0= pyhd8ed1ab_0
- wrapt= 1.14.1= py37h540881e_0
- xkeyboard-config= 2.41= hd590300_0
- xorg-kbproto= 1.0.7= h7f98852_1002
- xorg-libx11= 1.8.7= h8ee46fc_0
- xorg-libxau= 1.0.11= hd590300_0
- xorg-libxdmcp= 1.1.3= h7f98852_0
- xorg-xextproto= 7.3.0= h0b41bf4_1003
- xorg-xproto= 7.0.31= h7f98852_1007
- xz= 5.2.6= h166bdaf_0
- yaml= 0.2.5= h7f98852_2
- yarl= 1.7.2= py37h540881e_2
- zipp= 3.15.0= pyhd8ed1ab_0
- zlib= 1.2.13= hd590300_5
- zstd= 1.5.5= hfc55251_0
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Please also provide the error messages and command line used, otherwise we can't see what is going wrong.
I used this command: conda env create -f python_environment.yml -n P2B1
And there's no error message, just that it gets stuck on solving the environment for hours until my terminal times out.
You can also try using
mamba
, I find it can often solve environments that baseconda
struggles with.EDIT, only just noticed that it was
micromamba
that was suggested below as an answer, I originally misread that asminiconda
.Which system are you on? I also noticed that base conda is hardly usable anymore on our systems. In contrast, solving your environment with micromamba took 30 seconds.