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rstudio / keras3

R Interface to Keras
https://keras3.posit.co/
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GPU Installation Issue on Windows #1475

Open hcutler99 opened 1 month ago

hcutler99 commented 1 month ago

Hi,

Followed the installation instructions and to install keras3 with tensorflow in RStudio, however, it does not appear to have recognised my GPU. 

install.packages("keras3")
keras3::install_keras(backend = "tensorflow", gpu = TRUE)

tensorflow::as_tensor("Hello World") # Installation good
tf$config$list_physical_devices('GPU') # But this returns an empty list

This is my first time trying to configure a GPU so I am a bit out of my depth, but here are my machine specs. Would really appreciate any help you can provide.

Thanks and please let me know what other information I can provide to assist, Harry

t-kalinowski commented 1 month ago

Thanks for opening.

To use a GPU with TensorFlow on Windows, you need to be running R/Python/TensorFlow in WSL. It sounds like you're running the windows-native R and RStudio builds, and not via WSL.

If you want to use RStudio with WSL, the easiest way is via the open-source RStudio Server. This article helps you get set up: https://support.posit.co/hc/en-us/articles/360049776974-Using-RStudio-Server-in-Windows-WSL2

hcutler99 commented 1 month ago

Hi Tomasz,

Thanks for your help, really appreciate it. Followed those instructions but am now having trouble installing tensorflow into RStudio Server (using the code that you posted here: https://github.com/rstudio/keras3/issues/1311).

Would really appreciate if you had a minute to look at the below diagnostic ouputs.

Thanks again, Harry

> install.packages("remotes")
Installing package into ‘/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/remotes_2.5.0.tar.gz'
Content type 'application/x-gzip' length 164496 bytes (160 KB)
==================================================
downloaded 160 KB

* installing *source* package ‘remotes’ ...
** package ‘remotes’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (remotes)

The downloaded source packages are in
    ‘/tmp/Rtmp9r6qrA/downloaded_packages’
> remotes::install_github(sprintf("rstudio/%s", c("reticulate", "tensorflow", "keras")))
Downloading GitHub repo rstudio/reticulate@HEAD
Running `R CMD build`...
* checking for file ‘/tmp/Rtmp9r6qrA/remotes66ba167474a7/rstudio-reticulate-65e17a3/DESCRIPTION’ ... OK
* preparing ‘reticulate’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘reticulate_1.39.0.9000.tar.gz’
Installing package into ‘/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
* installing *source* package ‘reticulate’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c event_loop.cpp -o event_loop.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c libpython.cpp -o libpython.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c output.cpp -o output.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c pending_py_calls_notifier.cpp -o pending_py_calls_notifier.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c python.cpp -o python.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c readline.cpp -o readline.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c signals.cpp -o signals.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o reticulate.so RcppExports.o event_loop.o libpython.o output.o pending_py_calls_notifier.o python.o readline.o signals.o -L/usr/lib/R/lib -lR
installing to /home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/00LOCK-reticulate/00new/reticulate/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (reticulate)
Downloading GitHub repo rstudio/tensorflow@HEAD
Running `R CMD build`...
* checking for file ‘/tmp/Rtmp9r6qrA/remotes66ba259436e1/rstudio-tensorflow-4da7560/DESCRIPTION’ ... OK
* preparing ‘tensorflow’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘tensorflow_2.16.0.9000.tar.gz’
Installing package into ‘/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
* installing *source* package ‘tensorflow’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tensorflow)
Downloading GitHub repo rstudio/keras@HEAD
Running `R CMD build`...
* checking for file ‘/tmp/Rtmp9r6qrA/remotes66baf2c3bf8/rstudio-keras3-6729243/DESCRIPTION’ ... OK
* preparing ‘keras3’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘keras3_1.2.0.9000.tar.gz’
Installing package into ‘/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
* installing *source* package ‘keras3’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (keras3)
> reticulate::miniconda_uninstall() # start with a blank slate
> reticulate::install_miniconda()
* Installing Miniconda -- please wait a moment ...
* Downloading 'https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh' ...
trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh'
Content type 'application/octet-stream' length 148337011 bytes (141.5 MB)
==================================================
downloaded 141.5 MB

+ /usr/bin/bash /tmp/Rtmp9r6qrA/Miniconda3-latest-Linux-x86_64.sh -b -u -p '/home/doc_wsl2/.local/share/r-miniconda'
PREFIX=/home/doc_wsl2/.local/share/r-miniconda
Unpacking payload ...

Installing base environment...

Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
+ /home/doc_wsl2/.local/share/r-miniconda/bin/conda update --yes --name base conda
Channels:
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

# All requested packages already installed.

+ /home/doc_wsl2/.local/share/r-miniconda/bin/conda create --yes --name r-reticulate 'python=3.10' numpy --quiet -c conda-forge
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/doc_wsl2/.local/share/r-miniconda/envs/r-reticulate

  added / updated specs:
    - numpy
    - python=3.10

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |            2_gnu          23 KB  conda-forge
    bzip2-1.0.8                |       h4bc722e_7         247 KB  conda-forge
    ca-certificates-2024.8.30  |       hbcca054_0         155 KB  conda-forge
    ld_impl_linux-64-2.43      |       h712a8e2_2         654 KB  conda-forge
    libblas-3.9.0              |25_linux64_openblas          15 KB  conda-forge
    libcblas-3.9.0             |25_linux64_openblas          15 KB  conda-forge
    libffi-3.4.2               |       h7f98852_5          57 KB  conda-forge
    libgcc-14.2.0              |       h77fa898_1         829 KB  conda-forge
    libgcc-ng-14.2.0           |       h69a702a_1          53 KB  conda-forge
    libgfortran-14.2.0         |       h69a702a_1          53 KB  conda-forge
    libgfortran-ng-14.2.0      |       h69a702a_1          53 KB  conda-forge
    libgfortran5-14.2.0        |       hd5240d6_1         1.4 MB  conda-forge
    libgomp-14.2.0             |       h77fa898_1         450 KB  conda-forge
    liblapack-3.9.0            |25_linux64_openblas          15 KB  conda-forge
    libnsl-2.0.1               |       hd590300_0          33 KB  conda-forge
    libopenblas-0.3.28         |pthreads_h94d23a6_0         5.3 MB  conda-forge
    libsqlite-3.47.0           |       hadc24fc_0         854 KB  conda-forge
    libstdcxx-14.2.0           |       hc0a3c3a_1         3.7 MB  conda-forge
    libuuid-2.38.1             |       h0b41bf4_0          33 KB  conda-forge
    libxcrypt-4.4.36           |       hd590300_1          98 KB  conda-forge
    libzlib-1.3.1              |       hb9d3cd8_2          60 KB  conda-forge
    ncurses-6.5                |       he02047a_1         868 KB  conda-forge
    numpy-2.1.2                |  py310hd6e36ab_0         7.5 MB  conda-forge
    openssl-3.3.2              |       hb9d3cd8_0         2.8 MB  conda-forge
    pip-24.2                   |     pyh8b19718_1         1.2 MB  conda-forge
    python-3.10.15             |h4a871b0_2_cpython        24.1 MB  conda-forge
    python_abi-3.10            |          5_cp310           6 KB  conda-forge
    readline-8.2               |       h8228510_1         275 KB  conda-forge
    setuptools-75.1.0          |     pyhd8ed1ab_0         759 KB  conda-forge
    tk-8.6.13                  |noxft_h4845f30_101         3.2 MB  conda-forge
    tzdata-2024b               |       hc8b5060_0         119 KB  conda-forge
    wheel-0.44.0               |     pyhd8ed1ab_0          57 KB  conda-forge
    xz-5.2.6                   |       h166bdaf_0         409 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        55.3 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 
  ca-certificates    conda-forge/linux-64::ca-certificates-2024.8.30-hbcca054_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_2 
  libblas            conda-forge/linux-64::libblas-3.9.0-25_linux64_openblas 
  libcblas           conda-forge/linux-64::libcblas-3.9.0-25_linux64_openblas 
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5 
  libgcc             conda-forge/linux-64::libgcc-14.2.0-h77fa898_1 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1 
  libgfortran        conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1 
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_1 
  libgfortran5       conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1 
  libgomp            conda-forge/linux-64::libgomp-14.2.0-h77fa898_1 
  liblapack          conda-forge/linux-64::liblapack-3.9.0-25_linux64_openblas 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0 
  libopenblas        conda-forge/linux-64::libopenblas-0.3.28-pthreads_h94d23a6_0 
  libsqlite          conda-forge/linux-64::libsqlite-3.47.0-hadc24fc_0 
  libstdcxx          conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1 
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-he02047a_1 
  numpy              conda-forge/linux-64::numpy-2.1.2-py310hd6e36ab_0 
  openssl            conda-forge/linux-64::openssl-3.3.2-hb9d3cd8_0 
  pip                conda-forge/noarch::pip-24.2-pyh8b19718_1 
  python             conda-forge/linux-64::python-3.10.15-h4a871b0_2_cpython 
  python_abi         conda-forge/linux-64::python_abi-3.10-5_cp310 
  readline           conda-forge/linux-64::readline-8.2-h8228510_1 
  setuptools         conda-forge/noarch::setuptools-75.1.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 
  tzdata             conda-forge/noarch::tzdata-2024b-hc8b5060_0 
  wheel              conda-forge/noarch::wheel-0.44.0-pyhd8ed1ab_0 
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0 

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
* Miniconda has been successfully installed at "~/.local/share/r-miniconda".
[1] "/home/doc_wsl2/.local/share/r-miniconda"
> keras::install_keras()
sh: 1: nvidia-smi: not found
Virtual environment 'r-tensorflow' removed.
Using Python: /home/doc_wsl2/.pyenv/versions/3.10.15/bin/python3.10
Creating virtual environment 'r-tensorflow' ... 
+ /home/doc_wsl2/.pyenv/versions/3.10.15/bin/python3.10 -m venv /home/doc_wsl2/.virtualenvs/r-tensorflow
Done!
Installing packages: pip, wheel, setuptools
+ /home/doc_wsl2/.virtualenvs/r-tensorflow/bin/python -m pip install --upgrade pip wheel setuptools
Requirement already satisfied: pip in ./.virtualenvs/r-tensorflow/lib/python3.10/site-packages (23.0.1)
Collecting pip
  Using cached pip-24.3.1-py3-none-any.whl (1.8 MB)
Collecting wheel
  Using cached wheel-0.44.0-py3-none-any.whl (67 kB)
Requirement already satisfied: setuptools in ./.virtualenvs/r-tensorflow/lib/python3.10/site-packages (65.5.0)
Collecting setuptools
  Using cached setuptools-75.2.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 23.0.1
    Uninstalling pip-23.0.1:
      Successfully uninstalled pip-23.0.1
Successfully installed pip-24.3.1 setuptools-75.2.0 wheel-0.44.0
Virtual environment 'r-tensorflow' successfully created.
Using virtual environment 'r-tensorflow' ...
+ /home/doc_wsl2/.virtualenvs/r-tensorflow/bin/python -m pip install --upgrade --no-user 'numpy<2' 'tensorflow==2.15.*' tensorflow-hub tensorflow-datasets scipy requests Pillow h5py pandas pydot
Collecting numpy<2
  Using cached numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting tensorflow==2.15.*
  Using cached tensorflow-2.15.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.2 kB)
Collecting tensorflow-hub
  Using cached tensorflow_hub-0.16.1-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting tensorflow-datasets
  Using cached tensorflow_datasets-4.9.6-py3-none-any.whl.metadata (9.5 kB)
Collecting scipy
  Using cached scipy-1.14.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting requests
  Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting Pillow
  Using cached pillow-11.0.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
Collecting h5py
  Using cached h5py-3.12.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting pandas
  Using cached pandas-2.2.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
Collecting pydot
  Using cached pydot-3.0.2-py3-none-any.whl.metadata (10 kB)
Collecting absl-py>=1.0.0 (from tensorflow==2.15.*)
  Using cached absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting astunparse>=1.6.0 (from tensorflow==2.15.*)
  Using cached astunparse-1.6.3-py2.py3-none-any.whl.metadata (4.4 kB)
Collecting flatbuffers>=23.5.26 (from tensorflow==2.15.*)
  Using cached flatbuffers-24.3.25-py2.py3-none-any.whl.metadata (850 bytes)
Collecting gast!=0.5.0,!=0.5.1,!=0.5.2,>=0.2.1 (from tensorflow==2.15.*)
  Using cached gast-0.6.0-py3-none-any.whl.metadata (1.3 kB)
Collecting google-pasta>=0.1.1 (from tensorflow==2.15.*)
  Using cached google_pasta-0.2.0-py3-none-any.whl.metadata (814 bytes)
Collecting libclang>=13.0.0 (from tensorflow==2.15.*)
  Using cached libclang-18.1.1-py2.py3-none-manylinux2010_x86_64.whl.metadata (5.2 kB)
Collecting ml-dtypes~=0.3.1 (from tensorflow==2.15.*)
  Using cached ml_dtypes-0.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (20 kB)
Collecting opt-einsum>=2.3.2 (from tensorflow==2.15.*)
  Using cached opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB)
Collecting packaging (from tensorflow==2.15.*)
  Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
Collecting protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0dev,>=3.20.3 (from tensorflow==2.15.*)
  Using cached protobuf-4.25.5-cp37-abi3-manylinux2014_x86_64.whl.metadata (541 bytes)
Requirement already satisfied: setuptools in ./.virtualenvs/r-tensorflow/lib/python3.10/site-packages (from tensorflow==2.15.*) (75.2.0)
Collecting six>=1.12.0 (from tensorflow==2.15.*)
  Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting termcolor>=1.1.0 (from tensorflow==2.15.*)
  Using cached termcolor-2.5.0-py3-none-any.whl.metadata (6.1 kB)
Collecting typing-extensions>=3.6.6 (from tensorflow==2.15.*)
  Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting wrapt<1.15,>=1.11.0 (from tensorflow==2.15.*)
  Using cached wrapt-1.14.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.7 kB)
Collecting tensorflow-io-gcs-filesystem>=0.23.1 (from tensorflow==2.15.*)
  Using cached tensorflow_io_gcs_filesystem-0.37.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (14 kB)
Collecting grpcio<2.0,>=1.24.3 (from tensorflow==2.15.*)
  Using cached grpcio-1.67.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.9 kB)
Collecting tensorboard<2.16,>=2.15 (from tensorflow==2.15.*)
  Using cached tensorboard-2.15.2-py3-none-any.whl.metadata (1.7 kB)
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Collecting keras<2.16,>=2.15.0 (from tensorflow==2.15.*)
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Collecting tf-keras>=2.14.1 (from tensorflow-hub)
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Collecting click (from tensorflow-datasets)
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Collecting immutabledict (from tensorflow-datasets)
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Collecting etils>=1.6.0 (from etils[enp,epath,epy,etree]>=1.6.0; python_version < "3.11"->tensorflow-datasets)
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Requirement already satisfied: wheel<1.0,>=0.23.0 in ./.virtualenvs/r-tensorflow/lib/python3.10/site-packages (from astunparse>=1.6.0->tensorflow==2.15.*) (0.44.0)
Collecting fsspec (from etils[enp,epath,epy,etree]>=1.6.0; python_version < "3.11"->tensorflow-datasets)
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INFO: pip is looking at multiple versions of tf-keras to determine which version is compatible with other requirements. This could take a while.
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Installing collected packages: pytz, libclang, flatbuffers, dm-tree, zipp, wrapt, urllib3, tzdata, typing-extensions, tqdm, toml, termcolor, tensorflow-io-gcs-filesystem, tensorflow-estimator, tensorboard-data-server, six, pyparsing, pyasn1, psutil, protobuf, Pillow, packaging, opt-einsum, oauthlib, numpy, MarkupSafe, markdown, keras, importlib_resources, immutabledict, idna, grpcio, gast, fsspec, etils, docstring-parser, click, charset-normalizer, certifi, cachetools, absl-py, werkzeug, tensorflow-metadata, simple-parsing, scipy, rsa, requests, python-dateutil, pydot, pyasn1-modules, pyarrow, promise, ml-dtypes, h5py, google-pasta, astunparse, requests-oauthlib, pandas, google-auth, google-auth-oauthlib, array-record, tensorboard, tensorflow-datasets, tensorflow, tf-keras, tensorflow-hub
Successfully installed MarkupSafe-3.0.2 Pillow-11.0.0 absl-py-2.1.0 array-record-0.5.1 astunparse-1.6.3 cachetools-5.5.0 certifi-2024.8.30 charset-normalizer-3.4.0 click-8.1.7 dm-tree-0.1.8 docstring-parser-0.16 etils-1.10.0 flatbuffers-24.3.25 fsspec-2024.10.0 gast-0.6.0 google-auth-2.35.0 google-auth-oauthlib-1.2.1 google-pasta-0.2.0 grpcio-1.67.0 h5py-3.12.1 idna-3.10 immutabledict-4.2.0 importlib_resources-6.4.5 keras-2.15.0 libclang-18.1.1 markdown-3.7 ml-dtypes-0.3.2 numpy-1.26.4 oauthlib-3.2.2 opt-einsum-3.4.0 packaging-24.1 pandas-2.2.3 promise-2.3 protobuf-3.20.3 psutil-6.1.0 pyarrow-17.0.0 pyasn1-0.6.1 pyasn1-modules-0.4.1 pydot-3.0.2 pyparsing-3.2.0 python-dateutil-2.9.0.post0 pytz-2024.2 requests-2.32.3 requests-oauthlib-2.0.0 rsa-4.9 scipy-1.14.1 simple-parsing-0.1.6 six-1.16.0 tensorboard-2.15.2 tensorboard-data-server-0.7.2 tensorflow-2.15.1 tensorflow-datasets-4.9.6 tensorflow-estimator-2.15.0 tensorflow-hub-0.16.1 tensorflow-io-gcs-filesystem-0.37.1 tensorflow-metadata-1.16.1 termcolor-2.5.0 tf-keras-2.15.1 toml-0.10.2 tqdm-4.66.5 typing-extensions-4.12.2 tzdata-2024.2 urllib3-2.2.3 werkzeug-3.0.6 wrapt-1.14.1 zipp-3.20.2

Installation complete.

Restarting R session...

> tensorflow::as_tensor("Hello World")
Error: Valid installation of TensorFlow not found.

Python environments searched for 'tensorflow' package:
 /home/doc_wsl2/.pyenv/versions/3.10.15/bin/python3.10

Python exception encountered:
 Traceback (most recent call last):
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
    module = hook()
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
    return _find_and_load(name, import_)
  File "/home/doc_wsl2/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow/__init__.py", line 48, in <module>
    from tensorflow._api.v2 import __internal__
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _r
> reticulate::py_config()
python:         /home/doc_wsl2/.virtualenvs/r-tensorflow/bin/python
libpython:      /home/doc_wsl2/.pyenv/versions/3.10.15/lib/libpython3.10.so
pythonhome:     /home/doc_wsl2/.virtualenvs/r-tensorflow:/home/doc_wsl2/.virtualenvs/r-tensorflow
version:        3.10.12 (main, Sep 11 2024, 15:47:36) [GCC 11.4.0]
numpy:          /home/doc_wsl2/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/numpy
numpy_version:  1.26.4
tensorflow:     /home/doc_wsl2/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow

NOTE: Python version was forced by import("tensorflow")
> tensorflow::tf_config()
Valid installation of TensorFlow not found.

Python environments searched for 'tensorflow' package:
 /home/doc_wsl2/.pyenv/versions/3.10.15/bin/python3.10

Python exception encountered:
 Traceback (most recent call last):
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
    module = hook()
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
    return _find_and_load(name, import_)
  File "/home/doc_wsl2/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow/__init__.py", line 48, in <module>
    from tensorflow._api.v2 import __internal__
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
    module = hook()
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
    return _find_and_load(name, import_)
  File "/home/doc_wsl2/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow/_api/v2/__internal__/__init__.py", line 8, in <module>
    from tensorflow._api.v2.__internal__ import autograph
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
    module = hook()
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
    return _find_and_load(name, import_)
  File "/home/doc_wsl2/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow/_api/v2/__internal__/autograph/__init__.py", line 8, in <module>
    from tensorflow.python.autograph.core.ag_ctx import control_status_ctx # line: 34
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
    module = hook()
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
    return _find_and_load(name, import_)
  File "/home/doc_wsl2/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow/python/autograph/core/ag_ctx.py", line 21, in <module>
    from tensorflow.python.autograph.utils import ag_logging
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
    module = hook()
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
    return _find_and_load(name, import_)
  File "/home/doc_wsl2/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow/python/autograph/utils/__init__.py", line 17, in <module>
    from tensorflow.python.autograph.utils.context_managers import control_dependency_on_returns
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
    module = hook()
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
    return _find_and_load(name, import_)
  File "/home/doc_wsl2/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow/python/autograph/utils/context_managers.py", line 19, in <module>
    from tensorflow.python.framework import ops
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
    module = hook()
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
    return _find_and_load(name, import_)
  File "/home/doc_wsl2/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow/python/framework/ops.py", line 40, in <module>
    from tensorflow.python import pywrap_tensorflow
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
    module = hook()
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
    return _find_and_load(name, import_)
  File "/home/doc_wsl2/.virtualenvs/r-tensorflow/lib/python3.10/site-packages/tensorflow/python/pywrap_tensorflow.py", line 17, in <module>
    import ctypes
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
    module = hook()
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
    return _find_and_load(name, import_)
  File "/home/doc_wsl2/.pyenv/versions/3.10.15/lib/python3.10/ctypes/__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 96, in _run_hook
    module = hook()
  File "/home/doc_wsl2/R/x86_64-pc-linux-gnu-library/4.4/reticulate/python/rpytools/loader.py", line 120, in _hook
    return _find_and_load(name, import_)
ModuleNotFoundError: No module named '_ctypes'

You can install TensorFlow using the install_tensorflow() function.

> reticulate::import("tensorflow")
Error in py_module_import(module, convert = convert) : 
  ModuleNotFoundError: No module named '_ctypes'
Run `reticulate::py_last_error()` for details.
t-kalinowski commented 1 month ago

Hi,

reticulate::install_miniconda()

Please avoid using miniconda. Instead, use reticulate::install_python().

libpython: /home/doc_wsl2/.pyenv/versions/3.10.15/lib/libpython3.10.so

This shows that you're not using miniconda but the pyenv-installed Python from install_python(), so running reticulate::install_miniconda() was unnecessary.

ModuleNotFoundError: No module named '_ctypes'

This error suggests the Python installation is incomplete, likely due to missing system dependencies. Check the details in ?reticulate::install_python online link. Specifically, the man page links to the pyenv wiki, which provides instructions for installing system dependencies. For example, on Ubuntu, you can run the following in bash:

sudo apt update; sudo apt install build-essential libssl-dev zlib1g-dev \
libbz2-dev libreadline-dev libsqlite3-dev curl git \
libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev

Afterward, you'll likely need to remove the previous Python installation and force a rebuild by calling install_python() again in R. Watch for any errors during the build process.

unlink("~/.pyenv", recursive = TRUE, force = TRUE)
reticulate::install_python("3.11", force = TRUE)