Installation Issue

[william-denault]

Hello I aam trying to install Tensorflow on a Unix server that use to do some computation. I have followed your instruction below and I get the following error message when I run tensorflow::as_tensor("Hello World")

2024-03-04 06:52:39.913688: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2024-03-04 06:52:39.975193: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2024-03-04 06:52:39.975892: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-03-04 06:52:41.327400: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
Error: Valid installation of TensorFlow not found.

Python environments searched for 'tensorflow' package:
 /home/wdenault/.pyenv/versions/3.9.18/bin/python3.9

Python exception encountered:
 Traceback (most recent call last):
  File "/home/wdenault/R/x86_64-pc-linux-gnu-library/4.1/reticulate/python/rpytools/loader.py", line 119, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/wdenault/R/x86_64-pc-linux-gnu-library/4.1/reticulate/python/rpytools/loader.py", line 93, in _run_hook
    module = hook()
  File "/home/wdenault/R/x86_64-pc-linux-gnu-library/4.1/reticulate/python/rpytools/loader.py", line 117, in _hook
    return _find_and_load(name, import_)
  File "/home/wdenault/.virtualenvs/r-tensorflow/lib/python3.9/site-packages/tensorflow/__init__.py", line 52, in <module>
    from ._api.v2 import compat
  File "/home/wdenault/R/x86_64-pc-linux-gnu-library/4.1/reticulate/python/rpytools/loader.py", line 119, in _find_and_load_hook
    return _run_hook(name, _hook

Here is the output of sessionInfo()

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.12            lattice_0.20-44        here_1.0.1
 [4] png_0.1-8              rprojroot_2.0.4        grid_4.1.0
 [7] lifecycle_1.0.4        jsonlite_1.8.8         magrittr_2.0.3
[10] tfruns_1.5.2           rlang_1.1.3            cli_3.6.2
[13] whisker_0.4.1          Matrix_1.6-5           reticulate_1.35.0.9000
[16] compiler_4.1.0         base64enc_0.1-3        tensorflow_2.15.0.9000

Thank you in advance.

Best regards
William

Many installation issues are resolved by running the following in a fresh R session (you can restart R in Rstudio with Ctrl+Shift+F10) :

# install the development version of packages, in case the
# issue is already fixed but not on CRAN yet.
install.packages("remotes")
remotes::install_github(sprintf("rstudio/%s", c("reticulate", "tensorflow", "keras")))
if (is.null(reticulate::virtualenv_starter()))
  reticulate::install_python()
keras3::install_keras()

Test to see if installation was successful.

tensorflow::as_tensor("Hello World")

If the above snippet succeeded and you saw something like tf.Tensor(b'Hello World', shape=(), dtype=string), then 🎉, you've successfully installed Tensorflow.

If the above installation failed, please gather some diagnostic info:

reticulate::py_config()
tensorflow::tf_config()
reticulate::import("tensorflow")
reticulate::py_last_error()
sessionInfo()

Please copy and paste the FULL OUTPUT of running all three snippets, and be sure to enclose the output lines with three backticks (```) for monospace formatting.

[t-kalinowski]

Can you please post the full output from:

reticulate::install_python()
keras3::install_keras()

[william-denault]

Hi @t-kalinowski
Thanks for the quick feedback. here the output.

>tensorflow::as_tensor("Hello World")
2024-03-04 12:50:16.002903: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
Error: Valid installation of TensorFlow not found.

Python environments searched for 'tensorflow' package:
 /home/wdenault/.pyenv/versions/3.9.18/bin/python3.9

Python exception encountered:
 Traceback (most recent call last):
  File "/home/wdenault/R/x86_64-pc-linux-gnu-library/4.1/reticulate/python/rpytools/loader.py", line 119, in _find_and_load_hook
    return _run_hook(name, _hook)
  File "/home/wdenault/R/x86_64-pc-linux-gnu-library/4.1/reticulate/python/rpytools/loader.py", line 93, in _run_hook
    module = hook()
  File "/home/wdenault/R/x86_64-pc-linux-gnu-library/4.1/reticulate/python/rpytools/loader.py", line 117, in _hook
    return _find_and_load(name, import_)
  File "/home/wdenault/.virtualenvs/r-keras/lib/python3.9/site-packages/tensorflow/__init__.py", line 54, in <module>
    from tensorflow._api.v2 import compat
  File "/home/wdenault/R/x86_64-pc-linux-gnu-library/4.1/reticulate/python/rpytools/loader.py", line 119, in _find_and_load_hook
    return _run_hook(name,

[t-kalinowski]

Hi, Can you please post the output from running these commands:

reticulate::install_python()
keras3::install_keras()

(Not the output from running tensorflow::as_tensor("Hello World"))

[william-denault]

Sorry I did not understood it.
Please find the output below,

> reticulate::install_python()
+ /home/wdenault/.local/share/r-reticulate/pyenv/bin/pyenv update
+ /home/wdenault/.local/share/r-reticulate/pyenv/bin/pyenv install --skip-existing 3.9.18
[1] "/home/wdenault/.pyenv/versions/3.9.18/bin/python3.9"
> keras3::install_keras()
Virtual environment 'r-keras' removed.
Using Python: /home/wdenault/.pyenv/versions/3.9.18/bin/python3.9
Creating virtual environment 'r-keras' ...
+ /home/wdenault/.pyenv/versions/3.9.18/bin/python3.9 -m venv /home/wdenault/.virtualenvs/r-keras
Done!
Installing packages: pip, wheel, setuptools
+ /home/wdenault/.virtualenvs/r-keras/bin/python -m pip install --upgrade pip wheel setuptools
Requirement already satisfied: pip in ./.virtualenvs/r-keras/lib/python3.9/site-packages (23.0.1)
Collecting pip
  Using cached pip-24.0-py3-none-any.whl (2.1 MB)
Collecting wheel
  Using cached wheel-0.42.0-py3-none-any.whl (65 kB)
Requirement already satisfied: setuptools in ./.virtualenvs/r-keras/lib/python3.9/site-packages (58.1.0)
Collecting setuptools
  Using cached setuptools-69.1.1-py3-none-any.whl (819 kB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 58.1.0
    Uninstalling setuptools-58.1.0:
      Successfully uninstalled setuptools-58.1.0
  Attempting uninstall: pip
    Found existing installation: pip 23.0.1
    Uninstalling pip-23.0.1:
      Successfully uninstalled pip-23.0.1
Successfully installed pip-24.0 setuptools-69.1.1 wheel-0.42.0
Virtual environment 'r-keras' successfully created.
Using virtual environment 'r-keras' ...
+ /home/wdenault/.virtualenvs/r-keras/bin/python -m pip install --upgrade --no-user scipy pandas Pillow pydot ipython tensorflow_datasets packaging
Collecting scipy
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Collecting etils>=0.9.0 (from etils[enp,epath,etree]>=0.9.0->tensorflow_datasets)
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Collecting parso<0.9.0,>=0.8.3 (from jedi>=0.16->ipython)
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Collecting ptyprocess>=0.5 (from pexpect>4.3->ipython)
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Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas)
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Collecting charset-normalizer<4,>=2 (from requests>=2.19.0->tensorflow_datasets)
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Installing collected packages: wcwidth, pytz, pure-eval, ptyprocess, dm-tree, zipp, wrapt, urllib3, tzdata, typing-extensions, traitlets, tqdm, toml, termcolor, six, pyparsing, pygments, psutil, protobuf, prompt-toolkit, Pillow, pexpect, parso, packaging, numpy, idna, fsspec, executing, exceptiongroup, etils, decorator, click, charset-normalizer, certifi, absl-py, scipy, requests, python-dateutil, pydot, promise, matplotlib-inline, jedi, importlib_resources, googleapis-common-protos, asttokens, tensorflow-metadata, stack-data, pandas, ipython, array-record, tensorflow_datasets
Successfully installed Pillow-10.2.0 absl-py-1.4.0 array-record-0.5.0 asttokens-2.4.1 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 decorator-5.1.1 dm-tree-0.1.8 etils-1.5.2 exceptiongroup-1.2.0 executing-2.0.1 fsspec-2024.2.0 googleapis-common-protos-1.62.0 idna-3.6 importlib_resources-6.1.2 ipython-8.18.1 jedi-0.19.1 matplotlib-inline-0.1.6 numpy-1.26.4 packaging-23.2 pandas-2.2.1 parso-0.8.3 pexpect-4.9.0 promise-2.3 prompt-toolkit-3.0.43 protobuf-3.20.3 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 pydot-2.0.0 pygments-2.17.2 pyparsing-3.1.1 python-dateutil-2.9.0.post0 pytz-2024.1 requests-2.31.0 scipy-1.12.0 six-1.16.0 stack-data-0.6.3 tensorflow-metadata-1.14.0 tensorflow_datasets-4.9.3 termcolor-2.4.0 toml-0.10.2 tqdm-4.66.2 traitlets-5.14.1 typing-extensions-4.10.0 tzdata-2024.1 urllib3-2.2.1 wcwidth-0.2.13 wrapt-1.16.0 zipp-3.17.0
Using virtual environment 'r-keras' ...
+ /home/wdenault/.virtualenvs/r-keras/bin/python -m pip install --upgrade --no-user tensorflow-cpu 'jax[cpu]'
Collecting tensorflow-cpu
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Installing collected packages: libclang, flatbuffers, wrapt, tensorflow-io-gcs-filesystem, tensorflow-estimator, tensorboard-data-server, pyasn1, opt-einsum, oauthlib, ml-dtypes, MarkupSafe, keras, importlib-metadata, h5py, grpcio, google-pasta, gast, cachetools, astunparse, werkzeug, rsa, requests-oauthlib, pyasn1-modules, markdown, jaxlib, jax, google-auth, google-auth-oauthlib, tensorboard, tensorflow-cpu
  Attempting uninstall: wrapt
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Using virtual environment 'r-keras' ...
+ /home/wdenault/.virtualenvs/r-keras/bin/python -m pip install --upgrade --no-user 'keras==3.0.*'
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Installing collected packages: namex, mdurl, markdown-it-py, rich, keras
  Attempting uninstall: keras
    Found existing installation: keras 2.15.0
    Uninstalling keras-2.15.0:
      Successfully uninstalled keras-2.15.0
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
tensorflow-cpu 2.15.0.post1 requires keras<2.16,>=2.15.0, but you have keras 3.0.5 which is incompatible.
Successfully installed keras-3.0.5 markdown-it-py-3.0.0 mdurl-0.1.2 namex-0.0.7 rich-13.7.1
Finished installing Keras!

[t-kalinowski]

Thanks, it looks like installation succeeded.

I think the issue is:

• the tensorflow R package is looking for venv r-tensorflow, by default created by tensorflow::install_tensorflow() and keras::install_keras()
• With Keras 3, keras3::install_keras() no longer creates venv r-tensorflow, instead creating a venv named r-keras. This is because keras is now multi backend.

You can explicitely choose a venv:

library(keras3)
library(tensorflow)

use_virtualenv("r-keras")

[william-denault]

Ok but it seems that keras 3 has a different way to be written than keras do you have any doc about it

For example this would work in keras but not in keras 3

param_nnet =keras_model_sequential() %>%
  layer_dense(units = 64,
              activation = 'relu',
              input_shape = c(1)) %>%
  layer_dense(units = 64,
              activation = 'relu' ) %>% 
  layer_dense(units = 64,
              activation = 'relu' ) %>%
  layer_dense(units = 64,
              activation = 'relu' ) %>%
  layer_dense(units = 10,
              activation = 'softmax')

with keras 3 I got the following output

2024-03-07 14:55:41.383476: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
Error: ImportError: urllib3 v2 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'OpenSSL 1.0.2k-fips  26 Jan 2017'. See: https://github.com/urllib3/urllib3/issues/2168
Run `reticulate::py_last_error()` for details.

I have tried to update python ssl manual without success

[t-kalinowski]

The ssl error is likely due to the fact that you're on a relatively old OS (CentOS 7), but trying to use a relatively new Python. I think usually pyenv (what powers reticulate::install_python())takes care of issues like this, or reports useful error messages for how to resolve. A good first step would be to run

reticulate::install_python(force = TRUE)

And read the output carefully. See if there is anything that looks like an error message related to SSL.

This link might also be helpful for troubleshooting. https://github.com/pyenv/pyenv/wiki/Common-build-problems#error-the-python-ssl-extension-was-not-compiled-missing-the-openssl-lib

Bottom line, you don't have a valid Python installation that's currently not EOL'd.