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R Interface to Keras
https://keras3.posit.co/
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Ubuntu/R-3.5.0: install_keras() fails with "Error: Error 1 occurred installing TensorFlow" #434

Closed leonjessen closed 5 years ago

leonjessen commented 6 years ago

On Ubuntu 14.04 and R-3.5.0 I'm trying to install keras like so:

library(keras)
install_keras()

But then I get:

Using existing virtualenv at  ~/.virtualenvs/r-tensorflow 
Upgrading pip ...
Traceback (most recent call last):
  File "~/.virtualenvs/r-tensorflow/bin/pip", line 7, in <module>
    from pip import main
ImportError: cannot import name main
Error: Error 1 occurred installing TensorFlow

Any hints are very welcome?

jjallaire commented 6 years ago

I would try removing the virtualenv before upgrading. So virtualenv_remove("r-tensorflow")

leonjessen commented 6 years ago

Thanks for input - Unfortunately, this did not resolve the issue:

library(reticulate)
virtualenv_remove("r-tensorflow")
Remove virtualenv at ~/.virtualenvs/r-tensorflow? [Y/n]: Y
library(keras)
install_keras()
Creating virtualenv for TensorFlow at  ~/.virtualenvs/r-tensorflow 
Already using interpreter /usr/bin/python
New python executable in ~/.virtualenvs/r-tensorflow/bin/python
Installing setuptools, pip...done.
Upgrading pip ...
Downloading/unpacking pip
  Downloading pip-10.0.1-py2.py3-none-any.whl (1.3MB): 1.3MB downloaded
Installing collected packages: pip
Successfully installed pip
Cleaning up...
Upgrading wheel ...
Traceback (most recent call last):
  File "~/.virtualenvs/r-tensorflow/bin/pip", line 7, in <module>
    from pip import main
ImportError: cannot import name main
Error: Error 1 occurred installing TensorFlow
jjallaire commented 6 years ago

If you want to install for all server users you should do a regular sudo pip install of keras rather than trying to use the R base functions. Here are some docs on doing system-wide installs: https://tensorflow.rstudio.com/tensorflow/articles/installation_gpu.html#multiple-users

leonjessen commented 6 years ago

Thanks for the link - I will look into it!

leonjessen commented 6 years ago

Now I have tried working on the issue for a considerable amount of time, but alas, I am still stuck. The issue somehow seem to pertain to pip, the error I get is the following:

keras::install_keras(method = "virtualenv", tensorflow = "gpu")
Creating virtualenv for TensorFlow at  ~/.virtualenvs/r-tensorflow 
Already using interpreter /usr/bin/python
New python executable in /home/jessen/.virtualenvs/r-tensorflow/bin/python
Installing setuptools, pip...done.
Upgrading pip ...
Downloading/unpacking pip
  Downloading pip-10.0.1-py2.py3-none-any.whl (1.3MB): 1.3MB downloaded
Installing collected packages: pip
Successfully installed pip
Cleaning up...
Upgrading wheel ...
Traceback (most recent call last):
  File "/home/jessen/.virtualenvs/r-tensorflow/bin/pip", line 7, in <module>
    from pip import main
ImportError: cannot import name main
Error: Error 1 occurred installing TensorFlow

If I then try to get the pip version installed with keras, I get the same error:

$ .virtualenvs/r-tensorflow/bin/pip -V
Traceback (most recent call last):
  File ".virtualenvs/r-tensorflow/bin/pip", line 7, in <module>
    from pip import main
ImportError: cannot import name main

Any suggestions?

jjallaire commented 6 years ago

This is an issue that some (very few as far as I can tell) Python systems get into after an upgrade to pip 10. Here are some additional details: https://github.com/pypa/pip/issues/5240. I'm hoping that thread has a way to get your system out of this state.

leonjessen commented 6 years ago

Thanks for the link, I did come across it during the last couple of days. Unfortunately, so far I have yet to resolve the issue. I will make sure to come back to this thread, when I succeed.

leonjessen commented 6 years ago

Slight progress - The virtual environment pip looks like so:

$ cat .virtualenvs/r-tensorflow/bin/pip
#!/home/jessen/.virtualenvs/r-tensorflow/bin/python

# -*- coding: utf-8 -*-
import re
import sys

from pip import main

if __name__ == '__main__':
    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
    sys.exit(main())

and fails like so:

$ .virtualenvs/r-tensorflow/bin/pip -V
Traceback (most recent call last):
  File ".virtualenvs/r-tensorflow/bin/pip", line 7, in <module>
    from pip import main
ImportError: cannot import name main

However, if I change the import call from from pip import main to from pip._internal import main, I get:

$ .virtualenvs/r-tensorflow/bin/pip -V
pip 10.0.1 from /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip (python 2.7)

But, when I issue the command keras::install_keras(method = "virtualenv", tensorflow = "gpu") from within R, it overwrites my correction with the faulty call to import.

I need to somehow avoid the automatic update of pip when installing keras, so that it is left untouched after my manual edit...

jjallaire commented 6 years ago

My impression is that once you resolve the issue the automatic update should be okay. So you could simply comment out the automatic updates for one install and see if that makes the problem go away for good.

leonjessen commented 6 years ago

I was thinking something along those lines and I can see I need to look at tensorflow::install_tensorflow(), I am however not sure how/where to comment out the lines:

else if (is_ubuntu()) {
  if (!have_pip) {
    install_commands <- c(install_commands, paste0("$ sudo apt-get install python", 
      pyver, "-pip"))
    pip <- paste0("/usr/bin/pip", pyver)
}

I tried copying the entire function to my_install and then comment out, but then it cannot find is_windows(), is_osx(), etc.

(On a side note... In Danish "pip" is synonym for crazy, which is not far from my current state-of-mind...)

jjallaire commented 6 years ago

These are the lines to comment out: https://github.com/rstudio/tensorflow/blob/master/R/install.R#L427-L434

ewenharrison commented 6 years ago

@leonjessen Did you have any success. Having exactly the same problem.

ewenharrison commented 6 years ago

Ok, this works for me. 

# The attached file calls pip9.0.3, which doesn't have the pip10.0.1 issue that 
# many others have described 
source("install.R")
source("utils.R")

# I had a further issue with tensorflow 1.6 crashing R, which is not the case with v1.5.0.
install_tensorflow(version = "1.5.0")

# If wanting keras specifically, run:
install_tensorflow(version = "1.5.0", extra_packages = "keras")

# Check all is well.
library(tensorflow)
sess = tf$Session()
hello <- tf$constant('Hello, TensorFlow!')
sess$run(hello)

# Or
library(keras)
mnist <- dataset_mnist()
x_train <- mnist$train$x
y_train <- mnist$train$y
x_test <- mnist$test$x
y_test <- mnist$test$y

install_tensorflow.zip

leonjessen commented 6 years ago

Been away for the WhyR conference and currently semi-offline, I’ll check up on this asap

rotroff-lab commented 6 years ago

@ewenharrison Thank you! This has been driving me crazy for two days.

jjallaire commented 6 years ago

I've just made a change to only update pip (and related tools) when pip is < v8.1 (the recommended minimum for installing TF). This should eliminate this issue entirely on newer systems (that code is really there for the built-in Python on Mac OS X, which has an ancient pip v7.

https://github.com/rstudio/tensorflow/commit/87af53829c42f45ab2d08dabf10e1ac7538a53e1

leonjessen commented 6 years ago

Despite numerous attempts, I am still unable to get it to work. As it is clearly a pip issue and not R/Keras, I have opened an issue at pypa/pip.

ewenharrison commented 6 years ago

@leonjessen Does the output now show that you are calling pip 9.0.3? You should not get the "main" issue with this. You are definitely using the files I attached above?

pradyunsg commented 6 years ago

A pip maintainer here! 👋

You should be able to use python -m pip instead of pip -- the pip script might have been broken due to various reasons (outlined in a pip issue that's linked from the one @leonjessen opened).

leonjessen commented 6 years ago

Cheers @ewenharrison, back from holidays, we're on the same page with your files, right up until:

> sess = tf$Session()
Error: Installation of TensorFlow not found.

Python environments searched for 'tensorflow' package:
/home/jessen/.virtualenvs/r-tensorflow/bin/python
/usr/bin/python2.7
/usr/bin/python3.4

You can install TensorFlow using the install_tensorflow() function.
ewenharrison commented 6 years ago

Can you provide the output during installation.

leonjessen commented 6 years ago

Sure thing @ewenharrison:

> source("install_tensorflow/install.R")
> source("install_tensorflow/utils.R")
> install_tensorflow(version = "gpu", extra_packages = "keras")
Creating virtualenv for TensorFlow at  ~/.virtualenvs/r-tensorflow 
Already using interpreter /usr/bin/python
New python executable in /home/jessen/.virtualenvs/r-tensorflow/bin/python
Installing setuptools, pip...done.
Upgrading pip ...
Collecting pip==9.0.3
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
  SNIMissingWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
  InsecurePlatformWarning
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
  InsecurePlatformWarning
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Installing collected packages: pip
Successfully installed pip-10.0.1
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Upgrading wheel ...
Collecting wheel
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
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/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
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Installing collected packages: wheel
Successfully installed wheel-0.31.1
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Upgrading setuptools ...
Collecting setuptools
/home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ssl_.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
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  InsecurePlatformWarning
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Installing collected packages: setuptools
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You should consider upgrading via the 'pip install --upgrade pip' command.
Installing TensorFlow ...
Collecting tensorflow-gpu
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Successfully installed Pillow-5.2.0 absl-py-0.3.0 astor-0.7.1 backports.weakref-1.0.post1 certifi-2018.4.16 chardet-3.0.4 enum34-1.1.6 funcsigs-1.0.2 futures-3.2.0 gast-0.2.0 grpcio-1.14.0 h5py-2.8.0 idna-2.7 keras-2.2.2 keras-applications-1.0.4 keras-preprocessing-1.0.2 markdown-2.6.11 mock-2.0.0 numpy-1.15.0 pbr-4.2.0 protobuf-3.6.0 pyyaml-3.13 requests-2.19.1 scipy-1.1.0 setuptools-40.0.0 six-1.11.0 tensorboard-1.9.0 tensorflow-gpu-1.9.0 termcolor-1.1.0 urllib3-1.23 werkzeug-0.14.1 wheel-0.31.1
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Installation complete.
> library(tensorflow)

Attaching package: ‘tensorflow’

The following object is masked _by_ ‘.GlobalEnv’:

    install_tensorflow

> sess = tf$Session()
Error: Installation of TensorFlow not found.

Python environments searched for 'tensorflow' package:
 /home/jessen/.virtualenvs/r-tensorflow/bin/python
 /usr/bin/python2.7
 /usr/bin/python3.4

You can install TensorFlow using the install_tensorflow() function.

There is some sort of problem with which version installed python is being called, but I cannot seem to find a solution. Any input is much appreciated! 👍

ewenharrison commented 6 years ago

I'd try with the standard package before the GPU version.

On 6 August 2018 at 08:43, Leon Eyrich Jessen notifications@github.com wrote:

Sure thing @ewenharrison https://github.com/ewenharrison:

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For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/ff/f4/385715ccc461885f3cedf57a41ae3c12b5fec3f35cce4c8706b1a112a133/setuptools-40.0.0-py2.py3-none-any.whl (567kB) 100% |████████████████████████████████| 573kB 1.6MB/s Installing collected packages: setuptools Successfully installed setuptools-40.0.0 You are using pip version 10.0.1, however version 18.0 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Installing TensorFlow ... Collecting tensorflow-gpu /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings SNIMissingWarning /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. 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For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/68/45/8ed49fb2decd4ce7849fc9755d9e066f414fb29c40e811bf4c12287de0af/tensorflow_gpu-1.9.0-cp27-cp27mu-manylinux1_x86_64.whl (229.6MB) 100% |████████████████████████████████| 229.6MB 7.3kB/s Collecting h5py /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/33/0c/1c5dfa85e05052aa5f50969d87c67a2128dc39a6f8ce459a503717e56bd0/h5py-2.8.0-cp27-cp27mu-manylinux1_x86_64.whl (2.7MB) 100% |████████████████████████████████| 2.7MB 439kB/s Collecting pyyaml /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/9e/a3/1d13970c3f36777c583f136c136f804d70f500168edc1edea6daa7200769/PyYAML-3.13.tar.gz (270kB) 100% |████████████████████████████████| 276kB 3.8MB/s Collecting requests /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/65/47/7e02164a2a3db50ed6d8a6ab1d6d60b69c4c3fdf57a284257925dfc12bda/requests-2.19.1-py2.py3-none-any.whl (91kB) 100% |████████████████████████████████| 92kB 173kB/s Collecting Pillow /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/6e/27/709a8493071ec649a56d5a3194f648ec7cd792189e994bbd2ef5d285670d/Pillow-5.2.0-cp27-cp27mu-manylinux1_x86_64.whl (2.0MB) 100% |████████████████████████████████| 2.0MB 534kB/s Collecting keras /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/34/7d/b1dedde8af99bd82f20ed7e9697aac0597de3049b1f786aa2aac3b9bd4da/Keras-2.2.2-py2.py3-none-any.whl (299kB) 100% |████████████████████████████████| 307kB 3.0MB/s Collecting scipy /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/2a/f3/de9c1bd16311982711209edaa8c6caa962db30ebb6a8cc6f1dcd2d3ef616/scipy-1.1.0-cp27-cp27mu-manylinux1_x86_64.whl (30.8MB) 100% |████████████████████████████████| 30.8MB 57kB/s Collecting mock>=2.0.0 (from tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/e6/35/f187bdf23be87092bd0f1200d43d23076cee4d0dec109f195173fd3ebc79/mock-2.0.0-py2.py3-none-any.whl (56kB) 100% |████████████████████████████████| 61kB 9.4MB/s Collecting grpcio>=1.8.6 (from tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/ea/96/234eaae211b6b34739018735be33e1616bc3e73c62d842c5189b80a4bd72/grpcio-1.14.0-cp27-cp27mu-manylinux1_x86_64.whl (9.2MB) 100% |████████████████████████████████| 9.2MB 177kB/s Collecting termcolor>=1.1.0 (from tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/8a/48/a76be51647d0eb9f10e2a4511bf3ffb8cc1e6b14e9e4fab46173aa79f981/termcolor-1.1.0.tar.gz Collecting numpy>=1.13.3 (from tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/85/51/ba4564ded90e093dbb6adfc3e21f99ae953d9ad56477e1b0d4a93bacf7d3/numpy-1.15.0-cp27-cp27mu-manylinux1_x86_64.whl (13.8MB) 100% |████████████████████████████████| 13.8MB 127kB/s Collecting tensorboard<1.10.0,>=1.9.0 (from tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/d5/98/e2e9d5afbc86cef0b2dd0f4ab791519b9bd305ea207e1e5c2f9a9f2f6da6/tensorboard-1.9.0-py2-none-any.whl (3.3MB) 100% |████████████████████████████████| 3.3MB 465kB/s Collecting backports.weakref>=1.0rc1 (from tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/88/ec/f598b633c3d5ffe267aaada57d961c94fdfa183c5c3ebda2b6d151943db6/backports.weakref-1.0.post1-py2.py3-none-any.whl Collecting absl-py>=0.1.6 (from tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/96/5d/18feb90462c8edaae71305716c7e8bac479fc9dface63221f808a6b95880/absl-py-0.3.0.tar.gz (84kB) 100% |████████████████████████████████| 92kB 6.2MB/s Collecting wheel (from tensorflow-gpu) Using cached https://files.pythonhosted.org/packages/81/30/e935244ca6165187ae8be876b6316ae201b71485538ffac1d718843025a9/wheel-0.31.1-py2.py3-none-any.whl Collecting enum34>=1.1.6 (from tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl Collecting six>=1.10.0 (from tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. 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For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/5c/78/ff794fcae2ce8aa6323e789d1f8b3b7765f601e7702726f430e814822b96/gast-0.2.0.tar.gz Collecting protobuf>=3.4.0 (from tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/27/e7/bf96130ebe633b08a3913da4bb25e50dac5779f1f68e51c99485423f7443/protobuf-3.6.0-cp27-cp27mu-manylinux1_x86_64.whl (7.1MB) 100% |████████████████████████████████| 7.1MB 236kB/s Collecting astor>=0.6.0 (from tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/35/6b/11530768cac581a12952a2aad00e1526b89d242d0b9f59534ef6e6a1752f/astor-0.7.1-py2.py3-none-any.whl Collecting setuptools<=39.1.0 (from tensorflow-gpu) Downloading https://files.pythonhosted.org/packages/8c/10/79282747f9169f21c053c562a0baa21815a8c7879be97abd930dbcf862e8/setuptools-39.1.0-py2.py3-none-any.whl (566kB) 100% |████████████████████████████████| 573kB 3.1MB/s Collecting idna<2.8,>=2.5 (from requests) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/4b/2a/0276479a4b3caeb8a8c1af2f8e4355746a97fab05a372e4a2c6a6b876165/idna-2.7-py2.py3-none-any.whl (58kB) 100% |████████████████████████████████| 61kB 7.7MB/s Collecting urllib3<1.24,>=1.21.1 (from requests) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/bd/c9/6fdd990019071a4a32a5e7cb78a1d92c53851ef4f56f62a3486e6a7d8ffb/urllib3-1.23-py2.py3-none-any.whl (133kB) 100% |████████████████████████████████| 143kB 5.9MB/s Collecting chardet<3.1.0,>=3.0.2 (from requests) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB) 100% |████████████████████████████████| 143kB 5.5MB/s Collecting certifi>=2017.4.17 (from requests) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/7c/e6/92ad559b7192d846975fc916b65f667c7b8c3a32bea7372340bfe9a15fa5/certifi-2018.4.16-py2.py3-none-any.whl (150kB) 100% |████████████████████████████████| 153kB 4.8MB/s Collecting keras-applications==1.0.4 (from keras) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/54/90/8f327deaa37a71caddb59b7b4aaa9d4b3e90c0e76f8c2d1572005278ddc5/Keras_Applications-1.0.4-py2.py3-none-any.whl (43kB) 100% |████████████████████████████████| 51kB 6.3MB/s Collecting keras-preprocessing==1.0.2 (from keras) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning Downloading https://files.pythonhosted.org/packages/71/26/1e778ebd737032749824d5cba7dbd3b0cf9234b87ab5ec79f5f0403ca7e9/Keras_Preprocessing-1.0.2-py2.py3-none-any.whl Collecting funcsigs>=1; python_version < "3.3" (from mock>=2.0.0->tensorflow-gpu) /home/jessen/.virtualenvs/r-tensorflow/local/lib/python2.7/site-packages/pip/vendor/urllib3/util/ssl.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. 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You should consider upgrading via the 'pip install --upgrade pip' command.

Installation complete.

library(tensorflow)

Attaching package: ‘tensorflow’

The following object is masked by ‘.GlobalEnv’:

install_tensorflow

sess = tf$Session() Error: Installation of TensorFlow not found.

Python environments searched for 'tensorflow' package: /home/jessen/.virtualenvs/r-tensorflow/bin/python /usr/bin/python2.7 /usr/bin/python3.4

You can install TensorFlow using the install_tensorflow() function.

There is some sort of problem with which version installed python is being called, but I cannot seem to find a solution. Any input is much appreciated! 👍

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-- Ewen M Harrison MB ChB MSc PhD FRCS (Gen Surg) Senior Lecturer in General Surgery | Consultant Transplant and Hepatobiliary Surgeon ChM General Surgery http://www.chm.rcsed.ac.uk Programme Director| GlobalSurg http://globalsurg.org Research Collaborative Lead Surgical Informatics | Centre for Medical Informatics | Usher Institute | University of Edinburgh http://www.ed.ac.uk/schools-departments/surgery/staff/surgical-profiles/ewen-harrison Mobile: +44 (0) 797 442 0495 | mail@ewenharrison.com | Twitter: @ewenharrison | Web: DataSurg http://datasurg.net | SurgicalInformatics http://surgicalinformatics.org

leonjessen commented 6 years ago

I understand, but It has to be the GPU version... It's a petty letting a perfectly nice nvidia tesla card sitting idle - I need to put it to work 👍

ewenharrison commented 6 years ago

To debug your installation install the CPU version. Then start on the necessary systems required for the GPU system. https://tensorflow.rstudio.com/tools/local_gpu.html

On 6 August 2018 at 08:59, Leon Eyrich Jessen notifications@github.com wrote:

I understand, but It has to be the GPU version... It's a petty letting a perfectly nice nvidia tesla card sitting idle - I need to put it to work 👍

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-- Ewen M Harrison MB ChB MSc PhD FRCS (Gen Surg) Senior Lecturer in General Surgery | Consultant Transplant and Hepatobiliary Surgeon ChM General Surgery http://www.chm.rcsed.ac.uk Programme Director| GlobalSurg http://globalsurg.org Research Collaborative Lead Surgical Informatics | Centre for Medical Informatics | Usher Institute | University of Edinburgh http://www.ed.ac.uk/schools-departments/surgery/staff/surgical-profiles/ewen-harrison Mobile: +44 (0) 797 442 0495 | mail@ewenharrison.com | Twitter: @ewenharrison | Web: DataSurg http://datasurg.net | SurgicalInformatics http://surgicalinformatics.org

skeydan commented 6 years ago

Hi Leon,

were you able to solve this, so we could close the issue?

If not, I can understand this

I understand, but It has to be the GPU version... It's a petty letting a perfectly nice nvidia tesla card sitting idle

very well, so I'm just asking, very pragmatically, does it have to be virtualenv? So far, I've never had any problems using conda...

leonjessen commented 5 years ago

No need to re-open, just wanted to give my final verdict: I had to give up! I spend hours and hours looking online and tried all proposed solutions and nothing worked. Once your system is caught in an inconsistent state with pip, then you are in deep deep trouble. On my Ubuntu 14.04 I was able to get tensorflow up and running after installing miniconda3 and then in R-3.5.1 issue install_keras(method = "conda", tensorflow = "gpu"). However, I have decided to do, what would have been more time efficient, had I done so initially; clean install Ubuntu 18.04 LTS and then redo the whole Cuda/Keras/Tensorflow/R setup. You live you learn... Thanks for input during the process, much appreciated!