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jplu opened this issue Jun 7, 2016 · 35 comments · Fixed by #2958
Closed

"ERROR: Cannot find './util/python/python_lib'" #2703

jplu opened this issue Jun 7, 2016 · 35 comments · Fixed by #2958
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@jplu
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jplu commented Jun 7, 2016

Hello,

I have the following error when I try to compile the pip package from the source code.

Environment info

Operating System: Ubuntu 14.04

Installed version of CUDA and cuDNN:
(please attach the output of ls -l /path/to/cuda/lib/libcud*):

ls -l /usr/local/cuda/lib64/libcud*
-rw-r--r-- 1 root root   322936 Aug 15  2015 /usr/local/cuda/lib64/libcudadevrt.a
lrwxrwxrwx 1 root root       16 Aug 15  2015 /usr/local/cuda/lib64/libcudart.so -> libcudart.so.7.5
lrwxrwxrwx 1 root root       19 Aug 15  2015 /usr/local/cuda/lib64/libcudart.so.7.5 -> libcudart.so.7.5.18
-rwxr-xr-x 1 root root   383336 Aug 15  2015 /usr/local/cuda/lib64/libcudart.so.7.5.18
-rw-r--r-- 1 root root   720192 Aug 15  2015 /usr/local/cuda/lib64/libcudart_static.a
lrwxrwxrwx 1 root root       13 Feb  9 18:48 /usr/local/cuda/lib64/libcudnn.so -> libcudnn.so.4
lrwxrwxrwx 1 root root       17 Feb  9 18:48 /usr/local/cuda/lib64/libcudnn.so.4 -> libcudnn.so.4.0.7
-rwxrwxr-x 1 root root 61453024 Feb  8 23:12 /usr/local/cuda/lib64/libcudnn.so.4.0.7
-rw-rw-r-- 1 root root 62025862 Feb  8 23:12 /usr/local/cuda/lib64/libcudnn_static.a

If installed from sources, provide the commit hash: ea9e00a

Steps to reproduce

  1. git clone https://github.com/tensorflow/tensorflow
  2. cd tensorflow
  3. ./configure
  4. bazel build -c opt --config=cuda //tensorflow/cc:tutorials_example_trainer
  5. bazel build -c opt //tensorflow/tools/pip_package:build_pip_package --verbose_failures

Logs or other output that would be helpful

ERROR: /home/plu/git/tensorflow/util/python/BUILD:14:1: Executing genrule //util/python:python_check failed: bash failed: error executing command 
  (cd /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/tensorflow && \
  exec env - \
    PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/packages/bin:.:/homes/plu/docker/:/usr/local/cuda-7.5/bin/:/homes/plu/bin/:/usr/local/openmpi-1.10.1/bin/ \
  /bin/bash -c 'source external/bazel_tools/tools/genrule/genrule-setup.sh; OUTPUTDIR="bazel-out/host/genfiles/util/python/"; util/python/python_config.sh --check && touch $OUTPUTDIR/python_checked'): com.google.devtools.build.lib.shell.BadExitStatusException: Process exited with status 1: bash failed: error executing command 
  (cd /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/tensorflow && \
  exec env - \
    PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/packages/bin:.:/homes/plu/docker/:/usr/local/cuda-7.5/bin/:/homes/plu/bin/:/usr/local/openmpi-1.10.1/bin/ \
  /bin/bash -c 'source external/bazel_tools/tools/genrule/genrule-setup.sh; OUTPUTDIR="bazel-out/host/genfiles/util/python/"; util/python/python_config.sh --check && touch $OUTPUTDIR/python_checked'): com.google.devtools.build.lib.shell.BadExitStatusException: Process exited with status 1.


ERROR: Cannot find './util/python/python_lib'.  Did you run configure?

But, I do have this folder locally in the Tensorflow repository. Did I do something wrong? Or it is a bug coming from Tensorflow?

Thanks in advance for any help!

@girving
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girving commented Jun 7, 2016

Did you run configure?

@
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girving girving added the stat:awaiting response Status - Awaiting response from author label Jun 7, 2016
@jplu
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jplu commented Jun 8, 2016

Hello,

Yes I did run configure as it is written in the "Steps to reproduce" section of my previous post :-)

@girving
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girving commented Jun 8, 2016

@jplu: I saw that, but one can never be too careful when triaging hundreds of issues. :)

Can you add a pwd line to python_config.sh to see what directory it's in? I'm not sure how Bazel genrules work, so it's possible that the BUILD file should declare some dependencies.

@jplu
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jplu commented Jun 9, 2016

@girving: No worries I understand :)

I put a pwd command right after the licence header and run once again

bazel build -c opt //tensorflow/tools/pip_package:build_pip_package --verbose_failures

But nothing is displayed:

bazel build -c opt //tensorflow/tools/pip_package:build_pip_package --verbose_failures
WARNING: Output base '/homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7' is on NFS. This may lead to surprising failures and undetermined behavior.
......
INFO: Found 1 target...
ERROR: /home/plu/git/tensorflow/util/python/BUILD:14:1: Executing genrule //util/python:python_check failed: bash failed: error executing command 
  (cd /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/tensorflow && \
  exec env - \
    PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/packages/bin:.:/homes/plu/docker/:/usr/local/cuda-7.5/bin/:/homes/plu/bin/:/usr/local/openmpi-1.10.1/bin/ \
  /bin/bash -c 'source external/bazel_tools/tools/genrule/genrule-setup.sh; OUTPUTDIR="bazel-out/host/genfiles/util/python/"; util/python/python_config.sh --check && touch $OUTPUTDIR/python_checked'): com.google.devtools.build.lib.shell.BadExitStatusException: Process exited with status 1: bash failed: error executing command 
  (cd /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/tensorflow && \
  exec env - \
    PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/packages/bin:.:/homes/plu/docker/:/usr/local/cuda-7.5/bin/:/homes/plu/bin/:/usr/local/openmpi-1.10.1/bin/ \
  /bin/bash -c 'source external/bazel_tools/tools/genrule/genrule-setup.sh; OUTPUTDIR="bazel-out/host/genfiles/util/python/"; util/python/python_config.sh --check && touch $OUTPUTDIR/python_checked'): com.google.devtools.build.lib.shell.BadExitStatusException: Process exited with status 1.
/homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/tensorflow


ERROR: Cannot find './util/python/python_lib'.  Did you run configure?


Target //tensorflow/tools/pip_package:build_pip_package failed to build
INFO: Elapsed time: 15.143s, Critical Path: 2.45s

@girving
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girving commented Jun 9, 2016

@jplu You might need a flag to bazel to get it to not suppress stdout. Not sure which that is, though; bazel help build doesn't make it obvious. The high tech option is pwd > ~/blah.

@jplu
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jplu commented Jun 10, 2016

The redirect command did the thing, I had to think about this solution before...

Anyway, here the path:

/homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/tensorflow

@girving
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girving commented Jun 10, 2016

@damienmg We have a python_check genrule that verifies that a symbolic link to a directory exists. I think the check is failing since we don't depend on the symbolic link. Can one put a symbolic link to a directory in a normal filegroup, or is something special required?

https://github.com/tensorflow/tensorflow/blob/master/util/python/BUILD#L14

On the other hand, @martinwicke, I suppose if we add python_lib as a dependency then python_check will fail with a less informative error message. Thoughts? I imagine this error message has a significant role in reducing filed issues, so it'd be bad to make it worse.

@damienmg
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FWIW: the path was in the output :) /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/tensorflow

The test that check a symlink is printing a more comprehensive message about it not being a symlink, or did I read the script wrong?

@damienmg
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(and nothing special required with symlinks, but remember that when running, most files will actually be symlinks while directories will be recreated).

@martinwicke
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Can we just use all_files as a data depedency for python_check? That will not fail (since it's just a glob), and if nothing is there, we'll still see it's not there and get our nice message.

@girving girving added triaged and removed stat:awaiting response Status - Awaiting response from author labels Jun 11, 2016
@girving
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girving commented Jun 11, 2016

@martinwicke Seems reasonable. Want to assign it to someone?

@ebrevdo
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ebrevdo commented Jun 13, 2016

This used to work out of the box, no? Sounds like a bug was recently introduced.

@martinwicke
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Olivia, can you change the BUILD file in util/python to have a filegroup containing all files in the directory, like this:

filegroup(
name = "configure_files",
data = glob([
"*",
])
)

(syntax may be screwy), and add that as a data dependency to the python_check target?

And then make sure it works... I hadn't seen this before.

@martinwicke
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@jplu can you check whether #2958 fixes your problem?

martinwicke added a commit that referenced this issue Jun 21, 2016
caisq pushed a commit to caisq/tensorflow that referenced this issue Jun 21, 2016
martinwicke added a commit that referenced this issue Jun 21, 2016
@jplu
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jplu commented Jun 24, 2016

Sorry for the delay I was not able to use this computer until now.

Unfortunately the problem still remains :-(

WARNING: Output base '/homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7' is on NFS. This may lead to surprising failures and undetermined behavior.
WARNING: /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/protobuf/WORKSPACE:1: Workspace name in /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/protobuf/WORKSPACE (@__main__) does not match the name given in the repository's definition (@protobuf); this will cause a build error in future versions.
WARNING: /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/re2/WORKSPACE:1: Workspace name in /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/re2/WORKSPACE (@__main__) does not match the name given in the repository's definition (@re2); this will cause a build error in future versions.
WARNING: /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/highwayhash/WORKSPACE:1: Workspace name in /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/highwayhash/WORKSPACE (@__main__) does not match the name given in the repository's definition (@highwayhash); this will cause a build error in future versions.
WARNING: /home/plu/git/tensorflow/util/python/BUILD:11:16: in includes attribute of cc_library rule //util/python:python_headers: 'python_include' resolves to 'util/python/python_include' not in 'third_party'. This will be an error in the future.
INFO: Found 1 target...
ERROR: /home/plu/git/tensorflow/util/python/BUILD:14:1: Executing genrule //util/python:python_check failed: bash failed: error executing command 
  (cd /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/tensorflow && \
  exec env - \
    PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/packages/bin:.:/homes/plu/docker/:/usr/local/cuda-7.5/bin/:/homes/plu/bin/:/usr/local/openmpi-1.10.1/bin/ \
  /bin/bash -c 'source external/bazel_tools/tools/genrule/genrule-setup.sh; OUTPUTDIR="bazel-out/local_linux-opt/genfiles/util/python/"; util/python/python_config.sh --check && touch $OUTPUTDIR/python_checked'): com.google.devtools.build.lib.shell.BadExitStatusException: Process exited with status 1.


ERROR: Cannot find './util/python/python_lib'.  Did you run configure?


Target //tensorflow/tools/pip_package:build_pip_package failed to build
INFO: Elapsed time: 2.326s, Critical Path: 0.59s

I have done a fresh new clone corresponding to the commit 84225a2

@jmchen-g
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@caisq Could you take a look at this please?

@jmchen-g jmchen-g reopened this Jul 12, 2016
@pjoz
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pjoz commented Jul 12, 2016

I had this same issue in the closed tickets referenced above, @jmchen-g thanks for re-opening this one.

@jplu
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jplu commented Jul 21, 2016

Hello,

I have tested with the commit fefe52c that contains the fix proposed by @plutoshe. Unfortunately the issue still remains :(

bazel build -c opt --config=cuda //tensorflow/tools/pip_package:build_pip_package --verbose_failures
WARNING: Output base '/homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7' is on NFS. This may lead to surprising failures and undetermined behavior.
WARNING: /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/protobuf/WORKSPACE:1: Workspace name in /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/protobuf/WORKSPACE (@__main__) does not match the name given in the repository's definition (@protobuf); this will cause a build error in future versions.
WARNING: /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/re2/WORKSPACE:1: Workspace name in /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/re2/WORKSPACE (@__main__) does not match the name given in the repository's definition (@re2); this will cause a build error in future versions.
WARNING: /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/highwayhash/WORKSPACE:1: Workspace name in /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/external/highwayhash/WORKSPACE (@__main__) does not match the name given in the repository's definition (@highwayhash); this will cause a build error in future versions.
WARNING: /home/plu/git/tensorflow/util/python/BUILD:11:16: in includes attribute of cc_library rule //util/python:python_headers: 'python_include' resolves to 'util/python/python_include' not in 'third_party'. This will be an error in the future.
INFO: Found 1 target...
ERROR: /home/plu/git/tensorflow/util/python/BUILD:14:1: Executing genrule //util/python:python_check failed: bash failed: error executing command 
  (cd /homes/plu/.cache/bazel/_bazel_plu/5fecb6612d2e95475ff53a54e377c3f7/tensorflow && \
  exec env - \
    PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/packages/bin:.:/homes/plu/docker/:/usr/local/cuda-7.5/bin/:/homes/plu/bin/:/usr/local/openmpi-1.10.1/bin/ \
  /bin/bash -c 'source external/bazel_tools/tools/genrule/genrule-setup.sh; OUTPUTDIR="bazel-out/local_linux-opt/genfiles/util/python/"; util/python/python_config.sh --check && touch $OUTPUTDIR/python_checked'): com.google.devtools.build.lib.shell.BadExitStatusException: Process exited with status 1.


ERROR: Cannot find './util/python/python_lib'.  Did you run configure?


Target //tensorflow/tools/pip_package:build_pip_package failed to build
INFO: Elapsed time: 1.909s, Critical Path: 0.20s

Don't hesitate to ask me if you need other information to help you to debug.

@martinwicke
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what's your bazel version?

@jplu
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jplu commented Jul 22, 2016

I'm using Bazel 0.2.3

@pjoz
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pjoz commented Jul 22, 2016

I'm using bazel 0.2.2 with the same error

@martinwicke
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Which python did you specify when running configure? Also, can you run /bin/bash?

@pjoz
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pjoz commented Jul 24, 2016

Python specified is /usr/local/bin/python (version Python 2.7.11)

Ran /bin/bash before the install instructions with no change in result.

@jplu
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jplu commented Jul 25, 2016

The specified Python is:

/usr/bin/python --version
Python 2.7.6

I also can run /bin/bash:

/bin/bash --version
GNU bash, version 4.3.11(1)-release (x86_64-pc-linux-gnu)
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>

This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

@martinwicke
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Ok. I'm just stabbing at the dark -- I cannot reproduce this and I'm wondering what the difference between our installations might be.

Can you try running using docker just to see if that works?

< 9E88 div class="d-flex">

@jplu
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jplu commented Jul 26, 2016

It works via Docker:

docker run -it -p 8888:8888 gcr.io/tensorflow/tensorflow
Unable to find image 'gcr.io/tensorflow/tensorflow:latest' locally
latest: Pulling from tensorflow/tensorflow
759d6771041e: Pull complete 
8836b825667b: Pull complete 
c2f5e51744e6: Pull complete 
a3ed95caeb02: Pull complete 
b1a230d2f7d7: Pull complete 
f4bd848af23b: Pull complete 
9ff2d28f3bea: Pull complete 
de3ac9a732b6: Pull complete 
ba1ff7fd8338: Pull complete 
8b638dd1001b: Pull complete 
4c3f9ea22d7e: Pull complete 
Digest: sha256:8ae5229583adf18c1e50ac7fbf4c25301aef186eb3cc7c23d85999328a72ac4b
Status: Downloaded newer image for gcr.io/tensorflow/tensorflow:latest
[I 06:05:16.943 NotebookApp] Writing notebook server cookie secret to /root/.local/share/jupyter/runtime/notebook_cookie_secret
/usr/local/lib/python2.7/dist-packages/widgetsnbextension/__init__.py:30: UserWarning: To use the jupyter-js-widgets nbextension, you'll need to update
    the Jupyter notebook to version 4.2 or later.
  the Jupyter notebook to version 4.2 or later.""")
[W 06:05:16.965 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.
[W 06:05:16.966 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using authentication. This is highly insecure and not recommended.
[I 06:05:16.969 NotebookApp] Serving notebooks from local directory: /notebooks
[I 06:05:16.969 NotebookApp] 0 active kernels 
[I 06:05:16.969 NotebookApp] The Jupyter Notebook is running at: http://[all ip addresses on your system]:8888/
[I 06:05:16.969 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

@jplu
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jplu commented Jul 26, 2016

When I run:

util/python/python_config.sh --check

I get the same error.

@jplu
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jplu commented Jul 26, 2016

Once the run of ./configure is finished the environement variable $PYTHON_BIN_PATH is not set and makes crash the command:

util/python/python_config.sh --setup

@jplu
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jplu commented Jul 26, 2016

Ok, I found the issue, the script ./configure creates two symlinks in the folder util/python/:

  • python_include -> /usr/include/python2.7
  • python_lib -> /usr/lib/python2.7/site-packages

The problem is that the path /usr/lib/python2.7/site-packages doesn't exists for me. I don't have the site-packages folder. Mine is in /usr/local/python/lib/python2.7/site-packages/

Everything is working like a charm if I set the symlink python_lib to the proper path.

A possible fix could be to ask another question in the configure to set where the packages for Python are installed. WDYT?

@martinwicke
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Interesting. We actually ask distutils for this path (see utils/python/python_config.sh), so it appears distutils is misconfigured. We could switch to an alternative method, but I'm not at all sure it's better in general.

@jplu
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jplu commented Jul 26, 2016

The main problem is that people might have multiple location for their Python's packages. So why not checking the $PYTHONPATH variable? As this variable as to be updated to include all the path that are not "Python standardized" and that we want to use in general.

@martinwicke
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Let's see if I understood:

Let's say distutils lies to us and gives us a non-existent path (as in your case). What should we do next? We could ask the site module and see if it gives us an existing path (would it in your case?). If that fails also, we can ask the user. We should make sure the user gives us a path which is in $PYTHONPATH, otherwise it's very unlikely to work.

@jplu
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jplu commented Jul 26, 2016

Yes you have understood. If a Python lib is not in the standard location or in $PYTHONPATH then it is not possible to use it as Python will not know where are the files to import.

For example for my case, my $PYTHONPATH looks like this:

echo $PYTHONPATH
/home/plu/git/deepdetect/clients/python/:/usr/local/python/lib/python2.7/site-packages/:/home/plu/git/caffe/python

If I run the interactive python and do import caffe I can load all the files in my current environment. In the case I remove /home/plu/git/caffe/python from my $PYTHONPATH and redo an import caffe I will get an ImportError: No module named caffe

So I think, by just checking this environment variable we should be safe, but we never know. Nevertheless, checking the site is not enough, as for me:

>>> import site; site.getsitepackages()
['/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages']

I get only those two, and not the others contained in my $PYTHONPATH which mean that if someone prefer to compile every package itself and put them in a specific location, we will miss them. So for me the steps to do are the following:

  1. use site to get a first list
  2. merge the result with the content of $PYTHONPATH
  3. be sure that all the paths exists otherwise remove it from the list
  4. ask the user if all the path are well known, otherwise ask them to add the wanted other paths

@aselle aselle removed the triaged label Jul 28, 2016
@martinwicke
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@itsmeolivia can you look into modifying the python setup to include the workflow outlined by @jplu?

teamdandelion pushed a commit to teamdandelion/tensorflow that referenced this issue Aug 10, 2016
…on path from a list of possible known locations

Change: 129778433
@jplu
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jplu commented Aug 11, 2016

Perfect! Everything is compiling like a charm with this fix

Thanks a lot!

@jplu jplu closed this as completed Aug 11, 2016
copybara-service bot pushed a commit that referenced this issue Jul 29, 2023
CHANGELOG
=========
d4ae542ed - Fix nullptr dereference issue in triangular product.
7769eb1b2 - Fix problems with recent changes and Tensorflow in Power
ba1cb6e45 - Fixes #2703 by adding max_digits10 function
9995c3da6 - Fix -Wmaybe-uninitialized in SVD
4e9e493b4 - Fix -Waggressive-loop-optimizations
6e7abeae6 - fix arm build warnings
81fe2d424 - Fix more gcc compiler warnings / sort-of bugs
21cd3fe20 - Optimize check_rows_cols_for_overflow
9297aae66 - Fix AVX512 nomalloc issues in trsm.
1a2bfca8f - Fix annoying warnings
63dcb429c - Fix use of arg function in CUDA.
8f927fb52 - Altivec: fix compilation with C++20 and higher
d4b05454a - Fix argument for _mm256_cvtps_ph imm parameter
15ac3765c - Fix ivcSize return type in IndexedViewMethods.h
3791ac8a1 - Fix supportsMMA to obey EIGEN_ALTIVEC_MMA_DYNAMIC_DISPATCH compilation flag and compiler support.
bc57b926a - Add Quaternion constructor from real scalar and imaginary vector
31cd2ad37 - Ensure EIGEN_HAS_ARM64_FP16_VECTOR_ARITHMETIC is always defined on arm.
7465b7651 - Disable FP16 arithmetic for arm32.
b3267f693 - Remove unused variable in  test/svd_common.h.

PiperOrigin-RevId: 552130715
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