Using TBB with numba fails with pip install, works with apt install

[theahura]

Reporting a bug

• I have tried using the latest released version of Numba (most recent is
  visible in the change log (https://github.com/numba/numba/blob/master/CHANGE_LOG).
• I have included a self contained code sample to reproduce the problem.
  i.e. it's possible to run as 'python bug.py'.

Basically the title. Running the following commands fails:

python3 -m venv env
source env/bin/activate
pip install tbb numba
numba -s | grep TBB

Specifically, this returns:

TBB Threading Layer Available                 : False

The following does work:

sudo apt install libtbb-dev
numba -s | grep TBB

returning

TBB Threading Layer Available                 : True
+-->TBB imported successfully.

Two guesses.

1. The tbb version on pypi is bricked.
2. Numba is looking for a specific path that doesn't exist when installing with pip, but does exist when you install from apt.

[stuartarchibald]

@theahura Thanks for the report. Is the issue perhaps this: #6108 (comment) ?

[esc]

Which tbb and tbb-devel did you install from PyPi? I think you may need https://pypi.org/project/tbb/2020.3.254/ ?

[theahura]

@esc that version did not fix any issues.

@stuartarchibald seems like that could be related. I'm using a virtualenv, as the original post shows. I'm a bit confused by the linked comment's suggestion, however. It seems like you're saying the libtbb file isn't in the right place.

Where is the file located currently? (I see a bunch of libtbb.so files in env/lib).
And where does it need to go?

[esc]

Where is the file located currently? (I see a bunch of libtbb.so files in env/lib).
And where does it need to go?

I'm not sure anyone knows for certain. During our issue triage yesterday we discussed this and apparently the location of where to place libraries is a compile-time flag of the python interpreter. This means, the location will most likely be different depending on who compiled your python and thus, where you obtained it from.

Another issue, is that wheels were not designed as a binary packaging format. That is, the tbb package does not ship any Python code, only a compiled shared object / library and it's "not really" a properly supported use-case. We have asked about this before and you can read more here:

https://github.com/numba/numba/pulls?q=is%3Aopen+is%3Apr+milestone%3A%22Numba+0.54+RC%22

Incidentally, we actually have a script that unpacks the wheel we generate and removes libtbb.so again and repackages the wheel so that people can (if they are lucky). pip install tbb and have that work.

So, what I would recommend perhaps, is to point the LD_LIBRARY_PATH to the location of the libtbb.so file an try to launch it like that.

Hope that helps!

[esc]

I'm so sorry, I posted the wrong link, the correct one is here:

https://discuss.python.org/t/how-to-disable-vendoring-of-libraries-in-wheel/5010

[github-actions]

This issue is marked as stale as it has had no activity in the past 30 days. Please close this issue if no further response or action is needed. Otherwise, please respond with any updates and confirm that this issue still needs to be addressed.

[gmarkall]

Closing this issue as the question appears to be answered and no further feedback has been received.

[theahura]

FYI: this approach seems to break with newer versions of numba. I can confirm that it works with 0.52.0, but not with 0.55.1

[esc]

FYI: this approach seems to break with newer versions of numba. I can confirm that it works with 0.52.0, but not with 0.55.1

Question: with "this approach", you mean the approach of apt installing tbb? Is that broken with 0.55.1? Does tbb work with pip at all?

[theahura]

Question: with "this approach", you mean the approach of apt installing tbb?

Yes

Is that broken with 0.55.1? Does tbb work with pip at all?

Yes it's broken. I think it's a versioning thing, apt has tbb2020 but I believe numba is looking for tbb2021.

Pip tbb doesn't work at all, at least I couldn't get it working

[esc]

Is that broken with 0.55.1? Does tbb work with pip at all?

Yes it's broken. I think it's a versioning thing, apt has tbb2020 but I believe numba is looking for tbb2021.

W/o seeing the exact errors, this is probably correct.

Pip tbb doesn't work at all, at least I couldn't get it working

This may be worth opening a new issue about. If pip install tbb is really broken, the developers of that software should probably be notified. Do you perhaps recall or can you re-generate the error message you received with this?

[theahura]

This minimal example still replicates:

python3 -m venv env
source env/bin/activate
pip install tbb numba
numba -s | grep TBB

I get

__Threading Layer Information__                                                                      
TBB Threading Layer Available                 : False                                                
+--> Disabled due to Unknown import problem.                                                         

I had a hunch that the venv may have been the issue, but even a global install did not fix the issue. For my own project, I had to just pull tbb out because it was causing too many dependency issues 😞

I'm not even sure what pip install tbb does. The site-packages are basically empty, and I couldn't find where it dumped the libtbb.so files 🤔

[esc]

@theahura thank you, which platform is this?

[theahura]

Ubuntu 20 Desktop

[esc]

I can confirm this is still an issue that will need to be triaged.

zsh» python3 -m venv venv
zsh» source venv/bin/activate
zsh» pip install numba tbb
Collecting numba
  Downloading numba-0.55.1-1-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.4 MB)
     |████████████████████████████████| 3.4 MB 2.0 MB/s 
Collecting tbb
  Downloading tbb-2021.5.1-py2.py3-none-manylinux1_x86_64.whl (4.0 MB)
     |████████████████████████████████| 4.0 MB 4.6 MB/s 
Requirement already satisfied: setuptools in ./venv/lib/python3.8/site-packages (from numba) (44.0.0)
Collecting numpy<1.22,>=1.18
  Downloading numpy-1.21.5-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
     |████████████████████████████████| 15.7 MB 90 kB/s 
Collecting llvmlite<0.39,>=0.38.0rc1
  Downloading llvmlite-0.38.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB)
     |████████████████████████████████| 34.5 MB 3.5 MB/s 
Installing collected packages: numpy, llvmlite, numba, tbb
Successfully installed llvmlite-0.38.0 numba-0.55.1 numpy-1.21.5 tbb-2021.5.1
pip install numba tbb  9,43s user 1,95s system 46% cpu 24,336 total
zsh» which numba
/tmp/venv/bin/numba
zsh» numba -s | grep TBB 
TBB Threading Layer Available                 : False
zsh» cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=20.04
DISTRIB_CODENAME=focal
DISTRIB_DESCRIPTION="Ubuntu 20.04.3 LTS"

[stuartarchibald]

@esc is this issue down to this: #6108 (comment) ?

[esc]

@esc is this issue down to this: #6108 (comment) ?

It certainly sounds plausible.

[github-actions]

This issue is marked as stale as it has had no activity in the past 30 days. Please close this issue if no further response or action is needed. Otherwise, please respond with any updates and confirm that this issue still needs to be addressed.

[nathzi1505]

Where is the file located currently? (I see a bunch of libtbb.so files in env/lib).
And where does it need to go?

I'm not sure anyone knows for certain. During our issue triage yesterday we discussed this and apparently the location of where to place libraries is a compile-time flag of the python interpreter. This means, the location will most likely be different depending on who compiled your python and thus, where you obtained it from.

Another issue, is that wheels were not designed as a binary packaging format. That is, the tbb package does not ship any Python code, only a compiled shared object / library and it's "not really" a properly supported use-case. We have asked about this before and you can read more here:

https://github.com/numba/numba/pulls?q=is%3Aopen+is%3Apr+milestone%3A%22Numba+0.54+RC%22

Incidentally, we actually have a script that unpacks the wheel we generate and removes libtbb.so again and repackages the wheel so that people can (if they are lucky). pip install tbb and have that work.

So, what I would recommend perhaps, is to point the LD_LIBRARY_PATH to the location of the libtbb.so file an try to launch it like that.

Hope that helps!

TL;DR: This works.
After you install through pip install --upgrade tbb set your LD_LIBRARY_PATH to the .../venv/lib.