BUG: build issue on Ubuntu 22.04 about scipy

[dschmitz89]

How did you create your environment/install compilers etc.? Sounds like compiler version issue to me.

[nickodell]

Thanks for making this issue, Will.

One more point of comparison I want to check is dist-upgrade. When you got your 22.04.4 system, did you do so by installing it with a 22.04 ISO, or did you do a dist-upgrade? The reason why I ask is that the system where I'm having trouble was originally Ubuntu 20.10.

This SO issue has a few ways to check: https://askubuntu.com/questions/732334/how-to-check-if-an-ubuntu-installation-has-been-upgraded-from-previous-versions

[andyfaff]

Looking at how the various CI entries compile scipy is also a good source of build information (possibly not for total neophytes though). I often find docker to be useful in figuring out issues, because one is starting from a fresh slate. Crud that builds up can often lead to hard to reproduce issues.
Anyway, I've checkout out building on Ubuntu 22.04 and don't experience this problem. I start up the container with docker run -it ubuntu:22.04. I then issue the following commands:

apt-get update
apt-get install build-essential libopenblas-dev pkg-config gfortran python3-dev git python3-venv
git clone https://github.com/scipy/scipy.git scipy
python3 -m venv scipy-dev
source scipy-dev/bin/activate
pip install numpy cython meson ninja pythran pybind11 click rich-click doit pydevtool
cd scipy
git submodule update --init
python dev.py build

The build completes without issues.

root@baebf67a5dfc:/# uname -a
Linux baebf67a5dfc 6.4.16-linuxkit #1 SMP PREEMPT Tue Oct 10 20:38:06 UTC 2023 aarch64 aarch64 aarch64 GNU/Linux

[WillTirone]

@dschmitz89 I used the suggested code from the guide that uses mamba, but with conda did:

conda env create -f environment.yml # works with conda too

I actually have two machines - one where the build fails and one where it doesn't (an Ubuntu desktop and laptop). Both have gcc version == 11.4.0.

@andyfaff I agree, probably some weird hard to diagnose issue. As far as debugging, would you then just work on scipy development in the docker container? I haven't done this but should probably try :)

[andyfaff]

My main computers are all macOS. This means whenever I develop for Linux I do it in a docker container. Most of the development work I do on Linux is CI work: getting linux CI entries to work, working on wheel building in CI environments, etc. If one can't build in a fresh container there's something wrong. However, working continuously in a container would be draining.

I didn't try using conda/mamba. I usually only use conda/mamba for installing Python. Other tools are installed separately. e.g. pip for python packages and apt for build-essential, gfortran, etc.

[WillTirone]

Thanks for making this issue, Will.

One more point of comparison I want to check is dist-upgrade. When you got your 22.04.4 system, did you do so by installing it with a 22.04 ISO, or did you do a dist-upgrade? The reason why I ask is that the system where I'm having trouble was originally Ubuntu 20.10.

This SO issue has a few ways to check: https://askubuntu.com/questions/732334/how-to-check-if-an-ubuntu-installation-has-been-upgraded-from-previous-versions

I actually think the system that builds correctly was upgraded from 21.04 to 22.04 and works fine, while the system that doesn't build was a 22.04 ISO

[rgommers]

This seems to have been fixed in pythran 3 years ago: serge-sans-paille/pythran#1796. The traceback doesn't quite make sense, since #include <cstdlib> clearly is present already in that file. So not sure what's happening there, but it's probably some issue in the compiler toolchain you're using.

while the system that doesn't build was a 22.04 ISO

ISOs can often lack necessary upgraded. If you do sudo apt upgrade or sudo apt full-upgrade the problem will likely go away.

[WillTirone]

This seems to have been fixed in pythran 3 years ago: serge-sans-paille/pythran#1796. The traceback doesn't quite make sense, since #include <cstdlib> clearly is present already in that file. So not sure what's happening there, but it's probably some issue in the compiler toolchain you're using.

while the system that doesn't build was a 22.04 ISO

ISOs can often lack necessary upgraded. If you do sudo apt upgrade or sudo apt full-upgrade the problem will likely go away.

That makes sense, thanks for taking a look! Feel free to close the issue since, I agree, seems more like a local issue.

[rgommers]

Will do, thanks @WillTirone