Issues with IDE integration

[lsuchoy]

Hi @lmoresi @julesghub

I’ve installed a fresh copy of UW3 on one of our machines, but I’m having trouble getting it to work with any Python IDE, including Jupyter Notebook.

Here’s what I did:

1. I used Mamba to set up the environment.
2. I ran the tests successfully.
3. However, when I installed a new IDE (e.g., mamba install jupyter), some dependencies were overwritten.
4. When I reran the tests, I encountered the following error:

/opt/anaconda3/envs/uw3p/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_1050_VEstokesCart.py:3: in <module>
    import underworld3 as uw
src/underworld3/__init__.py:64: in <module>
    from mpi4py import MPI  # for initialising MPI
E   ImportError: libmpi.so.40: cannot open shared object file: No such file or directory

Have you encountered this issue before? How did you resolve it?
Should I be using a specific IDE or a particular version of Jupyter Notebook to avoid dependency conflicts?

Thanks,
Lior

[julesghub]

Hi @lsuchoy,
That's unexpected. I haven't seen this issue before. Mpi4py has lost the underlying shared libs after the new IDE install.
Can you tell me the steps you ran for 1,2 and I'll investigate.
Also which branch of the code you were using and on what platform, arm or intel?
Thanks.

[lsuchoy]

Hi @julesghub
Below are the exact steps I followed during the installation process (I’ve just redone everything to confirm):

(base) % git clone -b development --single-branch https://github.com/underworldcode/underworld3 /path/to/underworld3  
(base) % cd /path/to/underworld3  
(base) % mamba env create -n uw3new -f environment.yml  
(base) % mamba activate uw3new  
(uw3new) % pip install . --no-build-isolation  
(uw3new) % python setup.py build_ext --inplace  
(uw3new) % source test.sh       **--> tests pass ok**  
(uw3new) % mamba install jupyter  
(uw3new) % source test.sh       **--> this is where things fail**

I’m working on the development branch, using an Intel Xeon E5-2630 platform with Ubuntu 16.04.7. It’s not a new machine, but it’s a fresh install.

Lior

[julesghub]

Thanks for the notes @lsuchoy . I followed them but I wasn't able to recreate the issue using micromamba.
So I'm a bit confused what's happened with your build.

Note our environment.yml does have jupyter-lab, so you should be able to use that immediately after the mamba activate uw3new. Does that satisfy your IDE need?

Below I combined the uw3 pip installation commands into a single pip install ... (one less step).

(base) % git clone -b development --single-branch https://github.com/underworldcode/underworld3 /path/to/underworld3  
(base) % cd /path/to/underworld3  
(base) % mamba env create -n uw3new -f environment.yml  
(base) % mamba activate uw3new  
(uw3new) % pip install -e . --no-build-isolation  
(uw3new) % source test.sh       **--> tests pass ok**  
(uw3new) % mamba install jupyter  
(uw3new) % source test.sh       **--> this is where things fail**

Let me know if this helps.

[lsuchoy]

Hi @julesghub

I wasn’t aware that JupyterLab was already included in the environment (I didn’t realise you could have Lab without Notebook). Using JupyterLab without installing anything additional (i.e., skipping (uw3new) % mamba install jupyter) seems to work well. While this isn’t exactly a solution to the problem, it’s a good enough workaround for my needs.

Thanks so much for your help!
Lior

[lsuchoy]

Hi @julesghub,

Just one more note. After testing some features with JupyterLab, it seems that the modules trame and ipywidgets need to be added to the environment. I installed them manually using the following commands:

mamba install trame -c conda-forge  
mamba install ipywidgets  

Which seems to work well.

Lior

[julesghub]

Thanks for the tips. I'll add them into the environment.