Issue installing LibRoadRunner

[WilliamIX]

Hi Libroadrunner team - I'm trying to get the package to work (via Tellurium) on python 3.10 or 3.11 using linux via AWS. I'm getting an issue:

File "/usr/conda/envs/EPICpy310/lib/python3.10/site-packages/tellurium/__init__.py", line 14, in <module>
    from .tellurium import (
  File "/usr/conda/envs/EPICpy310/lib/python3.10/site-packages/tellurium/tellurium.py", line 150, in <module>
    import roadrunner
  File "/usr/conda/envs/EPICpy310/lib/python3.10/site-packages/roadrunner/__init__.py", line 10, in <module>
    from .roadrunner import *
  File "/usr/conda/envs/EPICpy310/lib/python3.10/site-packages/roadrunner/roadrunner.py", line 15, in <module>
    from . import _roadrunner
ImportError: libpython3.10.so.1.0: cannot open shared object file: No such file or directory

Googling this issue suggests that resetting LD_LIBRARY_PATH should fix the problem, however this does not seem to help in my case.

Have you ever encountered this issue before? Any advice would be appreciated.

[luciansmith]

Hmm, that is indeed odd.

My first question is just: does 'libpython3.10.so.1.0' actually exist somewhere? And was that the directory you used when you set LD_LIBRARY_PATH?

[WilliamIX]

Thanks for the fast reply @luciansmith!

I was able to find libpython3.10.so.1.0 and added its folder to LD_LIBRARY_PATH. It didn't solve the issue.

As a note, LD_LIBRARY_PATH this variable was unassigned when I echo'd it. I'm not really sure what this is used for.

Guessing from the fact that I have no other issues using any other python libraries, could this be something related to how Libroadrunner interfaces with C / Assembly / non-python languages?

[luciansmith]

It's used for anything in Python that has a C library that interfaces with Python under the hood. So, not that many packages, since most of them are written in pure Python, but for most things with SWIG wrappers (like roadrunner and numpy) it'll be important.

[carissableker]

Since there's no solution posted, and I came across the same issue:

I am using conda environments, and judging from the /usr/conda/envs/EPICpy310/lib in the errors of @WilliamIX, they are also, so it is probably related to the path (mis?)management of conda environment activation.

I created the environment:

mamba create -n tellurium python==3.12 conda-forge:pandas anaconda::ipykernel

And then used pip to install tellurium:

conda activate tellurium
pip install tellurium

To test (and get the sale error):

python -c "import tellurium as te"

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/.../envs/tellurium/lib/python3.12/site-packages/tellurium/__init__.py", line 14, in <module>
    from .tellurium import (
  File "/.../envs/tellurium/lib/python3.12/site-packages/tellurium/tellurium.py", line 150, in <module>
    import roadrunner
  File "/...envs/tellurium/lib/python3.12/site-packages/roadrunner/__init__.py", line 10, in <module>
    from .roadrunner import *
  File "/.../envs/tellurium/lib/python3.12/site-packages/roadrunner/roadrunner.py", line 15, in <module>
    from . import _roadrunner
ImportError: libpython3.12.so.1.0: cannot open shared object file: No such file or directory

However, the .so file is installed to the conda environment:

ls $(python3-config --prefix)/lib/libpython*

/.../envs/tellurium/lib/libpython3.12.so  /.../envs/tellurium/lib/libpython3.12.so.1.0  /.../envs/tellurium/lib/libpython3.so

I don't know enough about conda and libpython as to why this lib path is not available to roadrunner, but manually updating the LD_LIBRARY_PATH as follws (thanks to the tip here), works for me:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"$(python3-config --prefix)/lib"

To update the path every time the environment is activated, there are instructions here:
docs.conda.io#setting-environment-variables.
(basically conda env config vars set LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"$(python3-config --prefix)/lib")

[luciansmith]

Thank you for this! It sounds like we might need to figure out how to get a conda install built; just using pip all the time seems to not be 100% reliable.

[carissableker]

I found a few similar issues:

• libpython3.8.so.1.0: cannot open shared object file: No such file or directory lhotse-speech/lhotse#800
• Using conda from a system that just loads the libpython shared library conda/conda#9500
• https://stackoverflow.com/questions/46826497/conda-set-ld-library-path-for-env-only#comment97341958_46833531
• set LD_LIBRARY_PATH when activate conda/conda#12800

So it appears to be an issue of [conda] + [pip] + [shared libraries] not working together and pip alone/or in a different environment manager would find the correct library paths.

Interestingly, this was not an issue for me before, and I just tested again: libroadrunner==2.2.2 installed with pip into a conda environment (Python 3.10) was able to be imported without any errors.

On the otherside, a conda build would be nice, or this issue can just stay to be a source of info for those of us mixing conda and pip (in a somewhat unsupported way).

For info, conda-build uses patchelf to figure out the paths:
https://docs.conda.io/projects/conda-build/en/stable/resources/use-shared-libraries.html#

(someone seems to have figured out a conda build, but stopped updating 8 years ago? https://anaconda.org/sys-bio)