ImportError: libpython3.7m.so.1.0: cannot open shared object file: No such file or directory

[alejandroarmas]

I am having trouble running a python script on a computing cluster and the problem is reproduced when I run my job on slurm:

I get the error

2020-07-17 19:30:57.289439: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcudart.so.10.1: cannot open shared object file: No such file or directory
2020-07-17 19:30:57.289506: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
Traceback (most recent call last):
  File "test.py", line 4, in <module>
    from acme.agents.tf import dqn
  File "/home/armas/temp/dist_rl/lib/python3.7/site-packages/acme/agents/tf/dqn/__init__.py", line 18, in <module>
    from acme.agents.tf.dqn.agent import DQN
  File "/home/armas/temp/dist_rl/lib/python3.7/site-packages/acme/agents/tf/dqn/agent.py", line 20, in <module>
    from acme import datasets
  File "/home/armas/temp/dist_rl/lib/python3.7/site-packages/acme/datasets/__init__.py", line 17, in <module>
    from acme.datasets.reverb import make_reverb_dataset
  File "/home/armas/temp/dist_rl/lib/python3.7/site-packages/acme/datasets/reverb.py", line 22, in <module>
    from acme.adders import reverb as adders
  File "/home/armas/temp/dist_rl/lib/python3.7/site-packages/acme/adders/reverb/__init__.py", line 21, in <module>
    from acme.adders.reverb.base import DEFAULT_PRIORITY_TABLE
  File "/home/armas/temp/dist_rl/lib/python3.7/site-packages/acme/adders/reverb/base.py", line 26, in <module>
    import reverb
  File "/home/armas/temp/dist_rl/lib/python3.7/site-packages/reverb/__init__.py", line 27, in <module>
    from reverb import item_selectors as selectors
  File "/home/armas/temp/dist_rl/lib/python3.7/site-packages/reverb/item_selectors.py", line 19, in <module>
    from reverb import pybind
  File "/home/armas/temp/dist_rl/lib/python3.7/site-packages/reverb/pybind.py", line 1, in <module>
    import tensorflow as _tf; from .libpybind import *; del _tf
ImportError: libpython3.7m.so.1.0: cannot open shared object file: No such file or directory

On my local machine, I was struggling with same issue when I was running a virtual environment, I solved this problem simply with sudo apt-get install libpython3.7.

Here's some other things that may be helpful to know.

$which libpython
/usr/bin/which: no libpython in (/home/armas/temp/dist_rl/bin:/om2/user/armas/anaconda/bin:/om2/user/armas/anaconda/condabin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)

$echo $PATH
/home/armas/temp/dist_rl/bin:/om2/user/armas/anaconda/bin:/om2/user/armas/anaconda/condabin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin

If there's anything I missed please let me know and I'll be sure to add, thank you again!

[Juze1500]

Hello! Try export LD_LIBRARY_PATH=/path/to/libpython/directory before executing your python script. If you are using Conda, the path should be /path/to/conda/envs/your_env/lib.

[alejandroarmas]

@Juze1500 Thank you! I had done that many times before and it didn't work out. Turns out I had installed an outdated python version for my anaconda environment. After getting that figured out I got the same problem but changing my LD_LIBRARY_PATH variable fixed it. Appreciate the help man!

[jasonmeverett]

Hello! Try export LD_LIBRARY_PATH=/path/to/libpython/directory before executing your python script. If you are using Conda, the path should be /path/to/conda/envs/your_env/lib.

This worked for me. Thanks!

[wookayin]

Recommend putting the export LD_LIBRARY_PATH=.. into $CONDA_PREFIX/etc/conda/activate.d/env.sh, so that this environment variable set whenever the conda environment is activated.

You can do this with a one line command:

echo "export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:\$LD_LIBRARY_PATH" > $CONDA_PREFIX/etc/conda/activate.d/env.sh

[gattia]

@wookayin do you know how this same principle could be used to remove $CONDA_PREFIX/lib from LD_LIBRARY_PATH if the environment is deactivated? Or if you are using the base conda environment?

Thanks!

[gattia]

For anyone looking how to deactivate what I did is posted here: opensim-org/opensim-core#2968 (comment)

I still am not sure if there is anything that can be done to add/remove from path when the base conda is used.

[saltfishh]

Hello! Try export LD_LIBRARY_PATH=/path/to/libpython/directory before executing your python script. If you are using Conda, the path should be /path/to/conda/envs/your_env/lib.

thanks, it helps me!