Linux Path query

Question

[Bioinformatician_in_trouble]

Hello,

I am running gromacs commands on Putty and when I use:

python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a apolar.xvg

I get an error that there is "No module named builtins" Now, when I try to install it using

pip install future

I get the following error:

DEPRECATION: Python 2.6 is no longer supported by the Python core team, please upgrade your Python. A future version of pip will drop support for Python 2.6.

Pip is accessing this path: /usr/lib/python2.6/site-packages/pip/. So, there indeed is a python 2.6 installed in the path usr/lib but in my bashrc, I have the correct path to updated python3.7 as shown in the image below:

https://ibb.co/4JM1ZjT

why isn't that being read? Can someone please help? Linux is very new to me. Thank you!

Answer 1

[Mensur Dlakic]

Try running your original command with python3 instead if python. If that fails again with a similar message, try to update like this:

python3 -m pip install future

It will install the missing packages in your python3 directory. It may also work if you use pip3 instead of pip in your original update command.

[Bioinformatician_in_trouble]

Dear @Mensur Dlakic all three approaches are generating the same error: error while loading shared libraries: libpython3.7m.so.1.0: cannot open shared object file: No such file or directory

[cpad0112]

Check the python libraries path by locate libpython3.7m. In general, they would be in /usr/local/lib. If so, try this (in bash shell): export LD_LIBRARY_PATH=/lib:/usr/lib:/usr/local/lib:$PATH:. If this works, then run sudo ldconfig /usr/local/lib. If the libraries are not located in standard location, change /usr/local/lib with appropriate location. If you don't get a path, try installing libpython3.7 (sudo apt-get install libpython3.7 in ubuntu/debian/mint)