Python 3.x: can't install modules on the core cluster


I begin to test the core cluster with Python 3.x and realized that only ‘pip’ and ‘setuptools’ are pre-installed on the core cluster and I can’t install new modules like numpy.

I just built a virtual env, upgraded pip and ran “pip install numpy”. I got the error as follows:

"SystemError: Can not compile 'Python.h'. Perhaps you need to install python-dev|python-devel."

Would you think you would have the time to upgrade Python 3 soon? (just for information: maybe the simplest solution is to install the latest version of Anaconda. I have tested it, it’s easy to install and to maintain).


Juhui WANG


By default, there aren’t so many tools in the $PATH on the cluster.
The software are only available through conda and module. Actually, conda is behind module.

So please test the conda env python-3.7:

$ module load python
$ python
Python 3.7.1 | packaged by conda-forge | (default, Nov 13 2018, 18:33:04)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy

If you need extra library, you or we can add them.

By the way, about your primary issue, we will investigate the problem with virtualenv. We definitely need to allow user to create some.

Hi Gildas,

Everything is fine now! Thank you and bravo!