Setup environment on ITO at Kyushu University Supercomputer

Table of Content

The following is a memo of initial setup for subsystem A on ITO at Kyushu University.

Login environment

If you are using in Japanese, in [cci].bashrc[/cci], the following setting should be implemented to avoid garbled characters in the terminal.
[cc]
export LANG=en_US.UTF-8
[/cc]

Install Anaconda

To avoid conflict with the pre-installed Python system, pyenv is installed and used to create a virtual environment.

Install pyenv

Pyenv can be easily installed as follows:
[cc]
$ cd ~
$ git clone git://github.com/yyuu/pyenv.git .pyenv
[/cc]

Edit ~/.bashrc

Add the following in .bashrc:
[cc]
export PYENV_ROOT="${HOME}/.pyenv"
if [ -d "${PYENV_ROOT}" ]; then
export PATH=${PYENV_ROOT}/bin:$PATH
eval "$(pyenv init -)"
fi
[/cc]
You can take a look at available software and its versions:
[cc]
$ pyenv install -l
[/cc]

Install Anaconda

The newest version of Anaconda3 should be installed:
[cc]
$ pyenv install anaconda3-5.0.1
[/cc]

check available versions

You can check the available versions and find that "system" is the current environment because * is appended.
[cc]
$ pyenv versions
* system (set by /home/usr1/account/.pyenv/version)
anaconda3-5.0.1
[/cc]
You can switch to anaconda3-5.0.1 as follows:
[cc]
$ pyenv global anaconda3-5.0.1
[/cc]
Now you can confirm anaconda3-5.0.1 is the current environment as * is appended:
[cc]
$ pyenv versions
system
* anaconda3-5.0.1 (set by /home/usr1/m70161a/.pyenv/version)
[/cc]

Invoke python

Now you can invoke python 3.6.3 by Anaconda as follows:
[cc]
$ python
Python 3.6.3 |Anaconda, Inc.| (default, Oct 13 2017, 12:02:49)
[GCC 7.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>
[/cc]
You can exit by typing [cci]quit()[/cci].

Jupyter Notebook

Jupyter Notebook can be used on ITO. For this, you need to install Exceed onDemand (X client software) provided by Kyushu University. Installation guide is here (only in Japanese but you may translate it using Google translate).

Notice

When you build some software, including netcdf and FVCOM, the installed packages in [cci]./pyenv[/cci] may cause conflicts. To avoid this problem, rename [cci]./pyenv[/cci] like [cci]./pyenv2[/cci] to be hidden. After completion of building, restore to [cci]./pyenv[/cci].

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.