Working with Python

This page will tell you how to select a python distribution and start (and exit!) the python interpreterYou can then read the JYP's recommended steps for learning python for really working with python

Note: the former and outdated version (before the massive usage of conda) is still available for reference

Where to start

In order to start working with Python, you need to have a Python distribution installed on your local computer or on the remote Linux server(s) you work on. A distribution provides a Python interpreter, and Python extensions (aka Python modules or packages). You may have several distributions installed on your computer and you need to know how to initialize them, and which one you are using at a given time (type which python on Linux to determine where the python executable is located)

If you are using a Linux computer or a Mac, you should already have a default python installed. The following example shows where the python interpreter is installed on the obelix LSCE servers (if it's in /usr/bin, it's the default python) and which version it is (example below: version 2.7.5 compiled in April 2019)

# Which is the current python (e.g. where is it located)?
> which python
/usr/bin/python
# Where is it coming from ('rpm' works on a RedHat-like Linux machine)?
> rpm -qf /usr/bin/python
python-2.7.5-77.el7_6.x86_64
# You also get some information when you start the interpreter
> python
Python 2.7.5 (default, Apr 9 2019, 14:30:50)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-36)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>

Python distributions available for LSCE users

This section will help you choose a distribution in the big Python ecosystem (many distributions, python version 2.7.* or 3.*, …) on some of the servers used by LSCE users. You should use a distribution that is already available near your data (e.g. do the computation on a server near your data, do not move/duplicate the data!) and try to identify who is maintaining it, if you need help or additional packages.

Only install a distribution yourself if you need it on your local computer (desktop or laptop), or if you need to install some modules that can't be installed by the contacts listed below. A python distribution will require several Gb of disk space, so do not install it in a backed up home directory!

You can use either Python 2 or Python 3. Most packages are now available in both versions, but you should make sure that the most important package/s you need is/are available in the selected Python version. You can check the differences between both versions and try to write scripts that will work in both versions!

LSCE distribution

Contact: the LSCE system administrators (help-lsce@lsce.ipsl.fr)

Where: obelix interactive servers and cluster at LSCE

Initialization type: module based + conda

What's installed: type conda list after initializing the LSCE distribution

> module avail
[...]
4ARTIC/3.6 grib_api/1.14 netcdf/3 python/2.7.5
batch_env grib_api/1.14.0 netcdf/4 python/3.6
[...]
glost/0.3.1 ncview/2.1.7 python/2.7
[...]
> module load python/2.7
> which python
/usr/local/install/python-2.7/bin/python
> python
Python 2.7.15 |Anaconda, Inc.| (default, Oct 10 2018, 21:32:13)
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>

TGCC distribution

Contact: the TGCC hotline (hotline.tgcc@cea.fr)

Where: CEA TGCC

Initialization type: module based

What's installed: it depends…

# Get the default version of the Python based modules
$ module avail -t -d | egrep '(python|cdat)'
flavor/cdat/standard(default)
flavor/nest/python2(default)
flavor/pytorch/python2(default)
flavor/tensorflow/gpu_python2(default)
intelpython2/2019.0(default)
intelpython3/2019.0(default)
python/2.7.14(default)
python3/3.6.4(default)
cdat/8.0(default)
$ module load python
[...]
load module python/2.7.14 (Python)
$ which python
/ccc/products/python-2.7.14/intel--17.0.4.196__openmpi--2.0.2/default/bin/python
$ python
Python 2.7.14 (default, Jan 11 2018, 16:43:59)
[GCC 4.8.5] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>

CDAT

CDAT (Community Data Analysis Tools) is a powerful and complete front-end to a rich set of visual-data exploration and analysis capabilities well suited for climate data analysis problems, and is recommended by JYP.

CDAT is available for Mac, Linux and Windows 10 (Windows 10 + Windows Subsystem for Linux, and Ubuntu).

Contact: Jean-Yves Peterschmitt (JYP) @ LSCE

Where: obelix interactive servers and cluster at LSCE, ciclad interactive servers and cluster at IPSL, irene @ TGCC

Initialization type: conda based or module based

What's installed: type conda list after initializing a specific CDAT distribution

CDAT versions maintained by JYP

The following versions are maintained by JYP, on the Linux servers where LSCE users have accounts

CDAT version	JYP version	python version	Availability?	Available packages	Installation notes
8.1	18	2.7.15 3.6.7	LSCE, ciclad	Default CDAT packages Extra packages	8.1 notes

CDAT at TGCC

CDAT 8.0 is installed at TGCC and can be initialized with:

Python 2: module load cdat

Python 3: module load flavor/cdat/python3 cdat

The basics of CDAT initialization

The way you initialize CDAT depends on:

which server you want to use it on

which shell you are using in your terminals: tcsh or other shells

Read Which shell are you using? if you are not sure

Warning: the shell in a (batch) script may be different from your interactive shell!

which version of CDAT you want to use…

Note: if you get an error when importing cdms2 or vcs it means that either you have forgotten to initialize CDAT, or that something went wrong during the initialization. In both cases, you are either still using the default python installed on your system, or another (non-CDAT) python distribution!

$ python -c 'import cdms2, vcs'
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: No module named cdms2
# Am I using the correct python distribution?
$ which python
/usr/bin/python

conda-based versions of CDAT

The steps detailed in this section are for UV-CDAT 2.8.0 and later

Note: if you need to maintain a local version on your machine, you can read Installing and maintaining CDAT with conda and the versions specific notes.

Configuring .bashrc

You should add the following line at the end of your ~/.bashrc configuration file (create the ~/.bashrc file if it does not exist yet). This will basically make sure that your shell can find the conda executable it needs for initializing CDAT, and define a wp alias that you can use to find where the python executable is located

Server	Line to add to .bashrc
LSCE	source ~jypeter/.conda_jyp.sh Note:conda_jyp content
ciclad	source ~jypmce/.conda_jyp.sh

Note: when you add the specified line to your bashrc file, you will then always get the python supplied by conda, instead of the system's python, when you use bash. If you don't like this permanent behavior, just type source ~jyp_login_on_this_server/.conda_jyp.sh in the bash shell where you want to use conda+CDAT, rather than adding it to the .bashrc file…

Initializing CDAT

When you initialize CDAT, it will be available only in the current window/shell. In the other windows, you still get whatever your default python is. This should minimize potential side-effects

If your shell is not bash, start a bash shell by typing bash

You can later go back to your previous shell by typing exit or CTRL-D

Activate the conda environment that uses the version of UV-CDAT you want to use

source activate conda_env_name

Use the table below to determine which environments are available on which server

Use CDAT !

UV-CDAT version	Server	Environment name and activation line	Packages (conda list)
2.8.0	LSCE ciclad	cdatm14 (source activate cdatm14)	cdatm14 installed packages
2.10	LSCE	cdatm15 (source activate cdatm15)	cdatm14 installed packages
cdatm will always point to the latest stable version
latest stable version	LSCE	cdatm (source activate cdatm)	conda list

Canopy

Enthought Canopy is a Scientific and Analytic Python Deployment with Integrated Analysis Environment provided by Enthought. It used to be called EPD (Enthought Python Distribution)

Canopy is available for Windows, Mac and Linux. You can download the free Canopy Express that will already provide many extensions. If you are entitled to use Canopy Academic, login from inside Canopy Express and download the extra modules you need

Anaconda

Anaconda is a distribution similar to canopy provided by Continuum Analytics.

Anaconda is available for Windows, Mac and Linux

Note: Anaconda provides and uses conda for its installation. Since UV-CDAT is now also installed and maintained with conda, you can read the Installing and maintaining UV-CDAT with conda page for more information, even if you are not going to use UV-CDAT

Launching Python

Once you have initialized the python distribution you want to use, follow the instructions below to start the interpreter from a shell (on a Windows computer, you will have to start python from the Start menu or by clicking a shortcut on your desktop).

Remember that on Linux/Mac you can check which python you are using by typing which python!

Useful keyboard shortcuts

Key	Effect
CTRL-D	Exit the interpreter
↑ and ↓	Go to previous/next line(s)
CTRL-A	Go to the beginning of the line
CTRL-E	Go to the end of the line
CTRL-K	Erase from the cursor to the end of the line
CTRL-U	Erase from the beginning of the line to the cursor
TAB x 2	Do some TAB-completion (context dependent) e.g. a = np.cumTABTAB
CTRL-C	Interrupt a running script
CTRL-Z	Suspend the interpreter and go back to the shell Do not forget to go back to the interpreter with fg or to kill it (with jobs and kill %NN)

Stand-alone script

A python script is just like any other shell script. You don't have to explicitly call the python interpreter, if the interpreter is specified in a #! shebang comment on the first line of the script with, and the script has its execution bit set (chmod +x my_script.py).

jypeter@asterix1 - ...jypeter - 54 >cat basic_script.py
#!/usr/bin/env python
import sys
script_name = sys.argv[0]
print('Hello world, I am the ' + script_name + ' script')
# The end
jypeter@asterix1 - ...jypeter - 55 >chmod +x basic_script.py
ypeter@asterix1 - ...jypeter - 56 ># Type here what is required to initialize the distribution you want
jypeter@asterix1 - ...jypeter - 57 >./basic_script.py
Hello world, I am the ./basic_script.py script

Standard interpreter

python: start the interpreter

python script.py: execute script.py and exit

python -i script: execute script.py and stay in the interpreter (-i = Interactive)

Type man python if you want to see what other command line options are available

ipython interpreter

The ipython interpreter provides more options and commands than the standard python interpreter, but takes more time to load. If you are going to develop by starting and exiting the interpreter many times, it's faster to use the standard interpreter

Starting ipython: ipython

Using IPython for interactive work

Ipython-quick-ref-sheets

ipython notebook

The ipython notebook is a way to interact with python (and other supported interpreted languages) inside a web browser. You can mix cells with python commands, cells with the output of the python commands (possibly graphics generated by the commands), and text (using some wiki-like rich text format). This interactive web page, aka notebook, can be saved in a my_notebook.ipynb file and re-used later (e.g. the notebook provided in the introduction to Python, part 1).

Starting the notebook server: ipython notebook

Warning! When you start the notebook server, you will start a python process and a web browser, and a new python process will be started each time you open a new notebook.Please make sure that you shutdown cleanly each notebook and the server when you are finished, in order not to clutter the local computer or remote server with lots of python processes (especially a server shared by many users!). You may want to use the 'top' command in order to monitor what is happening

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