You can then read the JYP's recommended steps for learning python for really working with python
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 asterix LSCE server (if it's in
/usr/bin, it's the default python) and which version it is (example below: version 2.6.6 compiled in May 2015)
# 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-2.6.6-64.el6.x86_64 # You also get some information when you start the interpreter > python Python 2.6.6 (r266:84292, May 22 2015, 08:34:51) [GCC 4.4.7 20120313 (Red Hat 4.4.7-15)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>>
This section will help you choose a distribution in the big Python ecosystem (many distributions, python version 2.7.* or 3.*, …). 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 extra packages.
Only install a distribution yourself if you need it on your local computer, or if you need to install some modules that can't be installed by the contacts listed below. A python distribution can require several Gb of disk space, so do not install it in a backed up home directory!
We suggest that you use Python 2 rather than Python 3. Or you can check the differences between both versions and try to write scripts that will work in both versions!
Contact: the LSCE system administrators (email@example.com)
> module avail [...] castem/12 ferret/6.9.5 hdf5/1.8.9 netcdf/4p python/2.7.5 sun-java/7.0.45 [...] > module load python/2.7.5 > which python /usr/local/install/python-2.7.5/bin/python > python Python 2.7.5 (default, Sep 18 2013, 15:47:43) [GCC 4.4.7 20120313 (Red Hat 4.4.7-3)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>>
Contact: the TGCC hotline (firstname.lastname@example.org)
$ module avail [...] cmake/2.8.9(default) hwloc/1.5 netcdf-utils/184.108.40.206_hdf5 python/2.7.8 tix/8.4.3 cmake/3.2.2 hwloc/1.7.1(default) octave/3.6.3 python/3.3.2 tk/8.5(default) [...] $ module load python/2.7.8 load module python/2.7.8 (Python) $ which python /usr/local/ccc_python/2.7.8_201409/bin/python $ python Python 2.7.8 (default, Aug 27 2014, 17:50:16) [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>>
Contact: Jean-Yves Peterschmitt (JYP) @ LSCE
UV-CDAT (Ultrascale Visualization - Climate Data Analysis Tools) is a python distribution developed specifically for the climate scientists, and is recommended by JYP.
UV-CDAT is available for Mac and Linux.
You can find out which standard packages are installed in the Packages built by CDAT column below. UV-CDAT also provides some specific packages that you will not find in other python distributions: cdms2, cdutil, cdtime, genutil, vcs, cmor, …
Extra packages are listed:
The following versions are maintained by JYP, on the Linux servers where LSCE users have accounts
|CDAT version|| JYP|
|Availability?||Packages built by CDAT||Installation notes|
|1.1.0||08||2.7.3||LSCE, curie||n/a||1.1.0 notes|
|1.5.1||10||2.7.4||LSCE, ciclad||cdat-1.5.1_jyp-10_build_info.txt||1.5.1 notes|
|2.1.0||13||2.7.8||LSCE, ciclad||cdat-2.1.0_jyp-13_build_info.txt||2.1.0 notes|
2.8.0), you can get the list of currently available packages by typing:
cdat-VVV_jyp-NNN_build_info.txtfiles have been generated with
cd /my_build_directory_path; cat build_info.txt | sort > cdat-VVV_JYP-NNN_build_info.txt
The way you initialize UV-CDAT depends on:
Note: if you get an error when importing cdms2 or vcs it means that either you have forgotten to initialize UV-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 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
The steps detailed in this section are for UV-CDAT 2.8.0 and later
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
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
When you initialize UV-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
source activate conda_env_name
|UV-CDAT version||Server|| Environment name|
and activation line
|cdatm14 (||cdatm14 installed packages|
|2.10||LSCE||cdatm15 (||cdatm14 installed packages|
|cdatm will always point to the latest stable version|
|latest stable version||LSCE||cdatm (||
The steps detailed in this section are for UV-CDAT
2.1.0 and earlier
If you use tcsh as your login shell, you can define a
cdatm alias on all the IPSL servers on which UV-CDAT is installed (see details below), and move easily from one version of UV-CDAT to another:
cdatmto initialize the default version of UV-CDAT
cdatm --config CONFIG_NAMEto initialize a specific version
LSCE_13, …) in one of the tables below
> which python /usr/bin/python > cdatm ** CDAT 'uv-1.5.1' initialized! ** If you have problems with this installation, ** it is maintained by: Jean-Yves Peterschmitt - LSCE > which python /home/share/unix_files/cdat/versions/cdat_install_uv-1.5.1_x86_64_gcc4_10/bin/python
You need to add the following line to the
.cshrc file in your home directory, in order to define the
cdatm alias. You can also define the simple
wp alias, in order to always be able to determine quickly which python is initialized in the current terminal.
You first need to know where the
python program provided by UV-CDAT is installed, something like
Then, all you need to do in order to initialize UV-CDAT is to source the
setup_runtime file appropriate for your shell:
The table below lists, for each server and version, the path where you can find the setup_runtime files
On curie, you need to use setup_cdat.sh or setup_cdat.csh to initialize CDAT,
and also to load modules providing access to old librairies
Example: if you want to use UV-CDAT 2.1.0 at LSCE in a bash shell, you need to do the following (you only need the source line. The other lines are optional, just for checking that the initialization was OK)
bash-4.1$ source /home/share/unix_files/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/bin/setup_runtime.sh bash-4.1$ which python /home/share/unix_files/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/bin/python bash-4.1$ python -c 'import cdms2, vcs' bash-4.1$
You probably don't want to have to determine what you should type each time you want to use UV-CDAT in a window, so you should define a simple shortcut alias that you can type each time you need to initialize UV-CDAT. If, for example, you want to use UV-CDAT 2.1.0 at LSCE:
alias cdat13 'source /home/share/unix_files/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/bin/setup_runtime.csh'
alias wp 'which python'
~/.bash_profile(whichever works for you, or read
alias cdat13='source /home/share/unix_files/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/bin/setup_runtime.sh'
alias wp='which python'
If you are going to use a UV-CDAT python script on a cluster or supercomputer, using some kind of batch system using a bash or ksh script, use the following lines before you run the python script
source /home/share/unix_files/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/bin/setup_runtime.sh # Check which python we will be using mypython=`which python` echo echo -e "This script will use the following python: $mypython\n\n"
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 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
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
|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)
|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
or to kill it (with
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 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
python: start the interpreter
python script.py: execute script.py and exit
python -i script: execute script.py and stay in the interpreter (
man python if you want to see what other command line options are available
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
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:
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