Differences

This shows you the differences between two versions of the page.

--- other:python:starting [2016/05/19 15:52]
jypeter Started improving the CDAT section
+++ other:python:starting [2022/09/28 13:46]
jypeter [CDAT]
@@ Line 1: / Line 1: @@
 ====== Working with Python ======
-In order to begin using Python, you need to have a //Python distribution// installed. A //distribution// provides a Python interpreter, and Python extensions (aka Python //modules//). 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)
+<note tip>This page will tell you how to select a //python distribution// and start (and exit!) the python interpreter
-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 asterix1 server (if it's in ''/usr/bin'', it's the default python) and which version it is (version //2.6.6// compiled in May 2015)
+After reading this page, you can read the [[jyp_steps|JYP's recommended steps for learning python]] for really working with python
+</note>
-<code> > which python
+Note: the former and **outdated** version (before the massive usage of //conda//) is still [[other:python:starting_170810|available for reference]]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)
+<code># 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
+python-2.7.5-77.el7_6.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)
+Python 2.7.5 (default, Apr  9 2019, 14:30:50)
-[GCC 4.4.7 20120313 (Red Hat 4.4.7-15)] on linux2
+[GCC 4.8.5 20150623 (Red Hat 4.8.5-36)] on linux2
 Type "help", "copyright", "credits" or "license" for more information.
 >>>
 </code>
-===== Some python distributions =====
+===== Ultra quick-start on the interactive LSCE servers =====
-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!).
+==== Initialization ====
-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 be quite big, so do not install it in a backed up home directory!
+  - Start a terminal on an //obelix// server ([[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:newppl:starting#which_linux_servers_should_you_use|more info]])
+  - Type ''python'' to access the //default Python 2// interpreter available on the servers...
+  - ...or **follow the steps below to use the more complete //CDAT// distribution maintained by JYP**.\\ Remember that **you can exit the interpreter by typing CTRL-D** (or ''quit()'' or ''exit()'')
+    - Determine if you are using a [[other:newppl:starting#which_shell_are_you_using|bash or tcsh shell]] (all the new LSCE accounts use the //bash// shell), then type the following command to //initialize conda// (//conda// helps you manage your python environment)
+      * In a //bash// shell: ''source ~jypeter/.conda3_jyp.sh''
+      * In a //tcsh// shell: ''source ~jypeter/.conda3_jyp.csh''
+    - Choose which //flavor// of Python you want by typing the activation command:
+      * Python 2.7.x: ''conda activate cdatm_py2''
+      * Python 3.x: ''conda activate cdatm_py3''
+    - Type ''python'' to start the interpreter
+    - Note: if you will have to use python regularly, you should add the ''source'' line above to your ''.cshrc'' /''.login'' file (//tcsh// users) or ''.bashrc''/''.profile'' (//bash// users)
+      * **Do not** add the ''conda activate cdatm_pyN'' line to the shell config files, because this will create potential side-effects!\\ Only type the activation command in the terminal(s) where you will need to use this specific version of Python
-We suggest that you **use Python 2 rather than Python 3**. Or you can check the [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:jyp_steps#python_27_vs_python_3|differences between both versions]] and try to write scripts that will work in both versions! 8-)
+=== Example ===
-==== LSCE distribution ====
+<code> >ssh obelix
+Last login: Mon Jun  3 08:49:53 2019 from somewhere
-Contact: the LSCE system administrators
+bash-4.2$ which python
+/usr/bin/python
-<code>
+bash-4.2$ source ~jypeter/.conda3_jyp.sh
- > module avail
+bash-4.2$ which python
-[...]
+/usr/bin/python
-castem/12        ferret/6.9.5     hdf5/1.8.9       netcdf/4p        python/2.7.5     sun-java/7.0.45
+bash-4.2$ conda activate cdatm_py2
-[...]
+(cdatm_py2) bash-4.2$ which python
+/home/share/unix_files/cdat/miniconda3/envs/cdatm_py2/bin/python
- > module load python/2.7.5
+(cdatm_py2) bash-4.2$ python
+Python 2.7.15 | packaged by conda-forge | (default, Feb 28 2019, 04:00:11)
- > which python
+[GCC 7.3.0] on linux2
-/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.
->>>
+>>> print('hello!')
+hello!
+>>>   # Type CTRL-D to exit the python interpreter
 </code>
-==== TGCC distribution ====
+==== Useful keyboard shortcuts ====
-Contact: the TGCC hotline
+^  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.cum**TABTAB**''  |
+|  **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'')  |
-<code>
+==== Executing a python script ====
-$ module avail
-[...]
-cmake/2.8.9(default)      hwloc/1.5                 netcdf-utils/4.3.3.1_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
+Note: Python is an [[https://en.wikipedia.org/wiki/Interpreted_language|interpreted language]] and we speak of //Python scripts// rather than //Python programs//.
-load module python/2.7.8 (Python)
-$ which python
+  * ''python'': start the interpreter and start working interactively
-/usr/local/ccc_python/2.7.8_201409/bin/python
+  * ''python script.py'': execute //script.py// and **exit**
+  * ''python -i script'': execute //script.py// and **stay in the interpreter** (''-i'' = //**I**nteractive//)
-$ python
+Type ''man python'' if you want to see what other command line options are available
-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.
->>>
-</code>
-==== UV-CDAT ====
+==== Stand-alone script ====
-Contact: Jean-Yves @ LSCE
+You don't have to explicitly call the python interpreter, if the interpreter is specified in a ''#!'' [[https://en.wikipedia.org/wiki/Shebang_%28Unix%29|shebang comment]] on **the first line of the script** with, and the script has its //execution bit// set (''chmod +x my_script.py'').
-=== What is UV-CDAT? ===
+If you have a ''basic_script.py'' file with the following content in a directory...
+<code>
+#!/usr/bin/env python
-[[http://uv-cdat.llnl.gov/|UV-CDAT]] (//Ultrascale Visualization - Climate Data Analysis Tools//) is a python distribution developed specifically for the climate scientists.
+import sys
-You can find out which standard packages are installed by clicking on the ''cdat-VVV_JYP-NNN_build_info.txt'' files below and by visiting the [[other:uvcdat:extra|Extra packages installed in UV-CDAT by JYP]] page.
+script_name = sys.argv[0]
-UV-CDAT also provides some specific packages that you will not find in other python distributions: **cdms2**, **cdutil**, **cdtime**, **genutil**, **vcs**, **cmor2**, ...
+print('Hello world, I am the ' + script_name + ' script')
-=== UV-CDAT versions maintained by JYP ===
+# The end</code>
-The following versions are maintained by JYP, on the servers where LSCE users have accounts
+...and if you are in the same directory and have initialized the Python distribution you want, you can then run the script the following way:
-^  CDAT version  ^  JYP\\ version  ^  python\\ version  ^  Availability?  ^  Packages built by CDAT  ^  Installation notes  ^
+<code> > chmod +x basic_script.py
-|  **1.1.0**  |  08  |  2.7.3  |  LSCE, curie  |  n/a  |  [[other:uvcdat:installed#section110|1.1.0 notes]]  |
-|  **1.5.1**  |  10  |  2.7.4  |  LSCE, ciclad  |  {{:other:python:cdat-1.5.1_jyp-10_build_info.txt}}  |  [[other:uvcdat:installed#section151|1.5.1 notes]]  |
-|  **2.1.0**  |  13  |  2.7.8  |  LSCE, ciclad  |  {{:other:python:cdat-2.1.0_jyp-13_build_info.txt}}  |  [[other:uvcdat:installed#section210|2.1.0 notes]]  |
-|  **2.4.0**  |  14  |    |    |  //Not installed yet//  |    |
-Notes:
+ > ls -l basic_script.py
-  * The ''cdat-VVV_jyp-NNN_build_info.txt'' files have been generated with\\ ''cd /my_build_directory_path; cat build_info.txt | sort > cdat-VVV_JYP-NNN_build_info.txt''
+-rwxr-xr-x [...] basic_script.py
-=== Initializing UV-CDAT ===
+ > ./basic_script.py
+Hello world, I am the ./basic_script.py script
+</code>
-The way you initialize UV-CDAT depends on:
+==== What next? ====
-  * which **server** you want to use it
-  * which **shell** you are using: //tcsh// or other shells
-    * Note: the shell in a batch script may be different from your interactive shell!
-  * which **version** of UV-CDAT you want to use...
-    * Note: You should use the most recent version of UV-CDAT available on a given server, unless you have a good reason to use an older version (e.g. if you need to use the //old-style vcs// of version 1.5.1).
-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 probably still using the default python installed on your system!
+  - Read the rest of this page to get a better understanding of what you have learned in this section, and use Python more efficiently
+  - Learn Python by reading what you need on the [[other:python:jyp_steps|JYP's recommended steps for learning python]] page
-<code>$ python -c 'import cdms2, vcs'
-Traceback (most recent call last):
-  File "<string>", line 1, in <module>
-ImportError: No module named cdms2
-$ which python
+===== Using the LSCE jupyterhub server =====
-/usr/bin/python</code>
-== Initializing UV-CDAT for tcsh users ==
+The [[https://intranet.lsce.ipsl.fr/informatique/en/jupyter/index.php|LSCE jupyterhub notebook server]] is available for users with a LSCE Linux account:
+  * from a computer on the LSCE wired network: https://jupyter.lsce.ipsl.fr/
+  * from other computers: start the [[https://intranet.lsce.ipsl.fr/informatique/fr/vpn-forticlient.php#vpnlsce|LSCE VPN]] before opening https://jupyter.lsce.ipsl.fr/
-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:
+==== Using a non-standard kernel ====
-  * type ''cdatm'' to initialize the default version of UV-CDAT
-  * type ''cdatm %%--%%config //CONFIG_NAME//'' to initialize a specific version
-    * You can find the allowed values of //CONFIG_NAME// (e.g. ''LSCE_10'', ''LSCE_13'', ...) in one of the tables below
-<code> > which python
+Note: a //kernel// is a specific python environment/distribution
-/usr/bin/python
- > cdatm
+The LSCE jupyterhub server can be used to open //Notebooks// using pre-configured Python or R //kernels//. It is also possible to define additional per-user kernels by adding [[https://jupyter-client.readthedocs.io/en/stable/kernels.html#kernel-specs|kernel configuration directories]] in the user's home directory
-** CDAT 'uv-1.5.1' initialized!
-** If you have problems with this installation,
-** it is maintained by: Jean-Yves Peterschmitt - LSCE
- > which python
+The steps below show how to add a specific [[other:python:starting#cdat|CDAT environment]] kernel, but can be easily adapted for using other kernels
-/home/share/unix_files/cdat/versions/cdat_install_uv-1.5.1_x86_64_gcc4_10/bin/python
-</code>
-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.
+  - Initialize your (favorite) Python environment in a terminal, and (as usual) check which Python executable you are using\\ <code> >which python
+/usr/bin/python
-|  **LSCE**  | ''alias cdatm 'source ~jypeter/CDAT/Install/cdat_multi/cdat_multi.login ~jypeter/CDAT/Install/cdat_multi''' |
+ >source ~jypeter/.conda3_21-02_jyp.csh
-|  **ciclad**  | ''alias cdatm 'source ~jypmce/CDAT/Install/cdat_multi/cdat_multi.login ~jypmce/CDAT/Install/cdat_multi'''|
+ >conda activate cdatm_py3
-|  **curie**  | ''alias cdatm 'source ~p25jype/CDAT/Install/cdat_multi/cdat_multi.login ~p25jype/CDAT/Install/cdat_multi''' |
-|  **All** servers  | ''alias wp 'which python'' |
-== Initializing UV-CDAT when the cdatm alias is not available, or in a batch script ==
+(cdatm_py3)  >which python
+/home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm_py3/bin/python</code>
+  - Determine where the kernel configuration files of the **active** python are located\\ <code> >jupyter kernelspec list
+Available kernels:
+  python3     /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_nompi_py3/share/jupyter/kernels/python3</code>
+  - Copy the existing kernel directory that you have found to your home directory. You can use the existing kernel name, or use a new kernel name (using only ASCII letters, numbers,  ''-'' hyphen, ''.'' period and ''_'' underscore)\\ <code> >cp -pr /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_nompi_py3/share/jupyter/kernels/python3 ~/.local/share/jupyter/kernels
+ >cp -pr /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_nompi_py3/share/jupyter/kernels/python3 ~/.local/share/jupyter/kernels/my_favorite_kernel
-You first need to know which shell you are using
+ >ls ~/.local/share/jupyter/kernels/
+my_favorite_kernel/    python3/
+</code>
+  - Check that the ''kernelspec list'' command now finds the new kernel(s)\\ <code> >jupyter kernelspec list
+Available kernels:
+  my_favorite_kernel    your_home_dir/.local/share/jupyter/kernels/my_favorite_kernel
+  python3               your_home_dir/.local/share/jupyter/kernels/python3</code>
+  - You can optionally change the value of the ''display_name'' parameter in the ''kernel.json'' configuration file if you want to customize the name that will appear in the jupyterhub kernel menus\\ <code> >ls your_home_dir/.local/share/jupyter/kernels/my_favorite_kernel
+kernel.json  logo-32x32.png  logo-64x64.png
-<code>$ echo $SHELL
+ >cat your_home_dir/.local/share/jupyter/kernels/my_favorite_kernel/kernel.json
-/bin/bash</code>
+{
+ "argv": [
+  "/home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm19_nompi_py3/bin/python",
+  "-m",
+  "ipykernel_launcher",
+  "-f",
+  "{connection_file}"
+ ],
+ "display_name": "My favorite Python kernel",
+ "language": "python"
+</code>
+  - refresh the https://jupyter.lsce.ipsl.fr/ page and the new kernel(s) should appear in the kernels' related menus
+===== Python distributions available for LSCE users =====
-You then need to know where the ''python'' program provided by UV-CDAT is installed, something like ''/path/to/UV-CDAT/bin/python''
+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.
-Finally, all you need to do in order to initialize UV-CDAT is to source the ''setup_runtime'' file appropriate for your shell:
+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 your backed up //home// directory!
-  * tcsh: ''source /path/to/UV-CDAT/bin/setup_runtime.csh''
-  * bash, sh: ''source /path/to/UV-CDAT/bin/setup_runtime.sh''
-The table below lists, for each server and version, the path where you can find the //setup_runtime// files
+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 [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:jyp_steps#python_27_vs_python_3|differences between both versions]] and try to write scripts that will work in both versions!
-^  Server  ^  CDAT\\ version  ^  JYP\\ version  ^  Path  ^
+==== LSCE distribution ====
-|  LSCE  |  1.1.0  |  LSCE_08  |  ''/home/share/unix_files/cdat/versions/cdat_install_uv-1.1.0_x86_64_gcc4_08/bin''  |
-|  LSCE  |  1.5.1  |  LSCE_10  |  ''/home/share/unix_files/cdat/versions/cdat_install_uv-1.5.1_x86_64_gcc4_10/bin''  |
-|  LSCE  |  2.1.0  |  LSCE_13  |  ''/home/share/unix_files/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/bin''  |
-|  ciclad  |  1.5.1  |  ciclad_10-ng  |  ''/data/jypmce/cdat/versions/cdat_install_uv-1.5.1_x86_64_gcc4_10-ng/bin''  |
-|  ciclad  |  2.1.0  |  ciclad_13  |  ''/data/jypmce/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/bin''  |
-|  curie  |  1.1.0  |  curie_08  |  ''/ccc/work/cont003/dsm/p25jype/cdat/versions/cdat_install_uv-1.1.0_x86_64_gcc4_curie_08/bin''  |
-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)
+  * Contact: the LSCE system administrators ([[help-lsce@lsce.ipsl.fr]])
+  * Where: //obelix// interactive servers and //obelix// cluster at LSCE
+  * Initialization type: [[other:newppl:starting#using_module_to_access_optional_programs|module based]] + //conda//
+  * What's installed: type ''conda list'' after initializing the LSCE distribution
-<code>bash-4.1$ source /home/share/unix_files/cdat/versions/cdat_install_uv-2.1.0_x86_64_gcc4_13/bin/setup_runtime.sh
+<code>
+$ module -t avail
+[...]
+python/2.7
+python/2.7.5
+python/2-ramces
+python/3
+python/3.9
+python/4artic
+python/esmpy
+python/intel
+[...]
-bash-4.1$ which python
+$ module load python/3.9
-/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'
+$ which python
-bash-4.1$</code>
+/usr/local/install/python-3.9/bin/python
-You probably don't want to have to determine what you should type each time you want to use UV-CDAT in a window, so you should define a simple shortcut alias that you can type each time you need to initialize UV-CDAT. If, for example, you want to use UV-CDAT 2.1.0 at LSCE:
+$ python
-  * tcsh: add the following alias definitions to ''~/.cshrc''\\ ''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'''
+Python 3.9.7 (default, Sep 16 2021, 13:09:58)
-  * bash: add the following alias definition to ''~/.bashrc'', ''~/.profile'' or ''~/.bash_profile'' (whichever works for you, or read ''man bash''...)\\ ''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'''
+[GCC 7.5.0] :: Anaconda, Inc. on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>>
+</code>
-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
+==== CDAT ====
-<code>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
+[[https://cdat.llnl.gov/|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. CDAT is **recommended by JYP**.
-mypython=`which python`
-echo
-echo -e "This script will use the following python: $mypython\n\n"</code>
-==== Canopy ====
+CDAT is **available for Mac, Linux and Windows 10 (Windows 10 + [[other:win10wsl|Windows Subsystem for Linux, and Ubuntu]])**.
-[[https://www.enthought.com/products/canopy/|Enthought Canopy]] is //a Scientific and Analytic Python Deployment with Integrated Analysis Environment// provided by [[https://www.enthought.com/|Enthought]]. It 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
+  * 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
+  * What's installed: type ''conda list'' after initializing a specific CDAT distribution
+=== CDAT versions maintained by JYP ===
-==== Anaconda ====
+The following versions are maintained by JYP, on the Linux servers where LSCE users have accounts
-[[https://www.continuum.io/why-anaconda|Anaconda]] is a distribution similar to [[#canopy]] provided by [[https://www.continuum.io/|Continuum Analytics]]. It is available for Windows, Mac and Linux
+^  CDAT version  ^  JYP\\ version  ^  python\\ version  ^  Availability?  ^  Available packages ^  Installation notes  ^
+|  **8.2.1**  |  19  |  3.8.8  |  LSCE  |  {{  :other:uvcdat:cdat_conda:cdat_8.2.1_nompi_21-03-05.txt |Default CDAT 8.2.1 packages}}\\ [[other:uvcdat:cdat_conda:cdat_8_2_1#extra_packages_list|Extra packages]]  |  [[other:uvcdat:cdat_conda:cdat_8_2_1|8.2.1 notes]]  |
+|  **8.1**  |  18  |  2.7.15\\ 3.6.7  |  LSCE, ciclad  |  {{:other:uvcdat:cdat_conda:cdat-8.1_py2_list_190307.txt|Default CDAT 8.1 packages}}\\ [[other:uvcdat:cdat_conda:cdat_8_1#extra_packages_list|Extra packages]]  |  [[other:uvcdat:cdat_conda:cdat_8_1|8.1 notes]]  |
+== Initialization ==
-===== Launching Python =====
+Read the [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#ultra_quick-start_on_the_interactive_lsce_servers|Ultra quick-start on the LSCE servers]] above
-Once you have initialized the [[#some_python_distributions|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).
+Note: on the ciclad cluster, use ''source ~jypmce/.conda3_jyp.sh'' to initialize conda
-Remember that you can check which python you are using by typing ''which python''!
+=== CDAT at TGCC ===
-==== Useful keyboard shortcuts ====
+Note: TGCC also supports its own [[#tgcc_distribution|TGCC distribution]], that may be more up-to-date, if you don't need specific CDAT modules
-^  Key  ^  Effect  ^
+CDAT **8.0** is installed at TGCC and can be initialized with:
-|  **CTRL-D**  |  Exit the interpreter  |
+  * Python 2: ''module load cdat''
-|  **↑ and ↓**  |  Go to previous/next line(s)  |
+  * Python 3: ''module load flavor/cdat/python3 cdat''
-|  **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.cum**TABTAB**''  |
-|  **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 common CDAT-related error ===
-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 ''#!'' [[https://en.wikipedia.org/wiki/Shebang_%28Unix%29|shebang comment]] on the first line of the script with, and the script has it's execution bit set.
+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!
-<code>
+<code>$ python -c 'import cdms2, vcs'
-jypeter@asterix1 - ...jypeter - 54 >cat basic_script.py
+Traceback (most recent call last):
-#!/usr/bin/env python
+  File "<string>", line 1, in <module>
+ImportError: No module named cdms2
-import sys
+# Am I using the correct python distribution?
+$ which python
+/usr/bin/python</code>
-script_name = sys.argv[0]
+==== TGCC distribution ====
-print('Hello world, I am the ' + script_name + ' script')
+  * Contact: the TGCC hotline ([[hotline.tgcc@cea.fr]])
+  * Where: CEA TGCC
+  * Initialization type: [[other:newppl:starting#using_module_to_access_optional_programs|module based]]
+  * What's installed: it depends...
-# The end
+<code># 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)
-jypeter@asterix1 - ...jypeter - 55 >chmod +x basic_script.py
+$ module load python
+[...]
+load module python/2.7.14 (Python)
-ypeter@asterix1 - ...jypeter - 56 ># Type here what is required to initialize the distribution you want
+$ which python
+/ccc/products/python-2.7.14/intel--17.0.4.196__openmpi--2.0.2/default/bin/python
-jypeter@asterix1 - ...jypeter - 57 >./basic_script.py
+$ python
-Hello world, I am the ./basic_script.py script
+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.
+>>>
 </code>
-==== Standard interpreter ====
-  * ''python'': start the interpreter
+===== ipython =====
-  * ''python script.py'': execute //script.py// and **exit**
-  * ''python -i script'': execute //script.py// and **stay in the interpreter**
-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
+The //ipython// interpreter provides more options and commands than the standard python interpreter, but takes more time to start. 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''
@@ Line 257: / Line 306: @@
   * [[https://damontallen.github.io/IPython-quick-ref-sheets/|Ipython-quick-ref-sheets]]
+==== LSCE jupyter notebook server ====
+The different Python distributions available on the LSCE servers (interactive servers and cluster) can also be used on the [[https://intranet.lsce.ipsl.fr/informatique/en/jupyter/index.php|LSCE jupyter notebook server]]:
+  * If your computer is on the LSCE wired network
+  * Or if you are using the [[https://intranet.lsce.ipsl.fr/informatique/fr/vpn-forticlient.php|LSCE VPN]]
 ==== 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 [[other:python:jyp_steps#part_1|introduction to Python, part 1]]).
+<WRAP center round tip 60%>
+If you want to use ipython notebooks at LSCE, you should **use the [[other:python:starting#lsce_jupyter_notebook_server|LSCE notebook server]]** rather than trying to use (and probably overloading) the interactive servers!
+</WRAP>
+<note warning>FIXME Add a link to the new notebook page</note>
+[[https://www.dataquest.io/blog/jupyter-notebook-tutorial/|Jupyter Notebook for Beginners: A Tutorial]]
+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 [[other:python:jyp_steps#part_1|introduction to Python, part 1]]).
 Starting the notebook server: ''ipython notebook''
-<note warning>**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.
+<note warning>
+  * **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!).
+  * 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 an interactive server shared by many users!).
-You may want to [[other:newppl:starting#determining_the_load_of_a_linux_server|use the 'top' command]] in order to monitor what is happening</note>
+  * You may want to [[other:newppl:starting#determining_the_load_of_a_linux_server|use the 'top' command]] in order to monitor what is happening on the interactive server where you are using your notebook server
+</note>
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