Differences

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

--- other:python:starting [2016/02/03 10:56]
jypeter More CDAT stuff
+++ other:python:starting [2019/07/11 15:31]
jypeter [ipython notebook] Added link to a tutorial
@@ 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>jypeter@asterix1 - ...jypeter - 41 >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+Note: the former and **outdated** version (before the massive usage of //conda//) is still [[other:python:starting_170810|available for reference]]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
-jypeter@asterix1 - ...jypeter - 47 >rpm -qf /usr/bin/python
+# Where is it coming from ('rpm' works on a RedHat-like Linux machine)?
-python-2.6.6-64.el6.x86_64
+ > rpm -qf /usr/bin/python
+python-2.7.5-77.el7_6.x86_64
-jypeter@asterix1 - ...jypeter - 42 >python
+# You also get some information when you start the interpreter
-Python 2.6.6 (r266:84292, May 22 2015, 08:34:51)
+ > python
-[GCC 4.4.7 20120313 (Red Hat 4.4.7-15)] on linux2
+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.
 >>>
 </code>
-===== Some python distributions =====
+===== Ultra quick-start on the 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
+bash-4.2$ which python
+/usr/bin/python
+bash-4.2$ source ~jypeter/.conda3_jyp.sh
+bash-4.2$ which python
+/usr/bin/python
+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
+(cdatm_py2) bash-4.2$ python
+Python 2.7.15 | packaged by conda-forge | (default, Feb 28 2019, 04:00:11)
+[GCC 7.3.0] on linux2
+Type "help", "copyright", "credits" or "license" for more information.
+>>> print('hello!')
+hello!
+>>>   # Type CTRL-D to exit the python interpreter
+</code>
-Contact: the LSCE system administrators
+==== 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.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'')  |
+==== Executing a python script ====
+Note: Python is an [[https://en.wikipedia.org/wiki/Interpreted_language|interpreted language]] and we speak of //Python scripts// rather than //Python programs//.
+  * ''python'': start the interpreter and start working interactively
+  * ''python script.py'': execute //script.py// and **exit**
+  * ''python -i script'': execute //script.py// and **stay in the interpreter** (''-i'' = //**I**nteractive//)
+Type ''man python'' if you want to see what other command line options are available
+==== Stand-alone 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 its //execution bit// set (''chmod +x my_script.py'').
+If you have a ''basic_script.py'' file with the following content in a directory...
 <code>
-jypeter@asterix1 - ...jypeter - 43 >module avail
+#!/usr/bin/env python
-[...]
-castem/12        ferret/6.9.5     hdf5/1.8.9       netcdf/4p        python/2.7.5     sun-java/7.0.45
-[...]
-jypeter@asterix1 - ...jypeter - 44 >module load python/2.7.5
+import sys
-jypeter@asterix1 - ...jypeter - 45 >which python
+script_name = sys.argv[0]
-/usr/local/install/python-2.7.5/bin/python
-jypeter@asterix1 - ...jypeter - 46 >python
+print('Hello world, I am the ' + script_name + ' script')
-Python 2.7.5 (default, Sep 18 2013, 15:47:43)
-[GCC 4.4.7 20120313 (Red Hat 4.4.7-3)] on linux2
+# The end</code>
-Type "help", "copyright", "credits" or "license" for more information.
->>>
+...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:
+<code> > chmod +x basic_script.py
+ > ls -l basic_script.py
+-rwxr-xr-x [...] basic_script.py
+ > ./basic_script.py
+Hello world, I am the ./basic_script.py script
 </code>
-==== TGCC distribution ====
+==== What next? ====
-Contact: the TGCC hotline
+  - 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
+===== 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 your 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 [[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!
+==== LSCE distribution ====
+  * 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>
-[p25jype@curie70 ~]$ module avail
+ > module avail
+[...]
+ARTIC/3.6         grib_api/1.14      netcdf/3           python/2.7.5
+batch_env          grib_api/1.14.0    netcdf/4           python/3.6
 [...]
-cmake/2.8.9(default)      hwloc/1.5                 netcdf-utils/4.3.3.1_hdf5 python/2.7.8              tix/8.4.3
+glost/0.3.1        ncview/2.1.7       python/2.7
-cmake/3.2.2               hwloc/1.7.1(default)      octave/3.6.3              python/3.3.2              tk/8.5(default)
 [...]
-[p25jype@curie70 ~]$ module load python/2.7.8
+ > module load python/2.7
-load module python/2.7.8 (Python)
-[p25jype@curie70 ~]$ which python
+ > which python
-/usr/local/ccc_python/2.7.8_201409/bin/python
+/usr/local/install/python-2.7/bin/python
-[p25jype@curie70 ~]$ python
+ > python
-Python 2.7.8 (default, Aug 27 2014, 17:50:16)
+Python 2.7.15 |Anaconda, Inc.| (default, Oct 10 2018, 21:32:13)
-[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
+[GCC 7.3.0] on linux2
 Type "help", "copyright", "credits" or "license" for more information.
 >>>
 </code>
-==== UV-CDAT ====
+==== CDAT ====
-Contact: Jean-Yves @ LSCE
+[[https://uvcdat.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, and is recommended by JYP.
-=== What is UV-CDAT? ===
+CDAT is **available for Mac, Linux and Windows 10 (Windows 10 + [[other:win10wsl|Windows Subsystem for Linux, and Ubuntu]])**.
-[[http://uv-cdat.llnl.gov/|UV-CDAT]] (//Ultrascale Visualization - Climate Data Analysis Tools//) is a python distribution developed specifically for the climate scientists.
+  * 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 [[other:newppl:starting#using_module_to_access_optional_programs|module based]]
+  * What's installed: type ''conda list'' after initializing a specific CDAT distribution
-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]] page.
+=== CDAT versions maintained by JYP ===
-UV-CDAT also provides some specific packages: **cdms2**, **cdutil**, **cdtime**, **genutil**, **vcs**, **cmor2**, ...
+The following versions are maintained by JYP, on the Linux servers where LSCE users have accounts
-=== UV-CDAT versions maintained by JYP ===
+^  CDAT version  ^  JYP\\ version  ^  python\\ version  ^  Availability?  ^  Available packages ^  Installation 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 packages}}\\ [[other:uvcdat:cdat_conda:cdat_8_1#extra_packages_list|Extra packages]]  |  [[other:uvcdat:cdat_conda:cdat_8_1|8.1 notes]]  |
-The following versions are maintained by JYP on the servers where LSCE users have accounts
+== Initialization ==
-^  CDAT version  ^  JYP version  ^  python version  ^  Packages built by CDAT  ^  Installation notes  ^
+Read the [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#ultra_quick-start_on_the_lsce_servers|Ultra quick-start on the LSCE servers]] above
-|  1.1.0  |  08  |  2.7.3  |  n/a  |  [[other:uvcdat:installed#section110|1.1.0 notes]]  |
-|  1.5.1  |  10  |  2.7.4  |  {{: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  |  {{: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:
+Note: on the ciclad cluster, use ''source ~jypmce/.conda3_jyp.sh'' to initialize conda
-  * 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''
-=== Initializing UV-CDAT ===
+=== CDAT at TGCC ===
-The way you initialize UV-CDAT depends on which server, which version and which shell you are using!
+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
-==== Canopy ====
+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''
-[[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
+=== A common CDAT-related error ===
+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!
-==== Anaconda ====
+<code>$ python -c 'import cdms2, vcs'
+Traceback (most recent call last):
+  File "<string>", line 1, in <module>
+ImportError: No module named cdms2
-[[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
+# Am I using the correct python distribution?
+$ which python
+/usr/bin/python</code>
+==== TGCC distribution ====
-===== Launching Python =====
+  * 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...
-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).
+<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)
-Remember that you can check which python you are using by typing ''which python''!
+$ module load python
+[...]
+load module python/2.7.14 (Python)
-==== Useful keyboard shortcuts ====
+$ which python
+/ccc/products/python-2.7.14/intel--17.0.4.196__openmpi--2.0.2/default/bin/python
-^  Key  ^  Effect  ^
+$ python
-|  **CTRL-D**  |  Exit the interpreter  |
+Python 2.7.14 (default, Jan 11 2018, 16:43:59)
-|  **↑ and ↓**  |  Go to previous/next line(s)  |
+[GCC 4.8.5] on linux2
-|  **CTRL-A**  |  Go to the beginning of the line  |
+Type "help", "copyright", "credits" or "license" for more information.
-|  **CTRL-E**  |  Go to the end of the line  |
+>>>
-|  **CTRL-K**  |  Erase from the cursor to the end of the line  |
+</code>
-|  **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 ====
+==== Canopy ====
-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.
+[[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 used to be called EPD (//Enthought Python Distribution//)
-<code>
+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
-jypeter@asterix1 - ...jypeter - 54 >cat basic_script.py
-#!/usr/bin/env python
-import sys
-script_name = sys.argv[0]
+==== Anaconda ====
-print('Hello world, I am the ' + script_name + ' script')
+[[https://www.continuum.io/why-anaconda|Anaconda]] is a distribution similar to [[#canopy]] provided by [[https://www.continuum.io/|Continuum Analytics]].
-# The end
+Anaconda is **available for Windows, Mac and Linux**
-jypeter@asterix1 - ...jypeter - 55 >chmod +x basic_script.py
+Note: Anaconda provides and uses ''conda'' for its installation. Since CDAT is now also installed and maintained with ''conda'', you can read the [[other:uvcdat:conda_notes|Installing and maintaining UV-CDAT with conda]] page for more information, even if you are not going to use CDAT
-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
-</code>
-==== Standard interpreter ====
+===== ipython =====
-  * ''python'': start the interpreter
-  * ''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 172: / Line 264: @@
 ==== ipython notebook ====
+<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]]).

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