Differences

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--- other:python:starting [2022/01/04 23:06] – [Using the LSCE jupyterhub server] Added user kernel definition jypeter
+++ other:python:starting [2023/02/01 11:29] – [Initialization] Updated the instruction jypeter
@@ Line 40: / Line 40: @@
       * 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:
+    - Choose which environment you want by typing the activation command:
-      * Python 2.7.x: ''conda activate cdatm_py2''
       * Python 3.x: ''conda activate cdatm_py3''
+      * You can use ''conda env list'' to find out which environments are available, but the one you most likely want is ''cdatm_py3''
+    - If you need an (older) Python 2.7 environment, replace the steps above with:
+      * ''source ~jypeter/.conda3_19-06_jyp.sh''
+      * ''conda activate cdatm_py2''
     - Type ''python'' to start the interpreter
+    - If you need a list of the installed packages (and their version), use
+      * ''conda list''
+      * A partial list of what is installed is available in the [[other:uvcdat:cdat_conda:cdat_8_2_1#extra_packages_list|Extra packages list]]
     - 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
@@ Line 50: / Line 56: @@
 <code> >ssh obelix
-Last login: Mon Jun  3 08:49:53 2019 from somewhere
+Last login: Wed Feb  1 09:56:29 2023 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
+bash-4.2$ conda activate cdatm_py3
-/home/share/unix_files/cdat/miniconda3/envs/cdatm_py2/bin/python
-(cdatm_py2) bash-4.2$ python
+(cdatm_py3) bash-4.2$ which python
-Python 2.7.15 | packaged by conda-forge | (default, Feb 28 2019, 04:00:11)
+/home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm_py3/bin/python
-[GCC 7.3.0] on linux2
+(cdatm_py3) bash-4.2$ python
+Python 3.8.8 | packaged by conda-forge | (default, Feb 20 2021, 16:22:27)
+[GCC 9.3.0] on linux
 Type "help", "copyright", "credits" or "license" for more information.
 >>> print('hello!')
@@ Line 191: / Line 203: @@
 <code>
- > module avail
+$ module -t avail
 [...]
-ARTIC/3.6         grib_api/1.14      netcdf/3           python/2.7.5
+python/2.7
-batch_env          grib_api/1.14.0    netcdf/4           python/3.6
+python/2.7.5
-[...]
+python/2-ramces
-glost/0.3.1        ncview/2.1.7       python/2.7
+python/3
+python/3.9
+python/4artic
+python/esmpy
+python/intel
 [...]
- > module load python/2.7
+$ module load python/3.9
- > which python
+$ which python
-/usr/local/install/python-2.7/bin/python
+/usr/local/install/python-3.9/bin/python
- > python
+$ python
-Python 2.7.15 |Anaconda, Inc.| (default, Oct 10 2018, 21:32:13)
+Python 3.9.7 (default, Sep 16 2021, 13:09:58)
-[GCC 7.3.0] on linux2
+[GCC 7.5.0] :: Anaconda, Inc. on linux
 Type "help", "copyright", "credits" or "license" for more information.
 >>>
@@ Line 219: / Line 235: @@
   * 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]]
+  * Initialization type: conda based
   * What's installed: type ''conda list'' after initializing a specific CDAT distribution
@@ Line 232: / Line 248: @@
 == Initialization ==
-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
+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
 Note: on the ciclad cluster, use ''source ~jypmce/.conda3_jyp.sh'' to initialize conda
@@ Line 290: / Line 306: @@
 </code>
-==== Anaconda ====
-<note tip>This is the recommended Python distribution/environment. It is **available for Windows, Mac and Linux**</note>
-[[https://www.continuum.io/why-anaconda|Anaconda]] is a distribution provided by [[https://www.continuum.io/|Continuum Analytics]]. It is similar to [[#enthought_deployment_manager_edm|EDM]]
-Note: Anaconda provides and uses ''conda'' for its installation. Since [[#cdat|CDAT]] is 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
-==== Enthought Deployment Manager (EDM) ====
-<note tip>This was previously called //Enthought Python Distribution (EPD)// and then  //Enthought Canopy//</note>
-[[https://www.enthought.com/enthought-deployment-manager/|Enthought Deployment Manager (EDM)]] is Enthought’s mechanism to deliver scientific software applications and development environments
-There are native installers for Windows (.msi), Mac OS X (.pkg), RHEL/Fedora (.rpm), and Debian/Ubuntu (.deb)
 ===== ipython =====
@@ Line 319: / Line 318: @@
   * [[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 ====
+<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>
@@ Line 325: / Line 335: @@
 [[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]]).
+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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