Differences

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

--- other:python:starting [2022/08/11 14:11] – [CDAT] jypeter
+++ other:python:starting [2024/09/13 16:20] (current) – Updated the jupyter section 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 124: / Line 136: @@
-===== Using the LSCE jupyterhub server =====
+===== Using JupyterHub servers =====
+==== JupyterHub servers available for LSCE users ====
+  * [[https://intranet.lsce.ipsl.fr/informatique/en/jupyter/index.php|LSCE JupyterHub server information]]
+  * [[https://documentations.ipsl.fr/spirit/jupyterhub/documentation.html|IPSL JupyterHub server information]]
+  * You will **have to** be on the LSCE wired network, or use the [[https://intranet.lsce.ipsl.fr/informatique/en/intra-cea.php|LSCE VPN]], if you want to use the LSCE or IPSL JupyterHub servers !
+    * Otherwise, check the IPSL server documentation, if you want to try **accessing the IPSL server using an ssh tunnel**...
+==== Notebooks and jupyter servers documentation ====
+FIXME
-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/
 ==== Using a non-standard kernel ====
@@ Line 149: / Line 169: @@
 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
+  - 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> >mkdir -p ~/.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
  >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
@@ Line 185: / Line 206: @@
 ==== LSCE distribution ====
-  * Contact: the LSCE system administrators ([[help-lsce@lsce.ipsl.fr]])
+  * Contact: the [[other:newppl:starting#getting_help_from_the_lsce_system_administrators|LSCE system administrators]]
   * 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
+  * What's installed: type ''conda list'' after initializing on of the LSCE distributions
 <code>
-$ module -t avail
+$ module avail python
-[...]
+python/2.7      python/2-ramces python/3.9      python/intel
-python/2.7
+python/2.7.5    python/3        python/4artic
-python/2.7.5
-python/2-ramces
-python/3
-python/3.9
-python/4artic
-python/esmpy
-python/intel
-[...]
 $ module load python/3.9
@@ Line 209: / Line 222: @@
 $ python
-Python 3.9.7 (default, Sep 16 2021, 13:09:58)
+Python 3.9.15 (main, Nov 24 2022, 14:31:59)
-[GCC 7.5.0] :: Anaconda, Inc. on linux
+[GCC 11.2.0] :: Anaconda, Inc. on linux
 Type "help", "copyright", "credits" or "license" for more information.
 >>>
@@ Line 236: / Line 249: @@
 == 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 294: / Line 307: @@
 </code>
-==== Anaconda ====
-<note tip>This is the recommended (by JYP) Python distribution/environment. It is **available for Windows, Mac and Linux**</note>
-The [[https://www.anaconda.com/products/distribution|Anaconda distribution]] is  provided by the [[https://www.anaconda.com/about-us|Anaconda]] company (that was [[https://www.anaconda.com/blog/continuum-analytics-officially-becomes-anaconda|previously called Continuum Analytics]]). It is similar to [[#enthought_deployment_manager_edm|EDM]], but probably more widely used than 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 323: / Line 319: @@
   * [[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 329: / Line 336: @@
 [[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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