Differences

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

--- other:python:starting [2019/07/11 17:31] – [ipython notebook] Added link to a tutorial jypeter
+++ other:python:starting [2022/08/11 14:26] – Added jupyter server section jypeter
@@ Line 30: / Line 30: @@
 </code>
-===== Ultra quick-start on the LSCE servers =====
+===== Ultra quick-start on the interactive LSCE servers =====
 ==== Initialization ====
@@ Line 123: / Line 123: @@
   - Learn Python by reading what you need on the [[other:python:jyp_steps|JYP's recommended steps for learning python]] page
+===== Using the LSCE jupyterhub server =====
+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 ====
+Note: a //kernel// is a specific python environment/distribution
+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
+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
+  - Initialize your (favorite) Python environment in a terminal, and (as usual) check which Python executable you are using\\ <code> >which python
+/usr/bin/python
+ >source ~jypeter/.conda3_21-02_jyp.csh
+ >conda activate cdatm_py3
+(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
+ >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
+ >cat your_home_dir/.local/share/jupyter/kernels/my_favorite_kernel/kernel.json
+{
+ "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 =====
@@ Line 139: / Line 191: @@
 <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 161: / Line 217: @@
 ==== CDAT ====
-[[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.
+[[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**.
 CDAT is **available for Mac, Linux and Windows 10 (Windows 10 + [[other:win10wsl|Windows Subsystem for Linux, and Ubuntu]])**.
@@ Line 167: / Line 223: @@
   * 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 175: / Line 231: @@
 ^  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]]  |
+|  **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 ==
@@ Line 237: / Line 294: @@
 </code>
-==== Canopy ====
-[[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//)
-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 ====
-[[https://www.continuum.io/why-anaconda|Anaconda]] is a distribution similar to [[#canopy]] provided by [[https://www.continuum.io/|Continuum Analytics]].
-Anaconda is **available for Windows, Mac and Linux**
-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
 ===== ipython =====
@@ Line 263: / 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 ====