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other:python:starting [2019/07/11 15:31] jypeter [ipython notebook] Added link to a tutorial |
other:python:starting [2022/08/11 12:26] jypeter Added jupyter server section |
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</code> | </code> | ||
- | ===== Ultra quick-start on the LSCE servers ===== | + | ===== Ultra quick-start on the interactive LSCE servers ===== |
==== Initialization ==== | ==== Initialization ==== | ||
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- Learn Python by reading what you need on the [[other:python:jyp_steps|JYP's recommended steps for learning python]] page | - 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 ===== | ===== Python distributions available for LSCE users ===== | ||
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<code> | <code> | ||
- | > module avail | + | $ module -t avail |
[...] | [...] | ||
- | 4ARTIC/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. | Type "help", "copyright", "credits" or "license" for more information. | ||
>>> | >>> | ||
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==== CDAT ==== | ==== 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]])**. | CDAT is **available for Mac, Linux and Windows 10 (Windows 10 + [[other:win10wsl|Windows Subsystem for Linux, and Ubuntu]])**. | ||
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* Contact: Jean-Yves Peterschmitt (//JYP//) @ LSCE | * Contact: Jean-Yves Peterschmitt (//JYP//) @ LSCE | ||
* Where: //obelix// interactive servers and cluster at LSCE, //ciclad// interactive servers and cluster at IPSL, irene @ TGCC | * 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 | * What's installed: type ''conda list'' after initializing a specific CDAT distribution | ||
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^ CDAT version ^ JYP\\ version ^ python\\ version ^ Availability? ^ Available packages ^ Installation notes ^ | ^ 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 == | == Initialization == | ||
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</code> | </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 ===== | ===== ipython ===== | ||
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* [[https://damontallen.github.io/IPython-quick-ref-sheets/|Ipython-quick-ref-sheets]] | * [[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 ==== | ==== ipython notebook ==== | ||