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| other:python:starting [2019/04/26 09:35] – Added Ultra quick-start on the LSCE servers jypeter | other:python:starting [2025/07/03 16:18] (current) – [Using a non-standard kernel] jypeter |
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| ====== Working with Python ====== | ====== Working with Python ====== |
| |
| <note tip>This page will tell you how to select a python distribution and start (and exit!) the python interpreter | <note tip>This page will tell you how to select a //python distribution// and start (and exit!) the python interpreter |
| |
| You can then read the [[jyp_steps|JYP's recommended steps for learning python]] for really working with python | After reading this page, you can read the [[jyp_steps|JYP's recommended steps for learning python]] for really working with python |
| </note> | </note> |
| |
| 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) | 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) | 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)? | <code># Which is the current python (e.g. where is it located)? |
| </code> | </code> |
| |
| ===== Ultra quick-start on the LSCE servers ===== | ===== Ultra quick-start on the interactive LSCE servers ===== |
| |
| ==== Initialization ==== | ==== Initialization ==== |
| |
| - Start a terminal on an //obelix// server | - 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 or follow the steps below for a more advanced distribution. Remember that **you can exit the interpreter by typing CTRL-D** (or ''quit()'' or ''exit()'') | - Type ''python'' to access the //default Python 2// interpreter available on the servers... |
| - Determine if you are using a [[other:newppl:starting#which_shell_are_you_using|bash or tcsh shell]], then type the following command to initialize python | - ...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()'') |
| - In a //bash// shell: ''source ~jypeter/.conda3_jyp.sh'' | - 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 //tcsh// shell: ''source ~jypeter/.conda3_jyp.csh'' | * In a //bash// shell: ''source ~jypeter/.conda3_jyp.sh'' |
| | * In a //tcsh// shell: ''source ~jypeter/.conda3_jyp.csh'' |
| | - Choose which environment you want by typing the activation command: |
| | * 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 |
| |
| ===== Python distributions available for LSCE users ===== | === Example === |
| |
| 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. | <code> >ssh obelix |
| | Last login: Wed Feb 1 09:56:29 2023 from somewhere |
| |
| 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 a backed up //home// directory! | bash-4.2$ which python |
| | /usr/bin/python |
| |
| 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! | bash-4.2$ source ~jypeter/.conda3_jyp.sh |
| |
| ==== LSCE distribution ==== | bash-4.2$ which python |
| | /usr/bin/python |
| |
| * Contact: the LSCE system administrators ([[help-lsce@lsce.ipsl.fr]]) | bash-4.2$ conda activate cdatm_py3 |
| * Where: //obelix// interactive servers and 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> | (cdatm_py3) bash-4.2$ which python |
| > module avail | /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm_py3/bin/python |
| [...] | |
| 4ARTIC/3.6 grib_api/1.14 netcdf/3 python/2.7.5 | |
| batch_env grib_api/1.14.0 netcdf/4 python/3.6 | |
| [...] | |
| glost/0.3.1 ncview/2.1.7 python/2.7 | |
| [...] | |
| |
| > module load python/2.7 | (cdatm_py3) bash-4.2$ python |
| | Python 3.8.8 | packaged by conda-forge | (default, Feb 20 2021, 16:22:27) |
| > which python | [GCC 9.3.0] on linux |
| /usr/local/install/python-2.7/bin/python | |
| | |
| > python | |
| Python 2.7.15 |Anaconda, Inc.| (default, Oct 10 2018, 21:32:13) | |
| [GCC 7.3.0] on linux2 | |
| Type "help", "copyright", "credits" or "license" for more information. | Type "help", "copyright", "credits" or "license" for more information. |
| >>> | >>> print('hello!') |
| | hello! |
| | >>> # Type CTRL-D to exit the python interpreter |
| </code> | </code> |
| |
| ==== TGCC distribution ==== | ==== Useful keyboard shortcuts ==== |
| |
| * Contact: the TGCC hotline ([[hotline.tgcc@cea.fr]]) | ^ Key ^ Effect ^ |
| * Where: CEA TGCC | | **CTRL-D** | Exit the interpreter | |
| * Initialization type: [[other:newppl:starting#using_module_to_access_optional_programs|module based]] | | **↑ and ↓** | Go to previous/next line(s) | |
| * What's installed: it depends... | | **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'') | |
| |
| <code># Get the default version of the Python based modules | ==== Executing a python script ==== |
| $ 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) | |
| |
| $ module load python | Note: Python is an [[https://en.wikipedia.org/wiki/Interpreted_language|interpreted language]] and we speak of //Python scripts// rather than //Python programs//. |
| [...] | |
| load module python/2.7.14 (Python) | |
| |
| $ which python | * ''python'': start the interpreter and start working interactively |
| /ccc/products/python-2.7.14/intel--17.0.4.196__openmpi--2.0.2/default/bin/python | * ''python script.py'': execute //script.py// and **exit** |
| | * ''python -i script'': execute //script.py// and **stay in the interpreter** (''-i'' = //**I**nteractive//) |
| |
| $ python | Type ''man python'' if you want to see what other command line options are available |
| Python 2.7.14 (default, Jan 11 2018, 16:43:59) | |
| [GCC 4.8.5] on linux2 | |
| Type "help", "copyright", "credits" or "license" for more information. | |
| >>> | |
| </code> | |
| |
| ==== CDAT ==== | ==== Stand-alone script ==== |
| |
| [[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. | 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''). |
| |
| CDAT is **available for Mac, Linux and Windows 10 (Windows 10 + [[other:win10wsl|Windows Subsystem for Linux, and Ubuntu]])**. | If you have a ''basic_script.py'' file with the following content in a directory... |
| | <code> |
| | #!/usr/bin/env python |
| |
| * Contact: Jean-Yves Peterschmitt (//JYP//) @ LSCE | import sys |
| * 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 | |
| |
| === CDAT versions maintained by JYP === | script_name = sys.argv[0] |
| |
| The following versions are maintained by JYP, on the Linux servers where LSCE users have accounts | print('Hello world, I am the ' + script_name + ' script') |
| |
| ^ CDAT version ^ JYP\\ version ^ python\\ version ^ Availability? ^ Available packages ^ Installation notes ^ | # The end</code> |
| | **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]] | | |
| |
| === CDAT at TGCC === | ...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: |
| |
| CDAT **8.0** is installed at TGCC and can be initialized with: | <code> > chmod +x basic_script.py |
| * Python 2: ''module load cdat'' | |
| * Python 3: ''module load flavor/cdat/python3 cdat'' | |
| |
| === The basics of CDAT initialization === | > ls -l basic_script.py |
| | -rwxr-xr-x [...] basic_script.py |
| |
| The way you initialize CDAT depends on: | > ./basic_script.py |
| * which **server** you want to use it on | Hello world, I am the ./basic_script.py script |
| * which **shell** you are using in your terminals: //tcsh// or other shells | </code> |
| * Read [[other:newppl:starting#which_shell_are_you_using|Which shell are you using?]] if you are not sure | |
| * Warning: the shell in a (batch) script may be different from your interactive shell! | |
| * which **version** of CDAT you want to use... | |
| |
| 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! | ==== What next? ==== |
| |
| <code>$ python -c 'import cdms2, vcs' | - Read the rest of this page to get a better understanding of what you have learned in this section, and use Python more efficiently |
| Traceback (most recent call last): | - Learn Python by reading what you need on the [[other:python:jyp_steps|JYP's recommended steps for learning python]] page |
| File "<string>", line 1, in <module> | |
| ImportError: No module named cdms2 | |
| |
| # Am I using the correct python distribution? | |
| $ which python | |
| /usr/bin/python</code> | |
| |
| === conda-based versions of CDAT === | ===== Using JupyterHub servers ===== |
| |
| <WRAP center round important 60%> | ==== JupyterHub servers available for LSCE users ==== |
| \\ The steps detailed in this section are for [[other:uvcdat:cdat_conda:|UV-CDAT 2.8.0 and later]] | |
| </WRAP> | |
| |
| Note: if you need to maintain a **local** version on **your** machine, you can read [[other:uvcdat:conda_notes|Installing and maintaining CDAT with conda]] and the [[other:uvcdat:cdat_conda:index#versions|versions specific notes]]. | * [[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**... |
| |
| == Configuring .bashrc == | ==== Notebooks and jupyter servers documentation ==== |
| |
| You should **add** the following line at the end of your ''~/.bashrc'' configuration file (create the ''~/.bashrc'' file if it does not exist yet). This will basically make sure that your shell can find the ''conda'' executable it needs for initializing CDAT, and define a ''wp'' alias that you can use to find where the ''python'' executable is located | FIXME |
| |
| ^ Server ^ Line to add to ''.bashrc'' ^ | |
| | **LSCE** | ''source ~jypeter/.conda_jyp.sh''\\ \\ Note:{{ :other:python:conda_jyp.txt |conda_jyp}} content | | |
| | **ciclad** | ''source ~jypmce/.conda_jyp.sh'' | | |
| |
| | ==== Using a non-standard kernel ==== |
| |
| Note: when you add the specified line to your ''bashrc'' file, you will then always get the python supplied by conda, instead of the system's python, when you use ''bash''. If you don't like this permanent behavior, just type ''source ~jyp_login_on_this_server/.conda_jyp.sh'' in the bash shell where you want to use conda+CDAT, rather than adding it to the ''.bashrc'' file... | Note: a //kernel// is a specific python environment/distribution |
| |
| == Initializing CDAT == | 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 |
| |
| <WRAP center round tip 60%> | 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 |
| When you initialize CDAT, it will be available only in the **current** window/shell. In the other windows, you still get whatever your default python is. This should minimize potential side-effects | |
| </WRAP> | |
| |
| - If [[other:newppl:starting#which_shell_are_you_using|your shell]] is not //bash//, start a bash shell by typing ''bash'' | - Initialize your (favorite) Python environment in a terminal, and (as usual) check which Python executable you are using\\ <code> >which python |
| | /usr/bin/python |
| |
| * You can later go back to your previous shell by typing ''exit'' or ''CTRL-D'' | >source ~jypeter/.conda3_21-02_jyp.csh |
| - Activate the //conda environment// that uses the version of UV-CDAT you want to use | >conda activate cdatm_py3 |
| * ''source activate conda_env_name'' | |
| * Use the table below to determine which environments are available on which server | |
| - Use CDAT ! | |
| |
| ^ UV-CDAT version ^ Server ^ Environment name\\ and activation line ^ Packages\\ (''conda list'') ^ | (cdatm_py3) >which python |
| | [[:other:uvcdat:cdat_conda:cdat_2_8_0|2.8.0]] | **LSCE**\\ **ciclad** |**cdatm14** (''source activate cdatm14'') | {{ :other:uvcdat:cdat_conda:conda_list_lsce_cdatm14_170310.txt |cdatm14 installed packages}} | | /home/share/unix_files/cdat/miniconda3_21-02/envs/cdatm_py3/bin/python</code> |
| | [[:other:uvcdat:cdat_conda:cdat_2_10|2.10]] | **LSCE** |**cdatm15** (''source activate cdatm15'') | {{ :other:uvcdat:cdat_conda:uvcdat-2.10_list_170721.txt |cdatm14 installed packages}} | | - Determine where the kernel configuration files of the **active** python are located\\ <code> >jupyter kernelspec list |
| | **cdatm** will always point to the latest stable version |||| | Available kernels: |
| | //latest stable version// | **LSCE** |**cdatm** (''source activate cdatm'') | ''conda list'' | | 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 (more precisely to the ''~/.local/share/jupyter/kernels'' directory). You can use the existing kernel name (probably ''python3''), 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 |
| |
| | >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 ~/.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/'' (if you are using the LSCE notebook server) page and the new kernel(s) should appear in the kernels' related menus |
| | ===== Python distributions available for LSCE users ===== |
| |
| ==== Canopy ==== | 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. |
| |
| [[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//) | 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! |
| |
| 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 | 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 ==== |
| |
| ==== Anaconda ==== | * 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 on of the LSCE distributions |
| |
| [[https://www.continuum.io/why-anaconda|Anaconda]] is a distribution similar to [[#canopy]] provided by [[https://www.continuum.io/|Continuum Analytics]]. | <code> |
| | $ module avail python |
| | python/2.7 python/2-ramces python/3.9 python/intel |
| | python/2.7.5 python/3 python/4artic |
| |
| Anaconda is **available for Windows, Mac and Linux** | $ module load python/3.9 |
| |
| Note: Anaconda provides and uses ''conda'' for its installation. Since UV-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 UV-CDAT | $ which python |
| | /usr/local/install/python-3.9/bin/python |
| |
| ===== Launching Python ===== | $ python |
| | Python 3.9.15 (main, Nov 24 2022, 14:31:59) |
| | [GCC 11.2.0] :: Anaconda, Inc. on linux |
| | Type "help", "copyright", "credits" or "license" for more information. |
| | >>> |
| | </code> |
| |
| 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 or by clicking a shortcut on your desktop). | ==== CDAT ==== |
| |
| Remember that on Linux/Mac you can check which python you are using by typing ''which python''! | [[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**. |
| |
| ==== Useful keyboard shortcuts ==== | CDAT is **available for Mac, Linux and Windows 10 (Windows 10 + [[other:win10wsl|Windows Subsystem for Linux, and Ubuntu]])**. |
| |
| ^ Key ^ Effect ^ | * Contact: Jean-Yves Peterschmitt (//JYP//) @ LSCE |
| | **CTRL-D** | Exit the interpreter | | * Where: //obelix// interactive servers and cluster at LSCE, //ciclad// interactive servers and cluster at IPSL, irene @ TGCC |
| | **↑ and ↓** | Go to previous/next line(s) | | * Initialization type: conda based |
| | **CTRL-A** | Go to the beginning of the line | | * What's installed: type ''conda list'' after initializing a specific CDAT distribution |
| | **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'') | | |
| |
| ==== Stand-alone script ==== | === CDAT versions maintained by JYP === |
| |
| 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 its execution bit set (''chmod +x my_script.py''). | The following versions are maintained by JYP, on the Linux servers where LSCE users have accounts |
| |
| <code> | ^ CDAT version ^ JYP\\ version ^ python\\ version ^ Availability? ^ Available packages ^ Installation notes ^ |
| jypeter@asterix1 - ...jypeter - 54 >cat basic_script.py | | **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]] | |
| #!/usr/bin/env python | | **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]] | |
| |
| import sys | == Initialization == |
| |
| script_name = sys.argv[0] | 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 |
| |
| print('Hello world, I am the ' + script_name + ' script') | Note: on the ciclad cluster, use ''source ~jypmce/.conda3_jyp.sh'' to initialize conda |
| |
| # The end | === CDAT at TGCC === |
| |
| jypeter@asterix1 - ...jypeter - 55 >chmod +x basic_script.py | 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 |
| |
| ypeter@asterix1 - ...jypeter - 56 ># Type here what is required to initialize the distribution you want | 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'' |
| |
| jypeter@asterix1 - ...jypeter - 57 >./basic_script.py | === A common CDAT-related error === |
| Hello world, I am the ./basic_script.py script | |
| </code> | |
| |
| ==== Standard interpreter ==== | 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! |
| |
| * ''python'': start the interpreter | <code>$ python -c 'import cdms2, vcs' |
| * ''python script.py'': execute //script.py// and **exit** | Traceback (most recent call last): |
| * ''python -i script'': execute //script.py// and **stay in the interpreter** (''-i'' = //**I**nteractive//) | File "<string>", line 1, in <module> |
| | ImportError: No module named cdms2 |
| |
| Type ''man python'' if you want to see what other command line options are available | # Am I using the correct python distribution? |
| | $ which python |
| | /usr/bin/python</code> |
| | |
| | ==== TGCC distribution ==== |
| | |
| | * 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... |
| | |
| | <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) |
| | |
| | $ module load python |
| | [...] |
| | load module python/2.7.14 (Python) |
| | |
| | $ which python |
| | /ccc/products/python-2.7.14/intel--17.0.4.196__openmpi--2.0.2/default/bin/python |
| | |
| | $ python |
| | Python 2.7.14 (default, Jan 11 2018, 16:43:59) |
| | [GCC 4.8.5] on linux2 |
| | Type "help", "copyright", "credits" or "license" for more information. |
| | >>> |
| | </code> |
| | |
| | |
| | ===== ipython ===== |
| |
| ==== ipython interpreter ==== | ==== 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'' | Starting ipython: ''ipython'' |
| * [[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 ==== |
| |
| 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]]). | <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> |
| | |
| | [[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]]). |
| |
| Starting the notebook server: ''ipython notebook'' | 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> |
| |
| /* standard page footer */ | /* standard page footer */ |
