Differences

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

--- other:uvcdat:cdat_conda:miniconda3_install [2021/03/08 13:38]
jypeter created
+++ other:uvcdat:cdat_conda:miniconda3_install [2024/06/20 14:30] (current)
jypeter [Why is it vital to use only conda-forge ?] Add link to the mamba section
@@ Line 1: / Line 1: @@
 ====== JYP steps for installing Miniconda3 ======
-===== What? Why? =====
+===== Before installing Python on a shared computer =====
-  * //Miniconda3// is a minimal python environment/distribution that can be used for creating more complete working environments. It will basically make ''conda'' available on your computer, and then you can use ''conda'' to install and update more //stuff//.
+==== Desperately seeking a specific package ====
-  * A python //environment// is basically where and how you install python. A python //distribution// is more which packages you have chosen to install together in the environment. Hmmm, well, these are very similar things!
+Check if the Python package you are [[https://www.imdb.com/title/tt0089017/|desperately seeking]] is not already installed, before installing your own Python **on shared interactive Linux servers, or on batch computing clusters** !!
-  * You don't need to be (and **you should not be**) //root// when you install Miniconda3. You just need enough disk space where you have write access
+  * Ask other users who know the local environment
-  * If you are installing Miniconda3 in a Linux environment on a [[other:win10wsl|Windows 10 computer using Windows Subsystem for Linux (WSL)]], pay special attention to the instructions on the **WSL** lines
+  * Read the servers/clusters documentation: [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting|Python at LSCE by JYP]], [[https://intranet.lsce.ipsl.fr/informatique/index.php|LSCE]], [[https://documentations.ipsl.fr/spirit/|ESPRI Computing and Data Center]], ...
-  * The way you do things will depend on how you are going to use python? Are you installing the environment just for you, or for multiple users?
+  * Use ''[[other:newppl:starting#using_module_to_access_optional_programs|module avail [mod_name]]]'' to find out the Python versions available, and then ''module load'' and ''conda list'' to get more information on the available Python packages
+    * e.g. on ''spiritx'' ([[https://documentations.ipsl.fr/spirit/common/module_command.html|modules on spirit]])): <code>$ module avail python
+python/meso-3.8  python/meso-3.9  python/meso-3.10  python/meso-3.11
-  * We could also start with the //Anaconda// installer that will install a much more complete python environment, ready for use, but we choose not to do that because Anaconda requires more disk space at the beginning, with all its components coming from the //default// channel provided by the [[https://docs.conda.io/projects/conda/en/latest/glossary.html#conda-repository|conda repository]]. It's not useful because we will be mostly using (the same) packages provided by the [[https://conda-forge.org/feedstock-outputs/|conda-forge]] repository]].
+$ module avail anaconda
+anaconda-meso/2022.10    anaconda3-py/2020.11
+anaconda-meso/2023.09-0  anaconda3-py/2021.11
-The steps on this page are adapted from the much older (but with lots of extra and possibly useful details) [[other:uvcdat:conda_notes#installing_miniconda|installing miniconda]] instructions
+$ module avail pangeo
+pangeo-meso/2023.04.15  pangeo-meso/2024.01.22
-===== Installing miniconda3 =====
+$ module load pangeo-meso/2024.01.22
+(pangeo-meso-2024.01.22) $ which python
+/net/nfs/tools/u20/Python/miniconda3_py311_23.11.0-2/envs/pangeo-meso-2024.01.22/bin/python
+$ conda list | grep cartopy
+cartopy                   0.22.0          py311h320fe9a_1    conda-forge
+</code>
-  * Get the [[https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh|Python 3.8 Linux 64-bit (bash installer)]] (unless there is a [[https://conda.io/miniconda.html|more recent version?]])
+  * Lots of Python packages do very similar things. Maybe you can use another similar package that is already installed...
-    * Find some temporary space on Linux (or Windows, if you are using WSL)
-      * e.g. Linux at LSCE:\\ ''cd /home/scratch01/<your_login>''
-      * e.g. WSL, assuming that there is a ''C:\Scratch\<your_login>'' directory:\\ ''cd /mnt/c/Scratch/<your_login>''
-    * Use ''wget'' to download the installer:\\ ''wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh'' (90 Mb, 26 Feb 2021)
-  * Execute the installer
+  * If the packages you need are not available, it may be faster and easier to ask the local system administrators if they can install the packages, rather than doing everything yourself
-    * ''bash Miniconda3-latest-Linux-x86_64.sh''
-      * Accept the license
-      * Note: at the end of the installation (next step), **answer //no// to the following question**, so that the installer does not change your existing shell initialization files!\\ ''Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no]'' => **NO**
-      * Specify an explicit installation path **outside of your //home// directory**, with enough disk space (more than 3 Gb if you are going to install CDAT and some extra packages), preferably on a disk that is not backed up:
-        * Installations by //JYP//:
-          * Linux at LSCE: ''/home/share/unix_files/cdat/miniconda3'', or another subdirectory of ''/home/share/unix_files/cdat/''
-          * Linux on ciclad: ''/data/jypmce/cdat/miniconda3'', or another sub-directory of ''/data/jypmce/cdat/''
-        * WSL: installing to a directory that is not in ''/home/'' <wrap hi>does not work</wrap> (e.g. ''/mnt/h/CDAT/miniconda3'',assuming there is a ''H:\CDAT\'' directory, does not work)\\ You need to accept the installation in the default location: ''/home/<your_login>/miniconda3''
-      * The resulting ''miniconda3'' directory size is 342M\\ <code> > du -sh miniconda3
-M    miniconda3
- > cd miniconda3
+==== Using an unlisted Python distribution on a jupyter server ====
- > du -sh *
+If there is a //jupyter notebook server// connected to your system, and a Python environment providing all the packages you need, but that is not directly available on the notebook server, follow the [[other:python:starting#using_a_non-standard_kernel|using a non-standard kernel]] instructions, rather than starting your own local server
-M     bin
+===== Why should you use Miniconda3 ? =====
-       compiler_compat
-.0K    condabin
-K    conda-meta
-       envs
-K     etc
-.5M    include
-.0K    info
-M    lib
-K     LICENSE.txt
-M    pkgs
-K    share
-.0K    shell
-       ssl
-       x86_64-conda_cos6-linux-gnu</code>
-  * Initialize the newly installed conda environment:
+  * **//Miniconda3// is a minimal/bootstrap Python distribution** that can be used for creating more complex Python distributions.\\ It will basically make a recent ''conda'' command/executable available on your computer, and you can then use this ''conda'' executable to select an existing distribution, or create new and independent Python distributions.
-    * bash shell: ''source <installation_path>/miniconda3/etc/profile.d/conda.sh''
-    * tcsh shell: ''source <installation_path>/miniconda3/etc/profile.d/conda.csh''
-  * Check if you can use the ''conda'' command, and use it to initialize the //base// environment
+  * A **conda //environment//** is basically (the short name of the directory) where you install the Python that you will use (independently of //Miniconda3// itself). You have to ''activate'' this environment in order to use it\\ \\ A **Python //distribution//** is the collection of packages (and their dependencies) you have chosen to install together in a given environment.
-    * <code>$ which conda
+    * Example: initializing an environment named ''cdatm_py3'' (assuming it exists) in a //bash// shell <code>$ source /path_to_miniconda/etc/profile.d/conda.sh
-<installation_path>/miniconda3/condabin/conda
+$ which conda
+/path_to_miniconda/condabin/conda
+$ conda env list
+[...]
+cdatm_py3                /path_to_miniconda/envs/cdatm_py3
+some_other_env           /path_to_miniconda/envs/some_other_env
+$ conda activate cdatm_py3
+(cdatm_py3) $ which python
+/path_to_miniconda/envs/cdatm_py3/bin/python
+</code>
+    * The //special// environment where //Miniconda3// itself is installed is called ''base'' (it also used to be called ''root''). Note that the ''python'' binary of the //special// ''base'' environment is not located in the same directory hierarchy as the ''python'' of the other environments (i.e. there is no ''envs/'' subdirectory<code>$ conda activate base
+(base) $ which python
+/path_to_miniconda/bin/python
+</code>
+  * You **don't need to be (and you should not be !!) //root//** when you install //Miniconda3//. You just **need //enough// disk space** on a disk where you have write access
+    * **WARNING**: by default, //Miniconda3// will install itself and subsequent Python environments in a sub-directory of your home directory (''~/miniconda3'' on Linux). **Do not use the default installation location**, if you want to avoid disk space related problems (//disk full//, //quota exceeded//, ...) during the inittial installation or later
+      * **WARNING**: older versions of //Miniconda3// used a **hidden sub-directory** of the home directory of the person installing //Miniconda3// (''~/.conda'' on Linux)
+    * Choose carefully where you will install //Miniconda3//, because the size of the installation directory will start at a few Gb and will keep on growing
+  * You //could// also start with the full //Anaconda// (instead of //Miniconda//) installer, that will install a much more complete python environment, ready for use.\\ **We choose not to use the full //Anaconda// installer** because:
+    * It requires more disk space than //Miniconda3// during the initial installation,
+    * All the //Anaconda// installer packages come from the ''default'' //channel// (or //repository//) provided by the [[https://anaconda.org/|conda repository]].\\ This is not very useful for us (and could even cause complex dependency problems later) because we will be mostly using (the same) packages provided by the [[https://conda-forge.org/feedstock-outputs/|conda-forge]] //channel//, **in order to avoid complex package dependency problems**
+===== Downloading Miniconda3, and BASIC installation =====
+==== Miniconda3 on a Windows computer ====
+Some of the steps below are adapted from the [[https://docs.anaconda.com/free/miniconda/#quick-command-line-install|Windows section of "Quick command line install"]] to install a //pure Windows// version of Miniconda3
+=== Downloading the Miniconda3 installer on Windows ===
+  * We use a download link that always point to the [[https://docs.anaconda.com/free/miniconda/#latest-miniconda-installer-links|latest version of the Windows installer]]
+    * https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe
+    * The installer is based on **Python 3.12.2 and Conda 24.3.0 as of April 2024**
+  * Find some temporary disk space on Windows
+    * e.g. ''C:\Scratch\your_login'' or whatever you use as a [[other:win10config#local_scratch_folder|local Scratch folder]]
+  * Open a //terminal//, where you can type the required installation commands
+    * Windows //Powershell terminal//: ''Start'' => ''W'' => ''Windows PowerShell'' => ''Windows PowerShell''
+    * [[other:win10apps#windows_terminal|PowerShell in a Windows Terminal]]
+  * Use ''curl'' to download the latest installer (78 Mb as of April 2024): <code>PS C: cd C:\Scratch\your_login
+PS C:\Scratch\your_login> curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe -o miniconda.exe
+PS C:\Scratch\your_login> dir miniconda.exe
+[...]
+-a----        19/04/2024     11:18       81274240 miniconda.exe</code>
+=== BASIC Miniconda3 installation on Windows ===
+  * **Determine the folder where you will install Miniconda3 and ALL your future Python environments** based on this version of Miniconda3\\ **We will later refer to this installation location as ''/path_to_miniconda3/''** in the [[#miniconda3_on_a_linux-like_computer|Linux sections]] below
+    * Remember that **you will need a few Gb of available space**
+    * You should **avoid installing Miniconda3 in your Windows //home// folder** (''C:\Users\your_login'' or [[other:win10config#local_home_folder|<some_disk_different_from_c>:\Users\<your_login>]]), if you want to be able to easily make backups or your //home//, without backing up thousands of files related to your Python environments...
+    * We add some date or version information at the end of the folder name, in order to differentiate it from other (older of future) installations
+    * Example installation folder: ''C:\Utils\miniconda3_2024-03'' (if we start installing in March 2024)
+  * Launch the Miniconda3 installer with<code>PS C:\Scratch\your_login> .\miniconda.exe</code>
+  * In the installer window:
+    * (Review and) accept the License Agreement
+    * Choose to install for //Just Me// (the recommended default choice)
+    * Specify the //Destination Folder// selected above, e.g. ''C:\Utils\miniconda3_2024-03''
+    * Use the pre-selected //Advanced Installation Options//, i.e
+      * //Create start menu shortcutes//
+      * //Register Miniconda3 as my default Python 3.12// <= Useful?
+  * When the installer has finished running, you should have:
+    * A new ''C:\Utils\miniconda3_2024-03'' folder
+      * This folder size will be ~650 Mb and will keep on growing (up to several Gb) as you add more Python environments and packages
+        * => **Be sure to have enough space on this disk!**
+    * Two new shortcuts in the Windows ''Start''=>''M''=>''Miniconda3'' menu:
+      * ''Anaconda Prompt''
+      * ''Anaconda Powershell Prompt''
+        * **We will now use this //Anaconda PowerShell// shortcut each time we need to use Miniconda3 or Python**
+  * Remove the installer<code>PS C:\Scratch\your_login> del .\miniconda.exe</code>
+  * Open an //Anaconda PowerShell Prompt//, and type a few commands to make sure that ''conda'' is working
+    * ''Start''=>''M''=>''Miniconda3'' => ''Anaconda Powershell Prompt''
+    * <code>(base) PS C:\Users\your_login> conda env list
+base                  *  C:\Utils\miniconda3_2024-03
+(base) PS C:\Users\your_login> conda list
+# packages in environment at C:\Utils\miniconda3_2024-03:
+# Name                    Version                   Build  Channel
+[...]
+conda                     24.3.0          py312haa95532_0
+[...]
+python                    3.12.2               h1d929f7_0
+[...]
+(base) PS C:\Users\your_login> conda deactivate
+PS C:\Users\your_login> conda env list
+base                     C:\Utils\miniconda3_2024-03</code>
+  * **Next**: be sure to <wrap hi>follow the steps in the [[other:uvcdat:cdat_conda:miniconda3_install#fine-tuning_conda_to_use_only_conda-forge|Fine-tuning conda to use (only) conda-forge]], and **all** the other Miniconda3 related instructions</wrap>
+    * ''conda'' commands will work the same way on all Operating Systems (Windows and Linux-like)
+    * The ''.condarc'' is located in your Windows //home// folder\\ => ''C:\Users\your_login\.condarc'' (or ''$HOME\.condarc'')
+==== Miniconda3 on a Linux-like computer ====
+<WRAP center round tip 60%>
+By **//Linux-like//**, we mean:
+  * A **Linux** desktop/laptop
+    * The installation will be used by **one** person
+  * A **Linux** server
+    * The installation will be used by **one or more** persons
+  * A **windows computer with [[other:win10wsl|WSL+Ubuntu installed]]**
+    * You should use the [[#miniconda3_on_a_windows_computer|Windows installer]], if all the packages you need are available for Windows
+    * The installation will be used by **one** person
+  * A **Mac** where you can use Linux in a terminal
+    * The installation will be used by **one** person
+</WRAP>
+=== Downloading the Miniconda3 installer on Linux ===
+  * **Important**: <wrap hi>do not install your own Python environment(s) on shared computers before you have made sure that the packages you need are not already installed, or cannot be easily installed in an existing environment (by the person who maintains this environment)!</wrap>
+    * Read again the [[#before_installing_python_on_a_shared_computer|Before installing Python on a shared computer]] section
+  * We use a download link that always point to the [[https://docs.anaconda.com/free/miniconda/#latest-miniconda-installer-links|latest version of the Linux installer]]
+    * For the Linux computers we commonly use, we need the //Miniconda3 Linux 64-bit// link: https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+      * Note: Mac users should use the latest [[https://docs.anaconda.com/free/miniconda/#latest-miniconda-installer-links|macOS installer]] appropriate for their computer
+    * The installer is based on **Python 3.12.2 and Conda 24.3.0 as of April 2024**
+  * Find some temporary space on Linux (or Windows, if you are using [[other:win10wsl|WSL]])
+    * e.g. Linux on the **LSCE** servers:\\ ''$ cd /home/scratch01/$USER''
+    * e.g. Linux on the IPSL **spiritx** cluster:<code>$ mkdir /homedata/$USER/Scratch
+$ cd /homedata/$USER/Scratch</code>
+    * e.g. Linux on a **personal PC/Mac desktop/laptop**: use a local scratch/temporary directory with //enough// space
+  * Use ''wget'' to download the latest installer (138 Mb as of 22 Mar 2024):\\ <code>$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+$ ls -lh Miniconda3-latest-Linux-x86_64.sh
+[...] 138M Feb 27 20:40 Miniconda3-latest-Linux-x86_64.sh</code>
+=== Using the Miniconda3 installer on Linux ===
+We assume below that we are in the [[#downloading_the_miniconda3_installer_on_linux|directory where we have downloaded the installer]]
+  * **Determine the directory where you will install miniconda3 and all the Python environments** based on this version of miniconda3, but **do not create the directory** (the installation script will do it)\\ \\ **We will later refer to this location as ''/path_to_miniconda3/''**\\ \\
+    * Remember that **you will need a few Gb of available space**
+    * **If you want to share this installation with other users**, the directory has to be readable by these users
+    * Always **avoid installing in your //home// directory**, if you want to be able to easily make backups or your //home//, without backing up thousands of files related to your Python installation...
+    * We add some date or version information at the end of the directory, in order to differentiate it from other (older of future) installations
+      * e.g. //JYP// shared Linux installation at **LSCE**: ''/home/share/unix_files/cdat/miniconda3_2024-03''
+      * e.g. Linux at **spiritx**: ''/homedata/$USER/miniconda3_2024-03''
+  * Execute the installer with ''$ bash Miniconda3-latest-Linux-x86_64.sh''
+    * Review the license (type ''<SPACE>'' several times...) and accept it
+    * When asked for the installation directory, specify the directory location chosen in the previous step, and **not the default directory**
+      * e.g. specify\\ ''/path_to_miniconda3/''\\ instead of the default\\ ''$HOME/miniconda3''
+    * **Answer ''no'' to the question ''Do you wish to update your shell profile to automatically initialize conda?''**.\\ Otherwise the installation will make changes to your shell configuration files
+      * If you forget to answer ''no'', you can apparently:
+        * later remove the changes to your shell configuration files by typing: ''conda init %%--%%reverse $SHELL''
+        * or at least disable the automatic activation of the environment (that might have side effect) by typing: ''conda config %%--%%set auto_activate_base false''
+    * The resulting initial ''miniconda3'' directory size is 647 Mb (as of March 2024).\\ Remember that **this directory size will keep on growing**!\\ <code>$ du -sh miniconda3_2024-03
+M    miniconda3_2024-03
+$ du -sh miniconda3_2024-03/*
+M     miniconda3_2024-03/bin
+K     miniconda3_2024-03/cmake
+.0K    miniconda3_2024-03/compiler_compat
+M     miniconda3_2024-03/_conda
+.0K    miniconda3_2024-03/condabin
+K    miniconda3_2024-03/conda-meta
+.0K    miniconda3_2024-03/envs
+K     miniconda3_2024-03/etc
+M     miniconda3_2024-03/include
+M    miniconda3_2024-03/lib
+K     miniconda3_2024-03/LICENSE.txt
+.1M    miniconda3_2024-03/man
+M    miniconda3_2024-03/pkgs
+K    miniconda3_2024-03/sbin
+.5M    miniconda3_2024-03/share
+K     miniconda3_2024-03/shell
+.0K    miniconda3_2024-03/ssl
+.0K    miniconda3_2024-03/x86_64-conda_cos7-linux-gnu
+.0K    miniconda3_2024-03/x86_64-conda-linux-gnu
+</code>
+  * Initialize the newly installed conda environment. This will initialize the environment **only in the current terminal**. When you have checked that things work properly, you can later make the initialization easier by following the steps in [[#initializing_conda_on_a_linux-like_computer|Initializing conda on a Linux-like computer]]
+    * You have to execute a configuration script, and then activate the environment
+      - Run the **init** script: ''source /some_path/conda_init_script''
+      - **Activate** the base environment (these two commands have the same result):
+        * ''conda activate''
+        * or ''conda activate base''
+    * **bash shell**: ''source /path_to_miniconda3/etc/profile.d/conda.sh''
+      * e.g. (spiritx): ''source /homedata/jypmce/miniconda3_2024-03/etc/profile.d/conda.sh''
+    * **tcsh shell**: ''source /path_to_miniconda3/etc/profile.d/conda.csh''
+      * e.g. (LSCE): ''source /home/share/unix_files/cdat/miniconda3_2024-03/etc/profile.d/conda.csh''
+  * After initializing the environment, check if you can access the ''conda'' command, and use it to initialize the //base// environment
+    * e.g. on **spiritx1**: <code>$ which conda
+/homedata/jypmce/miniconda3_2024-03/condabin/conda
 $ which python
 /usr/bin/python
-$ conda activate
+$ conda activate base
+(base) $ which conda
+/homedata/jypmce/miniconda3_2024-03/bin/conda
 (base) $ which python
-<installation_path>/miniconda3/bin/python</code>
+/homedata/jypmce/miniconda3_2024-03/bin/python
-  * Update the new installation
-    * <code>$ conda update --all
-[...]</code>
-    * During the update, the ''miniconda3'' directory size goes from 432 Mb to 581 Mb. This directory will keep on growing, which is the reason why you should put it on a (preferably non backed up) disk where you have //enough// space
-  * Make sure we have the latest ''conda'' (just in case we did not get it with the //update//)\\ ''conda update -n base -c defaults conda''
+(base) $ conda deactivate
-  * Remove the installer:\\ ''rm Miniconda3-latest-Linux-x86_64.sh''
+$ which conda
+/homedata/jypmce/miniconda3_2024-03/condabin/conda
+$ which python
+/usr/bin/python
+</code>
-==== Post-Miniconda3 installation ====
+  * Remove the //Miniconda3// installer: ''$ rm Miniconda3-latest-Linux-x86_64.sh''
-The idea is to remove the miniconda3 initialization lines that were automatically added at the end of ''.bashrc'' and put them (and other useful commands) in a special initialization file, that can be sourced only when we actually want to use conda and CDAT (in order to avoid potentiel side effects)
+===== Fine-tuning conda to use (only) conda-forge =====
-=== New style initialization ===
+<note important>Be sure to **also follow these steps on a Windows installation** !</note>
-Note: this is the **new** ''conda activate some_version'' style
+==== Why is it vital to use only conda-forge ? ====
-See the ''~jypeter/.conda3_jyp.sh'' file below, and how to use it, **in a bash shell**. In a **tcsh shell**, see the ''~jypeter/.conda3_jyp.csh'' further down. In both shell cases, if you are installing your own version of python, you need to use your own location of the initialization files in the ''source'' lines, and you can use another file name than ''conda3_jyp''
+  * ''conda'' will probably work fine with the default settings **if you create simple new environments** with just one package and its dependencies.
-<code>$ which python
+  * ''conda'' works much better and faster since the end of 2023 (''conda'' versions starting at ''23.10''), now that it is [[https://conda.org/blog/2023-07-05-conda-libmamba-solver-rollout/|using the mamba solver]] instead of the default solver.
-/usr/bin/python
+    * Use ''conda %%--%%version'' version to determine which version you are using<code>$ conda --version
+conda 24.5.0
+</code>
-$ cat ~jypeter/.conda3_jyp.sh
+  * We are power users, and **we intend to create complex Python environments** combining lots (and lots) of packages available from ''conda-forge'', with complex dependencies, and we may run into dependency problems when combining packages coming from both //conda// and //conda-forge//.
-# Conda initialization by JYP, NEW style
+    * => **The sections below configure ''conda'' to always use //conda-forge//**, and completely update //Miniconda3// itself with packages coming only from //conda-forge//
-#
-# Use this for working with conda and CDAT centrally managed by JYP
-#
-# Execute this file in a BASH shell with
-#     source path/this_file
-# Then get the list of available python distributions with
-#     conda env list
-# Then activate a specific distribution with
-#     conda activate version_name
-#
-# More details in:
-#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_versions_of_uv-cdat
-#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:uvcdat:conda_notes
-#
-# Jean-Yves Peterschmitt - LSCE - 11/2018
-source /home/share/unix_files/cdat/miniconda3/etc/profile.d/conda.sh
+  * Very unlikely situation: if you use a recent version of ''conda'' (''>= 23.10''), and you have followed all the steps below, in order to **use only //conda-forge// packages**, and there are still some package installation problems, try to [[#adding_mamba_optional|install and use mamba]], as a drop-in replacement of ''conda''
+    * Historical note: before ''conda'' used ''libmamba'', we had to use ''mamba'' (instead of ''conda'') for dealing with our complex Python environments:
+      * [[https://wolfv.medium.com/making-conda-fast-again-4da4debfb3b7|Making conda fast again]]
+      * [[https://github.com/conda/conda/issues/9367#issuecomment-793968239|Solving environment: failed with initial frozen solve. Retrying with flexible solve.]]
-# Use the alias below to easily determine where your python
+==== Changing the .condarc file ====
-# interpreter is located
-alias wp="which python"
-# Where are ALL the python interpreters in the search path
+The following steps will **make sure that we only get packages from //conda-forge//**  (same thing as using the ''-c conda-forge'' option) **by default**, unless the requested packages really do not exist on //conda-forge//. More details in [[https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html|Managing channels]]
-alias wpa="which -a python"
-# The end
+<code>$ cat ~/.condarc  # On Windows use: cat $HOME\.condarc
+cat: /home/jypmce/.condarc: No such file or directory
-$ source ~jypeter/.conda3_jyp.sh
+$ conda config --get channels
-$ conda activate
+$ conda config --prepend channels conda-forge
-(base) $ which python
-/home/share/unix_files/cdat/miniconda3/bin/python
+$ conda config --set channel_priority strict
+$ conda config --get channels
+--add channels 'defaults'   # lowest priority
+--add channels 'conda-forge'   # highest priority
+$ cat ~/.condarc  # On Windows use: cat $HOME\.condarc
+channels:
+  - conda-forge
+  - defaults
+channel_priority: strict
 </code>
-**tcsh shell** usage example
+==== Updating Miniconda3 at least once! ====
-<code> >which python
+<wrap hi>Do not forget to [[#the_first_time_we_update_miniconda3|update conda at least once]] in order to take all the changes above into account!</wrap>
-/usr/bin/python
+===== Adding mamba (optional) =====
- >cat ~jypeter/.conda3_jyp.csh
+<WRAP center round alert 60%>
-# Conda initialization by JYP, NEW style
+  * Most people can (and should!) probably skip the ''mamba'' installation
+  * Only install ''mamba'' if you are sure that you will need some features that are not already provided by ''conda'' (e.g. ''conda repoquery'')
+</WRAP>
+[[https://mamba.readthedocs.io/|mamba]] is a fast, robust, and cross-platform package manager [...] fully compatible with conda packages, and supports most of conda’s commands
+==== Installing mamba ====
+  * ''mamba'' is used to manage environments, and **has to be installed in the //base// environment** (i.e. in the same environment as ''conda'')!
+  * If :
+    * You sure that [[https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html#existing-conda-install-not-recommended|you need ''mamba'', even the the developers advise not to mix conda and mamba]]
+    * You [[#fine-tuning_conda_to_use_only_conda-forge|use conda-forge by default]]
+    * Then you can use: ''conda install -n base mamba''
+==== Using mamba ====
+  * The useful mamba commands (wee need) are listed in the [[#useful_conda_commands|Useful conda commands section]]
+    * We mostly need ''[[https://mamba.readthedocs.io/en/latest/user_guide/mamba.html#repoquery|mamba repoquery]]''
+  * [[https://mamba.readthedocs.io/en/latest/user_guide/mamba.html|Mamba User Guide]]
+===== Keeping (Mini)conda up-to-date =====
+==== The update command ====
+  * Just type ''conda update -n base %%--%%all'', (review) and accept the changes
+    * Things should be OK if no package //downgrades// are requested
+  * The ''base'' (//Miniconda3// itself) and the other Python environments installed with the ''conda'' executable provided by the ''base'' environment are all independent, and can be updated independently
+  * It is up to you to decide if and when you want to update environments...
+    * ...but <wrap hi>you have to **update the ''base'' environment at least once** in order to replace all of its packages by their equivalent ''conda-forge'' packages
+</wrap>
+  * You can later update again the full //Miniconda3//, or just the ''conda'' command.\\ This should not make any changes to the other Python environment(s) installed with //Miniconda3//
+    * <code>$ conda update -n base --all
+[...]
+# All requested packages already installed.
+(base) $ conda update -n base conda
+[...]
+# All requested packages already installed.
+</code>
+  * Note: during our initial installation, the ''miniconda3'' directory size grew from 763 Mb to 1.6 Gb, and we have not installed any custom Python environment yet! This is the reason why you should install //Miniconda3// on a (preferably non backed up) disk where you have //enough// free space
+    * <code>$ du -sh /homedata/jypmce/miniconda3_2024-03
+M    /homedata/jypmce/miniconda3_2024-03
+[... update]
+$ du -sh /homedata/jypmce/miniconda3_2024-03
+.6G    /homedata/jypmce/miniconda3_2024-03
+</code>
+==== The first time we update Miniconda3... ====
+We have to **completely update //Miniconda3// at least once after installing //Miniconda3//** and [[#fine-tuning_conda_to_use_only_conda-forge|making conda-forge the highest priority channel]]
+  * Check the current version of ''conda''
+    * <code>$ conda --version
+conda 24.1.2</code>
+  * Completely update the //Miniconda3// installation
+    * <code>$ conda update -n base --all
+Channels:
+ - conda-forge
+ - defaults
+Platform: linux-64
+Collecting package metadata (repodata.json): done
+Solving environment: done
+## Package Plan ##
+  environment location: /homedata/jypmce/miniconda3_2024-03
+The following packages will be downloaded:
+    package                    |            build
+    ---------------------------|-----------------
+    conda-24.3.0               |  py312h7900ff3_0         1.1 MB  conda-forge
+    conda-libmamba-solver-24.1.0|     pyhd8ed1ab_0          40 KB  conda-forge
+    python-3.12.2              |hab00c5b_0_cpython        30.8 MB  conda-forge
+[...]
+The following NEW packages will be INSTALLED:
+[...]
+The following packages will be UPDATED:
+[...]
+  conda              pkgs/main::conda-24.1.2-py312h06a4308~ --> conda-forge::conda-24.3.0-py312h7900ff3_0
+[...]
+The following packages will be SUPERSEDED by a higher-priority channel:
+[...]
+Proceed ([y]/n)? y
+[...]
+Preparing transaction: done
+Verifying transaction: done
+Executing transaction: done
+</code>
+  * Check the updated version of ''conda'' and ''python''. Note that **(almost) all** the packages should now specify that they are provided by ''conda-forge''
+    * <code>$ conda list -n base
+[...]
+conda                     24.3.0          py312h7900ff3_0    conda-forge
+conda-libmamba-solver     24.1.0             pyhd8ed1ab_0    conda-forge
+[...]
+python                    3.12.2          hab00c5b_0_cpython    conda-forge
+[...]
+</code>
+    * You can use the following to determine if some packages were **not** available in ''conda-forge''
+      * <code>$ conda list -n base | grep -v conda-forge
+# Name                    Version                   Build  Channel
+libedit                   3.1.20230828         h5eee18b_0
+libffi                    3.4.4                h6a678d5_0
+xz                        5.4.5                h5eee18b_0
+</code>
+      * It should not be a major problem if a few packages are not provided by ''conda-forge''.\\ It only means that some packages provided by the ''anaconda'' //channel// were more recent than the same packages provided by the ''conda-forge'' //channel// when the packages were updated
+        * ''libedit'' example: [[https://anaconda.org/conda-forge/libedit|version 3.1.20191231 @ conda-forge]] and [[https://anaconda.org/anaconda/libedit|version 3.1.20230828 @ anaconda]]
+==== Cleaning up Miniconda3... ====
+<WRAP center round important 60%>
+It seems safe to reclaim some disk space by cleaning up the initial (//base//) installation.\\ \\ Use cleaning with caution after installing other environments...
+</WRAP>
+You can [[https://docs.conda.io/projects/conda/en/latest/commands/clean.html|clean]] the initial //Miniconda3// installation to free up some disk space.
+The documentation specifies //WARNING: This will break environments with packages installed using symlinks back to the package cache.//\\ **You should probably avoid using ''clean'' once you have installed new Python environments** (unless you are desperate for disk space and know how to do a complete re-installation if something breaks...)
+<code>(base) $ conda clean --all
+Will remove 154 (180.9 MB) tarball(s).
+Proceed ([y]/n)? y
+Will remove 1 index cache(s).
+Proceed ([y]/n)? y
+Will remove 74 (378.0 MB) package(s).
+Proceed ([y]/n)? y
+There are no tempfile(s) to remove.
+There are no logfile(s) to remove.
+(base) $ du -sh /homedata/jypmce/miniconda3_2024-03
+M    /homedata/jypmce/miniconda3_2024-03
+</code>
+===== Initializing conda in terminals =====
+==== Initializing conda on a Windows computer ====
+  * Open a ''PowerShell'' terminal with: ''Start''=> ''M'' => ''Miniconda3'' => ''Anaconda Powershell Prompt''
+  * The ''base'' environment will be activated by default
+    * If you need another environment, just type: ''conda activate name_of_the_environment_you_want''
+**TODO** FIXME
+  * Find out how to use ''menuinst'' in order to directly initialize an existing environment (different from ''base'') from the ''Start'' menu and from a ''Windows Terminal''
+    * [[https://docs.conda.io/projects/conda-build/en/latest/resources/add-win-start-menu-items.html|Adding Windows Start menu items]]
+    * [[https://conda.github.io/menuinst/|menuinst documentation]]
+    * [[https://github.com/conda/menuinst/issues/196|Add Windows Terminal profile option]]
+==== Initializing conda on a Linux-like computer ====
+When you open a terminal, your shell needs to know where to find the ''conda'' command used to initialize an environment, or switch between existing environments. This can be **configured in your //shell// configuration files** (''.bashrc'', ''.cshrc'', ...)
+=== conda in a single-user Linux-like installation ===
+You were asked the following question when installing //Miniconda3//: //Do you wish to update your shell profile to automatically initialize conda? [yes|no]//
+  * **If you answered //yes//**, the installer probably added some very complicated lines to your shell configuration files, and ''conda'' and the newly installed ''python'' are probably directly available when you open a new terminal.\\ \\ **Warning!** The automatic activation might have **subtle side effects**. You can:
+    * **Remove the changes** to your shell configuration files by typing: ''conda init %%--%%reverse $SHELL''
+    * Or at least **disable the automatic activation** of the environment by typing: ''conda config %%--%%set auto_activate_base false''
+  * **If you answered //no//** ([[#using_the_miniconda3_installer_on_linux|as suggested]]), use a [[other:newppl:starting#text_editors|text editor]] to add extra lines to the appropriate shell configuration file\\ The changes will apply to all the **new** terminals you open\\ \\
+    * **bash shell** user : add these lines to ''~/.bashrc''\\ <code>source /path_to_miniconda3/etc/profile.d/conda.sh
+alias pynit='conda activate base'</code>
+      * e.g. (spiritx):<code>source /homedata/jypmce/miniconda3_2024-03/etc/profile.d/conda.sh
+alias pynit='conda activate base'</code>
+    * **tcsh shell** user: add these lines to ''~/.cshrc''\\ <code>source /path_to_miniconda3/etc/profile.d/conda.csh''
+alias pynit 'conda activate base'</code>
+      * e.g. (LSCE):<code>source /home/share/unix_files/cdat/miniconda3_2024-03/etc/profile.d/conda.csh
+alias pynit 'conda activate base'</code>
+    * After changing your configuration file, just **type ''pynit'' in any (new) terminal you open, when you need to use Python**
+    * When you have a custom Python environment installed (e.g. ''my_power_env'', you can update the ''pynit'' alias to initialize this environment instead of the ''base'' environment (e.g. ''conda activate my_power_env'')
+    * You can also define other aliases, or use another name than ''pynit''!
+=== conda in a multi-user Linux installation ===
+<WRAP center round info 60%>
+We need to be extra-careful in the case of **python environments maintained by a single user, but used by several users**, in order not to break anything
+</WRAP>
+We could use the same configuration file as in the //single-user case//, but **it is more efficient to have the users //source// an intermediate initialization file**. The intermediate file will:
+  * //source// the initialization file used in the single-user case
+  * Define some useful aliases:
+    * ''pynit'' => initialize the base environment (or the environment the central maintainer chooses)
+    * ''wp'' => ''which python''
+    * ''wconda'' => ''which python''
+    * more aliases, if required
+  * If changes have to be made, it is very easy to update this central initialization file accordingly, without asking the other users to make changes
+    * Do not forget to keep a copy of the previous version!
+    * Use a symbolic link (''ln -s'') to point from the unchanging central initialization file name to the latest initialization file.\\ conda@LSCE example in ''/home/share/unix_files/cdat/conda_init_files/'':<code>$ ls -l
+-rw-r--r-- Jun 14 16:37 conda3_jyp_2024-03.csh
+-rw-r--r-- Jun 14 17:48 conda3_jyp_2024-03.sh
+lrwxrwxrwx Jun 17 15:56 conda3_jyp_latest.csh -> conda3_jyp_2024-03.csh
+lrwxrwxrwx Jun 17 15:57 conda3_jyp_latest.sh -> conda3_jyp_2024-03.sh
+</code>
+  * **''bash'' users** should add to their ''~/.bashrc'' file something like\\ ''source  /some_path_accessible_by_all_users/shared_conda_init_file.sh''\\ \\ with a ''shared_conda_init_file.sh'' file looking like {{ :other:uvcdat:cdat_conda:conda3_jyp_2024-03.sh.txt |}}\\ \\ Examples:
+    * **LSCE**:\\ ''source /home/share/unix_files/cdat/conda_init_files/conda3_jyp_2024-03.sh''\\ or ''source /home/share/unix_files/cdat/conda_init_files/conda3_jyp_**latest**.sh'' (link to the **latest** version)
+    * **''spiritx''** and **''spirit''**:
+      * We use the fact that file systems on ''spiritx'' are accessible in //read-only// mode on ''spirit''
+      * ''source /homedata/jypmce/conda_init_files/conda3_jyp_spiritx_2024-03.sh''\\ or ''source /homedata/jypmce/conda_init_files/conda3_jyp_spiritx_**latest**.sh'' (link to the **latest** version)
+  * **''tcsh'' users** should add to their ''~/.cshrc'' file something like\\ ''source  /some_path_accessible_by_all_users/shared_conda_init_file.csh''\\ \\ with a ''shared_conda_init_file.csh'' file looking like {{ :other:uvcdat:cdat_conda:conda3_jyp_2024-03.csh.txt |}}\\ \\ Examples:
+    * **LSCE**:\\ ''source /home/share/unix_files/cdat/conda_init_files/conda3_jyp_2024-03.csh''\\ or ''source /home/share/unix_files/cdat/conda_init_files/conda3_jyp_**latest**.csh'' (link to the **latest** version)
+===== conda resources =====
+==== Web sites ====
+  * [[https://docs.conda.io/projects/conda/en/stable/|Official conda website]]
+    * [[https://docs.conda.io/projects/conda/en/stable/user-guide/cheatsheet.html|Cheat sheet]] (2 pages, for people in a hurry)
+    * [[https://docs.conda.io/projects/conda/en/stable/commands/|Commands' reference]]
+  * Package repositories
+    * [[https://conda-forge.org/packages/|conda-forge]] <= recommended source of packages
+    * [[https://anaconda.org/|default]]
+==== Useful conda commands ====
+This is just a subset of some of the commands, and a subset of their options! For a complete reference, use the [[https://docs.conda.io/projects/conda/en/stable/|official conda website]]
+  * **Get help**
+    * ''conda -h''
+      * ''conda //command// %%--%%help'': help for a specific //command//
+  * **Version and configuration** information
+    * Version information: ''conda %%--%%version''
+    * Detailed information: ''conda info''
+    * Full configuration: ''conda config %%--%%show''
+      * [[https://docs.conda.io/projects/conda/en/latest/commands/config.html|conda config]] documentation
+  * **Available environments**
+    * ''conda env list''
+    * The currently active environment has a "*****" character on its line<code>(base) $ conda env list
+# conda environments:
 #
-# Use this for working with conda and CDAT centrally managed by JYP
+base                  *  /homedata/jypmce/miniconda3_2024-03</code>
-#
-# Execute this file in a TCSH shell with
+  * **Activate** an existing environment (available in ''conda env list'') or **deactivate**, in order to go back to the default Python
-#     source path/this_file
+    * ''conda activate existing_environment''
-# Then get the list of available python distributions with
+      * ''conda activate'' (without specifying an environment name) will **activate the ''base'' Miniconda3 environment**
-#     conda env list
+    * Go back to the default Python available on the system
-# Then activate a specific distribution with
+      * ''conda deactivate''
-#     conda activate version_name
+    * You can type ''which python'' to determine where is the current ''python'' executable you are using is\\ You should **always know which Python you are using!**
-#
+      * <code>(base) $ which python
-# More details in:
+/homedata/jypmce/miniconda3_2024-03/bin/python
-#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:python:starting#conda-based_versions_of_uv-cdat
-#   https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:uvcdat:conda_notes
+(base) $ conda deactivate
-#
-# Jean-Yves Peterschmitt - LSCE - 11/2018
+$ which python
+/usr/bin/python</code>
+    * Note: //before conda ''4.6''//, you had to type ''**source** activate existing_environment'' and ''**source** deactivate''
+  * Get the **list of installed packages**, their version, and where they come from (e.g. ''conda-forge'', ''pip'')
+    * ''conda list [-n existing_environment]''
+  * **Create an environment** and install a few packages and their dependencies
+    * ''conda create -n new_environment_name package1 package2 packageN''
+  * **Delete an environment**
+    * ''conda remove -n crap_environment %%--%%all''
+  * **Find out if a package is available** on the //conda-forge// channel (or other channels)
+    * Note: you should always install a package with ''conda'' instead of ''pip'', if it is available on a //conda channel//
+    * ''conda search package_exact_name''\\ ''conda search '*package_partial_name*'''
+      * Note: ''search'' with wildcards fails in a //tcsh// shell, as of April 2024 ([[https://github.com/conda/conda/issues/9771|CSH install/search fail with '*' variable in an argument]])
+    * **Get very detailed information about a package** (versions, size, dependencies) with:\\ ''conda search package_exact_name %%--%%info''
+    * FIXME: find an option to get only the latest version
+  * **Install and remove packages**\\ Add ''-n target_environment'' to make changes in another environment than the active one
+    * ''conda install package1 package2 packageN''
+      * ''conda'' should already be [[#fine-tuning_conda_to_use_only_conda-forge|configured to use conda-forge by default]] if you have read this page carefully
+      * Add ''-c channel_url_or_alias'' to install from a specific //channel//
+    * ''conda remove package1 package2 packageN''
+  * **Update a package** in the current, or a specific environment
+    * ''conda update -n existing_environment installed_package''
+    * Update only the ''conda'' package (not the full Miniconda3 //base// environment) in ''base'' environment\\ ''conda update -n base conda''
+  * **Completely update an environment** (all the packages)
+    * ''conda update -n existing_environment %%--%%all''
+  * **Cleaning... <wrap em>Dangerous</wrap>**!
+    * ''conda'' does not automatically clean the content of the ''pkgs'' directory
+    * If you have several environments, ''conda clean'' may remove packages that are not needed in an environment, but are still used in other environments, and **you may end up with a broken installation...**
+    * More details in [[#cleaning_up_miniconda3|Cleaning up Miniconda3...]]
+==== conda, pip and virtualenv ====
+  * Read the [[https://docs.conda.io/projects/conda/en/stable/commands/#conda-vs-pip-vs-virtualenv-commands|Conda vs. pip vs. virtualenv commands]] section
+  * Read the [[https://docs.conda.io/projects/conda/en/stable/user-guide/tasks/manage-environments.html#using-pip-in-an-environment|Using pip in an environment]]
+==== Installation history ====
+You can get the current list of installed packages with ''conda list -n existing_environment'', but it may also be useful to know in which order the packages were installed:
+  * ''conda list -n existing_environment %%--%%revisions'': display **exactly** what was installed and when (including the updates, and automatic dependencies installation)
+    * You can theoretically roll back to a previous ''RR'' //revision// number with: ''conda install -n existing_environment %%--%%revision RR''
+  * There is more information in the ''/path_to_miniconda/conda-meta/history'' installation log files.
+    * ''base'' history file: ''/path_to_miniconda/conda-meta/history''
+    * ''existing_environment'' history file: ''/path_to_miniconda/envs/existing_environment/conda-meta/history''
+    * e.g. installation commands for the ''base'' environment:\\ <code> $ egrep -e 'cmd:' -e '==>' /homedata/jypmce/miniconda3_2024-03/conda-meta/history
-source /home/share/unix_files/cdat/miniconda3/etc/profile.d/conda.csh
+==> 2024-02-23 18:39:23 <==
+# cmd: constructor /tmp/tmp.4um5tGKcqW/miniconda3/ --output-dir /tmp/tmp.4um5tGKcqW
+==> 2024-03-27 16:10:01 <==
+# cmd: /homedata/jypmce/miniconda3_2024-03/bin/conda update -n base --all
+==> 2024-03-28 11:38:08 <==
+[...]
+==> 2024-04-24 17:47:32 <==
+# cmd: /homedata/jypmce/miniconda3_2024-03/bin/conda update -n base --all</code>
+    * You can also, use a script and the ''conda'' module available **in the ''base'' environment**: [[https://github.com/conda/conda/issues/4545#issuecomment-469984684|example]]
+===== Uninstalling Miniconda3 =====
-# Use the alias below to easily determine where your python
+==== Windows computer ====
-# interpreter is located
-alias wp "which python"
-# The end
+Miniconda3 can be removed like a regular Windows application
- >source  ~jypeter/.conda3_jyp.csh
+  * Go to the //Apps & features// panel
+    * ''Start'' => ''Settings''  => ''Apps'' => ''Apps & features''
+  * Select ''Miniconda3 py3xxxxx''
+  * Click on ''Uninstall'' and follow the instructions displayed by the uninstaller window
+    * This will remove:
+      * The (very big) directory that you specified when you installed //Miniconda3//
+      * The ''conda'' shortcuts from the ''Start Menu''
+    * This will **not** remove your local configuration file ''C:\Users\your_login\.condarc''
- >conda activate
+==== Linux-like computer ====
-(base) >which python
+FIXME
-/home/share/unix_files/cdat/miniconda3/bin/python</code>
-You probably don't want to type the //source// line each time you need to use your conda based python, so you can add a ''source  ~jypeter/.conda3_jyp.sh'' line in your ''~/.bashrc'' file, and ''source  ~jypeter/.conda3_jyp.csh'' line in your ''~/.cshrc'' file. Then, when you need a specific python environment, just type ''conda activate name_of_the_specific_environment''
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