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other:uvcdat:cdat_conda:miniconda3_install [2024/03/26 10:41] jypeter [Using the installer] |
other:uvcdat:cdat_conda:miniconda3_install [2024/07/02 12:39] jypeter [Miniconda3 on a Windows computer] |
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====== JYP steps for installing Miniconda3 ====== | ====== JYP steps for installing Miniconda3 ====== | ||
+ | ===== Before installing Python on a shared computer ===== | ||
+ | |||
+ | ==== Desperately seeking a specific package ==== | ||
+ | |||
+ | 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** !! | ||
+ | |||
+ | * Ask other users who know the local environment | ||
+ | |||
+ | * 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]], ... | ||
+ | |||
+ | * 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 | ||
+ | |||
+ | $ module avail anaconda | ||
+ | anaconda-meso/2022.10 anaconda3-py/2020.11 | ||
+ | anaconda-meso/2023.09-0 anaconda3-py/2021.11 | ||
+ | |||
+ | $ module avail pangeo | ||
+ | pangeo-meso/2023.04.15 pangeo-meso/2024.01.22 | ||
+ | |||
+ | $ 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> | ||
+ | |||
+ | * Lots of Python packages do very similar things. Maybe you can use another similar package that is already installed... | ||
+ | |||
+ | * 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 | ||
+ | |||
+ | ==== Using an unlisted Python distribution on a jupyter server ==== | ||
+ | |||
+ | 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 | ||
===== Why should you use Miniconda3 ? ===== | ===== Why should you use Miniconda3 ? ===== | ||
- | * **//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 available on your computer, and you can then use this ''conda'' executable to select an existing distribution, or create new and independent Python distributions. | + | * **//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. |
- | * 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. | + | * 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. |
- | * Example: initializing an environment named ''cdatm_py3'' (assuming it exists)<code>$ source /path_to_miniconda/etc/profile.d/conda.sh | + | * Example: initializing an environment named ''cdatm_py3'' (assuming it exists) in a //bash// shell <code>$ source /path_to_miniconda/etc/profile.d/conda.sh |
$ which conda | $ which conda | ||
Line 21: | Line 57: | ||
/path_to_miniconda/envs/cdatm_py3/bin/python | /path_to_miniconda/envs/cdatm_py3/bin/python | ||
</code> | </code> | ||
- | * The special environment where //Miniconda3// itself is installed is called ''base''. Note that the ''python'' binary of the ''base'' environment is not located in the same directory hierarchy of the other environments (i.e. there is no ''envs/'' subdirectory<code>$ conda activate base | + | * 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 | (base) $ which python | ||
Line 27: | Line 63: | ||
</code> | </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 | + | * 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//, ...) | + | * **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 your home directory (''~/.conda'' on Linux) for the installation | + | * **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 | * 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 | ||
- | * 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 specific instructions on the **WSL** lines | + | * 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** | ||
- | * You could also start with the full //Anaconda// 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// at the beginning, and all its packages come from the ''default'' //channel// (or //repository//) provided by the [[https://docs.conda.io/projects/conda/en/latest/glossary.html#conda-repository|conda repository]]. This is not very useful (and could even cause complex dependency problems) 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**. | ||
- | Note: some extra details are available on the much older page //Installing and maintaining UV-CDAT with conda//. You can check later the [[other:uvcdat:conda_notes#useful_conda_commands|Useful conda commands]], but the [[https://docs.conda.io/projects/conda/en/latest/index.html|official conda documentation]] and the [[https://docs.conda.io/projects/conda/en/latest/user-guide/cheatsheet.html|Cheat sheet]] are probably more up-to-date. | + | ===== 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// folder, 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? | ||
+ | * There is no need to bookmark the web pages suggested by the installer at the end, since this web page gives all the required information | ||
+ | |||
+ | * 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 ==== | ||
- | ===== Installing miniconda3 on a Linux-like computer ===== | ||
<WRAP center round tip 60%> | <WRAP center round tip 60%> | ||
- | By //Linux-like//, we mean: | + | By **//Linux-like//**, we mean: |
- | * A native Linux computer (or server) | + | * A **Linux** desktop/laptop |
- | * A windows 10 computer with [[other:win10wsl|WSL+Ubuntu installed]] | + | * The installation will be used by **one** person |
- | * A Mac where you can use Linux in a terminal | + | * 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> | </WRAP> | ||
- | ==== Downloading the Minconda3 installer ==== | + | |
+ | === 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]] | * 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 | * 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 | * 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 as of March 2024** | + | * 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]]) | * Find some temporary space on Linux (or Windows, if you are using [[other:win10wsl|WSL]]) | ||
- | * e.g. Linux at **LSCE**:\\ ''$ cd /home/scratch01/$USER'' | + | * e.g. Linux on the **LSCE** servers:\\ ''$ cd /home/scratch01/$USER'' |
- | * e.g. Linux at **spiritx**:<code>$ mkdir /homedata/$USER/Scratch | + | * e.g. Linux on the IPSL **spiritx** cluster:<code>$ mkdir /homedata/$USER/Scratch |
$ cd /homedata/$USER/Scratch</code> | $ cd /homedata/$USER/Scratch</code> | ||
- | * e.g. Linux on a **personal PC/Mac desktop/laptop**: use a scratch/temporary directory with //enough// space | + | * e.g. Linux on a **personal PC/Mac desktop/laptop**: use a local scratch/temporary directory with //enough// space |
- | * e.g. **WSL**, assuming that there is a ''C:\Scratch\<your_login>'' directory:\\ ''cd /mnt/c/Scratch/<your_login>'' | + | |
* Use ''wget'' to download the latest installer (138 Mb as of 22 Mar 2024):\\ <code>$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh | * 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 | ||
Line 66: | Line 190: | ||
[...] 138M Feb 27 20:40 Miniconda3-latest-Linux-x86_64.sh</code> | [...] 138M Feb 27 20:40 Miniconda3-latest-Linux-x86_64.sh</code> | ||
- | ==== Using the Miniconda3 installer ==== | + | === Using the Miniconda3 installer on Linux === |
- | We assume below that we are in the [[#downloading_the_installer|directory where we have downloaded the installer]] | + | 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/''** | + | * **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 | + | * Remember that **you will need a few Gb of available space** |
- | * At LSCE, do not install in a subdirectory of your home directory! | + | * **If you want to share this installation with other users**, the directory has to be readable by these users |
- | * On other servers and computers, you should also **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... | + | * 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 | * 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. Linux at **LSCE**: ''/home/share/unix_files/cdat/miniconda3_2024-03'' | + | * e.g. //JYP// shared Linux installation at **LSCE**: ''/home/share/unix_files/cdat/miniconda3_2024-03'' |
- | * e.g. Linux at **spiritx**: ''/homedata/$USER/miniconda3_2024-03'' | + | * e.g. Linux at **spiritx**: ''/homedata/$USER/miniconda3_2024-03'' |
- | * Linux (including WSL) on a **personal PC/Mac desktop/laptop**: find a directory with enough space (including space for adding more packages and their future updates) | + | |
* Execute the installer with ''$ bash Miniconda3-latest-Linux-x86_64.sh'' | * Execute the installer with ''$ bash Miniconda3-latest-Linux-x86_64.sh'' | ||
Line 85: | Line 208: | ||
* **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 | * **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: | * If you forget to answer ''no'', you can apparently: | ||
- | * remove the changes to your shell configuration files by typing later: ''conda init --reverse $SHELL'' | + | * later remove the changes to your shell configuration files by typing: ''conda init %%--%%reverse $SHELL'' |
- | * or at least disable the automatic activation of the environment (that might have side effect) by typing: ''conda config --set auto_activate_base false'' | + | * or at least disable the automatic activation of the environment (that might have side effect) by typing: ''conda config %%--%%set auto_activate_base false'' |
- | * The resulting ''miniconda3'' directory size is 647 Mb (as of March 2024)\\ <code>$ du -sh miniconda3_2024-03 | + | * 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 |
647M miniconda3_2024-03 | 647M miniconda3_2024-03 | ||
Line 112: | Line 235: | ||
</code> | </code> | ||
- | * Initialize the newly installed conda environment (this will initialize the environment **only in the current terminal**): | + | * 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'' | * **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'' | * e.g. (spiritx): ''source /homedata/jypmce/miniconda3_2024-03/etc/profile.d/conda.sh'' | ||
Line 118: | Line 246: | ||
* e.g. (LSCE): ''source /home/share/unix_files/cdat/miniconda3_2024-03/etc/profile.d/conda.csh'' | * e.g. (LSCE): ''source /home/share/unix_files/cdat/miniconda3_2024-03/etc/profile.d/conda.csh'' | ||
- | * Check if you can use the ''conda'' command, and use it to initialize the //base// environment | + | * 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 | * e.g. on **spiritx1**: <code>$ which conda | ||
- | $ which python | ||
- | /usr/bin/python | ||
- | |||
- | $ source /homedata/jypmce/miniconda3_2024-03/etc/profile.d/conda.sh | ||
- | |||
- | $ which conda | ||
/homedata/jypmce/miniconda3_2024-03/condabin/conda | /homedata/jypmce/miniconda3_2024-03/condabin/conda | ||
$ which python | $ which python | ||
Line 145: | Line 267: | ||
</code> | </code> | ||
+ | * Remove the //Miniconda3// installer: ''$ rm Miniconda3-latest-Linux-x86_64.sh'' | ||
- | ==== Fine-tuning conda to use conda-forge ==== | + | ===== Fine-tuning conda to use (only) conda-forge ===== |
- | conda will probably work fine with the default settings **if you create simple new environments** with just one package and its dependencies. Besides, conda works much better and faster since the end of 2023, now that it is [[https://conda.org/blog/2023-07-05-conda-libmamba-solver-rollout/|using the mamba solver]] instead of the default solver. | + | <note important>Be sure to **also follow these steps on a Windows installation** !</note> |
- | We are power users, and **we intend to create complex environments** combining lots of packages available in ''conda-forge'', with complex dependencies, and we may run into dependency problems when combining packages coming from both conda and conda-forge. **The solution is to configure conda to always use conda-forge**, and completely update Miniconda3 itself with packages coming from conda-forge | + | ==== Why is it vital to use only conda-forge ? ==== |
- | === Changing the .condarc file === | + | * ''conda'' will probably work fine with the default settings **if you create simple new environments** with just one package and its dependencies. |
- | Most of the packages we will install will be provided by the //conda-forge// channel (''-c conda-forge'' option). The installation steps will also add dependencies that will theoretically come from //conda-forge//, but could also come from the //defaults// channel. | + | * ''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. |
+ | * Use ''conda %%--%%version'' version to determine which version you are using<code>$ conda --version | ||
+ | conda 24.5.0 | ||
+ | </code> | ||
- | The following will **make sure that we only get packages from //conda-forge//** unless the requested packages really don't exist on //conda-forge// (see [[https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html|Managing channels]] and [[https://conda-forge.org/docs/user/tipsandtricks.html#how-to-fix-it|Using multiple channels => How to fix it]]) | + | * 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//. |
+ | * => **The sections below configure ''conda'' to always use //conda-forge//**, and completely update //Miniconda3// itself with packages coming only from //conda-forge// | ||
- | <code>$ conda config --add channels conda-forge | + | * 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'' |
- | $ conda config --set channel_priority strict | + | * Historical note: before ''conda'' used ''libmamba'', we had to use ''mamba'' (instead of ''conda'') for dealing with our complex Python environments: |
- | $ cat ~/.condarc | + | * [[https://wolfv.medium.com/making-conda-fast-again-4da4debfb3b7|Making conda fast again]] |
- | channels: | + | * [[https://github.com/conda/conda/issues/9367#issuecomment-793968239|Solving environment: failed with initial frozen solve. Retrying with flexible solve.]] |
- | - conda-forge | + | |
- | - defaults | + | |
- | channel_priority: strict</code> | + | |
- | <code>$ cat ~/.condarc | + | ==== Changing the .condarc file ==== |
+ | |||
+ | 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]] | ||
+ | |||
+ | <code>$ cat ~/.condarc # On Windows use: cat $HOME\.condarc | ||
cat: /home/jypmce/.condarc: No such file or directory | cat: /home/jypmce/.condarc: No such file or directory | ||
+ | |||
$ conda config --get channels | $ conda config --get channels | ||
+ | |||
$ conda config --prepend channels conda-forge | $ conda config --prepend channels conda-forge | ||
+ | |||
$ conda config --set channel_priority strict | $ conda config --set channel_priority strict | ||
+ | |||
$ conda config --get channels | $ conda config --get channels | ||
--add channels 'defaults' # lowest priority | --add channels 'defaults' # lowest priority | ||
--add channels 'conda-forge' # highest priority | --add channels 'conda-forge' # highest priority | ||
- | $ cat ~/.condarc | + | |
+ | $ cat ~/.condarc # On Windows use: cat $HOME\.condarc | ||
channels: | channels: | ||
- conda-forge | - conda-forge | ||
Line 181: | Line 314: | ||
</code> | </code> | ||
- | === Getting conda configuration information === | + | ==== Updating Miniconda3 at least once! ==== |
- | * [[https://docs.conda.io/projects/conda/en/latest/commands/config.html|conda config]] documentation | + | <wrap hi>Do not forget to [[#the_first_time_we_update_miniconda3|update conda at least once]] in order to take all the changes above into account!</wrap> |
- | * Basic information: ''conda info'' | + | ===== Adding mamba (optional) ===== |
- | * Full configuration: ''conda config --show'' | + | |
- | ==== Updating conda ==== | + | <WRAP center round alert 60%> |
+ | * Most people can (and should!) probably skip the ''mamba'' installation | ||
- | * Update the new installation | + | * Only install ''mamba'' if you are sure that you will need some features that are not already provided by ''conda'' (e.g. ''mamba repoquery'') |
- | * <code>$ conda update --all | + | </WRAP> |
- | [...]</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'' package (just in case we did not get it with the //update//)\\ ''conda update -n base conda'' | + | [[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 |
- | * Remove the installer later, when you have tester your installation:\\ ''rm Miniconda3-latest-Linux-x86_64.sh'' | + | ==== Installing mamba ==== |
- | ===== Initializing conda in new terminals ===== | + | * ''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 are sure that [[https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html#existing-conda-install-not-recommended|you need ''mamba'', even if the developers advise not to mix conda and mamba]] | ||
+ | - You have configured ''conda'' to [[#fine-tuning_conda_to_use_only_conda-forge|use conda-forge by default]] | ||
+ | - Then (and only then!) you can install ''mamba'':\\ => ''conda install -n base mamba'' | ||
- | When you open a terminal, your shell needs to know where to find the ''conda'' command used to initialize an environment, or switch between environments | + | ==== Using mamba ==== |
- | ==== General case ==== | + | * The useful mamba commands (we 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]] | ||
- | You were asked the following question when installing miniconda3: //Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no]// | ||
- | * If you answered //yes//, the installer probably added some very complicated lines to your shell configuration files, but you probably have ''conda'' directly available when you open a new terminal | + | ===== Keeping (Mini)conda up-to-date ===== |
- | * if you answered //no// (as suggested), use a text editor to add an extra line to the appropriate configuration file | + | |
- | * //bash// user: add this line to ''~/.bashrc''\\ ''source <installation_path>/miniconda3/etc/profile.d/conda.sh'' | + | |
- | * //tcsh// user: add this line to ''~/.cshrc''\\ ''source <installation_path>/miniconda3/etc/profile.d/conda.csh'' | + | |
- | We choose **not** to add a ''conda activate env_name'' line to the shell configuration files, in order to avoid side effects. When we open a new terminal, we get the default python available on the system. When we need a specific python environment, we just open a new window and then explicitly type: ''conda activate env_name'' | + | ==== The update command ==== |
- | ==== Multi-user installation ==== | + | * Just type ''conda update -n base %%--%%all'', (review) and accept the changes |
+ | * Things should be OK if no package //downgrades// are requested | ||
- | In the case of **python environments maintained by a single user, but used by several users**, we could do the same as in the //General case//, but it can be useful to have the users //source// an intermediate initialization file, that will then //source// the initialization file used in the general case. This makes it easier to maintain and change the environments, without asking users to make changes. | + | * 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 | ||
+ | 736M /homedata/jypmce/miniconda3_2024-03 | ||
+ | [... update] | ||
+ | $ du -sh /homedata/jypmce/miniconda3_2024-03 | ||
+ | 1.6G /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 | ||
+ | 457M /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**. This intermediate init file will: | ||
+ | |||
+ | * **//source// the conda initialization file** used in the single-user case | ||
+ | * **Define some aliases** that will be useful to all the people using these environments: | ||
+ | * ''pynit'' => initialize the //base// environment (or another default environment chosen by the central maintainer) | ||
+ | * ''wp'' => ''which python'' | ||
+ | * ''wconda'' => ''which python'' | ||
+ | * more aliases, if required | ||
+ | * If changes have to be made later, 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 of the init file! | ||
+ | * 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**: | ||
+ | * **Add to ''~/.bashrc''**: ''source /home/share/unix_files/cdat/conda_init_files/conda3_jyp_**latest**.sh'' | ||
+ | * Note: ''conda3_jyp_**latest**.sh'' is a link to the **latest** version of the init file,\\ currently ''/home/share/unix_files/cdat/conda_init_files/conda3_jyp_2024-03.sh'' | ||
+ | * **''spiritx''** and **''spirit''**: | ||
+ | * We use the fact that file systems on ''spiritx'' are accessible in //read-only// mode on ''spirit'' | ||
+ | * The python environments are installed on **local disks of ''spiritx''**, but they can also be used on ''spirit'', even if the remote disks access will add some latency | ||
+ | * **Add to ''~/.bashrc''**: ''source /homedata/jypmce/conda_init_files/conda3_jyp_spiritx_**latest**.sh'' | ||
+ | * Note: ''conda3_jyp_spiritx_**latest**.sh'' is a link to the **latest** version of the init file,\\ currently ''/homedata/jypmce/conda_init_files/conda3_jyp_spiritx_2024-03.sh'' | ||
+ | |||
+ | * **''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**: | ||
+ | * **Add to ''~/.cshrc''**: ''source /home/share/unix_files/cdat/conda_init_files/conda3_jyp_**latest**.csh'' | ||
+ | * Note: ''conda3_jyp_**latest**.csh'' is a link to the **latest** version of the init file,\\ currently ''/home/share/unix_files/cdat/conda_init_files/conda3_jyp_2024-03.csh'' | ||
+ | |||
+ | |||
+ | |||
+ | ===== Using (mini)conda to create a new environment ===== | ||
+ | |||
+ | * Once ''conda'' is installed (in the ''base'' environment provided by //Miniconda3//), configured and updated, you can use it to create a new environment with the packages that you (or other users, in a shared environment) need | ||
+ | * Use the commands described in [[#useful_conda_commands|Useful conda commands]] | ||
+ | |||
+ | * Detailed example: the ''xcdat'' environment | ||
+ | * FIXME: update/rewrite the [[other:uvcdat:cdat_conda:cdat_2024_03]] page | ||
+ | |||
+ | ===== 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: | ||
+ | # | ||
+ | base * /homedata/jypmce/miniconda3_2024-03</code> | ||
+ | |||
+ | * **Activate** an existing environment (available in ''conda env list'') or **deactivate**, in order to go back to the default Python | ||
+ | * ''conda activate existing_environment'' | ||
+ | * ''conda activate'' (without specifying an environment name) will **activate the ''base'' Miniconda3 environment** | ||
+ | * Go back to the default Python available on the system | ||
+ | * ''conda deactivate'' | ||
+ | * 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!** | ||
+ | * On Linux:<code>(base) $ which python | ||
+ | /homedata/jypmce/miniconda3_2024-03/bin/python | ||
+ | |||
+ | (base) $ conda deactivate | ||
+ | |||
+ | $ which python | ||
+ | /usr/bin/python</code> | ||
+ | * On Windows:<code>(base) PS C:\> where.exe conda | ||
+ | C:\Utils\miniconda3_2024-03\Library\bin\conda.bat | ||
+ | C:\Utils\miniconda3_2024-03\Scripts\conda.exe | ||
+ | C:\Utils\miniconda3_2024-03\condabin\conda.bat | ||
+ | |||
+ | (base) PS C:\> where.exe python | ||
+ | C:\Utils\miniconda3_2024-03\python.exe | ||
+ | C:\Users\jypeter\AppData\Local\Microsoft\WindowsApps\python.exe | ||
+ | |||
+ | (base) PS C:\Users\jypeter> conda deactivate | ||
+ | |||
+ | PS C:\> where.exe conda | ||
+ | C:\Utils\miniconda3_2024-03\condabin\conda.bat | ||
+ | |||
+ | PS C:\> where.exe python | ||
+ | C:\Users\jypeter\AppData\Local\Microsoft\WindowsApps\python.exe</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'') | ||
+ | * All the packages: ''conda list [-n existing_environment]'' | ||
+ | * Some packages: ''conda list [-n existing_environment] full_or_partial_name'' <code>(base) $ conda list libmamba | ||
+ | # Name Version Build Channel | ||
+ | conda-libmamba-solver 24.1.0 pyhd8ed1ab_0 conda-forge | ||
+ | libmamba 1.5.8 had39da4_0 conda-forge | ||
+ | libmambapy 1.5.8 py312hd9e9ff6_0 conda-forge | ||
+ | |||
+ | (base) $ conda list lib | ||
+ | _libgcc_mutex 0.1 conda_forge conda-forge | ||
+ | conda-libmamba-solver 24.1.0 pyhd8ed1ab_0 conda-forge | ||
+ | [...] | ||
+ | urllib3 2.2.2 pyhd8ed1ab_1 conda-forge | ||
+ | zlib 1.3.1 h4ab18f5_1 conda-forge | ||
+ | </code> | ||
+ | |||
+ | * **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'' or ''mamba'', 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]]) | ||
+ | * Search **results can be filtered** by using the [[#the_conda_matchspec_format|conda MatchSpec format]] | ||
+ | * **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 available for the current platform | ||
+ | * Did not find a way to do that efficiently (June 20th 2024), even with ''mamba'' :-( | ||
+ | |||
+ | * **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// | ||
+ | * **Specific versions can be specified** by using the [[#the_conda_matchspec_format|conda MatchSpec format]] | ||
+ | * ''conda remove package1 package2 packageN'' | ||
+ | |||
+ | * Display the **dependencies of a package**, and the **packages that need a specific packages** | ||
+ | * e.g. the ''requests'' package | ||
+ | |||
+ | * **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 the ''base'' environment\\ ''conda update -n base conda'' | ||
+ | |||
+ | * **Completely update an environment** (i.e. update **all** the packages) | ||
+ | * ''conda update -n existing_environment %%--%%all'' | ||
+ | * [[#the_first_time_we_update_miniconda3|'base' environment update example]] | ||
+ | |||
+ | * **Determine the relationship between installed packages** | ||
+ | * It can be useful to determine: | ||
+ | * the packages that are required in order to use a given package => ''depends'' | ||
+ | * the packages that need a given package => ''whoneeds'' | ||
+ | * Packages relationships can be listed with ''[[#adding_mamba_optional|mamba]] repoquery'' | ||
+ | * Note: ''mamba repoquery'' currently [[https://github.com/mamba-org/mamba/issues/3334|only works in the currently active environment]] | ||
+ | |||
+ | * **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 | ||
+ | |||
+ | ==> 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]] | ||
+ | |||
+ | ==== The conda MatchSpec format ==== | ||
+ | |||
+ | * The ''conda search'' command uses the //MatchSpec// format | ||
+ | |||
+ | * ''conda install'' and ''conda search'' //probably// use the same syntax | ||
+ | |||
+ | * The //MatchSpec// format is poorly documented... | ||
+ | * Fortunately, you will usually only specify the package name, and want to install the latest version of a package | ||
+ | |||
+ | * Using ''=='' (//exact version//) is **different** from ''='' (//"fuzzy" value//), which can be confusing | ||
+ | * <code>$ conda search zlib==1.2 | ||
+ | No match found for: zlib==1.2. Search: *zlib*==1.2 | ||
+ | PackagesNotFoundError: The following packages are not available from current channels: | ||
+ | - zlib==1.2 | ||
+ | |||
+ | $ conda search zlib=1.2 | ||
+ | # Name Version Build Channel | ||
+ | zlib 1.2.8 0 conda-forge | ||
+ | zlib 1.2.8 1 conda-forge | ||
+ | [...] | ||
+ | zlib 1.2.13 h5eee18b_1 pkgs/main | ||
+ | zlib 1.2.13 hd590300_5 conda-forge | ||
+ | |||
+ | $ conda search zlib==1.2.12 | ||
+ | zlib 1.2.12 h166bdaf_0 conda-forge | ||
+ | [...] | ||
+ | zlib 1.2.12 h7f8727e_2 pkgs/main | ||
+ | |||
+ | </code> | ||
- | * ask //bash// users to add to ''~/.bashrc'' something like\\ ''source ~main_installer_login/.conda3_jyp.sh''\\ \\ with a ''.conda3_jyp.sh'' file looking like {{ :other:uvcdat:cdat_conda:conda3_jyp.sh.txt |}} | + | * Documentation: |
+ | * [[https://docs.conda.io/projects/conda-build/en/latest/resources/package-spec.html#package-match-specifications|conda Package match specifications]] | ||
+ | * [[https://conda.io/projects/conda/en/latest/dev-guide/api/conda/models/match_spec/index.html#conda.models.match_spec.MatchSpec|Documentation in the MatchSpec class]] | ||
+ | ===== Uninstalling Miniconda3 ===== | ||
- | * ask //tcsh// users to add to ''~/.cshrc'' something like\\ ''source ~main_installer_login/.conda3_jyp.csh''\\ \\ with a ''.conda3_jyp.csh'' file looking like {{ :other:uvcdat:cdat_conda:conda3_jyp.csh.txt |}} | + | ==== Windows computer ==== |
- | ==== Using mamba instead of conda ==== | + | Miniconda3 can be removed like a regular Windows application |
- | Even when using a proper ''.condarc'' in order to get packages coming only from //conda-forge//, ''conda install'' may fail to solve the dependencies after meditating during an enormous time (e.g. [[https://github.com/conda/conda/issues/9367#issuecomment-793968239|Solving environment: failed with initial frozen solve. Retrying with flexible solve.]]), when we try to deal with **complex environments** (i.e. we already have lots of installed packages and we want to add even more packages). | + | * 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'' | ||
- | Using CDAT as a base environment, and adding a lot of extra packages is a **complex environment**. | + | ==== Linux-like computer ==== |
- | The only solution seems to replace ''conda'' with [[https://github.com/mamba-org/mamba|mamba]], a reimplementation of the conda package manager in C++ ([[https://wolfv.medium.com/making-conda-fast-again-4da4debfb3b7|Making conda fast again]]): | + | FIXME |
- | * Install ''mamba'' in the //base// (i.e. //miniconda//) environment\\ ''conda install mamba -n base -c conda-forge'' | + | |
- | * Use ''mamba'' instead of ''conda'' when installing packages.\\ Theoretically, you don't need to specify ''install -c conda forge'' any more, because ''conda-forge'' is now the default source of new packages\\ ''mamba install lots_of_packages'' | + | |