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--- other:uvcdat:cdat_conda:miniconda3_install [2024/04/19 17:07] – [Miniconda3 on a Windows computer] More instructions jypeter
+++ other:uvcdat:cdat_conda:miniconda3_install [2024/04/25 16:24] – [Installation history] Added content jypeter
@@ Line 1: / Line 1: @@
 ====== 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 Linux servers, or on a shared cluster !!
+  * Ask other users who know the local environment
+  * Read the servers/cluster documentation
+  * 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
+    * e.g. on ''spiritx'': <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
+</code>
+  * Lots of Python packages do very similar things. Maybe you can use another installed package...
+  * 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 a specific Python on a jupyter server ====
+If there is a //jupyter notebook server// connected to your system, but the Python you want to use is not available on the 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 ? =====
@@ Line 41: / Line 66: @@
 ==== 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
+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 ===
@@ Line 54: / Line 79: @@
   * Open a //terminal//, where you can type the required installation commands
     * Windows //Powershell terminal//: ''Start'' => ''W'' => ''Windows PowerShell'' => ''Windows PowerShell''
-    * [[other:win10apps#windows_terminal|Windows Terminal]]
+    * [[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
@@ Line 64: / Line 89: @@
 === 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 location as ''/path_to_miniconda3/''** in the Linux sections
+  * **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 location as ''/path_to_miniconda3/''** in the Linux sections
     * 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''
+    * 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>
@@ Line 91: / Line 116: @@
   * 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<code>base) PS C:\Users\your_login> conda env list
+  * Open an //Anaconda PowerShell Prompt//, and type a few commands to make sure that ''conda'' is working<code>(base) PS C:\Users\your_login> conda env list
 base                  *  C:\Utils\miniconda3_2024-03
@@ Line 131: / Line 156: @@
 === Downloading the Miniconda3 installer ===
+  * 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>
+    * Check the output of ''module avail'', read your system documentation, ask other users...
   * 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]]
@@ Line 136: / Line 164: @@
       * 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 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/$USER/Scratch</code>
-    * e.g. Linux on a **personal PC/Mac desktop/laptop**: use a scratch/temporary directory with //enough// space
+    * e.g. Linux on a **personal PC/Mac desktop/laptop**: use a local scratch/temporary directory with //enough// space
   * Use ''wget'' to download the latest installer (138 Mb as of 22 Mar 2024):\\ <code>$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
@@ Line 373: / Line 402: @@
 </code>
 ===== Initializing conda in terminals =====
+<WRAP center round tip 60%>
+Reminder: if you have installed Miniconda3 on a Windows computer, you only have to open a terminal with
+  * ''Start'' menu => ''Anaconda Powershell Prompt''
+  * ''conda activate the_environment_you_want''
+</WRAP>
 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 the //shell// configuration files**
@@ Line 495: / Line 532: @@
 ==== 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]]
 ===== Uninstalling Miniconda3 =====
@@ Line 505: / Line 559: @@
     * ''Start'' => ''Settings''  => ''Apps'' => ''Apps & features''
   * Select ''Miniconda3 py3xxxxx''
-  * Click on ''Uninstall'' and follow the instructions displayed by the uninstaller window\\ This will remove:
+  * Click on ''Uninstall'' and follow the instructions displayed by the uninstaller window
-    * The (very big) directory that you specified when you installed //Miniconda3//
+    * This will remove:
-    * The ''conda'' shortcuts from the ''Start Menu''
+      * 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''
 ==== Linux-like computer ====
+FIXME