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--- conda [2020/07/17 08:32] – [Solutions to these pitfalls] jansen
+++ conda [2025/01/27 15:47] (current) – [Disk usage] jansen
@@ Line 7: / Line 7: @@
 ===== Installing Anaconda =====
-==== Method 1: Download and install ====
+==== Method 1: Use the provided version ====
+All our desktops and compute nodes currently have conda pre-installed, so you can skip the downlaod step, and with this version, the ''init'' step below can also be skipped. So if you choose this easiest solution. proceed to creating your environments (or tweaking the setup through config commands)
+==== Method 2: Download and install ====
 You can install anaconda or Miniconda (see anaconda website). This downloads a shell script you can run (either chmod 755 to make it executable, or run 'bash Miniconda3-latest-Linux-x86_64.sh' or whatever the name of your download is.
 Choose the location where you want to install the distribution (in a directory you own, but if you plan to install a lot of software, you should probably not install it in your home directory).
-==== Method 2: Use EasyBuild installed versions of Miniconda ====
+==== Method 3: Use EasyBuild installed versions of Miniconda ====
 We have pre-installed versions of Miniconda available through EasyBuild. Run
@@ Line 18: / Line 21: @@
 ===== Setup =====
 Now that you have the ''conda'' package manager available, you can use it to complete the setup.
+One bit of setup that ''conda'' insists on, is to add some initialization code to the login environment, so conda will always be active (''conda init bash'' or ''conda init tcsh''). However, see "pitfalls" section below.
+Note that with the system default version of conda, this init step is not necessary!
+Other bits of setup can be done through the ''conda config''  commands, see ''conda config --help'' for details. It is also possible to edit the ''$HOME/.condarc'' directly if you know what settings you want (eg by looking them up online).
 ===== Creating an environment =====
+One conda install can manage several environments, which are independent (except when set to inherit from another environment). The original install creates an environment ''base'', but it is best to create separate environments before using and modifying anything.
+To create an environment called ''TEST'', you run:
+  conda create --name TEST
+You can add package names and versions to add some packages immediately to the newly created environment, e.g.
+  conda create --name TEST python==3.6
+For more information, see the Anaconda websiete and output of ''conda create --help''
+Once created, you activate the environment using ''conda activate NAME''
 ===== Installing packages =====
+Install a package using ''conda install packagename'', optionally with a version as in ''conda install python==3.7'' to make sure that exact version gets installed, if available.
+If unsure what packages are available, use ''conda search packagename'' to search for any matching names (wildcards allowed, should be enclosed in quotes). To list installed packages, use ''conda list''.
 ===== Pitfalls =====
+==== Interference with system python environments ====
 As you can see above, the default behaviour when installing conda or running ''conda init'' is, to add some code to your .bashrc or .tcshrc to activate conda on every shell and in every window you open. That may sound like a nice feature, until you realize, that a custom version of python with a custom set of packages may wreak havoc on any environment that relies on the system default version. And there is a lot of software that happens to be written in python, or linked with it, including big parts of the Gnome and Cinnamon desktop applications. So, if you happen to set up a non-standard version of python as default, it might not be possible for you to log in in these desktop environments any more. Or even worse, if you need to install non-standard versions of gcc or its libraries, you might not be able to run a big part of the system software any more.
 ==== Solutions to these pitfalls ====
@@ Line 36: / Line 60: @@
+==== Disk usage ====
+Conda environments can be big. No wonder, since they can contain a full python install, libraries, compilers and many other tools. And as with most programs, conda defaults to store all of this in your $HOME since that is the one place that is known to exist on any UNIX system.
+So, you will want to change this location to something with more space, e.g. a local ''/data1'' or ''/data2'' disk.
+This can be done in ''.condarc'' by settings ''envs_dirs'' and ''pkgs_dirs'' to a chosen location. If you don't have a ''.condarc'' yet, create one with a text editor and add something like:
+  auto_activate_base: false
+  envs_dirs:
+    - /data2/yourname/conda/envs
+  pkgs_dirs:
+    - /data2/yourname/conda/pkgs
+Additional tip: having the environments locally on your workstation has advantages and disadvantages. One advantage is, that with the same setup, you can have a different instance of an environment on another machine, which is convenient if that other machine is not running the same Linux version as your desktop (eg compute nodes and vdesk).
+Disadvantage: if you occasionally use another desktop, you will not see your environments. In that case, use ''/net/computername/data2'' in stead of ''/data2''. in the configuration.
+If you are making this change when you already have some conda environments (in $HOME/.conda), you can move them to the new location. And just to be sure, in case there are already hard-coded path names in the environment, make a symbolic link. So, using the example .condarc shown above:
+  mv .conda /data2/yourname/conda
+  ln -s /data2/yourname/conda ~/.conda

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