Document how to use Spack to replace Homebrew/Conda (#13083)
* Document how to use Spack to replace Homebrew/Conda * Initial draft; can iterate more as features become available
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Adam J. Stewart
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@ -1095,6 +1095,248 @@ or filesystem views. However, it has some drawbacks:
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integrate Spack explicitly in their workflow. Not all users are
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willing to do this.
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-------------------------------------
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Using Spack to Replace Homebrew/Conda
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-------------------------------------
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Spack is an incredibly powerful package manager, designed for supercomputers
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where users have diverse installation needs. But Spack can also be used to
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handle simple single-user installations on your laptop. Most macOS users are
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already familiar with package managers like Homebrew and Conda, where all
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installed packages are symlinked to a single central location like ``/usr/local``.
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In this section, we will show you how to emulate the behavior of Homebrew/Conda
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using :ref:`environments`!
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^^^^^
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Setup
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^^^^^
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First, let's create a new environment. We'll assume that Spack is already set up
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correctly, and that you've already sourced the setup script for your shell.
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To create a new environment, simply run:
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.. code-block:: console
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$ spack env create myenv
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==> Updating view at /Users/me/spack/var/spack/environments/myenv/.spack-env/view
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==> Created environment 'myenv' in /Users/me/spack/var/spack/environments/myenv
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$ spack env activate myenv
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Here, *myenv* can be anything you want to name your environment. Next, we can add
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a list of packages we would like to install into our environment. Let's say we
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want a newer version of Bash than the one that comes with macOS, and we want a
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few Python libraries. We can run:
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.. code-block:: console
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$ spack add bash
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==> Adding bash to environment myenv
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==> Updating view at /Users/me/spack/var/spack/environments/myenv/.spack-env/view
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$ spack add python@3:
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==> Adding python@3: to environment myenv
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==> Updating view at /Users/me/spack/var/spack/environments/myenv/.spack-env/view
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$ spack add py-numpy py-scipy py-matplotlib
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==> Adding py-numpy to environment myenv
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==> Adding py-scipy to environment myenv
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==> Adding py-matplotlib to environment myenv
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==> Updating view at /Users/me/spack/var/spack/environments/myenv/.spack-env/view
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Each package can be listed on a separate line, or combined into a single line.
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Notice that we're explicitly asking for Python 3 here. You can use any spec
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you would normally use on the command line with other Spack commands.
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Next, we want to manually configure a couple of things. In the ``myenv``
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directory, we can find the ``spack.yaml`` that actually defines our environment.
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.. code-block:: console
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$ vim ~/spack/var/spack/environments/myenv/spack.yaml
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.. code-block:: yaml
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# This is a Spack Environment file.
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#
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# It describes a set of packages to be installed, along with
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# configuration settings.
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spack:
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# add package specs to the `specs` list
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specs: [bash, 'python@3:', py-numpy, py-scipy, py-matplotlib]
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view:
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default:
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root: /Users/me/spack/var/spack/environments/myenv/.spack-env/view
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projections: {}
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config: {}
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mirrors: {}
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modules:
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enable: []
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packages: {}
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repos: []
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upstreams: {}
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definitions: []
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concretization: separately
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You can see the packages we added earlier in the ``specs:`` section. If you
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ever want to add more packages, you can either use ``spack add`` or manually
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edit this file.
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We also need to change the ``concretization:`` option. By default, Spack
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concretizes each spec *separately*, allowing multiple versions of the same
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package to coexist. Since we want a single consistent environment, we want to
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concretize all of the specs *together*.
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Here is what your ``spack.yaml`` looks like with these new settings, and with
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some of the sections we don't plan on using removed:
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.. code-block:: diff
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spack:
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- specs: [bash, 'python@3:', py-numpy, py-scipy, py-matplotlib]
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+ specs:
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+ - bash
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+ - 'python@3:'
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+ - py-numpy
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+ - py-scipy
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+ - py-matplotlib
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- view:
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- default:
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- root: /Users/me/spack/var/spack/environments/myenv/.spack-env/view
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- projections: {}
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+ view: /Users/me/spack/var/spack/environments/myenv/.spack-env/view
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- config: {}
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- mirrors: {}
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- modules:
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- enable: []
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- packages: {}
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- repos: []
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- upstreams: {}
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- definitions: []
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+ concretization: together
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- concretization: separately
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""""""""""""""""
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Symlink location
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""""""""""""""""
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In the ``spack.yaml`` file above, you'll notice that by default, Spack symlinks
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all installations to ``/Users/me/spack/var/spack/environments/myenv/.spack-env/view``.
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You can actually change this to any directory you want. For example, Homebrew
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uses ``/usr/local``, while Conda uses ``/Users/me/anaconda``. In order to access
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files in these locations, you need to update ``PATH`` and other environment variables
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to point to them. Activating the Spack environment does this automatically, but
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you can also manually set them in your ``.bashrc``.
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.. warning::
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There are several reasons why you shouldn't use ``/usr/local``:
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1. If you are on macOS 10.11+ (El Capitan and newer), Apple makes it hard
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for you. You may notice permissions issues on ``/usr/local`` due to their
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`System Integrity Protection <https://support.apple.com/en-us/HT204899>`_.
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By default, users don't have permissions to install anything in ``/usr/local``,
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and you can't even change this using ``sudo chown`` or ``sudo chmod``.
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2. Other package managers like Homebrew will try to install things to the
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same directory. If you plan on using Homebrew in conjunction with Spack,
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don't symlink things to ``/usr/local``.
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3. If you are on a shared workstation, or don't have sudo priveleges, you
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can't do this.
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If you still want to do this anyway, there are several ways around SIP.
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You could disable SIP by booting into recovery mode and running
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``csrutil disable``, but this is not recommended, as it can open up your OS
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to security vulnerabilities. Another technique is to run ``spack concretize``
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and ``spack install`` using ``sudo``. This is also not recommended.
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The safest way I've found is to create your installation directories using
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sudo, then change ownership back to the user like so:
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.. code-block:: bash
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for directory in .spack bin contrib include lib man share
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do
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sudo mkdir -p /usr/local/$directory
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sudo chown $(id -un):$(id -gn) /usr/local/$directory
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done
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Depending on the packages you install in your environment, the exact list of
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directories you need to create may vary. You may also find some packages
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like Java libraries that install a single file to the installation prefix
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instead of in a subdirectory. In this case, the action is the same, just replace
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``mkdir -p`` with ``touch`` in the for-loop above.
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But again, it's safer just to use the default symlink location.
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^^^^^^^^^^^^
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Installation
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^^^^^^^^^^^^
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To actually concretize the environment, run:
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.. code-block:: console
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$ spack concretize
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This will tell you which if any packages are already installed, and alert you
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to any conflicting specs.
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To actually install these packages and symlink them to your ``view:``
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directory, simply run:
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.. code-block:: console
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$ spack install
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Now, when you type ``which python3``, it should find the one you just installed.
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In order to change the default shell to our newer Bash installation, we first
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need to add it to this list of acceptable shells. Run:
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.. code-block:: console
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$ sudo vim /etc/shells
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and add the absolute path to your bash executable. Then run:
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.. code-block:: console
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$ chsh -s /path/to/bash
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Now, when you log out and log back in, ``echo $SHELL`` should point to the
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newer version of Bash.
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^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Updating Installed Packages
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^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Let's say you upgraded to a new version of macOS, or a new version of Python
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was released, and you want to rebuild your entire software stack. To do this,
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simply run the following commands:
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.. code-block:: console
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$ spack env activate myenv
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$ spack concretize --force
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$ spack install
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The ``--force`` flag tells Spack to overwrite its previous concretization
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decisions, allowing you to choose a new version of Python. If any of the new
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packages like Bash are already installed, ``spack install`` won't re-install
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them, it will keep the symlinks in place.
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^^^^^^^^^^^^^^
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Uninstallation
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^^^^^^^^^^^^^^
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If you decide that Spack isn't right for you, uninstallation is simple.
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Just run:
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.. code-block:: console
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$ spack env activate myenv
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$ spack uninstall --all
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This will uninstall all packages in your environment and remove the symlinks.
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------------------------
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Using Spack on Travis-CI
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------------------------
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