Environments

An environment is used to group together a set of specs for the purpose of building, rebuilding and deploying in a coherent fashion. Environments provide a number of advantages over the à la carte approach of building and loading individual Spack modules:

  1. Environments separate the steps of (a) choosing what to install, (b) concretizing, and (c) installing. This allows Environments to remain stable and repeatable, even if Spack packages are upgraded: specs are only re-concretized when the user explicitly asks for it. It is even possible to reliably transport environments between different computers running different versions of Spack!

  2. Environments allow several specs to be built at once; a more robust solution than ad-hoc scripts making multiple calls to spack install.

  3. An Environment that is built as a whole can be loaded as a whole into the user environment. An Environment can be built to maintain a filesystem view of its packages, and the environment can load that view into the user environment at activation time. Spack can also generate a script to load all modules related to an environment.

Other packaging systems also provide environments that are similar in some ways to Spack environments; for example, Conda environments or Python Virtual Environments. Spack environments provide some distinctive features:

  1. A spec installed “in” an environment is no different from the same spec installed anywhere else in Spack. Environments are assembled simply by collecting together a set of specs.

  2. Spack Environments may contain more than one spec of the same package.

Spack uses a “manifest and lock” model similar to Bundler gemfiles and other package managers. The user input file is named spack.yaml and the lock file is named spack.lock

Using Environments

Here we follow a typical use case of creating, concretizing, installing and loading an environment.

Creating a named Environment

An environment is created by:

$ spack env create myenv

Spack then creates the directory var/spack/environments/myenv.

Note

All named environments are stored in the var/spack/environments folder.

In the var/spack/environments/myenv directory, Spack creates the file spack.yaml and the hidden directory .spack-env.

Spack stores metadata in the .spack-env directory. User interaction will occur through the spack.yaml file and the Spack commands that affect it. When the environment is concretized, Spack will create a file spack.lock with the concrete information for the environment.

In addition to being the default location for the view associated with an Environment, the .spack-env directory also contains:

  • repo/: A repo consisting of the Spack packages used in this environment. This allows the environment to build the same, in theory, even on different versions of Spack with different packages!

  • logs/: A directory containing the build logs for the packages in this Environment.

Spack Environments can also be created from either a spack.yaml manifest or a spack.lock lockfile. To create an Environment from a spack.yaml manifest:

$ spack env create myenv spack.yaml

To create an Environment from a spack.lock lockfile:

$ spack env create myenv spack.lock

Either of these commands can also take a full path to the initialization file.

A Spack Environment created from a spack.yaml manifest is guaranteed to have the same root specs as the original Environment, but may concretize differently. A Spack Environment created from a spack.lock lockfile is guaranteed to have the same concrete specs as the original Environment. Either may obviously then differ as the user modifies it.

Activating an Environment

To activate an environment, use the following command:

$ spack env activate myenv

By default, the spack env activate will load the view associated with the Environment into the user environment. The -v, --with-view argument ensures this behavior, and the -V, --without-vew argument activates the environment without changing the user environment variables.

The -p option to the spack env activate command modifies the user’s prompt to begin with the environment name in brackets.

$ spack env activate -p myenv
[myenv] $ ...

To deactivate an environment, use the command:

$ spack env deactivate

or the shortcut alias

$ despacktivate

If the environment was activated with its view, deactivating the environment will remove the view from the user environment.

Anonymous Environments

Any directory can be treated as an environment if it contains a file spack.yaml. To load an anonymous environment, use:

$ spack env activate -d /path/to/directory

Spack commands that are environment sensitive will also act on the environment any time the current working directory contains a spack.yaml file. Changing working directory to a directory containing a spack.yaml file is equivalent to the command:

$ spack env activate -d /path/to/dir --without-view

Anonymous specs can be created in place using the command:

$ spack env create -d .

In this case Spack simply creates a spack.yaml file in the requested directory.

Environment Sensitive Commands

Spack commands are environment sensitive. For example, the find command shows only the specs in the active Environment if an Environment has been activated. Similarly, the install and uninstall commands act on the active environment.

$ spack find
==> 0 installed packages

$ spack install zlib@1.2.11
==> Installing zlib
==> Searching for binary cache of zlib
==> Warning: No Spack mirrors are currently configured
==> No binary for zlib found: installing from source
==> Fetching http://zlib.net/fossils/zlib-1.2.11.tar.gz
######################################################################## 100.0%
==> Staging archive: /spack/var/spack/stage/zlib-1.2.11-3r4cfkmx3wwfqeof4bc244yduu2mz4ur/zlib-1.2.11.tar.gz
==> Created stage in /spack/var/spack/stage/zlib-1.2.11-3r4cfkmx3wwfqeof4bc244yduu2mz4ur
==> No patches needed for zlib
==> Building zlib [Package]
==> Executing phase: 'install'
==> Successfully installed zlib
  Fetch: 0.36s.  Build: 11.58s.  Total: 11.93s.
[+] /spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/zlib-1.2.11-3r4cfkmx3wwfqeof4bc244yduu2mz4ur

$ spack env activate myenv

$ spack find
==> In environment myenv
==> No root specs

==> 0 installed packages

$ spack install zlib@1.2.8
==> Installing zlib
==> Searching for binary cache of zlib
==> Warning: No Spack mirrors are currently configured
==> No binary for zlib found: installing from source
==> Fetching http://zlib.net/fossils/zlib-1.2.8.tar.gz
######################################################################## 100.0%
==> Staging archive: /spack/var/spack/stage/zlib-1.2.8-y2t6kq3s23l52yzhcyhbpovswajzi7f7/zlib-1.2.8.tar.gz
==> Created stage in /spack/var/spack/stage/zlib-1.2.8-y2t6kq3s23l52yzhcyhbpovswajzi7f7
==> No patches needed for zlib
==> Building zlib [Package]
==> Executing phase: 'install'
==> Successfully installed zlib
  Fetch: 0.26s.  Build: 2.08s.  Total: 2.35s.
[+] /spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/zlib-1.2.8-y2t6kq3s23l52yzhcyhbpovswajzi7f7

$ spack find
==> In environment myenv
==> Root specs
zlib@1.2.8

==> 1 installed package
-- linux-rhel7-x86_64 / gcc@4.9.3 -------------------------------
zlib@1.2.8

$ despacktivate
$ spack find
==> 2 installed packages
-- linux-rhel7-x86_64 / gcc@4.9.3 -------------------------------
zlib@1.2.8  zlib@1.2.11

Note that when we installed the abstract spec zlib@1.2.8, it was presented as a root of the Environment. All explicitly installed packages will be listed as roots of the Environment.

All of the Spack commands that act on the list of installed specs are Environment-sensitive in this way, including install, uninstall, activate, deactivate, find, extensions, and more. In the Configuring Environments section we will discuss Environment-sensitive commands further.

Adding Abstract Specs

An abstract spec is the user-specified spec before Spack has applied any defaults or dependency information.

Users can add abstract specs to an Environment using the spack add command. The most important component of an Environment is a list of abstract specs.

Adding a spec adds to the manifest (the spack.yaml file) and to the roots of the Environment, but does not affect the concrete specs in the lockfile, nor does it install the spec.

The spack add command is environment aware. It adds to the currently active environment. All environment aware commands can also be called using the spack -E flag to specify the environment.

$ spack activate myenv
$ spack add mpileaks

or

$ spack -E myenv add python

Concretizing

Once some user specs have been added to an environment, they can be concretized. The following command will concretize all user specs that have been added and not yet concretized:

[myenv]$ spack concretize

This command will re-concretize all specs:

[myenv]$ spack concretize -f

When the -f flag is not used to reconcretize all specs, Spack guarantees that already concretized specs are unchanged in the environment.

The concretize command does not install any packages. For packages that have already been installed outside of the environment, the process of adding the spec and concretizing is identical to installing the spec assuming it concretizes to the exact spec that was installed outside of the environment.

The spack find command can show concretized specs separately from installed specs using the -c (--concretized) flag.

[myenv]$ spack add zlib
[myenv]$ spack concretize
[myenv]$ spack find -c
==> In environment myenv
==> Root specs
zlib

==> Concretized roots
-- linux-rhel7-x86_64 / gcc@4.9.3 -------------------------------
zlib@1.2.11

==> 0 installed packages

Installing an Environment

In addition to installing individual specs into an Environment, one can install the entire Environment at once using the command

[myenv]$ spack install

If the Environment has been concretized, Spack will install the concretized specs. Otherwise, spack install will first concretize the Environment and then install the concretized specs.

As it installs, spack install creates symbolic links in the logs/ directory in the Environment, allowing for easy inspection of build logs related to that environment. The spack install command also stores a Spack repo containing the package.py file used at install time for each package in the repos/ directory in the Environment.

Loading

Once an environment has been installed, the following creates a load script for it:

$ spack env myenv loads -r

This creates a file called loads in the environment directory. Sourcing that file in Bash will make the environment available to the user; and can be included in .bashrc files, etc. The loads file may also be copied out of the environment, renamed, etc.

spack.yaml

Spack environments can be customized at finer granularity by editing the spack.yaml manifest file directly.

Configuring Environments

A variety of Spack behaviors are changed through Spack configuration files, covered in more detail in the Configuration Files section.

Spack Environments provide an additional level of configuration scope between the custom scope and the user scope discussed in the configuration documentation.

There are two ways to include configuration information in a Spack Environment:

  1. Inline in the spack.yaml file

  2. Included in the spack.yaml file from another file.

Inline configurations

Inline Environment-scope configuration is done using the same yaml format as standard Spack configuration scopes, covered in the Configuration Files section. Each section is contained under a top-level yaml object with it’s name. For example, a spack.yaml manifest file containing some package preference configuration (as in a packages.yaml file) could contain:

spack:
  ...
  packages:
    all:
      compiler: [intel]
  ...

This configuration sets the default compiler for all packages to intel.

Included configurations

Spack environments allow an include heading in their yaml schema. This heading pulls in external configuration files and applies them to the Environment.

spack:
  include:
  - relative/path/to/config.yaml
  - /absolute/path/to/packages.yaml

Environments can include files with either relative or absolute paths. Inline configurations take precedence over included configurations, so you don’t have to change shared configuration files to make small changes to an individual Environment. Included configs listed later will have higher precedence, as the included configs are applied in order.

Manually Editing the Specs List

The list of abstract/root specs in the Environment is maintained in the spack.yaml manifest under the heading specs.

spack:
    specs:
      - ncview
      - netcdf
      - nco
      - py-sphinx

Appending to this list in the yaml is identical to using the spack add command from the command line. However, there is more power available from the yaml file.

Spec Matrices

Entries in the specs list can be individual abstract specs or a spec matrix.

A spec matrix is a yaml object containing multiple lists of specs, and evaluates to the cross-product of those specs. Spec matrices also contain an excludes directive, which eliminates certain combinations from the evaluated result.

The following two Environment manifests are identical:

spack:
  specs:
    - zlib %gcc@7.1.0
    - zlib %gcc@4.9.3
    - libelf %gcc@7.1.0
    - libelf %gcc@4.9.3
    - libdwarf %gcc@7.1.0
    - cmake

spack:
  specs:
    - matrix:
        - [zlib, libelf, libdwarf]
        - ['%gcc@7.1.0', '%gcc@4.9.3']
      exclude:
        - libdwarf%gcc@4.9.3
    - cmake

Spec matrices can be used to install swaths of software across various toolchains.

The concretization logic for spec matrices differs slightly from the rest of Spack. If a variant or dependency constraint from a matrix is invalid, Spack will reject the constraint and try again without it. For example, the following two Environment manifests will produce the same specs:

spack:
  specs:
    - matrix:
        - [zlib, libelf, hdf5+mpi]
        - [^mvapich2@2.2, ^openmpi@3.1.0]

spack:
  specs:
    - zlib
    - libelf
    - hdf5+mpi ^mvapich2@2.2
    - hdf5+mpi ^openmpi@3.1.0

This allows one to create toolchains out of combinations of constraints and apply them somewhat indiscriminately to packages, without regard for the applicability of the constraint.

Spec List References

The last type of possible entry in the specs list is a reference.

The Spack Environment manifest yaml schema contains an additional heading definitions. Under definitions is an array of yaml objects. Each object has one or two fields. The one required field is a name, and the optional field is a when clause.

The named field is a spec list. The spec list uses the same syntax as the specs entry. Each entry in the spec list can be a spec, a spec matrix, or a reference to an earlier named list. References are specified using the $ sigil, and are “splatted” into place (i.e. the elements of the referent are at the same level as the elements listed separately). As an example, the following two manifest files are identical.

spack:
  definitions:
    - first: [libelf, libdwarf]
    - compilers: ['%gcc', '^intel']
    - second:
        - $first
        - matrix:
            - [zlib]
            - [$compilers]
  specs:
    - $second
    - cmake

spack:
  specs:
    - libelf
    - libdwarf
    - zlib%gcc
    - zlib%intel
    - cmake

Note

Named spec lists in the definitions section may only refer to a named list defined above itself. Order matters.

In short files like the example, it may be easier to simply list the included specs. However for more complicated examples involving many packages across many toolchains, separately factored lists make Environments substantially more manageable.

Additionally, the -l option to the spack add command allows one to add to named lists in the definitions section of the manifest file directly from the command line.

The when directive can be used to conditionally add specs to a named list. The when directive takes a string of Python code referring to a restricted set of variables, and evaluates to a boolean. The specs listed are appended to the named list if the when string evaluates to True. In the following snippet, the named list compilers is ['%gcc', '%clang', '%intel'] on x86_64 systems and ['%gcc', '%clang'] on all other systems.

spack:
  definitions:
    - compilers: ['%gcc', '%clang']
    - when: target == 'x86_64'
      compilers: ['%intel']

Note

Any definitions with the same named list with true when clauses (or absent when clauses) will be appended together

The valid variables for a when clause are:

  1. platform. The platform string of the default Spack architecture on the system.

  2. os. The os string of the default Spack architecture on the system.

  3. target. The target string of the default Spack architecture on the system.

  4. architecture or arch. The full string of the default Spack architecture on the system.

  5. re. The standard regex module in Python.

  6. env. The user environment (usually os.environ in Python).

  7. hostname. The hostname of the system (if hostname is an executable in the user’s PATH).

Environment-managed Views

Spack Environments can define filesystem views of their software, which are maintained as packages and can be installed and uninstalled from the Environment. Filesystem views provide an access point for packages from the filesystem for users who want to access those packages directly. For more information on filesystem views, see the section Filesystem Views.

Spack Environment managed views are updated every time the environment is written out to the lock file spack.lock, so the concrete environment and the view are always compatible.

Configuring environment views

The Spack Environment manifest file has a top-level keyword view. Each entry under that heading is a view descriptor, headed by a name. The view descriptor contains the root of the view, and optionally the projections for the view, and select and exclude lists for the view. For example, in the following manifest file snippet we define a view named mpis, rooted at /path/to/view in which all projections use the package name, version, and compiler name to determine the path for a given package. This view selects all packages that depend on MPI, and excludes those built with the PGI compiler at version 18.5.

spack:
  ...
  view:
    mpis:
      root: /path/to/view
      select: [^mpi]
      exclude: ['%pgi@18.5']
      projections:
        all: {name}/{version}-{compiler.name}

For more information on using view projections, see the section on Controlling View Projections. The default for the select and exclude values is to select everything and exclude nothing. The default projection is the default view projection ({}).

Any number of views may be defined under the view heading in a Spack Environment.

There are two shorthands for environments with a single view. If the environment at /path/to/env has a single view, with a root at /path/to/env/.spack-env/view, with default selection and exclusion and the default projection, we can put view: True in the environment manifest. Similarly, if the environment has a view with a different root, but default selection, exclusion, and projections, the manifest can say view: /path/to/view. These views are automatically named default, so that

spack:
  ...
  view: True

is equivalent to

spack:
  ...
  view:
    default:
      root: .spack-env/view

and

spack:
  ...
  view: /path/to/view

is equivalent to

spack:
  ...
  view:
    default:
      root: /path/to/view

By default, Spack environments are configured with view: True in the manifest. Environments can be configured without views using view: False. For backwards compatibility reasons, environments with no view key are treated the same as view: True.

From the command line, the spack env create command takes an argument --with-view [PATH] that sets the path for a single, default view. If no path is specified, the default path is used (view: True). The argument --without-view can be used to create an environment without any view configured.

The spack env view command can be used to change the manage views of an Environment. The subcommand spack env view enable will add a view named default to an environment. It takes an optional argument to specify the path for the new default view. The subcommand spack env view disable will remove the view named default from an environment if one exists. The subcommand spack env view regenerate will regenerate the views for the environment. This will apply any updates in the environment configuration that have not yet been applied.

Activating environment views

The spack env activate command will put the default view for the environment into the user’s path, in addition to activating the environment for Spack commands. The arguments -v,--with-view and -V,--without-view can be used to tune this behavior. The default behavior is to activate with the environment view if there is one.

The environment variables affected by the spack env activate command and the paths that are used to update them are in the following table.

Variable

Paths

PATH

bin

MANPATH

man, share/man

ACLOCAL_PATH

share/aclocal

LD_LIBRARY_PATH

lib, lib64

LIBRARY_PATH

lib, lib64

CPATH

include

PKG_CONFIG_PATH

lib/pkgconfig, lib64/pkgconfig

CMAKE_PREFIX_PATH

.

Each of these paths are appended to the view root, and added to the relevant variable if the path exists. For this reason, it is not recommended to use non-default projections with the default view of an environment.

The spack env deactivate command will remove the default view of the environment from the user’s path.