Package Settings (packages.yaml)¶

Spack allows you to customize how your software is built through the packages.yaml file. Using it, you can make Spack prefer particular implementations of virtual dependencies (e.g., MPI or BLAS/LAPACK), or you can make it prefer to build with particular compilers. You can also tell Spack to use external software installations already present on your system.

At a high level, the packages.yaml file is structured like this:

packages:
  package1:
    # settings for package1
  package2:
    # settings for package2
  # ...
  all:
    # settings that apply to all packages.

So you can either set build preferences specifically for one package, or you can specify that certain settings should apply to all packages. The types of settings you can customize are described in detail below.

Spack’s build defaults are in the default etc/spack/defaults/packages.yaml file. You can override them in ~/.spack/packages.yaml or etc/spack/packages.yaml. For more details on how this works, see Configuration Scopes.

External Packages¶

Spack can be configured to use externally-installed packages rather than building its own packages. This may be desirable if machines ship with system packages, such as a customized MPI that should be used instead of Spack building its own MPI.

External packages are configured through the packages.yaml file found in a Spack installation’s etc/spack/ or a user’s ~/.spack/ directory. Here’s an example of an external configuration:

packages:
  openmpi:
    externals:
    - spec: "openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64"
      prefix: /opt/openmpi-1.4.3
    - spec: "openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64+debug"
      prefix: /opt/openmpi-1.4.3-debug
    - spec: "openmpi@1.6.5%intel@10.1 arch=linux-debian7-x86_64"
      prefix: /opt/openmpi-1.6.5-intel

This example lists three installations of OpenMPI, one built with GCC, one built with GCC and debug information, and another built with Intel. If Spack is asked to build a package that uses one of these MPIs as a dependency, it will use the pre-installed OpenMPI in the given directory. Note that the specified path is the top-level install prefix, not the bin subdirectory.

packages.yaml can also be used to specify modules to load instead of the installation prefixes. The following example says that module CMake/3.7.2 provides cmake version 3.7.2.

cmake:
  externals:
  - spec: cmake@3.7.2
    modules:
    - CMake/3.7.2

Each packages.yaml begins with a packages: attribute, followed by a list of package names. To specify externals, add an externals: attribute under the package name, which lists externals. Each external should specify a spec: string that should be as well-defined as reasonably possible. If a package lacks a spec component, such as missing a compiler or package version, then Spack will guess the missing component based on its most-favored packages, and it may guess incorrectly.

Each package version and compiler listed in an external should have entries in Spack’s packages and compiler configuration, even though the package and compiler may not ever be built.

The packages configuration can tell Spack to use an external location for certain package versions, but it does not restrict Spack to using external packages. In the above example, since newer versions of OpenMPI are available, Spack will choose to start building and linking with the latest version rather than continue using the pre-installed OpenMPI versions.

To prevent this, the packages.yaml configuration also allows packages to be flagged as non-buildable. The previous example could be modified to be:

packages:
  openmpi:
    externals:
    - spec: "openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64"
      prefix: /opt/openmpi-1.4.3
    - spec: "openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64+debug"
      prefix: /opt/openmpi-1.4.3-debug
    - spec: "openmpi@1.6.5%intel@10.1 arch=linux-debian7-x86_64"
      prefix: /opt/openmpi-1.6.5-intel
    buildable: False

The addition of the buildable flag tells Spack that it should never build its own version of OpenMPI, and it will instead always rely on a pre-built OpenMPI. Similar to paths, buildable is specified as a property under a package name.

If an external module is specified as not buildable, then Spack will load the external module into the build environment which can be used for linking.

The buildable does not need to be paired with external packages. It could also be used alone to forbid packages that may be buggy or otherwise undesirable.

Virtual packages in Spack can also be specified as not buildable, and external implementations can be provided. In the example above, OpenMPI is configured as not buildable, but Spack will often prefer other MPI implementations over the externally available OpenMPI. Spack can be configured with every MPI provider not buildable individually, but more conveniently:

packages:
  mpi:
    buildable: False
  openmpi:
    externals:
    - spec: "openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64"
      prefix: /opt/openmpi-1.4.3
    - spec: "openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64+debug"
      prefix: /opt/openmpi-1.4.3-debug
    - spec: "openmpi@1.6.5%intel@10.1 arch=linux-debian7-x86_64"
      prefix: /opt/openmpi-1.6.5-intel

Implementations can also be listed immediately under the virtual they provide:

packages:
  mpi:
    buildable: False
      openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64: /opt/openmpi-1.4.3
      openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64+debug: /opt/openmpi-1.4.3-debug
      openmpi@1.6.5%intel@10.1 arch=linux-debian7-x86_64: /opt/openmpi-1.6.5-intel
      mpich@3.3 %clang@9.0.0 arch=linux-debian7-x86_64: /opt/mpich-3.3-intel

Spack can then use any of the listed external implementations of MPI to satisfy a dependency, and will choose depending on the compiler and architecture.

Automatically Find External Packages¶

You can run the spack external find command to search for system-provided packages and add them to packages.yaml. After running this command your packages.yaml may include new entries:

packages:
  cmake:
    externals:
    - spec: cmake@3.17.2
      prefix: /usr

Generally this is useful for detecting a small set of commonly-used packages; for now this is generally limited to finding build-only dependencies. Specific limitations include:

Packages are not discoverable by default: For a package to be discoverable with spack external find, it needs to add special logic. See here for more details.
The current implementation only collects and examines executable files, so it is typically only useful for build/run dependencies (in some cases if a library package also provides an executable, it may be possible to extract a meaningful Spec by running the executable - for example the compiler wrappers in MPI implementations).
The logic does not search through module files, it can only detect packages with executables defined in PATH; you can help Spack locate externals which use module files by loading any associated modules for packages that you want Spack to know about before running spack external find.
Spack does not overwrite existing entries in the package configuration: If there is an external defined for a spec at any configuration scope, then Spack will not add a new external entry (spack config blame packages can help locate all external entries).

Concretizer options¶

packages.yaml gives the concretizer preferences for specific packages, but you can also use concretizer.yaml to customize aspects of the algorithm it uses to select the dependencies you install:

# -------------------------------------------------------------------------
# This is the default spack configuration file.
#
# Settings here are versioned with Spack and are intended to provide
# sensible defaults out of the box. Spack maintainers should edit this
# file to keep it current.
#
# Users can override these settings by editing
# `$SPACK_ROOT/etc/spack/concretizer.yaml`, `~/.spack/concretizer.yaml`,
# or by adding a `concretizer:` section to an environment.
# -------------------------------------------------------------------------
concretizer:
  # Whether to consider installed packages or packages from buildcaches when
  # concretizing specs. If `true`, we'll try to use as many installs/binaries
  # as possible, rather than building. If `false`, we'll always give you a fresh
  # concretization.
  reuse: true
  # Options that tune which targets are considered for concretization. The
  # concretization process is very sensitive to the number targets, and the time
  # needed to reach a solution increases noticeably with the number of targets
  # considered.
  targets:
    # Determine whether we want to target specific or generic microarchitectures.
    # An example of the first kind might be for instance "skylake" or "bulldozer",
    # while generic microarchitectures are for instance "aarch64" or "x86_64_v4".
    granularity: microarchitectures
    # If "false" allow targets that are incompatible with the current host (for
    # instance concretize with target "icelake" while running on "haswell").
    # If "true" only allow targets that are compatible with the host.
    host_compatible: true
  # When "true" concretize root specs of environments together, so that each unique
  # package in an environment corresponds to one concrete spec. This ensures
  # environments can always be activated. When "false" perform concretization separately
  # on each root spec, allowing different versions and variants of the same package in
  # an environment.
  unify: false

Reuse already installed packages¶

The reuse attribute controls whether Spack will prefer to use installed packages (true), or whether it will do a “fresh” installation and prefer the latest settings from package.py files and packages.yaml (false). You can use:

% spack install --reuse <spec>

to enable reuse for a single installation, and you can use:

spack install --fresh <spec>

to do a fresh install if reuse is enabled by default. reuse: true is the default.

Selection of the target microarchitectures¶

The options under the targets attribute control which targets are considered during a solve. Currently the options in this section are only configurable from the concretization.yaml file and there are no corresponding command line arguments to enable them for a single solve.

The granularity option can take two possible values: microarchitectures and generic. If set to:

concretizer:
  targets:
    granularity: microarchitectures

Spack will consider all the microarchitectures known to archspec to label nodes for compatibility. If instead the option is set to:

concretizer:
  targets:
    granularity: generic

Spack will consider only generic microarchitectures. For instance, when running on an Haswell node, Spack will consider haswell as the best target in the former case and x86_64_v3 as the best target in the latter case.

The host_compatible option is a Boolean option that determines whether or not the microarchitectures considered during the solve are constrained to be compatible with the host Spack is currently running on. For instance, if this option is set to true, a user cannot concretize for target=icelake while running on an Haswell node.

Package Preferences¶

Spack can be configured to prefer certain compilers, package versions, dependencies, and variants during concretization. The preferred configuration can be controlled via the ~/.spack/packages.yaml file for user configurations, or the etc/spack/packages.yaml site configuration.

Here’s an example packages.yaml file that sets preferred packages:

packages:
  opencv:
    compiler: [gcc@4.9]
    variants: +debug
  gperftools:
    version: [2.2, 2.4, 2.3]
  all:
    compiler: [gcc@4.4.7, 'gcc@4.6:', intel, clang, pgi]
    target: [sandybridge]
    providers:
      mpi: [mvapich2, mpich, openmpi]

At a high level, this example is specifying how packages should be concretized. The opencv package should prefer using GCC 4.9 and be built with debug options. The gperftools package should prefer version 2.2 over 2.4. Every package on the system should prefer mvapich2 for its MPI and GCC 4.4.7 (except for opencv, which overrides this by preferring GCC 4.9). These options are used to fill in implicit defaults. Any of them can be overwritten on the command line if explicitly requested.

Each packages.yaml file begins with the string packages: and package names are specified on the next level. The special string all applies settings to all packages. Underneath each package name is one or more components: compiler, variants, version, providers, and target. Each component has an ordered list of spec constraints, with earlier entries in the list being preferred over later entries.

Sometimes a package installation may have constraints that forbid the first concretization rule, in which case Spack will use the first legal concretization rule. Going back to the example, if a user requests gperftools 2.3 or later, then Spack will install version 2.4 as the 2.4 version of gperftools is preferred over 2.3.

An explicit concretization rule in the preferred section will always take preference over unlisted concretizations. In the above example, xlc isn’t listed in the compiler list. Every listed compiler from gcc to pgi will thus be preferred over the xlc compiler.

The syntax for the provider section differs slightly from other concretization rules. A provider lists a value that packages may depend_on (e.g, MPI) and a list of rules for fulfilling that dependency.

Package Permissions¶

Spack can be configured to assign permissions to the files installed by a package.

In the packages.yaml file under permissions, the attributes read, write, and group control the package permissions. These attributes can be set per-package, or for all packages under all. If permissions are set under all and for a specific package, the package-specific settings take precedence.

The read and write attributes take one of user, group, and world.

packages:
  all:
    permissions:
      write: group
      group: spack
  my_app:
    permissions:
      read: group
      group: my_team

The permissions settings describe the broadest level of access to installations of the specified packages. The execute permissions of the file are set to the same level as read permissions for those files that are executable. The default setting for read is world, and for write is user. In the example above, installations of my_app will be installed with user and group permissions but no world permissions, and owned by the group my_team. All other packages will be installed with user and group write privileges, and world read privileges. Those packages will be owned by the group spack.

The group attribute assigns a Unix-style group to a package. All files installed by the package will be owned by the assigned group, and the sticky group bit will be set on the install prefix and all directories inside the install prefix. This will ensure that even manually placed files within the install prefix are owned by the assigned group. If no group is assigned, Spack will allow the OS default behavior to go as expected.