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. 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.

Prevent packages from being built from sources

Adding an external spec in packages.yaml allows Spack to use an external location, but it does not prevent Spack from building packages from sources. In the above example, Spack might choose for many valid reasons to start building and linking with the latest version of OpenMPI 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 from sources, and it will instead always rely on a pre-built OpenMPI.

Note

If concretizer:reuse is on (see Concretizer options for more information on that flag) pre-built specs include specs already available from a local store, an upstream store, a registered buildcache or specs marked as externals in packages.yaml. If concretizer:reuse is off, only external specs in packages.yaml are included in the list of pre-built specs.

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.

Non-buildable virtual packages

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

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.

In cases where the concretizer is configured to reuse specs, and other mpi providers (available via stores or buildcaches) are not wanted, Spack can be configured to require specs matching only the available externals:

packages:
  mpi:
    buildable: False
    require:
    - one_of: [
        "openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64",
        "openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64+debug",
        "openmpi@1.6.5%intel@10.1 arch=linux-debian7-x86_64"
      ]
  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 configuration prevents any spec using MPI and originating from stores or buildcaches to be reused, unless it matches the requirements under packages:mpi:require. For more information on requirements see Package Requirements.

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 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: true

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 Requirements

Spack can be configured to always use certain compilers, package versions, and variants during concretization through package requirements.

Package requirements are useful when you find yourself repeatedly specifying the same constraints on the command line, and wish that Spack respects these constraints whether you mention them explicitly or not. Another use case is specifying constraints that should apply to all root specs in an environment, without having to repeat the constraint everywhere.

Apart from that, requirements config is more flexible than constraints on the command line, because it can specify constraints on packages when they occur as a dependency. In contrast, on the command line it is not possible to specify constraints on dependencies while also keeping those dependencies optional.

The package requirements configuration is specified in packages.yaml keyed by package name:

packages:
  libfabric:
    require: "@1.13.2"
  openmpi:
    require:
    - any_of: ["~cuda", "%gcc"]
  mpich:
   require:
   - one_of: ["+cuda", "+rocm"]

Requirements are expressed using Spec syntax (the same as what is provided to spack install). In the simplest case, you can specify attributes that you always want the package to have by providing a single spec to require; in the above example, libfabric will always build with version 1.13.2.

You can provide a more-relaxed constraint and allow the concretizer to choose between a set of options using any_of or one_of:

  • any_of is a list of specs. One of those specs must be satisfied and it is also allowed for the concretized spec to match more than one. In the above example, that means you could build openmpi+cuda%gcc, openmpi~cuda%clang or openmpi~cuda%gcc (in the last case, note that both specs in the any_of for openmpi are satisfied).

  • one_of is also a list of specs, and the final concretized spec must match exactly one of them. In the above example, that means you could build mpich+cuda or mpich+rocm but not mpich+cuda+rocm (note the current package definition for mpich already includes a conflict, so this is redundant but still demonstrates the concept).

Note

For any_of and one_of, the order of specs indicates a preference: items that appear earlier in the list are preferred (note that these preferences can be ignored in favor of others).

Setting default requirements

You can also set default requirements for all packages under all like this:

packages:
  all:
    require: '%clang'

which means every spec will be required to use clang as a compiler.

Note that in this case all represents a default set of requirements - if there are specific package requirements, then the default requirements under all are disregarded. For example, with a configuration like this:

packages:
  all:
    require: '%clang'
  cmake:
    require: '%gcc'

Spack requires cmake to use gcc and all other nodes (including cmake dependencies) to use clang.

Setting requirements on virtual specs

A requirement on a virtual spec applies whenever that virtual is present in the DAG. This can be useful for fixing which virtual provider you want to use:

packages:
  mpi:
    require: 'mvapich2 %gcc'

With the configuration above the only allowed mpi provider is mvapich2 %gcc.

Requirements on the virtual spec and on the specific provider are both applied, if present. For instance with a configuration like:

packages:
  mpi:
    require: 'mvapich2 %gcc'
  mvapich2:
    require: '~cuda'

you will use mvapich2~cuda %gcc as an mpi provider.

Package Preferences

In some cases package requirements can be too strong, and package preferences are the better option. Package preferences do not impose constraints on packages for particular versions or variants values, they rather only set defaults – the concretizer is free to change them if it must due to other constraints. Also note that package preferences are of lower priority than reuse of already installed packages.

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 are preferably 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.

Package preferences accept the follow keys or components under the specific package (or all) section: 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 depends_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.

Assigning Package Attributes

You can assign class-level attributes in the configuration:

packages:
  mpileaks:
    # Override existing attributes
    url: http://www.somewhereelse.com/mpileaks-1.0.tar.gz
    # ... or add new ones
    x: 1

Attributes set this way will be accessible to any method executed in the package.py file (e.g. the install() method). Values for these attributes may be any value parseable by yaml.

These can only be applied to specific packages, not “all” or virtual packages.