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
etc/spack/packages.yaml. For more
details on how this works, see Configuration Scopes.
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
directory. Here’s an example of an external configuration:
packages: openmpi: externals: - spec: "firstname.lastname@example.orgemail@example.com arch=linux-debian7-x86_64" prefix: /opt/openmpi-1.4.3 - spec: "firstname.lastname@example.orgemail@example.com arch=linux-debian7-x86_64+debug" prefix: /opt/openmpi-1.4.3-debug - spec: "firstname.lastname@example.orgemail@example.com 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
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: firstname.lastname@example.org modules: - CMake/3.7.2
packages.yaml begins with a
packages: attribute, followed
by a list of package names. To specify externals, add an
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
packages: openmpi: externals: - spec: "email@example.comfirstname.lastname@example.org arch=linux-debian7-x86_64" prefix: /opt/openmpi-1.4.3 - spec: "email@example.comfirstname.lastname@example.org arch=linux-debian7-x86_64+debug" prefix: /opt/openmpi-1.4.3-debug - spec: "email@example.comfirstname.lastname@example.org 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
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.
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: "email@example.comfirstname.lastname@example.org arch=linux-debian7-x86_64" prefix: /opt/openmpi-1.4.3 - spec: "email@example.comfirstname.lastname@example.org arch=linux-debian7-x86_64+debug" prefix: /opt/openmpi-1.4.3-debug - spec: "email@example.comfirstname.lastname@example.org 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 email@example.comfirstname.lastname@example.org arch=linux-debian7-x86_64: /opt/openmpi-1.4.3 email@example.comfirstname.lastname@example.org arch=linux-debian7-x86_64+debug: /opt/openmpi-1.4.3-debug email@example.comfirstname.lastname@example.org arch=linux-debian7-x86_64: /opt/openmpi-1.6.5-intel email@example.com %firstname.lastname@example.org 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
After running this command your
packages.yaml may include new entries:
packages: cmake: externals: - spec: email@example.com 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
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 packagescan help locate all external entries).
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: [firstname.lastname@example.org] variants: +debug gperftools: version: [2.2, 2.4, 2.3] all: compiler: [email@example.com, 'firstname.lastname@example.org:', 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.
packages.yaml file begins with the string
package names are specified on the next level. The special string
applies settings to all packages. Underneath each package name is one
or more components:
target. Each component has an ordered list of
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
Spack can be configured to assign permissions to the files installed by a package.
packages.yaml file under
permissions, the attributes
group control the package
permissions. These attributes can be set per-package, or for all
all. If permissions are set under
all and for a
specific package, the package-specific settings take precedence.
write attributes take one of
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
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
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.