Manipulating dependencies

A couple of different ways are available to manipulate the list of dependencies that are specified for the software packages being installed.

Filtering out dependencies using --filter-deps

To avoid that certain dependencies are being installed, a list of software names can be specified to --filter-deps. Any time a dependency with a name from this list is specified, it will be simply filtered out by EasyBuild, and thus disregarded when resolving dependencies, loading modules for the dependencies in the build environment, and including ‘module load‘ statements in the generated module files.

This can be useful when particular tools and libraries are already provided by OS packages (or in some other way), and should not be reinstalled as modules by EasyBuild.

For example:

  • overview of dependencies of HDF5:

    $ eb HDF5-1.8.13-intel-2015a.eb -D
     ...
     * [ ] $CFGS/i/intel/intel-2015a.eb (module: intel/2015a)
     * [ ] $CFGS/z/zlib/zlib-1.2.8-intel-2015a.eb (module: zlib/1.2.8-intel-2015a)
     * [ ] $CFGS/s/Szip/Szip-2.1-intel-2015a.eb (module: Szip/2.1-intel-2015a)
     * [ ] $CFGS/h/HDF5/HDF5-1.8.13-intel-2015a.eb (module: HDF5/1.8.13-intel-2015a)
    
  • overview of dependencies of HDF5, with zlib and Szip excluded:

    $ eb HDF5-1.8.13-intel-2015a.eb --filter-deps=zlib,Szip -D
     ...
     * [ ] $CFGS/i/intel/intel-2015a.eb (module: intel/2015a)
     * [ ] $CFGS/h/HDF5/HDF5-1.8.13-intel-2015a.eb (module: HDF5/1.8.13-intel-2015a)
    

Installing dependencies as hidden modules using --hide-deps

Selected software packages can be marked to be installed as hidden modules (i.e., modules that are not visible via ‘module avail‘, but can be loaded) whenever they are included as a dependency, via the --hide-deps configuration option.

For example (note the preceding ‘.‘ in the last part of the module names for zlib and Szip):

$ eb HDF5-1.8.13-intel-2015a.eb --hide-deps=zlib,Szip -D
 ...
 * [ ] $CFGS/i/intel/intel-2015a.eb (module: intel/2015a)
 * [ ] $CFGS/z/zlib/zlib-1.2.8-intel-2015a.eb (module: zlib/.1.2.8-intel-2015a)
 * [ ] $CFGS/s/Szip/Szip-2.1-intel-2015a.eb (module: Szip/.2.1-intel-2015a)
 * [ ] $CFGS/h/HDF5/HDF5-1.8.13-intel-2015a.eb (module: HDF5/1.8.13-intel-2015a)

Note

Using Lmod (version >= 5.7.5), hidden modules can be made visible in the output of ‘module avail‘ using the --show-hidden option.

For example:

$ module avail bzip2

Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

$ module --show-hidden avail bzip2
----- /home/example/.local/easybuild/modules/all -----
bzip2/.1.0.6

Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

Using minimal toolchains for dependencies

By default, EasyBuild will try to resolve dependencies using the same toolchain as the one that is used for the software being installed, unless a specific toolchain is specified for the dependency itself (see Dependencies).

Using the --minimal-toolchains configuration option, you can instruct EasyBuild to consider subtoolchains for dependencies in the reverse order (from the bottom of the toolchain hierarchy to the top). This can be useful to refrain from having to frequently hardcode specific toolchains in order to avoid having the same dependency version installed with multiple toolchains that are compatible with each other. Although hardcoding the toolchain for dependencies will work fine, it severely limits the power of other EasyBuild features, like --try-toolchain for example.

When instructed to use minimal toolchains, EasyBuild will check whether an easyconfig file is available (in the robot search path, see Searching for easyconfigs: the robot search path) for that dependency using the different subtoolchains of the toolchain specified for the ‘parent’ software. Subtoolchains are considered ‘bottom-up’, i.e. starting with the most minimal subtoolchain (typically a compiler-only toolchain), and then climbing up towards the toolchain that is specified for the software being installed.

Note that if a specific toolchain is specified for a particular dependency, EasyBuild will stick to using it, even when instructed to use minimal toolchains. Also note that as of v3.0, if no easyconfig exists to resolve a dependency using the default toolchain EasyBuild will search for the dependency using a compatible subtoolchain (the difference being that the search order is from the top of the toolchain hierarchy to the bottom).

Considering dummy as minimal toolchain

The dummy toolchain is only considered as the most minimal subtoolchain if the --add-dummy-to-minimal-toolchains configuration option is enabled. By default, this configuration option is disabled.

Taking existing modules into account

You can instruct EasyBuild to take existing modules into account when determining which subtoolchain should be used for each of the dependencies, using the --use-existing-modules configuration option.

By default existing modules are ignored, meaning that the EasyBuild dependency resolution mechanism will pick a minimal toolchain for each dependency solely based on the available easyconfig files (if the --minimal-toolchains configuration option is enabled, that is).

With --use-existing-modules enabled, EasyBuild will first check whether modules exist for the dependencies that were built with the toolchain or any of the subtoolchains (searching top-down). If so, the toolchain of the first encountered existing module will determine the toolchain being selected. If not, the toolchain to use will be determined based on the available easyconfig files.

Example

Consider the following (partial) easyconfig file for Python v2.7.9 with the foss/2015b toolchain:

name = 'Python'
version = '2.7.9'

toolchain = {'name': 'foss', 'version': '2015b'}

dependencies = [
    ('zlib', '1.2.8'),
]

When the --minimal-toolchains configuration option is enabled, EasyBuild will also consider the subtoolchains GCC/4.9.3 and gompi/2015b of the foss/2015b toolchain (in that order) as potential minimal toolchains when determining the toolchain to use for dependencies.

So, for the zlib v1.2.8 dependency included in the example above, the following scenarios are possible:

  • without the use of --minimal-toolchains, the default behaviour of EasyBuild is to first consider the foss/2015b toolchain for zlib v1.2.8, if no such easyconfig file is found, it will continue searching using the gompi/2015b toolchain, and finally the GCC/4.9.3 toolchain
  • if (only) --minimal-toolchains is enabled, EasyBuild will search for an easyconfig file for zlib v1.2.8 using the GCC/4.9.3 toolchain; if no such easyconfig file is found, it will continue searching using the gompi/2015b toolchain, and finally the foss/2015b toolchain
  • if --add-dummy-to-minimal-toolchains is also enabled, EasyBuild will try locating an easyconfig file for zlib v1.2.8 that uses the dummy toolchain prior to consider the GCC/4.9.3 toolchain
  • additionally, with --use-existing-modules enabled, EasyBuild will first check whether a zlib module for version 1.2.8 built with the (sub)toolchains being considered exists; if not, it will search for an easyconfig file for zlib as outlined above