Modules (modules.yaml)

The use of module systems to manage user environment in a controlled way is a common practice at HPC centers that is sometimes embraced also by individual programmers on their development machines. To support this common practice Spack integrates with Environment Modules and Lmod by providing post-install hooks that generate module files and commands to manipulate them.

Modules are one of several ways you can use Spack packages. For other options that may fit your use case better, you should also look at spack load and environments.

Quick start

In the current version of Spack, module files are not generated by default. To get started, you can generate module files for all currently installed packages by running either

$ spack module tcl refresh

or

$ spack module lmod refresh

Spack can also generate module files for all future installations automatically through the following configuration:

$ spack config add modules:default:enable:[tcl]

or

$ spack config add modules:default:enable:[lmod]

Assuming you have a module system installed, you should now be able to use the module command to interact with them:

$ module avail

--------------------------------------------------------------- ~/spack/share/spack/modules/linux-ubuntu14-x86_64 ---------------------------------------------------------------
autoconf/2.69-gcc-4.8-qextxkq       hwloc/1.11.6-gcc-6.3.0-akcisez             m4/1.4.18-gcc-4.8-ev2znoc                   openblas/0.2.19-gcc-6.3.0-dhkmed6        py-setuptools/34.2.0-gcc-6.3.0-fadur4s
automake/1.15-gcc-4.8-maqvukj       isl/0.18-gcc-4.8-afi6taq                   m4/1.4.18-gcc-6.3.0-uppywnz                 openmpi/2.1.0-gcc-6.3.0-go2s4z5          py-six/1.10.0-gcc-6.3.0-p4dhkaw
binutils/2.28-gcc-4.8-5s7c6rs       libiconv/1.15-gcc-4.8-at46wg3              mawk/1.3.4-gcc-4.8-acjez57                  openssl/1.0.2k-gcc-4.8-dkls5tk           python/2.7.13-gcc-6.3.0-tyehea7
bison/3.0.4-gcc-4.8-ek4luo5         libpciaccess/0.13.4-gcc-6.3.0-gmufnvh      mawk/1.3.4-gcc-6.3.0-ostdoms                openssl/1.0.2k-gcc-6.3.0-gxgr5or         readline/7.0-gcc-4.8-xhufqhn
bzip2/1.0.6-gcc-4.8-iffrxzn         libsigsegv/2.11-gcc-4.8-pp2cvte            mpc/1.0.3-gcc-4.8-g5mztc5                   pcre/8.40-gcc-4.8-r5pbrxb                readline/7.0-gcc-6.3.0-zzcyicg
bzip2/1.0.6-gcc-6.3.0-bequudr       libsigsegv/2.11-gcc-6.3.0-7enifnh          mpfr/3.1.5-gcc-4.8-o7xm7az                  perl/5.24.1-gcc-4.8-dg5j65u              sqlite/3.8.5-gcc-6.3.0-6zoruzj
cmake/3.7.2-gcc-6.3.0-fowuuby       libtool/2.4.6-gcc-4.8-7a523za              mpich/3.2-gcc-6.3.0-dmvd3aw                 perl/5.24.1-gcc-6.3.0-6uzkpt6            tar/1.29-gcc-4.8-wse2ass
curl/7.53.1-gcc-4.8-3fz46n6         libtool/2.4.6-gcc-6.3.0-n7zmbzt            ncurses/6.0-gcc-4.8-dcpe7ia                 pkg-config/0.29.2-gcc-4.8-ib33t75        tcl/8.6.6-gcc-4.8-tfxzqbr
expat/2.2.0-gcc-4.8-mrv6bd4         libxml2/2.9.4-gcc-4.8-ryzxnsu              ncurses/6.0-gcc-6.3.0-ucbhcdy               pkg-config/0.29.2-gcc-6.3.0-jpgubk3      util-macros/1.19.1-gcc-6.3.0-xorz2x2
flex/2.6.3-gcc-4.8-yf345oo          libxml2/2.9.4-gcc-6.3.0-rltzsdh            netlib-lapack/3.6.1-gcc-6.3.0-js33dog       py-appdirs/1.4.0-gcc-6.3.0-jxawmw7       xz/5.2.3-gcc-4.8-mew4log
gcc/6.3.0-gcc-4.8-24puqve           lmod/7.4.1-gcc-4.8-je4srhr                 netlib-scalapack/2.0.2-gcc-6.3.0-5aidk4l    py-numpy/1.12.0-gcc-6.3.0-oemmoeu        xz/5.2.3-gcc-6.3.0-3vqeuvb
gettext/0.19.8.1-gcc-4.8-yymghlh    lua/5.3.4-gcc-4.8-im75yaz                  netlib-scalapack/2.0.2-gcc-6.3.0-hjsemcn    py-packaging/16.8-gcc-6.3.0-i2n3dtl      zip/3.0-gcc-4.8-rwar22d
gmp/6.1.2-gcc-4.8-5ub2wu5           lua-luafilesystem/1_6_3-gcc-4.8-wkey3nl    netlib-scalapack/2.0.2-gcc-6.3.0-jva724b    py-pyparsing/2.1.10-gcc-6.3.0-tbo6gmw    zlib/1.2.11-gcc-4.8-pgxsxv7
help2man/1.47.4-gcc-4.8-kcnqmau     lua-luaposix/33.4.0-gcc-4.8-mdod2ry        netlib-scalapack/2.0.2-gcc-6.3.0-rgqfr6d    py-scipy/0.19.0-gcc-6.3.0-kr7nat4        zlib/1.2.11-gcc-6.3.0-7cqp6cj

The names should look familiar, as they resemble the output from spack find. For example, you could type the following command to load the cmake module:

$ module load cmake/3.7.2-gcc-6.3.0-fowuuby

Neither of these is particularly pretty, easy to remember, or easy to type. Luckily, Spack offers many facilities for customizing the module scheme used at your site.

Module file customization

The table below summarizes the essential information associated with the different file formats that can be generated by Spack:

Hierarchical

Default root directory

Default template file

Compatible tools

tcl

No

share/spack/modules

share/spack/templates/modules/modulefile.tcl

Env. Modules/Lmod

lmod

Yes

share/spack/lmod

share/spack/templates/modules/modulefile.lua

Lmod

Spack ships with sensible defaults for the generation of module files, but you can customize many aspects of it to accommodate package or site specific needs. In general you can override or extend the default behavior by:

  1. overriding certain callback APIs in the Python packages

  2. writing specific rules in the modules.yaml configuration file

  3. writing your own templates to override or extend the defaults

The former method lets you express changes in the run-time environment that are needed to use the installed software properly, e.g. injecting variables from language interpreters into their extensions. The latter two instead permit to fine tune the filesystem layout, content and creation of module files to meet site specific conventions.

Setting environment variables dynamically in package.py

There are two methods that you can implement in any package.py to dynamically affect the content of the module files generated by Spack. The most important one is setup_run_environment, which can be used to set environment variables in the module file that depend on the spec:

def setup_run_environment(self, env):
    if self.spec.satisfies("+foo"):
        env.set("FOO", "bar")

The second, less commonly used, is setup_dependent_run_environment(self, env, dependent_spec), which allows a dependency to set variables in the module file of its dependents. This is typically used in packages like python, r, or perl to prepend the dependent’s prefix to the search path of the interpreter (PYTHONPATH, R_LIBS, PERL5LIB resp.), so it can locate the packages at runtime.

For example, a simplified version of the python package could look like this:

def setup_dependent_run_environment(self, env, dependent_spec):
    if dependent_spec.package.extends(self.spec):
        env.prepend_path("PYTHONPATH", dependent_spec.prefix.lib.python)

and would make any package that extends("python") have its library directory added to the PYTHONPATH environment variable in the module file. It’s much more convenient to set this variable here, than to repeat it in every Python extension’s setup_run_environment method.

The modules.yaml config file and module sets

The configuration files that control module generation behavior are named modules.yaml. The default configuration looks like this:

# -------------------------------------------------------------------------
# This is the default configuration for Spack's module file generation.
#
# 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 the following files.
#
# Per-spack-instance settings (overrides defaults):
#   $SPACK_ROOT/etc/spack/modules.yaml
#
# Per-user settings (overrides default and site settings):
#   ~/.spack/modules.yaml
# -------------------------------------------------------------------------
modules:
  # This maps paths in the package install prefix to environment variables
  # they should be added to. For example, <prefix>/bin should be in PATH.
  prefix_inspections:
    ./bin:
      - PATH
    ./man:
      - MANPATH
    ./share/man:
      - MANPATH
    ./share/aclocal:
      - ACLOCAL_PATH
    ./lib/pkgconfig:
      - PKG_CONFIG_PATH
    ./lib64/pkgconfig:
      - PKG_CONFIG_PATH
    ./share/pkgconfig:
      - PKG_CONFIG_PATH
    ./:
      - CMAKE_PREFIX_PATH

  # These are configurations for the module set named "default"
  default:
    # Where to install modules
    roots:
     tcl:    $spack/share/spack/modules
     lmod:   $spack/share/spack/lmod
    # What type of modules to use ("tcl" and/or "lmod")
    enable: []

    tcl:
      all:
        autoload: direct

    # Default configurations if lmod is enabled
    lmod:
      all:
        autoload: direct
      hierarchy:
        - mpi

You can define one or more module sets, each of which can be configured separately with regard to install location, naming scheme, inclusion and exclusion, autoloading, et cetera.

The default module set is aptly named default. All Spack commands that operate on modules apply to the default module set, unless another module set is specified explicitly (with the --name flag).

Changing the modules root

As shown in the table above, the default module root for lmod is $spack/share/spack/lmod and the default root for tcl is $spack/share/spack/modules. This can be overridden for any module set by changing the roots key of the configuration.

modules:
  default:
    roots:
      tcl: /path/to/install/tcl/modules
  my_custom_lmod_modules:
    roots:
      lmod: /path/to/install/custom/lmod/modules
      # ...

This configuration will create two module sets. The default module set will install its tcl modules to /path/to/install/tcl/modules (and still install its lmod modules, if any, to the default location). The set my_custom_lmod_modules will install its lmod modules to /path/to/install/custom/lmod/modules (and still install its tcl modules, if any, to the default location).

By default, an architecture-specific directory is added to the root directory. A module set may override that behavior by setting the arch_folder config value to False.

modules:
  default:
    roots:
      tcl: /path/to/install/tcl/modules
    arch_folder: false

Obviously, having multiple module sets install modules to the default location could be confusing to users of your modules. In the next section, we will discuss enabling and disabling module types (module file generators) for each module set.

Automatically generating module files

Spack can be configured to automatically generate module files as part of package installation. This is done by adding the desired module systems to the enable list.

modules:
  default:
    enable:
    - tcl
    - lmod

Configuring tcl and lmod modules

You can configure the behavior of either module system separately, under a key corresponding to the generator being customized:

modules:
  default:
    tcl:
      # contains environment modules specific customizations
    lmod:
      # contains lmod specific customizations

In general, the configuration options that you can use in modules.yaml will either change the layout of the module files on the filesystem, or they will affect their content. For the latter point it is possible to use anonymous specs to fine tune the set of packages on which the modifications should be applied.

Autoloading and hiding dependencies

A module file should set the variables that are needed for an application to work. But since an application often has many dependencies, where should all the environment variables for those be set? In Spack the rule is that each package sets the runtime variables that are needed by the package itself, and no more. This way, dependencies can be loaded standalone too, and duplication of environment variables is avoided.

That means however that if you want to use an application, you need to load the modules for all its dependencies. Of course this is not something you would want users to do manually.

Since Spack knows the dependency graph of every package, it can easily generate module files that automatically load the modules for its dependencies recursively. It is enabled by default for both Lmod and Environment Modules under the autoload: direct config option. The former system has builtin support through the depends_on function, the latter simply uses a module load statement. Both module systems (at least in newer versions) do reference counting, so that if a module is loaded by two different modules, it will only be unloaded after the others are.

The autoload key accepts the values:

  • none: no autoloading

  • run: autoload direct run type dependencies

  • direct: autoload direct link and run type dependencies

  • all: autoload all dependencies

In case of run and direct, a module load triggers a recursive load.

The direct option is most correct: there are cases where pure link dependencies need to set variables for themselves, or need to have variables of their own dependencies set.

In practice however, run is often sufficient, and may make module load snappier.

The all option is discouraged and seldomly used.

A common complaint about autoloading is the large number of modules that are visible to the user. Spack has a solution for this as well: hide_implicits: true. This ensures that only those packages you’ve explicitly installed are exposed by module avail, but still allows for autoloading of hidden dependencies. Lmod should support hiding implicits in general, while Environment Modules requires version 4.7 or higher.

Note

If supported by your module system, we highly encourage the following configuration that enables autoloading and hiding of implicits. It ensures all runtime variables are set correctly, including those for dependencies, without overwhelming the user with a large number of available modules. Further, it makes it easier to get readable module names without collisions, see the section below on Customize the naming of modules.

modules:
  default:
    tcl:
      hide_implicits: true
      all:
        autoload: direct # or `run`
    lmod:
      hide_implicits: true
      all:
        autoload: direct # or `run`

Setting environment variables for selected packages in config

In the configuration file you can filter particular specs, and make further changes to the environment variables that go into their module files. This is very powerful when you want to avoid modifying the package itself, or when you want to set certain variables on multiple selected packages at once.

For instance, in the snippet below:

modules:
  default:
    tcl:
      # The keyword `all` selects every package
      all:
        environment:
          set:
            BAR: 'bar'
      # This anonymous spec selects any package that
      # depends on mpi. The double colon at the
      # end clears the set of rules that matched so far.
      ^mpi::
        environment:
          prepend_path:
            PATH: '{^mpi.prefix}/bin'
          set:
            BAR: 'baz'
      # Selects any zlib package
      zlib:
        environment:
          prepend_path:
            LD_LIBRARY_PATH: 'foo'
      # Selects zlib compiled with gcc@4.8
      zlib%gcc@4.8:
        environment:
          unset:
          - FOOBAR

you are instructing Spack to set the environment variable BAR=bar for every module, unless the associated spec satisfies the abstract dependency ^mpi in which case BAR=baz, and the directory containing the respective MPI executables is prepended to the PATH variable. In addition in any spec that satisfies zlib the value foo will be prepended to LD_LIBRARY_PATH and in any spec that satisfies zlib%gcc@4.8 the variable FOOBAR will be unset.

Note

Order does matter

The modifications associated with the all keyword are always evaluated first, no matter where they appear in the configuration file. All the other changes to environment variables for matching specs are evaluated from top to bottom.

Warning

As general advice, it’s often better to set as few unnecessary variables as possible. For example, the following seemingly innocent and potentially useful configuration

all:
  environment:
    set:
      "{name}_ROOT": "{prefix}"

sets BINUTILS_ROOT to its prefix in modules for binutils, which happens to break the gcc compiler: it uses this variable as its default search path for certain object files and libraries, and by merely setting it, everything fails to link.

Exclude or include specific module files

You can use anonymous specs also to prevent module files from being written or to force them to be written. Consider the case where you want to hide from users all the boilerplate software that you had to build in order to bootstrap a new compiler. Suppose for instance that gcc@4.4.7 is the compiler provided by your system. If you write a configuration file like:

modules:
  default:
    tcl:
      include: ['gcc', 'llvm']  # include will have precedence over exclude
      exclude: ['%gcc@4.4.7']   # Assuming gcc@4.4.7 is the system compiler

you will prevent the generation of module files for any package that is compiled with gcc@4.4.7, with the only exception of any gcc or any llvm installation.

It is safe to combine exclude and autoload mentioned above. When exclude prevents a module file to be generated for a dependency, the autoload feature will simply not generate a statement to load it.

Customize the naming of modules

The names of environment modules generated by Spack are not always easy to fully comprehend due to the long hash in the name. There are three module configuration options to help with that. The first is a global setting to adjust the hash length. It can be set anywhere from 0 to 32 and has a default length of 7. This is the representation of the hash in the module file name and does not affect the size of the package hash. Be aware that the smaller the hash length the more likely naming conflicts will occur. The following snippet shows how to set hash length in the module file names:

modules:
  default:
    tcl:
      hash_length: 7

Tip

Using hide_implicits: true (see Autoloading and hiding dependencies) vastly reduces the number modules exposed to the user. The hidden modules always contain the hash in their name, and are not influenced by the hash_length setting. Hidden implicits thus make it easier to use a short hash length or no hash at all, without risking name conflicts.

To help make module names more readable, and to help alleviate name conflicts with a short hash, one can use the suffixes option in the modules configuration file. This option will add strings to modules that match a spec. For instance, the following config options,

modules:
  default:
    tcl:
      all:
        suffixes:
          ^python@3.12: 'python-3.12'
          ^openblas: 'openblas'

will add a python-3.12 version string to any packages compiled with Python matching the spec, python@3.12. This is useful to know which version of Python a set of Python extensions is associated with. Likewise, the openblas string is attached to any program that has openblas in the spec, most likely via the +blas variant specification.

The most heavyweight solution to module naming is to change the entire naming convention for module files. This uses the projections format covered in View Projections.

modules:
  default:
    tcl:
      projections:
        all: '{name}/{version}-{compiler.name}-{compiler.version}-module'
        ^mpi: '{name}/{version}-{^mpi.name}-{^mpi.version}-{compiler.name}-{compiler.version}-module'

will create module files that are nested in directories by package name, contain the version and compiler name and version, and have the word module before the hash for all specs that do not depend on mpi, and will have the same information plus the MPI implementation name and version for all packages that depend on mpi.

When specifying module names by projection for Lmod modules, we recommend NOT including names of dependencies (e.g., MPI, compilers) that are already in the Lmod hierarchy.

Note

Tcl and Lua modules also allow for explicit conflicts between modulefiles.

modules:
  default:
    enable:
      - tcl
    tcl:
      projections:
        all: '{name}/{version}-{compiler.name}-{compiler.version}'
      all:
        conflict:
          - '{name}'
          - 'intel/14.0.1'

will create module files that will conflict with intel/14.0.1 and with the base directory of the same module, effectively preventing the possibility to load two or more versions of the same software at the same time. The tokens that are available for use in this directive are the same understood by the format() method.

For Lmod and Environment Modules versions prior 4.2, it is important to express the conflict on both modulefiles conflicting with each other.

Note

Lmod hierarchical module files

When lmod is activated Spack will generate a set of hierarchical lua module files that are understood by Lmod. The hierarchy will always contain the two layers Core / Compiler but can be further extended to any of the virtual dependencies present in Spack. A case that could be useful in practice is for instance:

modules:
  default:
    enable:
      - lmod
    lmod:
      core_compilers:
        - 'gcc@4.8'
      core_specs:
        - 'python'
      hierarchy:
        - 'mpi'
        - 'lapack'

that will generate a hierarchy in which the lapack and mpi layer can be switched independently. This allows a site to build the same libraries or applications against different implementations of mpi and lapack, and let Lmod switch safely from one to the other.

All packages built with a compiler in core_compilers and all packages that satisfy a spec in core_specs will be put in the Core hierarchy of the lua modules.

Warning

Consistency of Core packages

The user is responsible for maintining consistency among core packages, as core_specs bypasses the hierarchy that allows Lmod to safely switch between coherent software stacks.

Warning

Deep hierarchies and lmod spider

For hierarchies that are deeper than three layers lmod spider may have some issues. See this discussion on the Lmod project.

Customize environment modifications

You can control which prefixes in a Spack package are added to environment variables with the prefix_inspections section; this section maps relative prefixes to the list of environment variables which should be updated with those prefixes.

The prefix_inspections configuration is different from other settings in that a prefix_inspections configuration at the modules level of the configuration file applies to all module sets. This allows users to make general overrides to the default inspections and customize them per-module-set.

modules:
  prefix_inspections:
    ./bin:
      - PATH
    ./man:
      - MANPATH
    ./:
      - CMAKE_PREFIX_PATH

Prefix inspections are only applied if the relative path inside the installation prefix exists. In this case, for a Spack package foo installed to /spack/prefix/foo, if foo installs executables to bin but no manpages in man, the generated module file for foo would update PATH to contain /spack/prefix/foo/bin and CMAKE_PREFIX_PATH to contain /spack/prefix/foo, but would not update MANPATH.

The default list of environment variables in this config section includes PATH, MANPATH, ACLOCAL_PATH, PKG_CONFIG_PATH and CMAKE_PREFIX_PATH, as well as DYLD_FALLBACK_LIBRARY_PATH on macOS. On Linux however, the corresponding LD_LIBRARY_PATH variable is not set, because it affects the behavior of system executables too.

Note

In general, the LD_LIBRARY_PATH variable is not required when using packages built with Spack, thanks to the use of RPATH. Some packages may still need the variable, which is best handled on a per-package basis instead of globally, as explained in Setting environment variables dynamically in package.py.

There is a special case for prefix inspections relative to environment views. If all of the following conditions hold for a module set configuration:

  1. The configuration is for an environment and will never be applied outside the environment,

  2. The environment in question is configured to use a view,

  3. The environment view is configured with a projection that ensures every package is linked to a unique directory,

then the module set may be configured to create modules relative to the environment view. This is specified by the use_view configuration option in the module set. If True, the module set is constructed relative to the default view of the environment. Otherwise, the value must be the name of the environment view relative to which to construct modules, or False-ish to disable the feature explicitly (the default is False).

If the use_view value is set in the config, then the prefix inspections for the package are done relative to the package’s path in the view.

spack:
  modules:
    view_relative_modules:
      use_view: my_view
    prefix_inspections:
      ./bin:
        - PATH
  view:
    my_view:
      projections:
        root: /path/to/my/view
        all:  '{name}-{hash}'

The spack key is relevant to environment configuration, and the view key is discussed in detail in the section on Configuring environment views. With this configuration the generated module for package foo would set PATH to include /path/to/my/view/foo-<hash>/bin instead of /spack/prefix/foo/bin.

The use_view option is useful when deploying a large software stack to users who are likely to inspect the modules to find full paths to software, when it is desirable to present the users with a simpler set of paths than those generated by the Spack install tree.

Filter out environment modifications

Modifications to certain environment variables in module files are there by default, for instance because they are generated by prefix inspections. If you want to prevent modifications to some environment variables, you can do so by using the exclude_env_vars:

modules:
  default:
    tcl:
      all:
        filter:
          # Exclude changes to any of these variables
          exclude_env_vars: ['CPATH', 'LIBRARY_PATH']

The configuration above will generate module files that will not contain modifications to either CPATH or LIBRARY_PATH.

Select default modules

By default, when multiple modules of the same name share a directory, the highest version number will be the default module. This behavior of the module command can be overridden with a symlink named default to the desired default module. If you wish to configure default modules with Spack, add a defaults key to your modules configuration:

modules:
  my-module-set:
    tcl:
      defaults:
      - gcc@10.2.1
      - hdf5@1.2.10+mpi+hl%gcc

These defaults may be arbitrarily specific. For any package that satisfies a default, Spack will generate the module file in the appropriate path, and will generate a default symlink to the module file as well.

Warning

If Spack is configured to generate multiple default packages in the same directory, the last modulefile to be generated will be the default module.

Maintaining Module Files

Each type of module file has a command with the same name associated with it. The actions these commands permit are usually associated with the maintenance of a production environment. Here’s, for instance, a sample of the features of the spack module tcl command:

$ spack module tcl --help
usage: spack module tcl [-h] [-n MODULE_SET_NAME] SUBCOMMAND ...

positional arguments:
  SUBCOMMAND
    refresh             regenerate module files
    find                find module files for packages
    rm                  remove module files
    loads               prompt the list of modules associated with a constraint
    setdefault          set the default module file for a package

options:
  -h, --help            show this help message and exit
  -n MODULE_SET_NAME, --name MODULE_SET_NAME
                        named module set to use from modules configuration

Refresh the set of modules

The subcommand that regenerates module files to update their content or their layout is refresh:

$ spack module tcl refresh --help
usage: spack module tcl refresh [-hy] [--delete-tree] [--upstream-modules] ...

positional arguments:
  installed_specs     constraint to select a subset of installed packages

options:
  --delete-tree       delete the module file tree before refresh
  --upstream-modules  generate modules for packages installed upstream
  -h, --help          show this help message and exit
  -y, --yes-to-all    assume "yes" is the answer to every confirmation request

A set of packages can be selected using anonymous specs for the optional constraint positional argument. Optionally the entire tree can be deleted before regeneration if the change in layout is radical.

Delete module files

If instead what you need is just to delete a few module files, then the right subcommand is rm:

$ spack module tcl rm --help
usage: spack module tcl rm [-hy] ...

positional arguments:
  installed_specs   constraint to select a subset of installed packages

options:
  -h, --help        show this help message and exit
  -y, --yes-to-all  assume "yes" is the answer to every confirmation request

Note

We care about your module files!

Every modification done on modules that are already existing will ask for a confirmation by default. If the command is used in a script it is possible though to pass the -y argument, that will skip this safety measure.

Using Spack modules in shell scripts

The easiest To enable additional Spack commands for loading and unloading module files, and to add the correct path to MODULEPATH, you need to source the appropriate setup file. Assuming Spack is installed in $SPACK_ROOT, run the appropriate command for your shell:

# For bash/zsh/sh
$ . $SPACK_ROOT/share/spack/setup-env.sh

# For tcsh/csh
$ source $SPACK_ROOT/share/spack/setup-env.csh

# For fish
$ . $SPACK_ROOT/share/spack/setup-env.fish

If you want to have Spack’s shell support available on the command line at any login you can put this source line in one of the files that are sourced at startup (like .profile, .bashrc or .cshrc). Be aware that the shell startup time may increase slightly as a result.

spack module tcl loads

In some cases, it is desirable to use a Spack-generated module, rather than relying on Spack’s built-in user-environment modification capabilities. To translate a spec into a module name, use spack module tcl loads or spack module lmod loads depending on the module system desired.

To load not just a module, but also all the modules it depends on, use the --dependencies option. This is not required for most modules because Spack builds binaries with RPATH support. However, not all packages use RPATH to find their dependencies: this can be true in particular for Python extensions, which are currently not built with RPATH.

Scripts to load modules recursively may be made with the command:

$ spack module tcl loads --dependencies <spec>

An equivalent alternative using process substitution is:

$ source <( spack module tcl loads --dependencies <spec> )

Module Commands for Shell Scripts

Although Spack is flexible, the module command is much faster. This could become an issue when emitting a series of spack load commands inside a shell script. By adding the --dependencies flag, spack module tcl loads may also be used to generate code that can be cut-and-pasted into a shell script. For example:

$ spack module tcl loads --dependencies py-numpy git
# bzip2@1.0.6%gcc@4.9.3=linux-x86_64
module load bzip2/1.0.6-gcc-4.9.3-ktnrhkrmbbtlvnagfatrarzjojmkvzsx
# ncurses@6.0%gcc@4.9.3=linux-x86_64
module load ncurses/6.0-gcc-4.9.3-kaazyneh3bjkfnalunchyqtygoe2mncv
# zlib@1.2.8%gcc@4.9.3=linux-x86_64
module load zlib/1.2.8-gcc-4.9.3-v3ufwaahjnviyvgjcelo36nywx2ufj7z
# sqlite@3.8.5%gcc@4.9.3=linux-x86_64
module load sqlite/3.8.5-gcc-4.9.3-a3eediswgd5f3rmto7g3szoew5nhehbr
# readline@6.3%gcc@4.9.3=linux-x86_64
module load readline/6.3-gcc-4.9.3-se6r3lsycrwxyhreg4lqirp6xixxejh3
# python@3.5.1%gcc@4.9.3=linux-x86_64
module load python/3.5.1-gcc-4.9.3-5q5rsrtjld4u6jiicuvtnx52m7tfhegi
# py-setuptools@20.5%gcc@4.9.3=linux-x86_64
module load py-setuptools/20.5-gcc-4.9.3-4qr2suj6p6glepnedmwhl4f62x64wxw2
# py-nose@1.3.7%gcc@4.9.3=linux-x86_64
module load py-nose/1.3.7-gcc-4.9.3-pwhtjw2dvdvfzjwuuztkzr7b4l6zepli
# openblas@0.2.17%gcc@4.9.3+shared=linux-x86_64
module load openblas/0.2.17-gcc-4.9.3-pw6rmlom7apfsnjtzfttyayzc7nx5e7y
# py-numpy@1.11.0%gcc@4.9.3+blas+lapack=linux-x86_64
module load py-numpy/1.11.0-gcc-4.9.3-mulodttw5pcyjufva4htsktwty4qd52r
# curl@7.47.1%gcc@4.9.3=linux-x86_64
module load curl/7.47.1-gcc-4.9.3-ohz3fwsepm3b462p5lnaquv7op7naqbi
# autoconf@2.69%gcc@4.9.3=linux-x86_64
module load autoconf/2.69-gcc-4.9.3-bkibjqhgqm5e3o423ogfv2y3o6h2uoq4
# cmake@3.5.0%gcc@4.9.3~doc+ncurses+openssl~qt=linux-x86_64
module load cmake/3.5.0-gcc-4.9.3-x7xnsklmgwla3ubfgzppamtbqk5rwn7t
# expat@2.1.0%gcc@4.9.3=linux-x86_64
module load expat/2.1.0-gcc-4.9.3-6pkz2ucnk2e62imwakejjvbv6egncppd
# git@2.8.0-rc2%gcc@4.9.3+curl+expat=linux-x86_64
module load git/2.8.0-rc2-gcc-4.9.3-3bib4hqtnv5xjjoq5ugt3inblt4xrgkd

The script may be further edited by removing unnecessary modules.

Module Prefixes

On some systems, modules are automatically prefixed with a certain string; spack module tcl loads needs to know about that prefix when it issues module load commands. Add the --prefix option to your spack module tcl loads commands if this is necessary.

For example, consider the following on one system:

$ module avail
linux-SuSE11-x86_64/antlr/2.7.7-gcc-5.3.0-bdpl46y

$ spack module tcl loads antlr    # WRONG!
# antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
module load antlr/2.7.7-gcc-5.3.0-bdpl46y

$ spack module tcl loads --prefix linux-SuSE11-x86_64/ antlr
# antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
module load linux-SuSE11-x86_64/antlr/2.7.7-gcc-5.3.0-bdpl46y