Modules

The use of module systems to manage user environment in a controlled way is a common practice at HPC centers that is often embraced also by individual programmers on their development machines. To support this common practice Spack provides integration with Environment Modules , LMod and Dotkit by:

  • generating module files after a successful installation
  • providing commands that can leverage the spec syntax to manipulate modules

In the following you will see how to activate shell support for commands in Spack that requires it, and discover what benefits this may bring with respect to deal directly with automatically generated module files.

Note

If your machine does not already have a module system installed, we advise you to use either Environment Modules or LMod. See Environment Modules for more details.

Shell support

You can enable shell support by sourcing the appropriate setup file in the $SPACK_ROOT/share/spack directory. For bash or ksh users:

$ . ${SPACK_ROOT}/share/spack/setup-env.sh

For csh and tcsh instead:

$ source $SPACK_ROOT/share/spack/setup-env.csh

Note

You can put the source line in your .bashrc or .cshrc to have Spack’s shell support available on the command line at any login.

Using module files via Spack

If you have shell support enabled you should be able to run either module avail or use -l spack to see what module/dotkit files have been installed. Here is sample output of those programs, showing lots of installed packages.

$ module avail

------- ~/spack/share/spack/modules/linux-debian7-x86_64 --------
adept-utils@1.0%gcc@4.4.7-5adef8da   libelf@0.8.13%gcc@4.4.7
automaded@1.0%gcc@4.4.7-d9691bb0     libelf@0.8.13%intel@15.0.0
boost@1.55.0%gcc@4.4.7               mpc@1.0.2%gcc@4.4.7-559607f5
callpath@1.0.1%gcc@4.4.7-5dce4318    mpfr@3.1.2%gcc@4.4.7
dyninst@8.1.2%gcc@4.4.7-b040c20e     mpich@3.0.4%gcc@4.4.7
gcc@4.9.1%gcc@4.4.7-93ab98c5         mpich@3.0.4%gcc@4.9.0
gmp@6.0.0a%gcc@4.4.7                 mrnet@4.1.0%gcc@4.4.7-72b7881d
graphlib@2.0.0%gcc@4.4.7             netgauge@2.4.6%gcc@4.9.0-27912b7b
launchmon@1.0.1%gcc@4.4.7            stat@2.1.0%gcc@4.4.7-51101207
libNBC@1.1.1%gcc@4.9.0-27912b7b      sundials@2.5.0%gcc@4.9.0-27912b7b
libdwarf@20130729%gcc@4.4.7-b52fac98
$ use -l spack

spack ----------
  adept-utils@1.0%gcc@4.4.7-5adef8da - adept-utils @1.0
  automaded@1.0%gcc@4.4.7-d9691bb0 - automaded @1.0
  boost@1.55.0%gcc@4.4.7 - boost @1.55.0
  callpath@1.0.1%gcc@4.4.7-5dce4318 - callpath @1.0.1
  dyninst@8.1.2%gcc@4.4.7-b040c20e - dyninst @8.1.2
  gmp@6.0.0a%gcc@4.4.7 - gmp @6.0.0a
  libNBC@1.1.1%gcc@4.9.0-27912b7b - libNBC @1.1.1
  libdwarf@20130729%gcc@4.4.7-b52fac98 - libdwarf @20130729
  libelf@0.8.13%gcc@4.4.7 - libelf @0.8.13
  libelf@0.8.13%intel@15.0.0 - libelf @0.8.13
  mpc@1.0.2%gcc@4.4.7-559607f5 - mpc @1.0.2
  mpfr@3.1.2%gcc@4.4.7 - mpfr @3.1.2
  mpich@3.0.4%gcc@4.4.7 - mpich @3.0.4
  mpich@3.0.4%gcc@4.9.0 - mpich @3.0.4
  netgauge@2.4.6%gcc@4.9.0-27912b7b - netgauge @2.4.6
  sundials@2.5.0%gcc@4.9.0-27912b7b - sundials @2.5.0

The names here should look familiar, they’re the same ones from spack find. You can use the names here directly. For example, you could type either of these commands to load the callpath module:

$ use callpath@1.0.1%gcc@4.4.7-5dce4318
$ module load callpath@1.0.1%gcc@4.4.7-5dce4318

spack load / unload

Neither of these is particularly pretty, easy to remember, or easy to type. Luckily, Spack has its own interface for using modules and dotkits. You can use the same spec syntax you’re used to:

Environment Modules Dotkit
spack load <spec> spack use <spec>
spack unload <spec> spack unuse <spec>

And you can use the same shortened names you use everywhere else in Spack. For example, this will add the mpich package built with gcc to your path:

$ spack install mpich %gcc@4.4.7

# ... wait for install ...

$ spack use mpich %gcc@4.4.7
Prepending: mpich@3.0.4%gcc@4.4.7 (ok)
$ which mpicc
~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4/bin/mpicc

Or, similarly with modules, you could type:

$ spack load mpich %gcc@4.4.7

These commands will add appropriate directories to your PATH, MANPATH, CPATH, and LD_LIBRARY_PATH. When you no longer want to use a package, you can type unload or unuse similarly:

$ spack unload mpich %gcc@4.4.7  # modules
$ spack unuse  mpich %gcc@4.4.7  # dotkit

Note

These use, unuse, load, and unload subcommands are only available if you have enabled Spack’s shell support and you have dotkit or modules installed on your machine.

Ambiguous module names

If a spec used with load/unload or use/unuse is ambiguous (i.e. more than one installed package matches it), then Spack will warn you:

$ spack load libelf
==> Error: Multiple matches for spec libelf.  Choose one:
libelf@0.8.13%gcc@4.4.7 arch=linux-debian7-x86_64
libelf@0.8.13%intel@15.0.0 arch=linux-debian7-x86_64

You can either type the spack load command again with a fully qualified argument, or you can add just enough extra constraints to identify one package. For example, above, the key differentiator is that one libelf is built with the Intel compiler, while the other used gcc. You could therefore just type:

$ spack load libelf %intel

To identify just the one built with the Intel compiler.

spack module loads

In some cases, it is desirable to load not just a module, but also all the modules it depends on. 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 loads --dependencies <spec>

An equivalent alternative is:

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

Warning

The spack load command does not currently accept the --dependencies flag. Use spack module loads instead, for now.

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 --shell flag, spack module find may also be used to generate code that can be cut-and-pasted into a shell script. For example:

$ spack module 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 loads needs to know about that prefix when it issues module load commands. Add the --prefix option to your spack module 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 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 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

Auto-generating Module Files

Module files are generated by post-install hooks after the successful installation of a package. The following table summarizes the essential information associated with the different file formats that can be generated by Spack:

  Hook name Default root directory Compatible tools
Dotkit dotkit share/spack/dotkit DotKit
TCL - Non-Hierarchical tcl share/spack/modules Env. Modules/LMod
Lua - Hierarchical lmod share/spack/lmod LMod

Though Spack ships with sensible defaults for the generation of module files, one can customize many aspects of it to accommodate package or site specific needs. These customizations are enabled by either:

  1. overriding certain callback APIs in the Python packages
  2. writing specific rules in the modules.yaml configuration file

The former method fits best cases that are site independent, e.g. injecting variables from language interpreters into their extensions. The latter instead permits to fine tune the content, naming and creation of module files to meet site specific conventions.

Package file API

There are two methods that can be overridden in any package.py to affect the content of generated module files. The first one is:

def setup_environment(self, spack_env, run_env):
    """Set up the compile and runtime environments for a package."""
    pass

and can alter the content of the same package where it is overridden by adding actions to run_env. The second method is:

def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
    """Set up the environment of packages that depend on this one"""
    pass

and has similar effects on module file of dependees. Even in this case run_env must be filled with the desired list of environment modifications.

Note

The r package and callback APIs

A typical example in which overriding both methods prove to be useful is given by the r package. This package installs libraries and headers in non-standard locations and it is possible to prepend the appropriate directory to the corresponding environment variables:

LIBRARY_PATH self.prefix/rlib/R/lib
LD_LIBRARY_PATH self.prefix/rlib/R/lib
CPATH self.prefix/rlib/R/include

with the following snippet:

    def setup_environment(self, spack_env, run_env):
        run_env.prepend_path('LIBRARY_PATH',
                             join_path(self.prefix, 'rlib', 'R', 'lib'))
        run_env.prepend_path('LD_LIBRARY_PATH',
                             join_path(self.prefix, 'rlib', 'R', 'lib'))
        run_env.prepend_path('CPATH',
                             join_path(self.prefix, 'rlib', 'R', 'include'))

The r package also knows which environment variable should be modified to make language extensions provided by other packages available, and modifies it appropriately in the override of the second method:


        If this isn't done, they'll have CC and CXX set to Spack's generic
    # ========================================================================

    @property
    def r_lib_dir(self):
        return join_path('rlib', 'R', 'library')

Configuration in modules.yaml

The name of the configuration file that controls module generation behavior is modules.yaml. The default configuration:

# -------------------------------------------------------------------------
# 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:
  enable:
    - tcl
    - dotkit
  prefix_inspections:
    bin:
      - PATH
    man:
      - MANPATH
    share/man:
      - MANPATH
    share/aclocal:
      - ACLOCAL_PATH
    lib:
      - LIBRARY_PATH
      - LD_LIBRARY_PATH
    lib64:
      - LIBRARY_PATH
      - LD_LIBRARY_PATH
    include:
      - CPATH
    lib/pkgconfig:
      - PKG_CONFIG_PATH
    lib64/pkgconfig:
      - PKG_CONFIG_PATH
    '':
      - CMAKE_PREFIX_PATH

activates generation for tcl and dotkit module files and inspects the installation folder of each package for the presence of a set of subdirectories (bin, man, share/man, etc.). If any is found its full path is prepended to the environment variables listed below the folder name.

Activation of other systems

Any other module file generator shipped with Spack can be activated adding it to the list under the enable key in the module file. Currently the only generator that is not activated by default is lmod, which produces hierarchical lua module files. For each module system that can be enabled a finer configuration is possible.

Directives that are aimed at driving the generation of a particular type of module files should be listed under a top level key that corresponds to the generator being customized:

modules:
  enable:
    - tcl
    - dotkit
    - lmod
  tcl:
    # contains environment modules specific customizations
  dotkit:
    # contains dotkit specific customizations
  lmod:
    # contains lmod specific customizations

All these module sections allow for both:

  1. global directives that usually affect the whole layout of modules or the naming scheme
  2. directives that affect only a set of packages and modify their content

For the latter point in particular it is possible to use anonymous specs to select an appropriate set of packages on which the modifications should be applied.

Selection by anonymous specs

The procedure to select packages using anonymous specs is a natural extension of using them to install packages, the only difference being that specs in this case are not required to have a root package. Consider for instance this snippet:

modules:
  tcl:
    # The keyword `all` selects every package
    all:
      environment:
        set:
          BAR: 'bar'
    # This anonymous spec selects any package that
    # depends on openmpi. The double colon at the
    # end clears the set of rules that matched so far.
    ^openmpi::
      environment:
        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

During module file generation, the configuration above will instruct Spack to set the environment variable BAR=bar for every module, unless the associated spec satisfies ^openmpi in which case BAR=baz. 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 spec constraints are instead evaluated top to bottom.

Blacklist or whitelist the generation of specific module files

Anonymous specs are also used to prevent module files from being written or to force them to be written. A common case for that at HPC centers is to hide from users all of the software that needs to be built with system compilers. Suppose for instance to have gcc@4.4.7 provided by your system. Then with a configuration file like this one:

modules:
  tcl:
    whitelist: ['gcc', 'llvm']  # Whitelist will have precedence over blacklist
    blacklist: ['%gcc@4.4.7']   # Assuming gcc@4.4.7 is the system compiler

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

Customize the naming scheme

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 two 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:
  tcl:
    hash_length: 7

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:
  tcl:
    all:
      suffixes:
        ^python@2.7.12: 'python-2.7.12'
        ^openblas: 'openblas'

will add a python-2.7.12 version string to any packages compiled with python matching the spec, python@2.7.12. 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.

Note

TCL module files

A modification that is specific to tcl module files is the possibility to change the naming scheme of modules.

modules:
  tcl:
    naming_scheme: '${PACKAGE}/${VERSION}-${COMPILERNAME}-${COMPILERVER}'
    all:
      conflict: ['${PACKAGE}', '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 Spec.format method.

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 generated hierarchy always contains the three layers Core / Compiler / MPI but can be further extended to any other virtual dependency present in Spack. A case that could be useful in practice is for instance:

modules:
  enable:
    - lmod
  lmod:
    core_compilers: ['gcc@4.8']
    hierarchical_scheme: ['lapack']

that will generate a hierarchy in which the lapack layer is treated as the mpi one. 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.

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.

Filter out environment modifications

Modifications to certain environment variables in module files are generated by default, for instance by prefix inspections in the default configuration file. There are cases though where some of these modifications are unwanted. Suppose you need to avoid having CPATH and LIBRARY_PATH modified by your dotkit modules:

modules:
  dotkit:
    all:
      filter:
        # Exclude changes to any of these variables
        environment_blacklist: ['CPATH', 'LIBRARY_PATH']

The configuration above will generate dotkit module files that will not contain modifications to either CPATH or LIBRARY_PATH and environment module files that instead will contain these modifications.

Autoload dependencies

In some cases it can be useful to have module files directly autoload their dependencies. This may be the case for Python extensions, if not activated using spack activate:

modules:
  tcl:
    ^python:
      autoload: 'direct'

The configuration file above will produce module files that will automatically load their direct dependencies. The allowed values for the autoload statement are either none, direct or all.

Note

TCL prerequisites
In the tcl section of the configuration file it is possible to use the prerequisites directive that accepts the same values as autoload. It will produce module files that have a prereq statement instead of automatically loading other modules.

Maintaining Module Files

Spack not only provides great flexibility in the generation of module files and in the customization of both their layout and content, but also ships with a tool to ease the burden of their maintenance in production environments. This tool is the spack module command:

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

manipulate module files

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

optional arguments:
  -h, --help  show this help message and exit

spack module refresh

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

$ spack module refresh --help
usage: spack module refresh [-h] [--delete-tree] [-m {tcl,dotkit}] [-y] ...

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

optional arguments:
  -h, --help            show this help message and exit
  --delete-tree         delete the module file tree before refresh
  -m {tcl,dotkit}, --module-type {tcl,dotkit}
                        type of module files [default: tcl]
  -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. The argument --module-type identifies the type of module files to refresh. Optionally the entire tree can be deleted before regeneration if the change in layout is radical.

spack module rm

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

$ spack module rm --help
usage: spack module rm [-h] [-m {tcl,dotkit}] [-y] ...

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

optional arguments:
  -h, --help            show this help message and exit
  -m {tcl,dotkit}, --module-type {tcl,dotkit}
                        type of module files [default: tcl]
  -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.