Skip to content

tutorial_configuration.rst

Latest commit

 

History

History
814 lines (593 loc) · 30 KB

tutorial_configuration.rst

File metadata and controls

814 lines (593 loc) · 30 KB

Configuration Tutorial

This tutorial will guide you through various configuration options that allow you to customize Spack's behavior with respect to software installation. There are many different configuration sections. A partial list of some key configuration sections is provided below.

Spack Configuration Sections
Name Description
config General settings (install location, number of build jobs, etc)
concretizer Specialization of the concretizer behavior (reuse, unification, etc)
compilers Define the compilers that Spack can use (required and system specific)
Mirrors Locations where spack can look for stashed source or binary distributions
Packages Specific settings and rules for packages
Modules Naming, location and additional configuration of Spack generated modules

The full list of sections can be viewed with spack config list. For further education, we encourage you to explore the Spack documentation on configuration files.

The principle goals of this section of the tutorial are:

  1. Introduce the configuration sections and scope hierarchy
  2. Demonstrate how to manipulate configurations
  3. Show how to configure system assets with Spack (compilers and packages)

As such, we will primarily focus on the compilers and packages configuration sections in this portion of the tutorial.

We will explain this by first covering how to manipulate configurations from the command line and then show how this impacts the configuration file hierarchy. We will then move into compiler and package configurations to help you develop skills for getting the builds you want on your system. Finally, we will give some brief attention to more generalized Spack configurations in the config section.

For all of these features, we will demonstrate how we build up a full configuration file. For some, we will then demonstrate how the configuration affects the install command, and for others we will use the spack spec command to demonstrate how the configuration changes have affected Spack's concretization algorithm. The provided output is all from a server running Ubuntu version 22.04.

Configuration from the command line

You can run spack config blame [section] at any point in time to see what your current configuration is. If you omit the section, then spack will dump all the configurations settings to your screen. Let's go ahead and run this for the concretizer section.

$ spack config blame concretizer

Notice that the spack:concretizer:reuse option is defaulted to true. For this section we'd actually like to turn reuse off so that when we demonstrate package configuration our preferences are weighted higher than available binaries for the concretizer solution selection procedure.

One of the most convenient ways to set configuration options is through the command line.

$ spack config add concretizer:reuse:false

If we rerun spack config blame concretizer we can see that the change was applied.

$ spack config blame concretizer

Notice that the reference file for this option is now different. This indicates the scope where the configuration was set in, and we will discuss how Spack chooses the default scope shortly. For now, it is important to note that the spack config command accepts an optional --scope flag so we can be more precise in the configuration process. This will make more sense after the next section which provides the definition of Spack's configuration scopes and their hierarchy.

Configuration Scopes

Depending on your use case, you may want to provide configuration settings common to everyone on your team, or you may want to set default behaviors specific to a single user account. Spack provides six configuration scopes to handle this customization. These scopes, in order of decreasing priority, are:

Scope Directory
Command Line N/A
Environment In environment base directory (in spack.yaml)
Custom Custom directory, specified with --config-scope
User ~/.spack/
Site $SPACK_ROOT/etc/spack/
System /etc/spack/
Defaults $SPACK_ROOT/etc/spack/defaults/

Spack's default configuration settings reside in $SPACK_ROOT/etc/spack/defaults. These are useful for reference, but should never be directly edited. To override these settings, create new configuration files in any of the higher-priority configuration scopes.

A particular cluster may have multiple Spack installations associated with different projects. To provide settings common to all Spack installations, put your configuration files in /etc/spack. To provide settings specific to a particular Spack installation, you can use the $SPACK_ROOT/etc/spack directory.

For settings specific to a particular user, you will want to add configuration files to the ~/.spack directory. When Spack first checked for compilers on your system, you may have noticed that it placed your compiler configuration in this directory.

Configuration settings can also be placed in a custom location, which is then specified on the command line via --config-scope. An example use case is managing two sets of configurations, one for development and another for production preferences.

Settings specified on the command line have precedence over all other configuration scopes.

Platform-specific scopes

Some facilities manage multiple platforms from a single shared file system. In order to handle this, each of the configuration scopes listed above has two sub-scopes: platform-specific and platform-independent. For example, compiler settings can be stored in the following locations:

  1. $ENVIRONMENT_ROOT/spack.yaml
  2. ~/.spack/<platform>/compilers.yaml
  3. ~/.spack/compilers.yaml
  4. $SPACK_ROOT/etc/spack/<platform>/compilers.yaml
  5. $SPACK_ROOT/etc/spack/compilers.yaml
  6. /etc/spack/<platform>/compilers.yaml
  7. /etc/spack/compilers.yaml
  8. $SPACK_ROOT/etc/defaults/<platform>/compilers.yaml
  9. $SPACK_ROOT/etc/defaults/compilers.yaml

These files are listed in decreasing order of precedence, so files in ~/.spack/<platform> will override settings in ~/.spack.

YAML Format

Spack configurations are nested YAML dictionaries with a specified schema. The configuration is organized into sections based on theme (e.g., a 'compilers' section) and the highest-level keys of the dictionary specify the section. Spack generally maintains a separate file for each section, although environments keep them together (in spack.yaml).

When Spack checks its configuration, the configuration scopes are updated as dictionaries in increasing order of precedence, allowing higher precedence files to override lower. YAML dictionaries use a colon ":" to specify key-value pairs. Spack extends YAML syntax slightly to allow a double-colon "::" to specify a key-value pair. When a double-colon is used, instead of adding that section, Spack replaces what was in that section with the new value. For example, consider a user's compilers configuration file as follows:

compilers::
- compiler:
    spec: gcc@11.4.0
    paths:
      cc: /usr/bin/gcc
      cxx: /usr/bin/g++
      f77: /usr/bin/gfortran
      fc: /usr/bin/gfortran
    flags: {}
    operating_system: ubuntu22.04
    target: x86_64
    modules: []
    environment: {}
    extra_rpaths: []

This ensures that no other compilers are used, as the user configuration scope is the last scope searched and the compilers:: line replaces information from all previous configuration files. If the same configuration file had a single colon instead of the double colon, it would add the GCC version 11.3.0 compiler to whatever other compilers were listed in other configuration files.

A configuration section appears nearly the same when managed in an environment's spack.yaml file except that the section is nested 1 level underneath the top-level 'spack' key. For example the above compilers.yaml could be incorporated into an environment's spack.yaml like so:

spack:
  specs: []
  view: true
  compilers::
  - compiler:
      spec: gcc@11.4.0
      paths:
        cc: /usr/bin/gcc
        cxx: /usr/bin/g++
        f77: /usr/bin/gfortran
        fc: /usr/bin/gfortran
      flags: {}
      operating_system: ubuntu22.04
      target: x86_64
      modules: []
      environment: {}
      extra_rpaths: []

Compiler Configuration

For most tasks, we can use Spack with the compilers auto-detected the first time Spack runs on a system. As discussed in the basic installation tutorial, we can also tell Spack where compilers are located using the spack compiler add command. However, in some circumstances, we want even more fine-grained control over the compilers available. This section will teach you how to exercise that control using the compilers configuration file.

We will start by opening the compilers configuration file:

$ spack config edit compilers

We start with no active environment, so this will open a compilers.yaml file for editing (you can also do this with an active environment):

compilers:
- compiler:
    spec: clang@=14.0.0
    paths:
      cc: /usr/bin/clang
      cxx: /usr/bin/clang++
      f77:
      fc:
    flags: {}
    operating_system: ubuntu22.04
    target: x86_64
    modules: []
    environment: {}
    extra_rpaths: []
- compiler:
    spec: gcc@=10.5.0
    paths:
      cc: /usr/bin/gcc-10
      cxx: /usr/bin/g++-10
      f77: /usr/bin/gfortran-10
      fc: /usr/bin/gfortran-10
    flags: {}
    operating_system: ubuntu22.04
    target: x86_64
    modules: []
    environment: {}
    extra_rpaths: []
- compiler:
    spec: gcc@=11.4.0
    paths:
      cc: /usr/bin/gcc
      cxx: /usr/bin/g++
      f77: /usr/bin/gfortran
      fc: /usr/bin/gfortran
    flags: {}
    operating_system: ubuntu22.04
    target: x86_64
    modules: []
    environment: {}
    extra_rpaths: []

This specifies two versions of the GCC compiler and one version of the Clang compiler with no Flang compiler. Now suppose we have a code that we want to compile with the Clang compiler for C/C++ code, but with gfortran for Fortran components. We can do this by adding another entry to the compilers.yaml file:

- compiler:
    spec: clang@=14.0.0-gfortran
    paths:
      cc: /usr/bin/clang
      cxx: /usr/bin/clang++
      f77: /usr/bin/gfortran
      fc: /usr/bin/gfortran
    flags: {}
    operating_system: ubuntu22.04
    target: x86_64
    modules: []
    environment: {}
    extra_rpaths: []

Let's talk about the sections of this compiler entry that we've changed. The biggest change we've made is to the paths section. This lists the paths to the compilers to use for each language/specification. In this case, we point to the Clang compiler for C/C++ and the gfortran compiler for both specifications of Fortran. We've also changed the spec entry for this compiler. The spec entry is effectively the name of the compiler for Spack. It consists of a name and a version number, separated by the @ sigil. The name must be one of the supported compiler names in Spack (aocc, apple-clang, arm, cce, clang, dpcpp, fj, gcc, intel, msvc, nag, nvhpc, oneapi, pgi, rocmcc, xl, xl_r). The version number can be an arbitrary string of alphanumeric characters, as well as -, ., and _. The target and operating_system sections we leave unchanged. These sections specify when Spack can use different compilers, and are primarily useful for configuration files that will be used across multiple systems.

We can verify that our new compiler works by invoking it now:

$ spack install --no-cache zlib %clang@14.0.0-gfortran
...

This new compiler also works on Fortran codes. We'll show this by compiling a small package using cmake%gcc@11.4.0 as a build dependency, since it is already available in our binary cache:

$ spack install --reuse cmake %gcc@11.4.0
...
$ spack install --no-cache --reuse json-fortran %clang@=14.0.0-gfortran ^cmake%gcc@11.4.0
...

Compiler flags

Some compilers may require specific compiler flags to work properly in a particular computing environment. Spack provides configuration options for setting compiler flags every time a specific compiler is invoked. These flags become part of the package spec and therefore of the build provenance. As on the command line, the flags are set through the implicit build variables cflags, cxxflags, cppflags, fflags, ldflags, and ldlibs.

Let's open our compilers configuration file again and add a compiler flag:

- compiler:
    spec: clang@=14.0.0-gfortran
    paths:
      cc: /usr/bin/clang
      cxx: /usr/bin/clang++
      f77: /usr/bin/gfortran
      fc: /usr/bin/gfortran
    flags:
      cppflags: -g
    operating_system: ubuntu22.04
    target: x86_64
    modules: []
    environment: {}
    extra_rpaths: []

We can test this out using the spack spec command to show how the spec is concretized:

.. literalinclude:: outputs/config/0.compiler_flags.out
   :language: console

We can see that cppflags="-g" has been added to every node in the DAG.

Advanced compiler configuration

There are four fields of the compiler configuration entry that we have not yet talked about.

The target field of the compiler defines the cpu architecture family that the compiler supports.

- compiler:
    ...
    target: ppc64le
    ...

The modules field of the compiler was originally designed to support older Cray systems, but can be useful on any system that has compilers that are only usable when a particular module is loaded. Any modules in the modules field of the compiler configuration will be loaded as part of the build environment for packages using that compiler:

- compiler:
    ...
    modules:
    - PrgEnv-gnu
    - gcc/5.3.0
    ...

The environment field of the compiler configuration is used for compilers that require environment variables to be set during build time. For example, if your Intel compiler suite requires the INTEL_LICENSE_FILE environment variable to point to the proper license server, you can set this in compilers.yaml as follows:

- compiler:
    ...
    environment:
      set:
        INTEL_LICENSE_FILE: 1713@license4
    ...

In addition to set, environment also supports unset, prepend_path, and append_path.

The extra_rpaths field of the compiler configuration is used for compilers that do not rpath all of their dependencies by default. Since compilers are often installed externally to Spack, Spack is unable to manage compiler dependencies and enforce rpath usage. This can lead to packages not finding link dependencies imposed by the compiler properly. For compilers that impose link dependencies on the resulting executables that are not rpath'ed into the executable automatically, the extra_rpaths field of the compiler configuration tells Spack which dependencies to rpath into every executable created by that compiler. The executables will then be able to find the link dependencies imposed by the compiler. As an example, this field can be set by:

- compiler:
    ...
    extra_rpaths:
    - /apps/intel/ComposerXE2017/compilers_and_libraries_2017.5.239/linux/compiler/lib/intel64_lin
    ...

Configuring Package Preferences

Package preferences in Spack are managed through the packages configuration section. First, we will look at the default packages.yaml file.

$ spack config --scope defaults edit packages
.. literalinclude:: _spack_root/etc/spack/defaults/packages.yaml
   :language: yaml
   :emphasize-lines: 18,45

This sets the default preferences for compilers and for providers of virtual packages. To illustrate how this works, suppose we want to change the preferences to prefer the Clang compiler and to prefer MPICH over OpenMPI. Currently, we prefer GCC and OpenMPI.

.. literalinclude:: outputs/config/0.prefs.out
   :language: console
   :emphasize-lines: 16

Let's override these default preferences in an environment. When you have an activated environment, you can edit the associated configuration with spack config edit (you don't have to provide a section name):

$ spack env create config-env
$ spack env activate config-env
$ spack config edit

Warning

You will get exactly the same effects if you make these changes without using an environment, but you must delete the associated packages.yaml file after the config tutorial or the commands you run in later tutorial sections will not produce the same output (because they weren't run with the configuration changes made here)

spack:
  specs: []
  view: true
  packages:
    all:
      compiler: [clang, gcc, intel, pgi, xl, nag, fj]
      providers:
        mpi: [mpich, openmpi]

Because of the configuration scoping we discussed earlier, this overrides the default settings just for these two items.

.. literalinclude:: outputs/config/1.prefs.out
   :language: console
   :emphasize-lines: 18

Variant preferences

As we've seen throughout this tutorial, HDF5 builds with MPI enabled by default in Spack. If we were working on a project that would routinely need serial HDF5, that might get annoying quickly, having to type hdf5~mpi all the time. Instead, we'll update our preferences for HDF5.

spack:
  specs: []
  view: true
  packages:
    all:
      compiler: [clang, gcc, intel, pgi, xl, nag, fj]
      providers:
        mpi: [mpich, openmpi]
    hdf5:
      require: ~mpi

Now hdf5 will concretize without an MPI dependency by default.

.. literalinclude:: outputs/config/3.prefs.out
   :language: console
   :emphasize-lines: 8

In general, every attribute that we can set for all packages we can set separately for an individual package.

External packages

The packages configuration file also controls when Spack will build against an externally installed package. Spack has a spack external find command that can automatically discover and register externally installed packages. This works for many common build dependencies, but it's also important to know how to do this manually for packages that Spack cannot yet detect.

On these systems, we have a pre-installed curl. Let's tell Spack about this package and where it can be found:

spack:
  specs: []
  view: true
  packages:
    all:
      compiler: [clang, gcc, intel, pgi, xl, nag, fj]
      providers:
        mpi: [mpich, openmpi]
    hdf5:
      require: ~mpi
    curl:
      externals:
      - spec: curl@7.81.0 %gcc@11.4.0
        prefix: /usr

Here, we've told Spack that Curl 7.81.0 is installed on our system. We've also told it the installation prefix where Curl can be found. We don't know exactly which variants it was built with, but that's okay.

.. literalinclude:: outputs/config/0.externals.out
   :language: console

You'll notice that Spack is now using the external Curl installation, but the compiler used to build Curl is now overriding our compiler preference of clang. If we explicitly specify Clang:

.. literalinclude:: outputs/config/1.externals.out
   :language: console

Spack concretizes to both HDF5 and Curl being built with Clang. This has a side-effect of rebuilding Curl. If we want to force Spack to use the system Curl, we have two choices. We can either specify it on the command line, or we can tell Spack that it's not allowed to build its own Curl. We'll go with the latter.

spack:
  specs: []
  view: true
  packages:
    all:
      compiler: [clang, gcc, intel, pgi, xl, nag, fj]
      providers:
        mpi: [mpich, openmpi]
    hdf5:
      require: ~mpi
    curl:
      externals:
      - spec: curl@5.34.0 %gcc@11.4.0
        prefix: /usr
      buildable: false

Now Spack will be forced to choose the external Curl.

.. literalinclude:: outputs/config/2.externals.out
   :language: console

This gets slightly more complicated with virtual dependencies. Suppose we don't want to build our own MPI, but we now want a parallel version of HDF5. Well, fortunately, we have MPICH installed on these systems.

Instead of manually configuring an external for MPICH like we did for Curl we will use the spack external find command. For packages that support this option, this is a useful way to avoid typos and get more accurate external specs.

.. literalinclude:: outputs/config/0.external_find.out
   :language: console

To express that we don't want any other MPI installed, we can use the virtual mpi package as a key. While we're editing the spack.yaml file, make sure to configure HDF5 to be able to build with MPI again:

spack:
  specs: []
  view: true
  packages:
    all:
      compiler: [clang, gcc, intel, pgi, xl, nag, fj]
      providers:
        mpi: [mpich, openmpi]
    curl:
      externals:
      - spec: curl@7.81.0 %gcc@11.4.0
        prefix: /usr
      buildable: false
    mpich:
      externals:
      - spec: mpich@4.0+hydra device=ch4 netmod=ofi
        prefix: /usr
    mpi:
      buildable: false

Now that we have configured Spack not to build any possible provider for MPI, we can try again.

.. literalinclude:: outputs/config/3.externals.out
   :language: console
   :emphasize-lines: 15

Notice that we still haven't build hdf5 with our external mpich. The concretizer has instead turned off mpi support in hdf5. To debug this, we will force Spack to use hdf5+mpi.

$ spack spec hdf5%clang+mpi
==> Error: concretization failed for the following reasons:

   1. hdf5: '+mpi' conflicts with '^mpich@4.0:4.0.3'
   2. hdf5: '+mpi' conflicts with '^mpich@4.0:4.0.3'
        required because conflict applies to spec ^mpich@4.0:4.0.3
          required because hdf5%clang+mpi requested from CLI
        required because conflict is triggered when +mpi
          required because hdf5%clang+mpi requested from CLI

In this case, we cannot use the external mpich. The version is incompatible with hdf5. At this point, the best option is to give up and let Spack build mpi for us. The alternative is to try to find a version of hdf5 which doesn't have this conflict.

By configuring most of our package preferences in packages.yaml, we can cut down on the amount of work we need to do when specifying a spec on the command line. In addition to compiler and variant preferences, we can specify version preferences as well. Except for specifying dependencies via ^, anything that you can specify on the command line can be specified in packages.yaml with the exact same spec syntax.

Installation permissions

The packages configuration also controls the default permissions to use when installing a package. You'll notice that by default, the installation prefix will be world-readable but only user-writable.

Let's say we need to install converge, a licensed software package. Since a specific research group, fluid_dynamics, pays for this license, we want to ensure that only members of this group can access the software. We can do this like so:

packages:
  converge:
    permissions:
      read: group
      group: fluid_dynamics

Now, only members of the fluid_dynamics group can use any converge installations.

At this point we want to discard the configuration changes we made in this tutorial section, so we can deactivate the environment:

$ spack env deactivate

Warning

If you do not deactivate the config-env environment, then specs will be concretized differently in later tutorial sections and your results will not match.

High-level Config

In addition to compiler and package settings, Spack allows customization of several high-level settings. These settings are managed in the config section (in config.yaml when stored as an individual file outside of an environment). You can see the default settings by running:

$ spack config --scope defaults edit config
.. literalinclude:: _spack_root/etc/spack/defaults/config.yaml
   :language: yaml

As you can see, many of the directories Spack uses can be customized. For example, you can tell Spack to install packages to a prefix outside of the $SPACK_ROOT hierarchy. Module files can be written to a central location if you are using multiple Spack instances. If you have a fast scratch file system, you can run builds from this file system with the following config.yaml:

config:
  build_stage:
    - /scratch/$user/spack-stage

Note

It is important to distinguish the build stage directory from other directories in your scratch space to ensure spack clean does not inadvertently remove unrelated files. This can be accomplished by including a combination of spack and or stage in each path as shown in the default settings and documented examples. See Basic Settings for details.

On systems with compilers that absolutely require environment variables like LD_LIBRARY_PATH, it is possible to prevent Spack from cleaning the build environment with the dirty setting:

config:
  dirty: true

However, this is strongly discouraged, as it can pull unwanted libraries into the build.

One last setting that may be of interest to many users is the ability to customize the parallelism of Spack builds. By default, Spack installs all packages in parallel with the number of jobs equal to the number of cores on the node (up to a maximum of 16). For example, on a node with 16 cores, this will look like:

$ spack install --no-cache --verbose --overwrite --yes-to-all zlib
==> Installing zlib
==> Executing phase: 'install'
==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.3.0/zlib-1.2.12-fntvsj6xevbz5gyq7kfa4xg7oxnaolxs'
...
==> 'make' '-j16'
...
==> 'make' '-j16' 'install'
...
[+] /home/user/spack/opt/spack/linux-ubuntu22.04-x86_64/gcc-11.3.0/zlib-1.2.12-fntvsj6xevbz5gyq7kfa4xg7oxnaolxs

As you can see, we are building with all 16 cores on the node. If you are on a shared login node, this can slow down the system for other users. If you have a strict ulimit or restriction on the number of available licenses, you may not be able to build at all with this many cores. To limit the number of cores our build uses, set build_jobs like so:

$ spack config edit config
config:
  build_jobs: 2

If we uninstall and reinstall zlib-ng, we see that it now uses only 2 cores:

$ spack install --no-cache --verbose --overwrite --yes-to-all zlib-ng
==> Installing zlib
==> Executing phase: 'install'
==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu22.04...
...
==> 'make' '-j2'
...
==> 'make' '-j2' 'install'
...
[+] /home/user/spack/opt/spack/linux-ubuntu22.04...

Obviously, if you want to build everything in serial for whatever reason, you would set build_jobs to 1.

Last, we'll unset concretizer:reuse:false since we'll want to enable concretizer reuse for the rest of this tutorial.

$ spack config rm concretizer:reuse

Warning

If you do not do this step, the rest of the tutorial will not reuse binaries!

Conclusion

In this tutorial, we covered basic Spack configuration using compilers.yaml, packages.yaml, and config.yaml. Spack has many more configuration files, including modules.yaml, which will be covered in the :ref:`modules-tutorial`. For more detailed documentation on Spack's many configuration settings, see the configuration section of Spack's main documentation.

For examples of how other sites configure Spack, see https://github.com/spack/spack-configs. If you use Spack at your site and want to share your config files, feel free to submit a pull request!