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Using user Spack module for software installations

Spack is a package manager for supercomputers, Linux and MacOS. It can be used to install complicated scientific software packages easily. CSC installs the development stack, including compilers, MPI libraries and also many other libraries and applications using Spack. CSC provides also a user module for customers that enables per-project software installations using Spack.

Note

Spack is an advanced tool and it requires understanding of compiling and linking programs.

Note

This tutorial assumes you are on Puhti, which has spack/v0.18-user installed. Mahti has another version of Spack available for users, spack/v0.17-user. Aside from the module versions, the outlined procedure is identical on the two systems.

Creating a Spack instance

Before running the Spack module for the first time, you have to prepare an installation location that can reside either on /projappl or /scratch disk areas. You also have to set an environment variable that points to the location of the Spack instance.

For example, if you want to create a Spack instance in the /projappl directory, you can initialize the environment as follows:

[maijam@puhti-login11 ~]$ module purge
The following modules were not unloaded:
  (Use "module --force purge" to unload all):

  1) csc-tools
[maijam@puhti-login11 ~]$ export USER_SPACK_ROOT=/projappl/project_2001234/spack-instance-1
[maijam@puhti-login11 ~]$ mkdir -p ${USER_SPACK_ROOT}
[maijam@puhti-login11 ~]$ module load spack/v0.18-user
Run user-spack-init to initialize user installation in /projappl/project_2001234/spack-instance-1
[maijam@puhti-login11 ~]$ user-spack-init
[INFO] USER_SPACK_GROUP not set, defaulting to project_2001234 based on target directory

Purge before loading

Before loading Spack, you have to run module purge to purge all default environment compilers and library modules as they may interfere with Spack builds.

Several Spack instances

You can have several Spack instances under the same project. The used instance is specified with the $USER_SPACK_ROOT environment variable that points to the root directory of the instance.

Initializing

Before accessing the Spack instance for the first time, you have to initialize it by running the user-spack-init command.

Using the Spack instance

An initialized instance can be activated by purging the module environment, setting the root path of the instance and loading the Spack module:

[maijam@puhti-login11 ~]$ module purge
The following modules were not unloaded:
  (Use "module --force purge" to unload all):

  1) csc-tools
[maijam@puhti-login11 ~]$ export USER_SPACK_ROOT=/projappl/project_2001234/spack-instance-1
[maijam@puhti-login11 ~]$ module load spack/v0.18-user
Found existing user spack installation at /projappl/project_2001234/spack-instance-1

Example build

[maijam@puhti-login11 ~]$ spack spec -I --reuse kakoune
Input spec
--------------------------------
 -   kakoune

Concretized
--------------------------------
 -   kakoune@2021.11.08%gcc@11.3.0 arch=linux-rhel8-cascadelake
[^]      ^ncurses@6.2%gcc@11.3.0~symlinks+termlib abi=none arch=linux-rhel8-cascadelake
[^]          ^pkgconf@1.8.0%gcc@11.3.0 arch=linux-rhel8-cascadelake

The spack spec command shows what would be installed given a certain input. It is good practice to run it before installing to ensure that the build looks like intended. The -I flag is used to display the current install status of the package and its dependencies, while the --reuse flag is provided in order to reuse already installed dependencies whenever possible. Actual installation is then performed via the spack install command.

[maijam@puhti-login11 ~]$ spack install --reuse kakoune
[+] /appl/spack/v018/install-tree/gcc-11.3.0/pkgconf-1.8.0-2hkydh
[+] /appl/spack/v018/install-tree/gcc-11.3.0/ncurses-6.2-n4phtn
==> Installing kakoune-2021.11.08-yh4nmfid4st4l7gsmuzqv43o6qt6ckrm
==> No binary for kakoune-2021.11.08-yh4nmfid4st4l7gsmuzqv43o6qt6ckrm found: installing from source
==> Using cached archive: /local_scratch/maijam/spack-build-project_2002567/source-cache/_source-cache/archive/aa/aa30889d9da11331a243a8f40fe4f6a8619321b19217debac8f565e06eddb5f4.tar.bz2
==> No patches needed for kakoune
==> kakoune: Executing phase: 'edit'
==> kakoune: Executing phase: 'build'
==> kakoune: Executing phase: 'install'
==> kakoune: Successfully installed kakoune-2021.11.08-yh4nmfid4st4l7gsmuzqv43o6qt6ckrm
  Fetch: 0.00s.  Build: 34.31s.  Total: 34.31s.
[+] /projappl/project_2001234/spack-instance-1/install_tree/gcc-11.3.0/kakoune-2021.11.08-yh4nmf

Spec syntax

The string that specifies which package should be installed (the spec) can be simply just the package name, as above, but often you might want to install a specific version, perhaps using a specific compiler and with some optional installation flags (e.g. a GPU-enabled version of the software). Spack uses a special syntax for specifying this information as explained in the official documentation.

Using modules with user Spack installations

By default, Spack creates module files under $USER_SPACK_ROOT/modules and you can add that path to your $MODULEPATH with the command:

[maijam@puhti-login11 ~]$ module use ${USER_SPACK_ROOT}/modules

After installing a new package, you need to regenerate the module files. For example:

[maijam@puhti-login11 ~]$ spack module tcl refresh kakoune

Now you can see the modules with regular module avail and module spider commands. For example, the kakoune editor built in the previous example can be searched and loaded with:

[maijam@puhti-login11 ~]$ module spider kakoune

--------------------------------
  kakoune: kakoune/2021.11.08-gcc-11.3.0-yh4n
--------------------------------

    This module can be loaded directly: module load kakoune/2021.11.08-gcc-11.3.0-yh4n

[maijam@puhti-login11 ~]$ module load kakoune/2021.11.08-gcc-11.3.0-yh4n

Further reading

Last update: October 28, 2022