Spack: software package manager

Starting August 2020, Palmetto utilizes Spack to manage the installation and configuration of its research software packages. As a package management tool developed by the Lawrence Livermore National Lab (LLNL), Spack helps managing the installation and configuration of many research software packages and their dependencies in a streamlined and transparent manner.

In the remainder of this documentation, we will show how Palmetto users can also use Spack to manage their own software libraries.

Setup Spack inside user directory

The following command needs to be run to setup Spack:

$ cd
$ mkdir software
$ cd software
$ git clone https://github.com/spack/spack.git
$ source ~/software/spack/share/spack/setup-env.sh

You can also append this line to your .bashrc file for it to be automatically loaded as follows:

$ echo "source ~/software/spack/share/spack/setup-env.sh" >> ~/.bashrc
$ source ~/.bashrc

Copy the default configurations for Spack from Palmetto. You can customize these configurations as necessary. 

$ cp -R /software/spack-src/spack-yaml ~/.spack

Modify the config.yaml file inside ~/.spack/linux/ with the following content:

...

  # This is the path to the root of the Spack install tree.
  install_tree: ~/software/spackages

  # Locations where templates should be found
  template_dirs:
    - ~/software/spack/share/spack/templates/

  # Default directory layout
  install_path_scheme: "${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}"

  # Locations where different types of modules should be installed.
  module_roots:
    tcl:    ~/software/ModuleFiles/modules
    lmod:   ~/software/ModuleFiles/lmod

...

In the file above: - install_tree specifies where in your home directory you want to install your software. - template_dirs uses the same template to generate the modulefiles as Palmetto's. You can change to your own template if you'd like. - install_path_scheme provides the subdirectory structure within install_tree. - tcl and lmod are two different modulefiles specification. Palmetto currently uses tcl. The generated modulefiles will be placed into the corresponding location.

Installing a software package using Spack.

To view a list of all software supported by Spack, you can run the spack list command. At the moment (July 29, 2020), there are 4483 software packages supported by Spack (ls -l ~/software/spack/var/spack/repos/builtin/packages/ | wc -l).

Let's assume that you want to install R 3.3.0, which is not currently available on Palmetto (oldest version is 3.5.3).

First, run the following command to view information about R on Spack

$ spack info r

  • Safe versions list all versions that the Spack team inspected and considered safe/stable to use. You can see that 3.3.0 is listed among them.
  • Variants list different configuration options that are possible. As we will use R on Palmetto, X11 might not be neccessary, but we will want external-lapack and memory_profiling.
  • The value inside the backet, [on] or [off], tell you the default setting of these variants. To turn on a variant that is defaulted to [off], use +VARIANT_NAME. To turn off a variant that is defaulted to [on], use ~VARIANT_NAME.

Before running the installation, we want to run a specification check. This is done by running

$ spack spec -I -l r@3.3.0 arch=x86_64 +external-lapack +memory_profiling
  • The -I flag provides information about dependencies. In the display, a gray - sign in the first column indicates that the dependency is not available and needs to be installed.
  • The -l flag provides the unique hash string that identifies each software package installed and managed by Spack.
  • If there is any problem with the installation specification (version conflicts, etc), the spec call will catch the majority of them here.

If there is no error reported during spack spec, we can start the installation process:

$ spack install r@3.3.0 arch=x86_64 +external-lapack +memory_profiling

After finishing the installation, you will need to add the path to your new module file directory to $MODULEPATH:

$ export MODULEPATH=$MODULEPATH:~/software/ModuleFiles/modules/linux-centos8-x86_64/
$ module avail

You can see your newly install R package:

Using module allows you to manage the primary installed software, R 3.3.0. However, Spack also installed a number of dependencies for you. To view all dependencies, run:

$ spack find

These dependencies will be reused by Spack when you install other software packages that require the same dependencies. For example, if you run spack spec -Il r@4.0.0 arch=x86_64, you will see that many of the dependency lines have the green [+] sign, indicating that that dependency is already installed.

Further information about installing packages using Spack can be found on Spack's documentation page