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Install software with Spack

Spack is an open source package manager that simplifies building, installing, customizing, and sharing HPC software stacks. Spack helps installing software with much less efforts. It is a very simple and efficient way for installing packages with cumbersome structures and lots of dependencies. Spack is an open source package manger and developing and maintaining by community of HPC developers.

To learn more about Sapck review:

Usage

Spack has a very simple workflow. Basically, it is a Git repo of package files are written in pure Python including software build requirements and dependencies. We can Clone and setup Spack by:

git clone https://github.com/spack/spack.git
cd spack
git fetch origin releases/latest:latest
git checkout latest
source spack/share/spack/setup-env.sh # setup Spack

To list a specific software and it’s specifications we can use:

spack list <software-name> # list a software
spack info <software-name> # show information and variants of a software
spack spec -I <software-name> # show specifications (dependencies)

Option -I or --install-status shows status of the software dependencies i.e. installed (+) or will be installed during the installation (-).

Now let’s install a new software’s from Spack:

spack install <software_name> or <software_name@version> or <software_name@version %compiler@version>

In general, @version for both software and compiler could be removed. Spack installs the most stable version by default (see spack versions -s <software-name>). You may find complete list of software that you can install by using spack list or in Spack online package list. Also. we can use --verbose option to see more details during the installation, --no-cache to install a package directly from the source, and --overwrite to overwrite an installed package.

After installation, we can find the software by:

spack find # to see all installed software
spack find <software-name> # to find a software (use -lfvp to see hashes, flags, variants and pathes)
spack location -i <software-name> # to find location of a software

And we can load the software:

spack load <software_name>
spack find --loaded # see what is loaded

To uninstall a software we can use:

spack uninstall <software_name@version> or <software_name/hash>
spack uninstall --all arch=<arch-name> # uninstall by architecture
spack uninstall --all %<compiler@version> # uninstall by compiler

We can use -R or --dependents option to uninstall any packages that depend on that package and -f or --force to force to remove. Note that after uninstalling a software, using spack gc will uninstall dependencies of the software.

More details about Spack commands can be found by:

  • spack --help or spack -h getting help
  • spack command -h print information for a particular command (eg. spack view -h)
  • spack command subcommand -h print information for a particular subcommand (eg. spack view add -h)

To see full list of commands visit Spack Command Reference.

Specs & dependencies

In general, we can specify versions by @, compilers by %, dependencies by ^ and hashes by / for install/uninstall commands. The following example from Spack Basic Usage show these specs:

mpileaks@1.2:1.4 %gcc@4.7.5 +debug ~qt arch=bgq_os ^callpath@1.1 %gcc@4.7.2

If provided to spack install, this will install the mpileaks library at some version between 1.2 and 1.4 (inclusive), built using gcc at version 4.7.5 for the Blue Gene/Q architecture, with debug options enabled, and without Qt support. Additionally, it says to link it with the callpath library (which it depends on), and to build callpath with gcc 4.7.2.

Compilers

We can select compiler version and settings. To find and list compilers, use:

spack compiler list
spack compiler find

Compilers can be added to the Spack compilers list or removed from the list by:

spack compiler add <compiler-name@ver> # for example $(spack location -i gcc@10.1.0) add gcc 10 compiler that already is installed by Spack
spack compiler remove <compiler-name@ver>

Also, we can directly modify compilers.yaml file by:

spack config edit compilers

Moreover, we can add specific compiler’s options during the installation. Valid flag names are cflags, cxxflags, fflags, cppflags, ldflags, and ldlibs. For instance, spack install libdwarf cppflags="-g" will install libdwarf with the -g flag injected into their compile line.

Architecture specifiers

Also, we can specify architecture of a machine by arch. For example, the following will unistall all software installed with gcc 4.8.5 in linux-centos7-haswell machine:

spack uninstall --all %gcc@4.8.5 arch=linux-centos7-haswell

We can specify these values separately by platform=linux, os=centos7 and target=haswell.

Create and edit package files

If the package that you are looking for is not among Spack repo list, you can create a package file in Python by spack create <tarball link> and add to the Spack reop. Review Package Creation Tutorial to learn how to build and debug a package.

If the package that you are looking for is outdated or has wrong dependencies, you can modify the package Python file by:

spack edit <software-name>

To update version of the package, install the package tar file from the developer web-page or GitHub and extract the related hash number by md5sum or shasum -a 256 command and add version and hash number to the package file. For example, spack edit octopus:

class Octopus(Package):
    """A real-space finite-difference (time-dependent) density-functional
    theory code."""

    homepage = "https://octopus-code.org/"
    url      = "http://octopus-code.org/down.php?file=10.0/octopus-10.0.tar.gz"

    version('10.0',   sha256='ccf62200e3f37911bfff6d127ebe74220996e9c09383a10b1420c81d931dcf23')

In the above example, we have added Octopus version 10 to the package file.

Also, we can open the packages configuration file and update preferences by:

spack config edit packages

Note: if you prefer to use Emacs to edit Spack config files, use export EDITOR=emacs to make Emacs the default text editor.

Environment modules

Lmod is a Lua-based module system that easily handles the MODULEPATH Hierarchical problem. To install Lmode, use the following (note this may take a while):

source spack/share/spack/setup-env.sh
spack install lmod

To use Lmode for installing and loading new packages use:

unset MODULEPATH
unset MODULESHOME
source $(spack location -i lmod)/lmod/lmod/init/bash
source spack/share/spack/setup-env.sh

spack install <software-name>
module load <software-name>

Now we can use module avail to see list of the available (installed) modules.

We can also, use lomd to manage modules by editing the module configuration file. Let’s open the file:

spack config edit modules

And add the following configuration from Spack tutorial to the config file:

modules:
  enable:
    - lmod
  lmod:
    core_compilers:
      - 'gcc@7.5.0'
    hierarchy:
      - mpi
      - lapack
    hash_length: 0
    whitelist:
      - gcc
    blacklist:
      - '%gcc@3.8.0' 
      - readline
    all:
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"
      environment:
        set:
          '{name}_ROOT': '{prefix}'
    openmpi:
      environment:
        set:
          SLURM_MPI_TYPE: pmi2
          OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
    netlib-scalapack:
      template: 'group-restricted.lua'

Note that in the above example, we seleceted gcc@7.5.0 as core compiler and hided gcc@3.8.0 from the tree. Also, we supposed the hierarchy of installed modules are depends on mpi and lapack.

To apply these changes, we need to refresh the modules tree and update MODULEPATH by:

module purge
spack module lmod refresh --delete-tree -y
module unuse $HOME/spack/share/spack/modules/<os-arch>
module use $HOME/spack/share/spack/lmod/<os-arch>/Core

Note that in above commands, I assumed that Spack directory is located on $HOME. You need to update path and <os-arch> based on the Sapck directory and, the operating system and architecture of your machine (for example linux-ubuntu18.04-x86_64). To keep the new module path for latter, you can add the following to the .bashrc file.

export MODULEPATH=$HOME/spack/share/spack/lmod/<os-arch>/Core

Now use module avail to see changes. You can learn more about modules and Lmod in here.

To learn more about management and projection of modulefile, review module-projection repository.

Copyright, Ashkan Mirzaee | Content is available under CC BY-SA 3.0 | Sourcecode licensed under GPL-3.0