Using Spack

Modules provided by Spack

Care must be taken when using modules provided by Spack as they behave differently from standard Linux modules.

The Spack package management tool is used to manage much of the software and libraries installed on CSD3. Spack allows us to automatically resolve dependencies and have multiple versions of tested software installed simultaneously without them interfering with each other.

To achieve this, Spack makes use of RPATH to hardcode the paths of dependencies into libraries. This means that when you load a module for a particular library you do not need to load any further modules for dependencies of that library.

For example, the boost toolkit depends on the MPI, zlib and bzip2 libraries:

boost@1.64.0
    ^bzip2@1.0.6
    ^mpich@2.14
    ^zlib@1.2.10

Spack arranges things so that if you load the boost module:

module load boost-1.64.0-gcc-6.2.0-pftxg46

then you do not also need to load the bzip2, mpich and zlib modules.

This, however, can lead to behaviour that is unexpected for modules. For example, on CSD3 there are two versions of zlib available: 1.2.8 and 1.2.10. You may imagine that you can use boost with zlib 1.2.8 with the following commands:

module load zlib-1.2.8-gcc-6.2.0-epathtp
module load boost-1.64.0-gcc-6.2.0-pftxg46

but this will not work. boost will still use zlib 1.2.10 as the path to this is hardcoded into boost itself via RPATH. If you wish to use the older version of zlib then you must load it and then compile boost yourself.

If you wish to see what versions of libraries are hardcoded into a particular Spack module then you must use Spack commands available after loading the spack module, e.g.:

[auser@login-e-1 ~]$ module avail boost

------------ /lustre/sw/spack/share/spack/modules/linux-centos7-x86_64 ------------
boost-1.63.0-intel-17.0.2-fl25xqn boost-1.64.0-gcc-6.2.0-pftxg46

[auser@login-e-1 ~]$ module load spack

[auser@login-e-1 ~]$ spack find -dl boost
==> 2 installed packages.
-- linux-centos7-x86_64 / gcc@6.2.0 -----------------------------
pftxg46    boost@1.64.0
545wezu        ^bzip2@1.0.6
kskvysh        ^mpich@2.14
4og3my2        ^zlib@1.2.10


-- linux-centos7-x86_64 / intel@17.0.2 --------------------------
fl25xqn    boost@1.63.0
nq2yt4x        ^bzip2@1.0.6
jbjvxs7        ^zlib@1.2.10

This shows their are two boost modules installed (one for the Intel compilers and one for the GCC compilers), they both depend on bzip2 1.0.6 and zlib 1.2.10 and the GCC version also depends on MPICH 2.14. The paths for these dependencies are hardcoded into the boost RPATH.