SPACK - migration to setup without environment

Having worked with spack environments for some time, we have encountered several severe issues which have convinced us that we need to find a more practical way of maintaining software packages on VSC. In particular we came across the following drawbacks:

• hard to read and lengthy output of spack find commands.
• long response times of all spack commands when the number of installed packages grows.
• difficult and for practical purposes impossible maintenance of a consistent database of software packages (spack.yaml, spack.lock files).
• unresolvable discrepancies between the list of software packages found in spack as compared to those found in modules.
• unreliable concretisation procedure (discrepancies between what is shown in spack spec -I .. and what is actually installed with spack install …).

There are now three separate spack installation trees corresponding to the CPU/GPU architectures on VSC:

• skylake - Intel CPUs; works on Intel Skylake and Cascadelake CPUs
• zen - AMD CPUs; works on Zen 2 and 3 CPUs
• cuda-zen - AMD CPUs + NVIDIA GPUs; works on all nodes equipped with graphics cards

By default the spack installation tree suitable for the current compute/login node is activated and will be indicated by a prefix on the command line, e.g.:

zen [user@l51 ~]$

The installation trees can be found in:

/opt/sw/skylake/spack-0.19.0
/opt/sw/zen/spack-0.19.0
/opt/sw/cuda-zen/spack-0.19.0

Only the software packages and modules of the currently active tree (denoted by the prefix) will be searched by spack find/load and module avail/load commands.

It is easily possible to switch between installation trees with the short commands:

alias cuz='spackup cuda-zen'
alias sky='spackup skylake'
alias zen='spackup zen'

This will be required e.g. when software intended to run on GPU nodes needs to be compiled on a login node of VSC-5.

zen [userl51 ~]$ cuz
cuz [userl51 ~]$ 
... build your software ...

The command spackup will

• set PATH
• set MODULEPATH
• set PS1 prompt
• source /path/to/spack/instance/share/spack/setup-env.sh

If you need to find a list of packages or modules which correspond to the software you have been using until now, you can use the alias spacksearch to do that

alias spacksearch='/usr/bin/python3.9 /opt/sw/spack-scripts/search/search.py'

The script can be used like in the following example:

zen [user@l51 ~] spacksearch <hash>

where <hash> is the 7 character hash of the package that you see at the end of the module name or in the output of spack find -l <package>

Let's assume you have used this netcdf-c module:

netcdf-c/4.8.1-gcc-11.2.0-jsfjwaz

which can be found with spack find -l netcdf-c %gcc as:

jsfjwaz netcdf-c@4.8.1

You can use the migration script to find netcdf-c installations with identical build options:

zen [user@l51 ~]$ spacksearch jsfjwaz

==> The package hash jsfjwaz refers to netcdf-c and belongs to vsc5 as:
     netcdf-c ~dap~fsync~hdf4~jna+mpi~parallel-netcdf+pic+shared

==> Searching similar netcdf-c modules at zen...

---/gpfs/opt/sw/zen/spack-0.19.0/share/spack/modules/linux-almalinux8-zen3---
netcdf-c/4.9.0-aocc-4.0.0-6fetjps
netcdf-c/4.9.0-aocc-4.0.0-vyf5okn
netcdf-c/4.9.0-gcc-12.2.0-usqc3ay
netcdf-c/4.9.0-gcc-12.2.0-oljzgqt
netcdf-c/4.9.0-gcc-12.2.0-hbo7ve6
netcdf-c/4.9.0-gcc-12.2.0-62buxj4
netcdf-c/4.9.0-gcc-12.2.0-awvdfta
netcdf-c/4.9.0-gcc-12.2.0-oppx7bm

---/gpfs/opt/sw/zen/spack-0.19.0/share/spack/modules/linux-almalinux8-zen---
netcdf-c/4.9.0-gcc-8.5.0-7qwm3uz

==> Load any one of these packages with 'module load mypackage', e.g.:
module load netcdf-c/4.9.0-gcc-8.5.0-7qwm3uz

==> Get some additional info with 'spack find -lvd mypackage', e.g.:
spack find -lvd /7qwm3u

To search for packages in a different spack tree you can just change to that tree and then run spacksearch there.

For example to search in the 'cuda-zen' spack tree:

zen [user@l51 search]$ cuz
cuda-zen [user@l51 search]$ spacksearch jsfjwaz

==> The package hash jsfjwaz refers to netcdf-c and belongs to vsc5 as:
     netcdf-c ~dap~fsync~hdf4~jna+mpi~parallel-netcdf+pic+shared

==> Searching similar netcdf-c modules at cuda-zen...

---/gpfs/opt/sw/cuda-zen/spack-0.19.0/share/spack/modules/linux-almalinux8-zen---
netcdf-c/4.9.0-gcc-9.5.0-fx6pjb6
netcdf-c/4.9.0-gcc-9.5.0-4gdf6vm
netcdf-c/4.9.0-gcc-9.5.0-o5eb5rf
netcdf-c/4.9.0-gcc-9.5.0-upkxxip

==> Load any one of these packages with 'module load mypackage', e.g.:
module load netcdf-c/4.9.0-gcc-9.5.0-upkxxip

==> Get some additional info with 'spack find -lvd mypackage', e.g.:
spack find -lvd /upkxxi

Add this function to your .bashrc file:

## spack command wrapper, so we can include our own `spack something`
## commands, like `spack search`:
spack () {
    case "$1" in
        "search")
            python3 /opt/sw/spack-scripts/search/search.py "$2"
            ;;
        *)
            command spack "$@"
    esac
}

Usage example:

skylake [user@l41 ~]$ spack search asd

==> The package hash asd refers to python and belongs to vsc4 as:
     python +bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib

==> Searching similar python modules at skylake...

---/gpfs/opt/sw/skylake/spack-0.19.0/share/spack/modules/linux-almalinux8-skylake_avx512---
python/3.10.8-gcc-9.5.0-qh22vnd
python/3.10.8-gcc-12.2.0-apbi5uz
python/3.10.8-intel-2021.7.1-p4x6jid

==> Load any one of these packages with 'module load mypackage', e.g.:
module load python/3.10.8-intel-2021.7.1-p4x6jid

==> Get some additional info with 'spack find -lvd mypackage', e.g.:
spack find -lvd /p4x6ji

You may continue to use modules from the spack environments skylake and zen3 by adjusting the MODULEPATH variable:

For zen3:

export MODULEPATH=/opt/sw/vsc4/VSC/Modules/TUWien:/opt/sw/vsc4/VSC/Modules/Intel/oneAPI:/opt/sw/vsc4/VSC/Modules/Parallel-Environment:/opt/sw/vsc4/VSC/Modules/Libraries:/opt/sw/vsc4/VSC/Modules/Compiler:/opt/sw/vsc4/VSC/Modules/Debugging-and-Profiling:/opt/sw/vsc4/VSC/Modules/Applications:/opt/sw/vsc4/VSC/Modules/p71545::/opt/sw/spack-0.17.1/var/spack/environments/zen3/modules/linux-almalinux8-zen:/opt/sw/spack-0.17.1/var/spack/environments/zen3/modules/linux-almalinux8-zen2:/opt/sw/spack-0.17.1/var/spack/environments/zen3/modules/linux-almalinux8-zen3

For skylake:

export MODULEPATH=/opt/sw/vsc4/VSC/Modules/TUWien:/opt/sw/vsc4/VSC/Modules/Intel/oneAPI:/opt/sw/vsc4/VSC/Modules/Parallel-Environment:/opt/sw/vsc4/VSC/Modules/Libraries:/opt/sw/vsc4/VSC/Modules/Compiler:/opt/sw/vsc4/VSC/Modules/Debugging-and-Profiling:/opt/sw/vsc4/VSC/Modules/Applications:/opt/sw/vsc4/VSC/Modules/p71545:/opt/sw/vsc4/VSC/Modules/p71782::/opt/sw/spack-0.19.0/var/spack/environments/skylake/modules/linux-almalinux8-x86_64:/opt/sw/spack-0.19.0/var/spack/environments/skylake/modules/linux-almalinux8-skylake

Some module have prerequisites which need to be loaded in addition to the module. You can check if a module has prerequisites with module show <module>, e.g.:

zen [user@l51 ~]$ module show py-numpy/1.23.4-gcc-12.2.0-xbac5zw |grep prereq
prereq          openblas/0.3.21-gcc-12.2.0-gcn6jxp
prereq          py-setuptools/59.4.0-gcc-12.2.0-qphisr6
prereq          python/3.9.15-gcc-12.2.0-my6jxu2

These prerequisites can be loaded together with the module automatically module load –auto <module>, e.g.:

zen [user@l51 ~]$ module load --auto py-numpy/1.23.4-gcc-12.2.0-xbac5zw
Loading py-numpy/1.23.4-gcc-12.2.0-xbac5zw
  Loading requirement: openblas/0.3.21-gcc-12.2.0-gcn6jxp python/3.9.15-gcc-12.2.0-my6jxu2 py-setuptools/59.4.0-gcc-12.2.0-qphisr6

Loading a module does no longer automatically set the LD_LIBRARY_PATH environment variable, as with some software packages this has lead to conflicts with system libraries. If you have to set LD_LIBRARY_PATH you may use:

export LD_LIBRARY_PATH=$LIBRARY_PATH

Alternatively you may have to set it to specific paths where the needed libraries can be found.