Apparently 'missing' dependency when installing on a clean OS

[sassy-crick]

Dear all,

I ran into that issue the other day when I was installing software on our new HPC cluster. Instead of first installing foss first and then software, here I simply tried to install the final software package and that failed with the error below:

== FAILED: Installation ended unsuccessfully (build directory: 
/dev/shm/hpcsw/AlphaFold/2.3.4/foss-2022a-CUDA-11.7.0-ColabFold): build failed (first 300 
chars): Module command '/usr/share/lmod/lmod/libexec/lmod python load 
OpenMM/8.0.0-foss-2022a-CUDA-11.7.0' failed with exit code 1; stderr: Lmod has detected the 
following error: The following module(s) are unknown:
"SWIG/4.0.2-GCCcore-11.3.0"


eb -M ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb
== Temporary log file in case of crash /dev/shm/hpcsw/eb-wf7bpgg4/easybuild-rq6zem6p.log
== found valid index for /gpfs/easybuild/dev/software/EasyBuild/4.8.0/easybuild/easyconfigs, so using it...
== found valid index for /gpfs/easybuild/dev/software/EasyBuild/4.8.0/easybuild/easyconfigs, so using it...

9 out of 147 required modules missing:

* M4/1.4.18 (M4-1.4.18.eb)
* Autoconf/2.71 (Autoconf-2.71.eb)
* Automake/1.16.5 (Automake-1.16.5.eb)
* libtool/2.4.7 (libtool-2.4.7.eb)
* Autotools/20220317 (Autotools-20220317.eb)
* PCRE/8.45-GCCcore-11.3.0 (PCRE-8.45-GCCcore-11.3.0.eb)
* SWIG/4.0.2-GCCcore-11.3.0 (SWIG-4.0.2-GCCcore-11.3.0.eb)
* AlphaFold/2.3.4-foss-2022a-CUDA-11.7.0-ColabFold (AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb)
* ColabFold/1.5.2-foss-2022a-CUDA-11.7.0 (ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb)

Apptainer> eb -r --parallel=48 --cuda-compute-capabilities=8.0 ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb
== Temporary log file in case of crash /dev/shm/hpcsw/eb-p2g7gr27/easybuild-ue4kt4b5.log
== found valid index for /gpfs/easybuild/dev/software/EasyBuild/4.8.0/easybuild/easyconfigs, so using it...
== found valid index for /gpfs/easybuild/dev/software/EasyBuild/4.8.0/easybuild/easyconfigs, so using it...
== resolving dependencies ...
== processing EasyBuild easyconfig 
/gpfs/easybuild/dev/software/EasyBuild/4.8.0/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.
4-foss-2022a-CUDA-11.7.0-ColabFold.eb
== building and installing AlphaFold/2.3.4-foss-2022a-CUDA-11.7.0-ColabFold...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== ... (took 9 secs)
== FAILED: Installation ended unsuccessfully (build directory: 
/dev/shm/hpcsw/AlphaFold/2.3.4/foss-2022a-CUDA-11.7.0-ColabFold): build failed (first 300 
chars): Module command '/usr/share/lmod/lmod/libexec/lmod python load 
OpenMM/8.0.0-foss-2022a-CUDA-11.7.0' failed with exit code 1; stderr: Lmod has detected the 
following error: The following module(s) are unknown:
"SWIG/4.0.2-GCCcore-11.3.0"

The solution was of course to install SWIG-4.0.2-GCCcore-11.3.0.eb but that should in my humble opinion not be required. I did not mess around with OpenMM at all, I simply fired up the installation and let it work its way through.

The log file is here.

I know that is a bit of an unusual situation but I thought I mention it, just in case there is an issue within EasyBuild.

Thanks.