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I'm having my first tinker with modules. I've installed lmod and easybuild and have built a package (SAMtools) with its dependencies.

Running module av shows the modules are available. It lists them twice, once in the 'all' category and also in their relevant category. If I try to load a module like bio/SAMtools, it complains that it can't find the dependencies. I assume this is because it's looking for ncurses when it needs to look for all/ncurses or devel/ncurses.

I know I could just change the modulepath to point straight at the all directory instead of the directory containing the category directories but wanted to know if this was the correct approach or if I'm doing something wrong and module should be able to locate the module dependencies..

Gaspode
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1 Answers1

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module (whether it is Environment Modules or Lmod) looks for the module name as a directory under the enabled modulepath. So if your enabled modulepath is /path/to/modulefiles, if you try to load devel/ncurses it will look at version files under /path/to/modulefiles/devel/ncurses directory.

As the modules generated by easybuild defines dependency as ncurses and not all/ncurses or devel/ncurses, it means the modulepath to enable should be /path/to/modulefiles/all or /path/to/modulefiles/devel.

Locating modulefile section in modulefile(4) man page gives details on how modules are searched. This is the documentation for Environment Modules, but the mechanism is quite similar on Lmod.

Xavier Delaruelle
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  • Thanks. Kind of what I was thinking - just wanted to confirm I hadn't got it wrong. Just seems a bit of a waste for easybuild to nicely categorise the packages, just to point lmod at 'all' and ignore the categories.. – Gaspode Jul 27 '23 at 08:41
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    The reason that EasyBuild has the categorized modules as well is so you can pick: either you add the `/modules/all` directory to `$MODULEPATH`, or you add all the different `/modules/` paths to `$MODULEPATH` (except for `.../all`). With the latter, you'll have more structure in the output of "`module avail`" compared to just having one "bag" of modules when using `/modules/all` – Kenneth Hoste Aug 13 '23 at 16:40