Ho Fotis, On 19 Nov 2012, at 13:24, Fotis Georgatos wrote:
> > Hi there, > > Thanks to EasyBuild, we at Uni.Lu are more than half in our way on the HPC > platforms > to provide the 1st generation of a reproducible bioinformatics environment. > Applause ! > http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2011-94.html Sounds great! > Since I have been preparing a good bunch of bioinformatics packages: > https://github.com/fgeorgatos/easybuild.experimental/tree/master/users/fgeorgatos/bioinfo > I'd like to have a dedicated moduleclass "bio" for them now; *Do you agree?* > > IMHO, in fact, more generally, we should ideally get exactly what the HLRS > guys have done: > https://github.com/fgeorgatos/easybuild.experimental/wiki/Package-categories > ie. bio cae chem compiler debugger devel ide lib math mpi numlib performance > phys system tools vis > And, now tell me, doesn't this appear to be nicely backward-compatible? ;-) Instead of adding custom module classes hardcoded in EasyBuild, we'll just make if more flexible, for example by adding an EasyBuild configuration parameter to specify a list of possible classes. How does that sound? There's already an issue for that, see https://github.com/hpcugent/easybuild-framework/issues/209 . I've just upped the priority on this from low (1) to medium (2). > > Perhaps also having a "metamodule" moduleclass would make sense, to serve > items > like "goalf"/"ictce" and HPCBIOS's policies; do you have any objections to > that? > (after all, they aren't exactly "compiler" modules; it seems pending work to > me!) They're toolchain modules, but you can categorize them on your end as you please once #209 is implemented. Why would you say they're pending work? > Finally, has anybody seen something like the following? > (I know modules sometime play tricks on you and metamodules seem to tickle > dragon's tail) > > fgeorgatos@gaia-13:~/easybuild.experimental/users/fgeorgatos/bioinfo$ module > purge > fgeorgatos@gaia-13:~/easybuild.experimental/users/fgeorgatos/bioinfo$ module > load GSL goalf > fgeorgatos@gaia-13:~/easybuild.experimental/users/fgeorgatos/bioinfo$ module > load GSL goalf PETSc > ERROR: module load GSL goalf PETSc failed > fgeorgatos@gaia-13:~/easybuild.experimental/users/fgeorgatos/bioinfo$ module > load PETSc If you see something like this, check whether this is caused by a segmentation fault of modulecmd, i.e. run: modulecmd bash load GSL goalf PETSc If it is, this is most likely the issue with v3.2.9 that I resolved a while ago. There's an improved patch for that available, that will make it into v3.2.10, see http://sourceforge.net/mailarchive/attachment.php?list_name=modules-interest&message_id=CAGYkfXD4OFCmkDg9%2B6bcXT9R_KhsD2nergJUVN0XtJfeoC0qsA%40mail.gmail.com&counter=2 K.
