Hi jpr! On Feb 18, 2016, at 7:43 PM, Kenneth Hoste <[email protected]> wrote: > One thing you should be aware of is --try-toolchain, and the fact that it > works nicely together with --robot. > > See for example the output of "eb pBWA-0.5.9_1.21009-goolf-1.4.10.eb -D > --try-toolchain-version=1.7.20"; > new easyconfigs for both BWA and pBWA will be generated for you, in which the > toolchain version is replaced. > > That should make it significantly easier to 'bump' the toolchain.
This. In principle, it should be possible to use the above technique combined with the existing HPCBIOS bundles and actually arrive quite far. I’ve done it several times, the LifeSciences cases tend to be very robust. It is true that they all have started showing their age, due to toolchains though: - first generation goolf/1.4.10 includes the gcc version with the issues you mentioned; we could agree on a fi. 1.4.11 strain just to get by - nothing complicated with that. - the ictce/5.3.0 is even more problematic: Intel has ceased releasing those particular sources, on the premise of some compiler instability (among all icc/ifort variants, that particular one); But: you can still do --try-toolchain=ictce,5.5.0 and get very useful things produced so, good as-is. Since you are looking into it, we now have the chance to improve on a number of fronts such as: [0] Refresh both goolf & intel variants with their more modern equivalent toolchains [1] Reconcile LifeSciences, Bioinfo & Math common dependencies by ironing out annoying Boost collisions [2] Weed out/fix problematic dependencies from Bioinfo (Intel ipp in goolf variant, I am looking at you) [3] Push out a few more HPCBIOS targets which are collecting dust in some (of my) digital corners :) [4] Test against multiple distros to stabilise the deps into convenient choices (more art than science here) [5] New configs should rather use new yaml like easyconfig format (more suitable for this activity). I especially like feature [1] because it permits to mix’n’match bundles at will, but it takes some good effort until things start to melt together nicely. In an ideal world, we would have an intern or two with some good CI/docker/distros skills, isolate her or them from daily systems firefighting, and the above would occur quite fast. Alas... If anybody is available to put man-hours into this, please step forward, to follow up with a hangout. Fotis -- echo "sysadmin know better bash than english" | sed s/min/mins/ \ | sed 's/better bash/bash better/' # signal detected in a CERN forum
