Hi Robert,
thanks, this is useful - please do. All: start collecting your wish lists - to see what people are interested for! I personally aim for some progress along easyconfig issues #1689 and #383, #384. This is also worthy of a bundle and a compiler refresh, so it’s in my radar too: http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2015-01.html F. On Feb 24, 2016, at 9:03 PM, Robert Schmidt <[email protected]> wrote: > Can we have a call on HPCBIOS stuff? > > I think we are due to talk about bumping the base toolchain and I'd like to > talk about dependencies and such again. > > I'll put up a doodle tomorrow to work out a time if there is interest. > > On Mon, Feb 22, 2016 at 2:48 PM Kenneth Hoste <[email protected]> wrote: > Hi John-Paul, > > On 22/02/16 17:48, John-Paul Robinson wrote: > > Thanks for the update on the status and thoughts around HPCBIOS. I'm > > interested in exploring these options. > > > > We are in the process of migrating from ROCKS5 (CentOS5) to a platform > > based on CentOS7. As part of this, we're adopting EasyBuild to manage > > builds. A large part of our community is bioinformatics oriented. They > > use a mix of popular tools on the cli HPC side which have been > > self-managed. On the web interface side, we have a Galaxy instance > > with it's own tool collection. A curated reference model like HPCBIOS > > could be useful reference for our community. > > > > We will attempt the --try-toolchain-version as a first pass. I did > > attempt this bump approach to move Cufflinks to an updated goolf but ran > > into a number of cross dependencies. Cufflinks has some complex > > dependencies and I was new to EasyBuild so that may have had something > > to do with it. I eventually had to correct a number of easyconfigs to > > move to goolf-1.7.20 > > https://github.com/hpcugent/easybuild-easyconfigs/pull/2058 > > > > After some reflection, I've come up with an Easy* solution. I created a > > texinfo-4.13a easyconfig which will allow GCC 4.7.2 to build when > > loaded. This bootstraps the goolf-1.4.10 chain and should enable using > > most of the HPCBIOS easyconfigs directly. (eb --from-pr 2543) > > This makes sense, and you can even fix it once and for all by issuing a > PR to include textinfo 4.13a as a build dep in the GCC 4.7.2 easyconfig > file: > > name = 'GCC' > version = '4.7.2' > > ... > > # make sure dependencies are loaded when building/installing GCC, > # by using an empty version (rather than using 'dummy' as version) > toolchain = {'name': 'dummy', 'version': ''} > > ... > > # less strict texinfo version required, which allowed document > parsing error > # (this is fixed in more recent versions of GCC) > builddependencies = [('texinfo', '4.13a')] > > > The easiest way is to provide an easyconfig file for texinfo 4.13a that > is built with the dummy toolchain (i.e. texinfo-4.13a.eb), to avoid that > one version of GCC is required to build another version of GCC. > That does leave us at the mercy of the OS-provided compiler to get > texinfo 4.13a built, but that may be acceptable here... > > > > > > This seems like a reasonable short term solution for seeding our > > environment and may provide reproducibility over the long term. It will > > also be worth the effort to update to goolf-1.7.20 and newer chains. > > I'm not deeply familiar with version motivations and build options for > > bioinformatics pipelines but do want to provide our users with the most > > efficient execution on newer hardware. Having an updated HPCBIOS and > > easyconfigs seems like a good way to accomplish that and prepare for the > > improvements promised by the phi later this year > > (http://software.intel.com/XeonPhiCatalog). > > Promises, promises. ;-) > > > regards, > > Kenneth > > > > Thanks again and look forward to continuing this conversation, > > > > ~jpr > > > > On 02/19/2016 07:37 PM, Fotis Georgatos wrote: > >> 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
