Hi Stijn et al, -sorry in advance for the lengthy email-
Some more news on the upcoming robot script "pkg2eb" follow. As said, it simply reads NetBSD's pkgsrc Makefile's and produces a stock .eb; No claims for anything else than that ;-) >> 2) Contribution, part #2: package descriptions generated via pkg2eb >> >> OK, this is a wild ride. I had a little bit too much time yesterday afternoon >> and decided to peek & poke on NetBSD's pkgsrc. The Makefiles contain much of >> the information needed to feed easybuild with and, a tool was born... pkg2eb! >> >> It is a blind robot really: it will try to best-guess the possible >> parameters; >> I am still debugging it and a release should rather wait, but here's the >> first >> bunch of builds that were done fully automated: On 24/07/2012 21:10, Stijn De Weirdt wrote: > a first step in providing easybuild support should be that one reads (and > tries to understand) the configure options and dependencies of a package. Yeap, this is the tough part of the task; a robot can't help too much in this, unless there is some consistent aspect in the original files; *there* is where the sysadmin will have to kick in and work; so, yes, we get to keep our jobs! ;-) The original list I sent was a bit uninteresting (many examples from audio/*) so it just kept compiling overnight and arrived at a list of >600 modules now. Worthy stuff are the (~100) libraries and some (untested!) scientific modules: gmp, gsl, gromacs, prng; yes, these are plain non-mpi compilations. Even openmpi/1.6 & slurm-2.4.0-0.pre4 appear to build out of the box. (I have yet to see a system having a resource manager -> modules dependency :) Anyway, as a minimum, pkg2eb is a tool to automate the boring part of making the skeleton for a first build; it certainly cannot do much of sysadmin work. After all, 9315 templates is not too bad for a start: https://github.com/fgeorgatos/easybuild/tree/master/experimental2 Only a small fraction of it has, yet, become modules; see attached list. To be sure, even less will actually work. Consider them as without quality control and simply templates; eg. libraries are not truly made as such etc. > second, one should try to build with something else then gcc (eg intel): it > will show how good the default package is wrt building/installing and will > identify which packages need an easyblock. At this point it's relatively trivial to prepare .eb files for the next steps: * intel compiler/stack * parallel build mpicc-style * any other such combinations >> Our team will produce more and announce them as they become available. btw. the above comment regarded mainly bioinformatics packages; these are produced by human flesh and controlled daily by multiple eyeballs. They are production and will remain so, so *these* are the ones to consider merging with the existing .eb package set. Cedric notified of having cufflinks ready which will soon arrive upstream. > we will see if we can send you a copy of our not-yet publsihed .eb and old > style blocks, to avoid duplication of work and to speedup the porting to the > new version. Yeah, I think that's unavoidable to avoid duplication of work. Since you are the tool developers, you should play the clearing house of this, yet, allow for a bigger ecosystem of easybuild maintainers to develop. Look at OS/OSS repositories to pick ideas how this could be organized best. > what also could be useful (i think there's an internal ticket for that) is > that based on such source packages (eg like the .src.rpm for rpm based > systems), you have an easyblock that takes these source packages as source and > builds and install them as they were intended by the distribution. and since > you are a debian expert, we also need an easyblock to install binary .deb in > easybuild (we have that for rpms, it's how java is installed atm). Interestingly, I'm more of an .rpm expert than .deb; I'm only learning *deb :) But I'm pretty certain we'll arrive at such a need quickly and we will need to do something about it. fyi. I'm somewhat experienced with rpm's .spec files & OpenSuseBuild service, which itself is an excellent *non-OS-specific* resource; look at this example: https://build.opensuse.org/package/show?package=qtop&project=home%3Ageorgatos btw. I would be glad to help you using that tool; it runs fine in user-space. > this is ofcourse a problem, we already have that with toolkits. module load > Python in easybuild actually means module load > Python/someversion-numpy-someversion-scipy-someversion-matplotlib-someversion-mpi4py-someversion... ack that. > this is a matter of organising i think: i prefer a good, well featured base > version, with some possible exceptions so you would have to do > module load Python/vX-1 > module load Python-scipy/vX-Python-vX-1 (i have no clue how this should be > organised or named) [...] > anyway, i don't think there's a silver bullet here. I think the "goalf" bunching technique shows what is the proper way here: * Pick an acronym of tools which correspond to >80% of the needs & go for it. >> And since Python v3 requires a manual hack to build on Debian (dep: tcsh), >> this bring us to the next topic... Hm... I think I have an elegant way to propose how to get past this: """ fgeorgatos@gaia-16:~/easybuild$ eb easybuild/easyconfigs/w/WRF/WRF-3.4-goalf-1.1.0-no-OFED-dmpar.eb ERROR: Failed to process easyconfig /home/clusterusers/fgeorgatos/easybuild/easybuild/easyconfigs/w/WRF/WRF-3.4-goalf-1.1.0-no-OFED-dmpar.eb: EasyBuild crashed with an error (at easybuild/framework/application.py:513 in check_osdeps): One or more OS dependencies were not found: ['tcsh'] """ What if there was a (perhaps empty) "tcsh" module provided in the namespace, in order to silent such messages? Easybuild has to be modified for that, to take it into account (and makes much sense anyway, to fine-tuning sw!). Yes, I'm greedy: I have now a latest tcsh available via pkg2eb. :-P >> 4) Wishlist [...] >> * Consider category-oriented module sets (eg. `module load >> bioinformatics-tools`) # may be done outside of EB logic > what should this do: load modules or change the modulepath so a module > available becomes readable again I was thinking it -simply- as changing the MODULEPATH variable and, hence, no real change from EB tool is needed (just enforce the destination dirs and do some scripting to automate the tasks). I have the impression that either way, it's not Easybuild's job to take care of that, modulo some logic to manage multiple categories (or filter actions according to that). This is rather a question of best practices, IMHO. """How is it best to manage >1000 modules?""" Note that this number is not exaggerated: some HPC sites which do purely bioinformatics have an upwards of 400 tools setup. That's a good number! > i'm missing something here: you have some concrete examples? Yes, the concrete examples copy-pasted from real HPC sites exist at that URL: https://github.com/fgeorgatos/easybuild/wiki/Wishlist # Look at the gray box It is a collection I've been building over the last couple of years. > i think what could be interesting is that the default easyblock is as complete > as possible, and that we have an easy way to generate symlinks to these module > files so anyone can use there own naming convention This might prove to be the correct (tm) practice. >> class_name = name[0].upper() + name[1:].replace('-','_') >> Yes, I mean "r" vs "R" ;-) > ;) >> I can accept the logic of needing to create a case-insensitive namespace >> for clarity on the user side but, is there another systems reason for it? > we tried to follow some PEP standard OK. If we talk about this one, http://www.python.org/dev/peps/pep-0008/ , I think that Easybuild_mypackage is somewhat better than Mypackage, because it a) reduces collisions & b) allows more freedom in the namespace (ie. the sysadmin gets to choose if there is a case-insensitive policy) And we still are PEP compliant, then! > i can understand the freedom on the actual enduser part (ie the module naming > or renaming), but what other degrees of freedom are you thinking of? Naming is of course a major one. Not forcing the easyblock paths to live under an [a-z] dir structure, too. I think the rest is just about building best practices experience, across different implementation scenarios! > anyway, thanks for trying it out and giving feedback. it's much appreciated! You're very welcome, -- Drs./Eng. Fotis Georgatos ------------------------------------------------------- Scientific Collaborator LCSB (University of Luxembourg) ------------------------------------------------------- Mail: [email protected] Phone: +352 466644 5609
----------------------- /opt/apps/easybuild/modules/all/ ----------------------- ATLAS/3.8.4-GCC-4.6.3-LAPACK-3.4.0 BLACS/1.1-GCC-4.6.3-OpenMPI-1.4.5-no-OFED FFTW/3.3.1-GCC-4.6.3-OpenMPI-1.4.5-no-OFED GCC/4.6.3 HDF5/1.8.7-goalf-1.1.0-no-OFED HPL/2.0-goalf-1.1.0-no-OFED JasPer/1.900.1-goalf-1.1.0-no-OFED LAPACK/3.4.0-GCC-4.6.3 OpenMPI/1.4.5-GCC-4.6.3-no-OFED Python/2.7.3-goalf-1.1.0-no-OFED ScaLAPACK/1.8.0-GCC-4.6.3-OpenMPI-1.4.5-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1 Szip/2.1-goalf-1.1.0-no-OFED WRF/3.3.1-goalf-1.1.0-no-OFED-dmpar goalf/1.1.0-no-OFED netCDF/4.1.3-goalf-1.1.0-no-OFED zlib/1.2.5-goalf-1.1.0-no-OFED zlib/1.2.7-goalf-1.1.0-no-OFED ------------- /home/clusterusers/fgeorgatos/easybuild/modules/all/ ------------- AfterStep/2.1.2-goalf-1.1.0-no-OFED-20120724 CUnit/2.1-goalf-1.1.0-no-OFED-20120724 ETL/0.04.11-goalf-1.1.0-no-OFED-20120724 Gauche/0.9.3.3-goalf-1.1.0-no-OFED-20120724 GeoIP/1.4.8-goalf-1.1.0-no-OFED-20120724 Judy/1.0.5-goalf-1.1.0-no-OFED-20120724 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