Hello, I just have a little comment to add to point 4 :)
On 03.08.12 16:25, "Fotis Georgatos" <[email protected]> wrote: > >Hi, > >here's my regular TGIF email ;-) > >(1) Skipping certain EasyBuild steps > >On 26/07/2012 17:07, Fotis Georgatos wrote:> * Allow to skip certain steps >easily (we notice it is often required): >> ** skip_configure=true >> ** skip_make=true >> ** skip_make_installdir=true >> That reduces LOC (lines of code) and hence human error. It's more easy, >>too. > >Finally, we've arrived to a trully elegant way to override certain steps: > preconfigopts='/bin/true' > premakeopts='/bin/true' >It certainly helps to minimize legth of easyblocks or, eliminate them. > > > >(2) Contribution towards v0.9 > >This regards the list at: >https://github.com/hpcugent/easybuild/wiki/List-of-supported-software-pack >ages > >(2a) >Cedric has made some more progress, intermediate results are visible here: >https://github.com/fgeorgatos/easybuild/tree/master/experimental > >(2b) >Some more simple easyconfig files are available; review/cleanup needed. > >These ones appear to build fine (for goalf), but they are otherwise >untested: >(to be precise, they do not seem fail in the 3 basic steps & give >modulefile) >(also, the libraries need to be declared as such) > >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/c/curl-7 >.26.0.eb > >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/a/autoco >nf-2.69.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/f/flex-2 >.5.35.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/g/geos-3 >.3.4.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/g/glpk-4 >.47.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/g/gmp-5. >0.5.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/g/gnuplo >t-4.4.4.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/g/gsl-1. >15.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/l/libpng >-1.5.11.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/l/libxml >2-2.8.0.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/m/mhash- >0.9.9.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/m/mono-2 >.10.6.eb ># and some more in the same directory >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/m/mpc-0. >9.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/m/mpfr-3 >.1.0.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/o/openmp >i-1.6.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/p/pcre-8 >.30.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/q/qhull- >2003.1.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/r/raptor >-1.4.21.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/r/raptor >2-2.0.7.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/r/readli >ne-6.2.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/s/swig-1 >.3.36.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/s/szip-2 >.1.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/u/unixOD >BC-2.3.0.eb > >A couple of users are already working with these; no problems reported so >far: >(presumably ready for .eb cleanup & release) > >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/g/gromac >s-4.5.5.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental3/octave-3 >.4.3-goalf-1.1.0-no-OFED.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental3/octave-3 >.6.2-goalf-1.1.0-no-OFED.eb > >These ones are just mockups -have issues- and require more effort: > >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/a/apache >-ant-1.8.4-bin.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/a/arpack >96.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/b/bison- >2.5.1.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/b/bzip2- >1.0.6.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/d/doxyge >n-1.6.3.src.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/g/gdal-. >eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/g/ghc-6. >8.3.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/h/h5util >s-1.12.1.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/i/ipytho >n-0.12.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/l/libctl >-2.2.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/l/libmat >heval-1.1.4.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/l/libxsl >t-1.1.26.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/m/mpich2 >-1.4.1p1.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/m/mysql2 >-0.3.11.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/o/OpenCV >-2.4.1.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/p/primer >3-.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/p/proj-. >eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/p/pytabl >e-0.8.3a.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/r/root_v >5.26.00b.source.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/r/rpy2-2 >.1.3.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/s/schroe >dinger-1.0.11.eb >https://github.com/fgeorgatos/easybuild/blob/master/experimental2/x/x264-s >napshot--2245.eb > >(2c) >Some more experiments are ongoing and may be fixed anytime soon: >https://github.com/fgeorgatos/easybuild/tree/master/experimental3 > > >(3) Wishlist updates: select logfile location > >OK, the wishlist has been amended with one worthy to check idea: >https://github.com/fgeorgatos/easybuild/wiki/Wishlist >""" >Add possibility to save the logfile somewhere even when failures happen >(/tmp >is no good for queue submitted jobs) >""" > >This is actually quite critical for me to speed up operations, >since I run them in batch mode (cluster jobs) and the logfiles >-with all the interesting error information- are scattered around. >(the interesting info, are actually the failures, which go in /tmp!!!) > >Can we do something about it? Am I missing some other option here? > > >(4) Compiling/Linking against boost and such libraries > >While building Cufflinks, Cedric came across this issue: >http://stackoverflow.com/questions/11688893/decoding-gcc-specs-file-line > >To summarize what I understand, there is a subtle difference in the gcc >spec strings and we wonder if there is some funny interaction between >Debian/Easybuild/gcc; can you supply the following command from your side? > >$ gcc -dumpspecs|grep -A1 multilib: ># Most RHEL clones give: . !m64 !m32;64:../lib64 m64 !m32;32:../lib !m64 >m32; >(check it character-per-character, it's hard exercise for the human >reader) Actually, there is no problem in the compilation of Cufflinks (we are interested in the most recent version, being 2.0.2 IIRC). It is building fine and linking correctly against the (by us) specified boost-version 1.50. Needed some patching and renaming, but this is nicely handled via the easyconfig and easyblock. The problem arised when I wanted to link against the as-a-dependency easybuild-built boost version (1.50) with a simple C++ program. Even though the easybuild does specify the LIBRARY_PATH environment variable (set using make_module_req_guess() ) to point correctly to the "local" libs (the easybuild ones, in opposite to the default system libraries), when using the GCC with goalf (eventually coming from easybuild) the order of the paths in LIBRARY_PATH is somehow mixed up thus making the gcc pick the system libs (under /usr...) instead of the "local" libs (1.50). Interestingly, using the dummy gcc does not cause this problem and uses LIBRARY_PATH as it is found e.g. With the env command - no mix up seems to occur. If you wonder why Cufflinks worked fine: this is simply because it uses "-L/with/boost/libs/dir" and this gets top-priority in linking, even before LIBRARY_PATH. > >(5) Next steps > >Finally, I think we reach a point that a mini-hackathon would be welcome; >Especially, to touch on matters like the following and integrate current >work: >https://github.com/fgeorgatos/HPC-RFC/blob/master/0001/0001.md >https://github.com/fgeorgatos/easybuild/wiki/Wishlist > > >have a nice weekend, > >Fotis > >-- >echo "sysadmin know better bash than english" | sed s/min/mins/ \ > | sed 's/better bash/bash better/' # Yelling in a CERN forum These were my two cents :) Best and have a nice weekend, Cedric Cedric Laczny, PhD Student UNIVERSITÉ DU LUXEMBOURG LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE Campus Belval | House of Biomedicine 7, avenue des Hauts-Fourneaux L-4362 Esch-sur-Alzette T +352 46 66 44 6398 F +352 46 66 44 6949 [email protected] http://lcsb.uni.lu <http://lcsb.uni.lu/> ----- This message is confidential and may contain privileged information. 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