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-packages (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/autoconf-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/gnuplot-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/libxml2-2.8.0.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/openmpi-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/raptor2-2.0.7.eb https://github.com/fgeorgatos/easybuild/blob/master/experimental2/r/readline-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/unixODBC-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/gromacs-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/arpack96.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/doxygen-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/h5utils-1.12.1.eb https://github.com/fgeorgatos/easybuild/blob/master/experimental2/i/ipython-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/libmatheval-1.1.4.eb https://github.com/fgeorgatos/easybuild/blob/master/experimental2/l/libxslt-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/primer3-.eb https://github.com/fgeorgatos/easybuild/blob/master/experimental2/p/proj-.eb https://github.com/fgeorgatos/easybuild/blob/master/experimental2/p/pytable-0.8.3a.eb https://github.com/fgeorgatos/easybuild/blob/master/experimental2/r/root_v5.26.00b.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/schroedinger-1.0.11.eb https://github.com/fgeorgatos/easybuild/blob/master/experimental2/x/x264-snapshot--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) (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
