Hi Kenneth and Fotis, thank you for your answers. Well in the end I decided to pursue Gentoo:Prefix path which gave me isolated Gentoo Linux with its optimized apps in a separate directory location, not conflicting with the host RedHat instance. It is very nice and all I had to to was to run a /scratch/mmokrejs/gentoo/startprefix shellscript to get my environment setup and my bash. Unfortunately, the Gentoo:Prefix does not allow me to use a different glibc and it turned out I need for many java apps newer glibc (2.14 or newer). For those curious what the java issues were about, see: https://bugs.gentoo.org/show_bug.cgi?id=586716 https://bugs.gentoo.org/show_bug.cgi?id=588578
There were/are more issues with some packages in the Gentoo::Prefix path as it uses a modified portage tree (with fixes relating to the $EPREFIX, etc.) but on the other hand, some packages are a bit outdated compared to the MAIN Gentoo portage tree. Anyway, it was not a complete solution for me, although I compiled many apps using the old, glibc-2.12 from RedHat. Finally, I discovered Gentoo::RAP which has a bit cryptic documentation and the table at the top of the https://wiki.gentoo.org/wiki/Prefix/libc page drives me always crazy (I have more questions than which the table tries to document&explain). Gentoo::RAP uses Gentoo's MAIN portage repository (so less confusion for me but issues fixed in Gentoo::Prefix repository may still be broken in the MAIN tree ... ;)). You cannot get everything at once. What is very important for me, on Gentoo::RAP I got glibc-2.23 installed and more or less all apps including lots of java stuff can be run there. So, it is an amazing system how to get all the bells and whistles of Gentoo Linux on almost any platform. In my case, I could compile many apps with 'gcc -march=native' and because the Gentoo's build system is ready-made for non-gcc compilers as well (icc, f77, f90, clang, etc), I will recompile some of the applications using "CC=icc CXX=icc CFLAGS=opts CXXFLAG=opts emerge foo" with no effort. The process will either succeed and overwrite the gcc-made binaries, or not. I won't cry if some fail. Here is merely the whole trickery to get you :-) running: #export PORTAGE_TMPDIR=/dev/shm # to speedup compile process using a fast temp space #EPREFIX/etc/locale.gen export GENTOO_MIRRORS="http://gentoo.mirror.dkm.cz/pub/gentoo/"; export EPREFIX="/scratch/mmokrejs/gentoo_rap" # the place where you want to install the whole Gentoo thing # either fetch bootstrap-prefix.sh or bootstrap-rap.sh, refer to https://wiki.gentoo.org/wiki/Prefix/libc ./bootstrap-rap.sh $EPREFIX/startprefix # voila, you are done, you get your environment and without any mount/chroot calls! # inside prefixed/RAP-ed Gentoo execute the following # emerge app-portage/emerge-delta-webrsync emerge-webrsync # if you are behind a ftp/rsync firewall fetch snapshots via http emerge cpuinfo2cpuflags # figure out your CPUFLAGS or study /proc/cpuinfo yourself cpuinfo2cpuflags-x86 # read https://wiki.gentoo.org/wiki/Handbook:AMD64/Installation/Stage#CFLAGS_and_CXXFLAGS # edit/tune CFLAGS/CXXFLAGS/CC/CXX in $EPREFIX/etc/portage/make.conf emerge system # below is how I continued with installation of the latest&greatest apps from science and haskell overlays (supplementing the apps from MAIN portage tree) emerge layman layman -a science layman -a haskell echo "sci-biology/* **" >> $EPREFIX/etc/portage/package.accept_keywords echo 'PORTDIR_OVERLAY="/scratch/mmokrejs/gentoo_rap/var/lib/layman"' >> $EPREFIX/etc/portage/make.conf echo 'source /scratch/mmokrejs/gentoo_rap/var/lib/layman/make.conf' >> $EPREFIX/etc/portage/make.conf gcc-config -l eselect profile list echo "en_US ISO-8859-1" >> "$EPREFIX"/etc/locale.gen echo "en_US.UTF-8 UTF-8" >> "$EPREFIX"/etc/locale.gen locale-gen emerge =sys-devel/gcc-4.7.3-r1 =sys-devel/gcc-4.9.3 =sys-devel/gcc-4.8.5 =sys-devel/gcc-4.2.4-r2 =sys-devel/gcc-4.1.2 =sys-devel/gcc-3.4.6-r2 --keep-going cd $EPREFIX/var/lib/layman/science/sci-biology for p in *; do emerge -uN --keep-going --autounmask=y --backtrack=1000 $p; done So in summary, I myself did not see a reason to try to convert *.ebuild files to *.eb, and from a brief inspection of some easybuild files in the HPCugent github repository I realized the packages in Gentoo have more patches. Anyway, our cluster admins feel they want to create new *.eb files for some packages, so I can only wish them good luck and enough time to port the known/existing patches from other Linux distro's to easybuild. Anyway, thank you for you work, easybuild is a nice way to keep clean isolated environment, which Gentoo tries to yield using SLOTs and gcc-config/java-config, etc. Both approaches offer binaries compiled using your wished compiler and its options but the Gentoo:RAP approach was faster then even thinking about converting *.ebuild files to *.eb. :-)) So, now I hope some of you try now Gentoo and eventually join the community. ;-) Martin Fotis Georgatos wrote:
Hi Martin, this could become a very interesting direction. The script Kenneth mentioned is actually this one, it won't won any prizes other than antediluvian hackery: https://github.com/fgeorgatos/easybuild.experimental/blob/master/bin/pkg2eb_v2.sh More broadly, I would love to see more concerted efforts across distros, to keep their processes and entropy in check. Currently, it is all VERY ad-hoc about experience is exchanged across different build systems. F. p.s. At some point we could have a skype/hangout to swap knowledge and interests - just to catch up with the news. On 10 June 2016 at 11:00, Kenneth Hoste <[email protected] <mailto:[email protected]>> wrote: Hi Martin, On 09/06/16 11:55, Martin MOKREJŠ wrote: Hi, I would like to know if there is some automated way to install Gentoo packages through EasyBuild. I want to take packages available in science overlay of Gentoo Linux at http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git and install them on a non-Gentoo host. Is it doable? ;-) I foresee some difficulty because there can be classes inherited in the ebuild files, complicating the conversion. Also syntax (EAPI) is changing time to time. Interesting! I'm currently unaware of any effort on this, but Fotis (in CC) has done some work like this for pkgsrc recipes, cfr. https://github.com/fgeorgatos/easybuild.experimental/tree/master/contrib/pkgsrc. I'm not sure if the script he used for this is availble anywhere (can't seem to find it in the repo), or if it would be helpful at all for this... regards, Kenneth Thank you, Martin P.S.: Do not confuse official Gentoo portage tree which has far less packages, the packages in the overlay are of more testing quality but mostly work fine. On the other hand, there are many more available. P.P.S.: Do not confuse a github tree of science overlay, it is manually synced in both directions with the official http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git science overlay tree.. That is because some users prefer more the github access including pull requests and issue reports, etc. But devs have to pull/cherrypick the changes in both directions. -- echo "sysadmin know better bash than english"|sed s/min/mins/ \ | sed 's/better bash/bash better/' # signal detected in a CERN forum
