reproducible and user-controlled software management in HPC
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1 reproducible and user-controlled software management in HPC with GNU Guix Ricardo Wurmus + Pjotr Prins + Ben Woodcroft + Altuna Akalin BOSC 2017, Prague
2 System Admins prefer mature software, no variants, only apply unavoidable updates Users want fresh software, multiple variants, latest tools, flexibility use stable software for systems manage user software stack on their own
3 ad-hoc volatile primitive There is no way to reproduce the environment, even on the same machine at a different point in time. Due to a lack of isolation, the environment will change or even break when the host system changes. No safe upgrades or roll-backs. No separation for different workflows. Unportable.
4 ?
5 Installing software is easy now!...but reproducibility is still out of reach
6 Installing software is easy now!...but reproducibility is still out of reach
7
8
9 100% reproducible We have all the bits!
10 100% reproducible We have all the bits! 100% stateful We only have the bits!
11 App bundles are convenient lack means of abstraction don't compose well are like giant statically linked aries
12
13 Functional packaging headers sources build tools libraries... cabba9e-emacs-24.5/ emacs lib...
14 Functional packaging Same inputs? Same output! cabba9e-emacs-24.5/ emacs lib... Different inputs? Different outputs. dedbeef-emacs-24.5/ emacs lib...
15 coreutils-8.24 perl tar-1.28 gzip-1.6 bzip xz file-5.25 diffutils-3.3 patch sed findutils gawk grep-2.22 coreutils-8.24 make-4.1 bash ld-wrapper-0 utils gcc glibc-2.22 glibc-utf8-locales-2.22 acl gmp libcap-2.24 glibc-utf8-locales-2.22 gcc ld-wrapper-boot3-0 utils-cross-boot make-boot0-4.1 diffutils-boot0-3.3 findutils-boot file-boot bootstrap-aries-0 ed-1.12 libsigsegv-2.10 perl-boot perl acl gmp libcap-2.24 pkg-config-0.29 guile bison readline-6.3 ncurses-6.0 gcc-cross-boot0-wrapped texinfo-6.0 bash-static libstdc zlib perl-boot gettext-boot gcc-cross-boot glibc-bootstrap-0 gcc-bootstrap-0 linux-libre-headers gzip-1.6 gettext attr m gzip-1.6 guile-bootstrap-2.0 utils-bootstrap-0 gettext attr m gcc-cross-boot0-wrapped glibc-intermediate-2.22 m expat lzip-1.16 pkg-config-0.29 libffi readline-6.3 libunistring libltdl libgc gmp ncurses-6.0 libatomic-ops m expat-2.1.0
16 guix gc --references /gnu/store/ -foo-0.9 /gnu/store/ -glibc-2.25 /gnu/store/ -gcc lib /gnu/store/ -bar-0.7b /gnu/store/ -baz /gnu/store/ -foo-0.9
17 guix package -i baz --with-input=foo=bar guix package -i baz --with-source=baz-1.0.tgz
18 guix pack bedtools /gnu/store/ -pack.tar.gz
19 guix pack -f docker bedtools /gnu/store/ -docker-pack.tar.gz LOL
20 guix package --manifest=genenetwork All you need is: Guix version + package manifest (+ source code)
21 The level of abstraction matters Guix enables reproducible and safe experimentation Guix makes environment sharing easy There are ways to use Guix without root access Like Conda? 5. guix package -i conda
22 Learn more! Poster A-142 #guix on irc.freenode.net
23 /home/rekado/.guix-profile /var/guix/... /gnu/store... guix-profile 42 hscq14x...-profile bowtie2 rhrdst11m include lud0v1c...-bowtie bowtie2
24 /home/rekado/.guix-profile /var/guix/... /gnu/store... guix-profile hscq14x...-profile bowtie2 rhrdst11m include lud0v1c...-bowtie bowtie2 z3braf1sh...-profile
25 /home/rekado/.guix-profile /var/guix/... /gnu/store... guix-profile hscq14x...-profile bowtie2 rhrdst11m include lud0v1c...-bowtie bowtie2 z3braf1sh...-profile
26 /home/rekado/.guix-profile /var/guix/... /gnu/store... guix-profile 43 hscq14x...-profile bowtie2 rhrdst11m include lud0v1c...-bowtie bowtie2 z3braf1sh...-profile
27 /home/rekado/.guix-profile /var/guix/... /gnu/store... guix-profile 43 rhrdst11m include lud0v1c...-bowtie bowtie2 z3braf1sh...-profile
28 /home/rekado/.guix-profile /var/guix/... /gnu/store... guix-profile 43 rhrdst11m include z3braf1sh...-profile
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