Simon Tournier

Reproducible Research and Guix

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npub1rgkatvlde7ms8whrqj2f4rhm9lp7xc2jea8a56qmywyqumtkf34qrpgj6x

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zimoun_at_social.sciences.re@mostr.pub

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nprofile1qqsp5tw4k0kuldcrht3sf9y63majlslrv9fv7n76dqdj8zqwd4myc6s66dcvh

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npub1rgkatvlde7ms8whrqj2f4rhm9lp7xc2jea8a56qmywyqumtkf34qrpgj6x

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Last Notes

2024-10-22 13:52:05

French RR netwwork Webinar: @npub1a75…w8nq and Arnaud Legrand explained their feedback on 2 MOOCs about #ReproducibleResearch.
Interested by producing better scientific results, check out the both MOOCs!
How to make your scientific workflow more robust? These MOOCs’re a very good start. You’ll learn concepts applied with tools such as: #Guix, #Emacs + #OrgMode, #Git and #GitAnnex, etc.
https://www.fun-mooc.fr/en/courses/reproducible-research-ii-practices-and-tools-for-managing-comput
https://www.fun-mooc.fr/en/courses/reproducible-research-methodological-principles-transparent-scie
https://www.recherche-reproductible.fr
#OpenScience

2024-10-11 09:35:33

Mardi 15 oct. Café #Guix : «Installer et utiliser facilement et de façon reproductible ses logiciels avec Guix» par Pierre-Antoine Bouttier
https://hpc.guix.info/events/2024-2025/café-guix
🤔 Qu’est-ce que Guix ?
En quête de quoi “télévorer“ ?
https://replay.jres.org/w/3TuYmocHwKtzs7q1VtL1GB
https://10years.guix.gnu.org/video/guix-as-a-tool-for-computational-science
https://hpc.guix.info/events/2023/workshop/video/caring-for-your-environment-s-/
https://hpc.guix.info/events/2023/workshop/video/what-is-guix-/
https://hpc.guix.info/events/2023/workshop/video/everyone-can-learn-how-to-guix/
Plus de télévoration ? Bah le MOOC: « #ReproducibleResearch II: Practices and tools for managing computations and data »
https://www.fun-mooc.fr/en/courses/reproducible-research-ii-practices-and-tools-for-managing-comput

2024-08-30 07:58:48

The #Guix manual does not suit your needs: connect some dots with @npub160m…lu4t’s series!
Well written posts that turn the spotlight on some features and explain them.
https://www.futurile.net/resources/guix

2024-07-24 16:50:31

Oh, I discover that #Scheme supports transparent conversion between Arabic numbers to Roman numerals, and even “exotic“ ones.
Fun!
$ guix repl
scheme@(guix-user)> (format #t "~&~@r~%" 1234)
MCCXXXIV
$1 = #t
scheme@(guix-user)> (format #t "~&~:@r~%" 1234)
MCCXXXIIII
$2 = #t
#Guix

2024-06-23 16:59:44

Voilà bientôt le train de nuit, le sac est bouclé, un bon bouquin dedans, les jumelles, à manger pour quelques jours… bref de quoi rester percher quelques jours autour du Pic de Rulhe ! Petite semaine vacances de rando-observation loin du brouaha… <3
Hé oui #LAriegeCestMoche ! ;-)

2024-06-15 22:17:27

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@npub19am…qjn6 L’étape suivante de la banalisation sera de ne même plus prévenir…
Allez je mets mes pantoufles du vieux ronchon : « hé oui c’est le progrès ! »

2024-05-31 12:59:21

The blog post: « Source code archiving in Guix: new publication » quickly summarizes how #Guix is connected to #SoftwareHeritage.
https://guix.gnu.org/en/blog/2024/source-code-archiving-in-guix-new-publication
#ReproducibleResearch

2024-04-29 11:40:59

What’s G-expressions? Quoting #Guix manual:
« To describe a derivation and its build actions, one typically needs to embed build code inside host code. It boils down to manipulating build code as data, and the homoiconicity of Scheme — code has a direct representation as data — comes in handy for that. But we need more than the normal quasiquote mechanism in Scheme to construct build expressions. »
https://guix.gnu.org/manual/devel/en/guix.html#G_002dExpressions
[1/3]

2024-04-19 13:58:09

Prochain Café #Guix, jeudi 30 avril 13h: Introduction aux G-expressions.
Après la lecture de la section « Définition des paquets », et après quelques itérations test/erreur, nous devons ici ou là mettre des symboles comme #~(#$(%. Ce petit Caf’ essaiera de les rendre moins cryptiques. Nous introduirons quelques ingrédients de la boite à outils #Scheme / #Guile (quote, quasiquote, unquote) ce qui nous mènera aux G-exps… Vaste programme ! ;-)
N’hésitez pas à poser des questions ici ou là :-)

2024-04-15 10:29:24

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@npub19am…qjn6 Why? Because GC? Else?

2024-03-18 15:43:31

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@npub19d9…f02p This minimization looks like a part of a complete "technology system" as defined by Ellul's book https://en.wikipedia.org/wiki/The_Technological_Society
It's a paradoxical position: a tool (e.g., proposals) is first designed as a mean to make a situation more efficient, then this tool becomes a complete system that transforms "itself" as inefficient.
The question is thus: how to design a tool that avoids the paradox? Maybe Illich's book sketches ideas https://en.wikipedia.org/wiki/Tools_for_Conviviality

2024-03-15 10:28:00

#ReproducibleResearch in #HPC context using #Guix by @npub19am…qjn6
Reflection on HPC motto:
+ OpenMPI
+ CPU specilization (AVX, etc.)
+ GPU
Conclusion: Reproducible Deployement is possible without sacrifing on performances!
Links:
https://hpc.guix.info/blog/2022/07/is-reproducibility-practical
https://hpc.guix.info/blog/2019/12/optimized-and-portable-open-mpi-packaging
https://hpc.guix.info/blog/2022/01/tuning-packages-for-a-cpu-micro-architecture
https://hpc.guix.info/blog/2024/01/hip-and-rocm-come-to-guix
https://hpc.guix.info/blog/2018/01/pre-built-binaries-vs-performance
From http://orap.irisa.fr/52ieme-forum-reproductibilite

2024-03-04 19:05:07

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@npub1f6a…pnql Is the complete carbon footprint included in these prices?

2024-03-04 17:29:30

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@npub19am…qjn6 We are at the beginning of a vicious circle about water, no?
Its lack will imply high constraints on electricity production; see International Energy Agency https://www.iea.org/reports/electricity-2024. Hydroelectricity, obviously. And more. Even nuclear; with low water level, poor perfs because low cooling.
And dry area will consume more energy or resources to secure water's supply; e.g. desalination or else.
Barcelona is maybe an example of this dichotomy.
@npub1l5u…0adz

2024-03-03 22:12:10

Wanting the analysis with R reproducible, checkout the package r-guix-install!
https://hpc.guix.info/package/r-guix-install
It provides the R procedure guix.install(): it allows to install R packages via #Guix right from within the running R session. If this R package doesn't exist in Guix, it and all its missing dependencies will be imported recursively.
Channel guix-cran provides 18853 packages from CRAN and guix-bioc 2871 packages from BioConductor
https://hpc.guix.info/channel/guix-cran
https://hpc.guix.info/channel/guix-bioc

2024-02-27 13:06:13

Awesome Café #Guix about Guix Packager and how to exploit it.
https://guix-hpc.gitlabpages.inria.fr/guix-packager/
It allows to quickly have a package recipe without diving in all the “parenthetical” details. :-)
Thanks Alice Brenon and Philippe Virouleau.

2024-02-19 10:09:26

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@npub19am…qjn6 Somehow I do not feel that way. :-)
« when you work with (say) Guile or Lout, you go to the manual and work from that canonical reference. »
Maybe because you contributed to internals of Guile or Lout? ;-)
Have you read the canonical reference of TeX or LaTeX?
« With JS or LaTeX, I feel more like I’m doing things I don’t really understand »
Ah! Like many of us with Guile or Lout. :-) Except that I do not find examples or packages to copy. ;-)
@npub1nxc…pa3h

2024-02-12 10:15:17

Café #Guix mardi 27 février 13h
https://meet.univ-grenoble-alpes.fr/b/cel-dyj-m93-arv
« Comment faire un paquet Guix avec l'outil d'aide Guix Packager ? »
animé par Alice Brenon (ICAR / LIRIS) et Philippe Virouleau (Inria).
https://guix-hpc.gitlabpages.inria.fr/guix-packager/

2024-02-11 09:20:09

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@npub1zgl…rqd7 Thanks for explaining. Indeed more than a short message. :-D
Well, I will elaborate later more on guix-devel mailing list – old style. :-)
About slowness, sadly yeah )-: Well, we need to chase some unnecessary extra work. One attempt: https://issues.guix.gnu.org/issue/65787
About 2. I agree something is missing; see “Mechanism for helping in multi-channels configuration” https://yhetil.org/guix/87v875kf5u.fsf@gmail.com
So work on our plate… :-)
@npub19am…qjn6

2024-02-10 09:58:32

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« The most powerful CPU in the table is from […]. Compared with the Apollo 11
Guidance Computer it runs at ~48 times the clock speed with 1.8x the program
space. It's very tempting to claim that […] could fly me to the moon. But we
need more analysis. »
Are we on a path for more sobriety?
[2/2]

2024-02-10 09:56:36

https://forrestheller.com/Apollo-11-Computer-vs-USB-C-chargers.html
« Let's see how the CPUs contained in recent USB-C wall chargers compare to
the power of the Apollo 11 Guidance Computer (AGC). The Apollo 11 spacecraft
carried 3 humans to the moon and back in 1969. »
[1/2]

2024-02-09 12:18:07

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@npub19am…qjn6 @npub1zgl…rqd7 Mine looks like:
guix time-machine -- describe -f channels > channels.scm
guix time-machine -C channels.scm -- shell -m manifest.scm
while unhappy do test … ; add stuff to manifest.scm ;done
git add channels.scm manifest.scm; git commit -m ’update’
Well it could be nice to ease two things:
+ channels.scm management (add/remove channels)
+ manifest.scm management (add/remove packages)
instead of manually editing these files.

2024-02-07 08:18:45

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@npub19am…qjn6 @npub14h4…hpj0
The hidden O(n) is not obvious from the Guile manual:
« This expression returns the first element of each list within LST. For
proper lists of proper lists, it is equivalent to ‘(map car lst)’. However,
it performs additional checks to make sure that LST and the lists therein are
proper lists, as prescribed by the pattern, raising an error if they are
not. »
Well “additional checks” is vague… :-)
https://www.gnu.org/software/guile/manual/html_node/Pattern-Matching.html

2024-02-06 14:43:18

Follow-up of a discussion at FOSDEM with @npub19am…qjn6 and
@npub14h4…hpj0 about #Guile builtin implementation (C vs Scheme):
A post comparing Guile builtin merge sort in C against merge sort in Scheme
https://simon.tournier.info/posts/2024-02-05-guile-sort/index.html
My conclusions:
1. Guile needs more love!
2. Better Guile makes better #Guix!
#structuredprocrastination

2024-02-06 08:37:49

Le Monde: https://www.lemonde.fr/sciences/article/2024/02/05/supercalculateur-du-cnrs-un-magnifique-projet-et-des-degats-collateraux_6214897_1650684.html
« En dernière année de thèse, ses délais vont déraper, le temps d’organiser la
migration de ses calculs vers une autre machine. »
« […] mais le temps de migration des applications, c’est environ trois mois. »
Parmi les questions que je me pose: Est-ce que #guix faciliterait cette
migration ? Et quelques liens pour y réfléchir:
https://hpc.guix.info/blog/2018/01/pre-built-binaries-vs-performance/
https://archive.fosdem.org/2023/schedule/event/cpu_tuning_gnu_guix/

2024-02-01 10:22:28

Yesterday, I attended to #swh community meeting. Nice event and fruitful experience.
Thanks @npub128s…wgul for organizing and thanks Mélissa (La Dérivation) for facilitating.
For what it is worth, I wrote down some notes for keeping a trace for myself.
https://simon.tournier.info/posts/2023-01-31-swh-meeting.html
Checkout my personal answers of Software Heritage FAQ: https://simon.tournier.info/posts/2023-02-07-unesco-swh.html