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talks: Add BE-RSE talk.

* talks/be-rse-2020: New directory.
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Ludovic Courtès 2020-11-20 17:54:44 +01:00
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45 changed files with 4186 additions and 9 deletions

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/talks/fosdem-2020/containers/talk.vrb
/talks/fosdem-2020/containers/talk.dvi
/talks/jdev-2020/images/hwloc-graph.pdf
/talks/jdev-2020/talk.aux
/talks/jdev-2020/talk.log
/talks/jdev-2020/talk.nav
/talks/jdev-2020/talk.out
/talks/jdev-2020/talk.pdf
/talks/jdev-2020/talk.pdf.log
/talks/jdev-2020/talk.snm
/talks/jdev-2020/talk.toc
/talks/jdev-2020/talk.vrb
talk.aux
talk.log
talk.nav
talk.out
talk.pdf
talk.pdf.log
talk.snm
talk.toc
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;; Rules for Rubber.
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% The comment below tells Rubber to compile the .dot files.
%
% rubber: module graphics
% rubber: rules rules.ini
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\newcommand{\highlight}[1]{\alert{\textbf{#1}}}
\title{The role of software deployment in reproducible research}
\author{Ludovic Courtès}
\date{5 November 2020}
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\begin{frame}[plain, fragile]
\vspace{10mm}
\Huge{\textbf{The role of software deployment \\
in reproducible research}}
\\[2cm]
\large{Ludovic Courtès}
\\[2mm]
\alert{BE-RSE seminar, \oldstylenums{5 November 2020}}
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%% \screenshot{images/nature-reviewing-computational-methods}
% http://blogs.nature.com/methagora/2014/02/guidelines-for-algorithms-and-software-in-nature-methods.html
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\Huge{\textbf{HPC = cutting edge?}}
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% https://docs.conda.io/en/latest/_images/conda_logo.svg
\end{tikzpicture}
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%% \screenshot[width=\paperwidth]{images/easybuild-bug}
% https://github.com/spack/spack/issues?q=is%3Aissue+is%3Aopen+label%3Abuild-error
%% \screenshot[width=\paperwidth]{images/spack-bug}
\screenshot[width=\paperwidth]{images/spack-build-errors}
\screenshot[width=.9\paperwidth]{images/conda-broke-tweet}
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\begin{frame}[plain]
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% https://xkcd.com/1988/
\screenshot[height=0.95\paperheight]{images/singularity-def-file}
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\setbeamercolor{normal text}{fg=white,bg=black}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% \begin{frame}
%% \LARGE{
%% \begin{enumerate}
%% \item transactional package manager
%% \item software environment manager
%% \item APIs \& tools to customize environments
%% \item container provisioning tools
%% \end{enumerate}
%% }
%% \end{frame}
\begin{frame}
\Large{
\begin{itemize}
\item Guix started in 2012
\item \highlight{$\approx$15,000 packages}, all free software
\item \highlight{4 architectures}:\\
x86\_64, i686, ARMv7, AArch64
%% \item binaries available
\item \highlight{Guix-HPC effort (Inria, MDC, UBC, UTHCS) started in 2017}
\item<2-> \textbf{Guix 1.2 coming up!}
\end{itemize}
}
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%% \setbeamercolor{normal text}{bg=white}
%% \screenshot[width=.7\paperwidth]{images/Guix-1-0}
%% \setbeamercolor{normal text}{bg=black}
\begin{frame}[fragile]
\begin{semiverbatim}
\LARGE{
guix \alert{install} gcc-toolchain openmpi hwloc
eval `guix package \alert{--search-paths}=prefix`
guix package \alert{--roll-back}
guix \alert{environment} --ad-hoc \\
gcc-toolchain@5.5 hwloc@1
}
\end{semiverbatim}
\end{frame}
\begin{frame}[fragile]
\begin{semiverbatim}
\LARGE{
guix package \alert{--manifest}=my-packages.scm
(\alert{specifications->manifest}
'("gcc-toolchain" "openmpi"
"scotch" "mumps"))
}
\end{semiverbatim}
\end{frame}
\setbeamercolor{normal text}{bg=guixdarkgrey}
\begin{frame}[fragile]
\begin{semiverbatim}
\Large{
bob@laptop$ guix package \alert{--manifest}=my-packages.scm
bob@laptop$ guix \alert{describe}
guix cabba9e
repository URL: https://git.sv.gnu.org/git/guix.git
commit: cabba9e15900d20927c1f69c6c87d7d2a62040fe
\pause
alice@supercomp$ guix \alert{pull} --commit=cabba9e
alice@supercomp$ guix package \alert{--manifest}=my-packages.scm
}
\end{semiverbatim}
\end{frame}
\begin{frame}[fragile]
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\node [at=(current page.center), inner sep=0pt]
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at (current page.center) {
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};
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\setbeamercolor{normal text}{bg=guixgrey}
\begin{frame}[fragile]
\begin{semiverbatim}
\LARGE{
guix \alert{time-machine} --commit=cabba9e -- \\
install hello
}
\end{semiverbatim}
\end{frame}
\begin{frame}[fragile]
\begin{semiverbatim}
(define pastix
(\alert{package}
(name "pastix")
(home-page "https://gitlab.inria.fr/solverstack/pastix")
(\alert{source} (origin
(method git-fetch)
(uri (git-reference
(\alert{url} home-page)
(\alert{commit} "2f30ff07a")\tikz{\node(commit){};}
(recursive? #t)))
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\end{semiverbatim}
\begin{tikzpicture}[overlay]
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% https://annex.softwareheritage.org/public/logo/
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};
\node<2-> [at=(current page.south), anchor=south,
inner sep=2mm, rounded corners, fill=black, text width=13cm,
opacity=.3, text opacity=1] {
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(swh) edge [out=-90, in=0, ->] (commit);
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\setbeamercolor{normal text}{bg=guixred3}
\begin{frame}[fragile]%{Container provisioning}
\begin{tikzpicture}[overlay]
\node<2> [at=(current page.south), anchor=south,
inner sep=2mm, rounded corners, fill=black, text width=10cm,
opacity=.3, text opacity=1] {
\url{https://hpc.guix.info/blog/2020/05/faster-relocatable-packs-with-fakechroot/}
};
\end{tikzpicture}
\LARGE{
\begin{semiverbatim}
\$ guix \alert{pack}\only<2>{ --relocatable}\only<3>{ --format=squashfs}\only<4->{ --format=docker} \\
python python-numpy python-scipy
\textrm{...}
/gnu/store/\textrm{...}-\only<1-2>{pack.tar.gz}\only<3>{singularity-image.tar.gz}\only<4->{docker-image.tar.gz}
\end{semiverbatim}
}
\end{frame}
\setbeamercolor{normal text}{bg=white}
\screenshot[width=.9\paperwidth]{images/docker-guix-lol}
\setbeamercolor{normal text}{bg=guixdarkgrey}
\begin{frame}[fragile]
\begin{semiverbatim}
\LARGE{
guix pack hwloc \\
\alert{--with-source}=./hwloc-2.1rc1.tar.gz
guix install mumps \\
\alert{--with-input}=scotch=pt-scotch
}
\end{semiverbatim}
\end{frame}
\setbeamercolor{normal text}{bg=guixgreen1}
\begin{frame}[plain]
\Huge{\textbf{Reproducible deployment\\ is the key.}}
\end{frame}
\setbeamercolor{normal text}{fg=white,bg=black}
\screenshot{images/pigx1}
\screenshot{images/pigx2}
\setbeamercolor{normal text}{bg=white}
\begin{frame}[plain]
\begin{tikzpicture}[remember picture, overlay]
\node [at=(current page.center), inner sep=0pt]{
\includegraphics[height=.7\textheight]{images/workflow-management-3}
};
\node [at=(current page.south), anchor=south,
text=guixdarkgrey, fill=white, text opacity=1]{
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};
\node [at=(current page.north west), anchor=north west, opacity=0,
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inner sep=3mm]
{\url{https://hpc.guix.info/blog/2019/10/towards-reproducible-jupyter-notebooks}};
\end{tikzpicture}
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%% \screenshot{images/jupyter-select-kernel}
\screenshot{images/environment}
%% \begin{frame}[plain]
%% \begin{tikzpicture}[remember picture, overlay]
%% \node [at=(current page.center), inner sep=0pt]{
%% \includegraphics[width=.95\textwidth]{images/guix-kernel-python}
%% };
%% \node [at=(current page.south), anchor=south,
%% text=guixdarkgrey, fill=white, text opacity=1]{
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%% \node [at=(current page.north west), anchor=north west, opacity=0,
%% inner sep=5mm, text=guixdarkgrey, fill=white, text opacity=1]{
%% \Large{\textbf{Guix-Jupyter}}
%% };
%% \end{tikzpicture}
%% \end{frame}
\setbeamercolor{normal text}{bg=rescienceyellow}
\begin{frame}[fragile, plain]
\begin{tikzpicture}[remember picture, overlay]
\node [at=(current page.south), anchor=south, inner sep=0pt]{
\includegraphics[height=0.95\textheight]{images/ten-years-challenge}
};
\node [at=(current page.north), anchor=north, text=guixgrey] {
\small{\url{https://rescience.github.io/ten-years/}}
};
\end{tikzpicture}
\end{frame}
\setbeamercolor{normal text}{bg=white}
\screenshot{images/end-to-end-1}
\screenshot[height=\textheight]{images/end-to-end-2}
\begin{frame}[fragile, plain]
\begin{tikzpicture}[remember picture, overlay]
\node [at=(current page.center), inner sep=0pt]{
\includegraphics[width=.9\textwidth]{images/re-storage-tradeoffs}
};
\node [at=(current page.center), anchor=south, inner sep=8mm, text=guixgrey] {
\small{\url{https://doi.org/10.5281/zenodo.3886739}}
};
\end{tikzpicture}
\end{frame}
\setbeamercolor{normal text}{bg=guixblue2}
\begin{frame}[plain]
\Huge{\textbf{Wrap-up.}}
\end{frame}
\setbeamercolor{normal text}{bg=white}
\screenshot[width=\textwidth]{images/big-picture-3}
%% \setbeamercolor{normal text}{fg=white,bg=black}
%% \begin{frame}
%% \LARGE{
%% \begin{itemize}
%% \item \highlight{reproduce} software environments
%% \item \highlight{declare \& publish} complete environments
%% \item beyond replication: precision \highlight{experimentation}
%% \item a foundation for \highlight{``deployment-aware'' apps}
%% \end{itemize}
%% }
%% \end{frame}
\screenshot{images/guix-scope}
\setbeamercolor{normal text}{bg=white}
\begin{frame}[fragile]
\vspace{-2cm}
\begin{tikzpicture}
\matrix[row sep=10mm, column sep=1cm]{
% https://git-scm.com/downloads/logos
\node {\includegraphics[width=0.2\textwidth]{images/Git-Logo-2Color}}; &
\node {\includegraphics[width=0.15\textwidth]{images/arrow-right}}; &
\node {\includegraphics[width=0.24\textwidth]{images/Guix-horizontal-print}};
\\
};
\end{tikzpicture}
\begin{tikzpicture}[overlay]
\node [at=(current page.center), anchor=north,
text=black, text width=.9\textwidth]{
\Huge{Let's add\\ \textbf{reproducible deployment}\\
to our best practices book. \par
}};
\end{tikzpicture}
\end{frame}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\setbeamercolor{normal text}{bg=black}
\begin{frame}[plain]
\vfill{
\vspace{3cm}
\center{\includegraphics[width=0.5\textwidth]{images/guixhpc-logo-transparent}}\\[1.0cm]
\texttt{ludovic.courtes@inria.fr |} @GuixHPC
\center{\alert{\url{https://hpc.guix.info}}}
\\[1cm]
}
\end{frame}
\setbeamercolor{normal text}{bg=guixred2}
\begin{frame}
\Huge{\textbf{Bonus slides!}}
\end{frame}
\setbeamercolor{normal text}{bg=black}
\begin{frame}[fragile]
%% \frametitle{Bit-Reproducible Builds$^*$}
%% \framesubtitle{$^*$ almost!}
\begin{semiverbatim}
\Large{
\$ guix build hwloc
\uncover<2->{/gnu/store/\tikz[baseline]{\node[anchor=base](nixhash){\alert<2>{h2g4sf72\textrm{...}}};}-hwloc-1.11.2}
\uncover<3->{\$ \alert<3>{guix gc --references /gnu/store/\textrm{...}-hwloc-1.11.2}
/gnu/store/\textrm{...}-glibc-2.24
/gnu/store/\textrm{...}-gcc-4.9.3-lib
/gnu/store/\textrm{...}-hwloc-1.11.2
}}
\end{semiverbatim}
\begin{tikzpicture}[overlay]
\node<1>(labelnixhash) [fill=white, text=black, inner sep=0.5cm,
rounded corners] at (current page.center) {%
\Large{\textbf{isolated build}: chroot, separate name spaces, etc.}
};
\node<2>(labelnixhash) [fill=white, text=black] at (4cm, 2cm) {%
hash of \textbf{all} the dependencies};
\path[->]<2>(labelnixhash.north) edge [bend left, in=180, out=-45] (nixhash.south);
\draw<4-> (-10pt, 105pt) [very thick, color=guixorange2, rounded corners=8pt]
arc (10:-50:-50pt and 110pt);
\node<4->[fill=white, text=black, text opacity=1, opacity=.7,
rounded corners=2mm, inner sep=5mm]
at (7, 2) {\textbf{\Large{(nearly) bit-identical for everyone}}};
\end{tikzpicture}
\end{frame}
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\begin{tikzpicture}[remember picture, overlay]
\node [at=(current page.center), inner sep=0pt]
{\includegraphics[width=0.95\paperwidth]{images/snap-crypto-miner}};
\node [at=(current page.south east), anchor=south east,
text=black, text opacity=1, fill=white]{
\small{\url{https://github.com/canonical-websites/snapcraft.io/issues/651}}
};
\end{tikzpicture}
\end{frame}
\begin{frame}[plain]
\begin{tikzpicture}[remember picture, overlay]
\node [at=(current page.center), inner sep=0pt]
{\includegraphics[width=0.9\paperwidth]{images/lwn-docker-hello-world}};
\node [at=(current page.south east), anchor=south east,
text=white, fill=black, text opacity=1]{
\small{\url{https://lwn.net/Articles/752982/}}
};
\end{tikzpicture}
\end{frame}
\setbeamercolor{normal text}{bg=white}
\begin{frame}[plain]
\begin{tikzpicture}[remember picture, overlay]
\node [at=(current page.center), inner sep=0pt]
{\includegraphics[height=\paperheight]{images/hwloc-graph}};
\end{tikzpicture}
\end{frame}
\setbeamercolor{normal text}{fg=white,bg=black}
\begin{frame}{cluster deployments}
\Large{
\begin{itemize}
% http://zvfak.blogspot.ch/2015/07/gnu-guix-for-easily-managing.html
\item \highlight{Max Delbrück Center} (DE): 250-node cluster +
workstations
% https://ubc.uu.nl/infrastructure/
% https://wiki.bioinformatics.umcutrecht.nl/pub/HPC/WebHome/HPC_Flyer.png
\item \highlight{UMC Utrecht} (NL): 68-node cluster (1,000+ cores)
% https://www.qriscloud.org.au/support/qriscloud-documentation/75-euramoo-datasheet
% https://www.qriscloud.org.au/support/qriscloud-documentation/76-flashlite-datasheet
\item \highlight{University of Queensland} (AU): 20-node cluster
(900 cores)
\item \highlight{PlaFRIM} (FR): Inria Bordeaux (3,000+ cores)
\end{itemize}
}
\end{frame}
%% \screenshot[width=.9\paperwidth]{images/openhub-activity}
\screenshot[width=\paperwidth]{images/openhub-contributors}
\begin{frame}{}
\begin{textblock}{12}(2, 6)
\tiny{
Copyright \copyright{} 2010, 2012--2019 Ludovic Courtès \texttt{ludo@gnu.org}.\\[3.0mm]
GNU Guix logo, CC-BY-SA 4.0, \url{https://gnu.org/s/guix/graphics}.
\\[1.5mm]
Smoothie image and hexagon image \copyright{} 2019 Ricardo Wurmus,
CC-BY-SA 4.0.
\\[1.5mm]
Hand-drawn arrows by Freepik from flaticon.com.
\\[1.5mm]
DeLorean time machine picture \copyright{} 2014 Oto Godfrey and
Justin Morton, CC-BY-SA 4.0,
\url{https://commons.wikimedia.org/wiki/File:TeamTimeCar.com-BTTF_DeLorean_Time_Machine-OtoGodfrey.com-JMortonPhoto.com-07.jpg}.
\\[1.5mm]
Copyright of other images included in this document is held by
their respective owners.
\\[3.0mm]
This work is licensed under the \alert{Creative Commons
Attribution-Share Alike 3.0} License. To view a copy of this
license, visit
\url{https://creativecommons.org/licenses/by-sa/3.0/} or send a
letter to Creative Commons, 171 Second Street, Suite 300, San
Francisco, California, 94105, USA.
\\[2.0mm]
At your option, you may instead copy, distribute and/or modify
this document under the terms of the \alert{GNU Free Documentation
License, Version 1.3 or any later version} published by the Free
Software Foundation; with no Invariant Sections, no Front-Cover
Texts, and no Back-Cover Texts. A copy of the license is
available at \url{https://www.gnu.org/licenses/gfdl.html}.
\\[2.0mm]
% Give a link to the 'Transparent Copy', as per Section 3 of the GFDL.
The source of this document is available from
\url{https://git.sv.gnu.org/cgit/guix/maintenance.git}.
}
\end{textblock}
\end{frame}
\end{document}
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