talks: Add beginning of FOSDEM HPC talk.

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Ludovic Courtès 2017-02-02 14:42:44 +01:00
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#+TITLE: Optimized & Reproducible HPC Software Deployment
* current HPC software environments are broken
** distros are old and inflexible, not upgraded
** thus, sysadmins write their own modules
** hand-maintained modules break, still inflexible
** modules may be removed behind your feet
** thus, users hand-build software in $HOME
** possibly using language-specific package managers
** => it's a mess
* fixing this chaos
** first approach: easybuild & spack
*** layered on top of the existing distro
*** good: packaging work is shared among HPC users, some QA
*** bad: everyone builds in $HOME -> waste of resources
*** bad: uses host tools -> not reproducible [screenshots]
** second approach: app bundles
*** we have the bits, not the source
*** 100% reproducibility, but prevents experimentation
** third approach: can we have our cake and eat it too?
* Guix
** what it is
** example commands
** isolated builds: 100% reproducible
** reproducible *yet* customizable [RepPar paper]
** package variants, personal packages
* HPC & non-root usage (switch to Pjotr here?)
** the problem: guix-daemon runs as root because that's the only way to get repro build envs
** solutions:
*** running guix-daemon as non-root: doesn't work
*** user namespaces: unfortunately not widely available
*** relocation: yay!

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\title{Optimized \& Reproducible HPC Software Deployment}
\subtitle{... with GNU~Guix and free software}
\author{Pjotr Prins\footnote{UMC Utrecht, UTHSC GeneNetwork.org} \& Ludovic Courtès\footnote{Inria}}
\date{\small{FOSDEM, February 2017}}
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\maketitle
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\begin{frame}
\Huge{\textbf{Recipe for a contemporary HPC cluster environment.}}
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\Huge{\#1. Start with an old \& inflexible distro.}
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\Huge{\#2. Add a layer of home-made ``modules''.}
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\uncover<3->{\\\#2d. Tweak build flags for user A.}
\uncover<4->{\\\#2e. New versions are out, rebuild!}
\uncover<5->{\\\#2f. User B unhappy cuz we upgraded. Ignore?}
\uncover<6->{\\...}}
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\Huge{\#3. Spice up with user-built software!}
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\Huge{\textbf{Fixing HPC cluster environments.}}
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\Huge{\textbf{Give up on packaging?}}
\\[1.0cm]
\uncover<2->{\Large{$\rightarrow$ ``app bundles'' (Docker images \& co.)}}
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%% \begin{frame}[plain]
%% \begin{quotation}
%% \noindent
%% \LARGE{``Debian and other distributions are going to be \textbf{that
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%% \end{quotation}
%% \hfill{--- Jos Poortvliet, ownCloud developer}
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%% {\includegraphics[height=\paperheight]{images/docker-security}};
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%% \small{\url{https://www.banyanops.com/blog/analyzing-docker-hub/}}
%% };
%% \node [at=(current page.south west), anchor=south west,
%% text=black, text opacity=1, fill=white]{
%% \small{May 2015}
%% };
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%% \end{frame}
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\tiny{\url{https://www.hpcwire.com/2016/10/20/singularity-containers-easing-scientific-computing}}
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\begin{frame}[plain]{``app bundles'' are headed wrong}
\Large{
\begin{itemize}
\item difficulty to \highlight{compose} software packages
\item wrong \highlight{abstraction level}: image vs. package
\item \highlight{hardly reproducible}: we have the bits, not the
source
\item makes it hard to \highlight{customize \& experiment}
\end{itemize}
}
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\Huge{\textbf{Can we eat it too?}}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\LARGE{
\begin{enumerate}
\item transactional package manager
\item software environment manager
\item APIs \& tools to customize environments
\item packaging tools
\end{enumerate}
}
\end{frame}
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\begin{semiverbatim}
\$ guix package -i gcc-toolchain openmpi hwloc
\textrm{...}
\$ eval `guix package --search-paths`
\textrm{...}
\$ guix package --manifest=my-software.scm
\textrm{...}
\end{semiverbatim}
%% \begin{tikzpicture}[overlay]
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%% fill=guixorange1, text width=3cm,
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%% \textbf{\large{demo}}
%% };
%% \end{tikzpicture}
\end{frame}
%% \setbeamercolor{normal text}{bg=guixdarkgrey,fg=guixred3}
%% \begin{frame}[fragile]
%% \Huge{Want to get started hacking on hwloc?}
%% \\[2cm]
%% \uncover<2->{\Large{A simple matter of installing the deps, right?}}
%% \end{frame}
%% \setbeamercolor{normal text}{bg=white}
%% \begin{frame}[plain]
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%% \end{tikzpicture}
%% \end{frame}
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\begin{frame}[fragile]
%% \frametitle{Bit-Reproducible Builds$^*$}
%% \framesubtitle{$^*$ almost!}
\begin{semiverbatim}
\$ guix build hello
\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}
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\node [at=(current page.south east), anchor=south east,
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\url{https://hal.inria.fr/hal-01161771/en}
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\Huge{Creating package variants at the command line}
\end{frame}
\begin{frame}[fragile]
\begin{semiverbatim}
\$ guix build hwloc \\
\alert<1>{--with-source}=./hwloc-42.0rc1.tar.gz
\textrm{...}
\pause
\$ guix package -i mumps \\
\alert<2>{--with-input}=scotch=pt-scotch
\textrm{...}
\end{semiverbatim}
\end{frame}
\begin{frame}[plain]
\Huge{Your personal packages or variants in
\texttt{GUIX\_PACKAGE\_PATH}!}
\end{frame}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\setbeamercolor{normal text}{bg=guixblue2}
\begin{frame}
\Huge{\textbf{HPC \& non-root usage.}}
\end{frame}
\setbeamercolor{normal text}{fg=white,bg=black}
\begin{frame}[fragile]{}
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text width=35mm, minimum height=4cm,
text centered,
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fill=white, text=black
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tool/.style = {
fill=white, text=black, text width=3cm,
text centered
},
daemon/.style = {
rectangle, text width=50mm, text centered,
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bottom color=guixyellow,
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\node(builders)[builders, text height=5cm]{}
node[fill=black, text=white] at (0, 2) {\large{\textbf{build processes}}}
node[fill=black, text=white] at (0, 1.5) {chroot, separate UIDs}
node[builder] at (-1,-0.5) {\alert{Guile}, make, etc.}
node[builder] at ( 0,-0.5) {\alert{Guile}, make, etc.}
node[builder] at ( 1,-0.5) {\alert{Guile}, make, etc.}; &
\node[tools]{}
node[fill=white, text=black] at (0, 1) {\large{\textbf{Guile Scheme}}}
node[tool] at (0, 0) {\texttt{(guix packages)}}
node(client)[tool] at (0, -1) {\texttt{(guix store)}};
\\
\node(daemon)[daemon]{\large{\textbf{build daemon}}}; &
&
\\
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\end{tikzpicture}
\begin{tikzpicture}[overlay]
\path[very thick, draw=guixorange1]
(client.south) edge [out=-90, in=0, ->] node[below, sloped]{RPCs} (daemon.east);
\path[->, very thick, draw=guixorange1]
(daemon) edge (builders);
\end{tikzpicture}
\end{frame}
\begin{frame}{Allowing for non-root usage}
\Large{
\begin{enumerate}
\setcounter{enumi}{-1}
\item {run build daemon \highlight{as non-root}
\begin{itemize}
\item<2-> not reproducible
\item<2-> prevents use of pre-built binaries
\end{itemize}}
\item {rely on Linux ``\highlight{user namespaces}''
\begin{itemize}
\item<3-> awesome!
\item<3-> ... but support is missing on some systems
\end{itemize}}
\item make binaries \highlight{relocatable}
\end{enumerate}
}
\end{frame}
\setbeamercolor{normal text}{bg=guixblue2}
\begin{frame}
\Huge{\textbf{Relocatable binaries (Pjotr).}}
\end{frame}
\setbeamercolor{normal text}{fg=white,bg=black}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\setbeamercolor{normal text}{bg=guixblue2}
\begin{frame}[plain]
\Huge{\textbf{Status.}}
\end{frame}
\setbeamercolor{normal text}{fg=white,bg=black}
\begin{frame}
\Large{
\begin{itemize}
\item started in 2012
\item \highlight{4,800+ packages}, all free software
\item \highlight{4 architectures}:\\
x86\_64, i686, ARMv7, mips64el
\item binaries at \url{https://hydra.gnu.org}
\item 0.12.0 released in December 2016
\end{itemize}
}
\end{frame}
\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{Utrecht Bioinformatics Center} (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<2-> \emph{more to come!}
\end{itemize}
}
\end{frame}
\setbeamercolor{normal text}{bg=white}
\screenshot[width=.9\paperwidth]{images/openhub-activity}
\screenshot[width=.9\paperwidth]{images/openhub-contributors}
\setbeamercolor{normal text}{bg=black}
\setbeamercolor{normal text}{bg=guixblue2}
\begin{frame}[plain]
\Huge{\textbf{Wrap-up.}}
\end{frame}
\setbeamercolor{normal text}{fg=white,bg=black}
\begin{frame}{Summary}
\Large{
\begin{itemize}
\item Guix supports \highlight{reproducible software environments}
\item ... allows for \highlight{experimentation} through customization
\item relocation allows unprivileged Guix usage in HPC
\end{itemize}
}
\end{frame}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}[plain]
\vfill{
\vspace{2.5cm}
\center{\includegraphics[width=0.2\textwidth]{images/GuixSD}}\\[1.0cm]
\texttt{ludo@gnu.org}\hfill{\alert{\url{https://gnu.org/software/guix/}}}
}
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\begin{frame}{}
\begin{textblock}{12}(2, 8)
\tiny{
Copyright \copyright{} 2010, 2012--2017 Ludovic Courtès \texttt{ludo@gnu.org}.\\[3.0mm]
GNU GuixSD logo, CC-BY-SA 4.0, \url{http://gnu.org/s/guix/graphics}
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{http://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{http://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{http://git.sv.gnu.org/cgit/guix/maintenance.git}.
}
\end{textblock}
\end{frame}
\end{document}
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