02/10: talks: fosdem-2017/hpc: Incorporate Pjotr's part.

[Ludovic Courtès]

civodul pushed a commit to branch master
in repository maintenance.

commit 255fa874b0d9b2195fe93549ec5da10a15f1bef6
Author: Ludovic Courtès <address@hidden>
Date:   Thu Feb 2 23:46:20 2017 +0100

    talks: fosdem-2017/hpc: Incorporate Pjotr's part.
---
 .gitignore                         |    1 +
 talks/fosdem-2017/hpc/outline.org  |    3 +
 talks/fosdem-2017/hpc/section2.tex |  164 ++++++++++++++++++++++++++++++++++++
 talks/fosdem-2017/hpc/talk.tex     |   33 +++++++-
 4 files changed, 197 insertions(+), 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index 824224e..27413cc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -102,3 +102,4 @@
 /talks/fosdem-2017/hpc/talk.snm
 /talks/fosdem-2017/hpc/talk.toc
 /talks/fosdem-2017/hpc/talk.vrb
+/talks/fosdem-2017/hpc/section2.tex.aux
diff --git a/talks/fosdem-2017/hpc/outline.org 
b/talks/fosdem-2017/hpc/outline.org
index 374cbc4..3505152 100644
--- a/talks/fosdem-2017/hpc/outline.org
+++ b/talks/fosdem-2017/hpc/outline.org
@@ -1,5 +1,8 @@
 #+TITLE: Optimized & Reproducible HPC Software Deployment
 
+https://fosdem.org/2017/schedule/event/hpc_deployment_guix/
+Sat. 11:30, H.2213
+
 * current HPC software environments are broken
 ** distros are old and inflexible, not upgraded
 ** thus, sysadmins write their own modules
diff --git a/talks/fosdem-2017/hpc/section2.tex 
b/talks/fosdem-2017/hpc/section2.tex
new file mode 100644
index 0000000..32aad77
--- /dev/null
+++ b/talks/fosdem-2017/hpc/section2.tex
@@ -0,0 +1,164 @@
+%% \begin{frame}{The stated problem}
+%% \begin{itemize}
+%% \item HPC environments generally run old software (kernel, glibc, build 
tools)
+%% \item Newer software is installed through other routes
+%% \item Software targeting architectures such as Intel PHI require cross 
compilation
+%% \end{itemize}
+%% \end{frame}
+
+%% \begin{frame}{Supercomputer}
+%% \begin{itemize}
+%% \item \emph{Propriety} Intel/NVIDIA/Oracle software is up-to-date
+%% \item Python, R, gcc and llvm tend to be out of date
+%% \item Modern languages Dlang, Go, Julia are not supported
+%% \item Also Openblas and OpenCL libraries may not be supported
+%% \item True on most HPC systems
+%% \end{itemize}
+%% \end{frame}
+
+%% \begin{frame}{FOSS}
+%% \begin{itemize}
+%% \item We are FOSS people - we want recent FOSS tools - how do we cope?
+%% \item Docker? Brew? Conda? From source?
+%% \item And, yes, we want reproducibility too
+%% \end{itemize}
+%% \end{frame}
+
+%% \begin{frame}{GNU Guix on HPC}
+%% \begin{itemize}
+%% \item Guix installs in a root mounted /gnu/store ...
+%% \item Allow for running a privileged Guix daemon?
+%% \item Perhaps allow for a mounted /gnu/store?
+%% \item If not, what to do?
+%% \item Answer: relocatable Guix
+%% \end{itemize}
+%% \end{frame}
+
+\begin{frame}[fragile]{Insight 1}
+  The first key insight: Guix store paths provide unique fingerprints:
+
+\small
+\begin{verbatim}
+/gnu/store/m9vxvhdj691bq1f85lpflvnhcvrdilih-glibc-2.23/lib/libc.so
+\end{verbatim}
+\end{frame}
+
+\begin{frame}[fragile]{Linked libraries}
+  \small
+ldd `which ldc2`
+\begin{verbatim}
+libconfig.so.9  /gnu/store/1v4an...-libconfig-1.5/lib/libconfig.so.9
+librt.so.1      /gnu/store/m9vxv...-glibc-2.23/lib/librt.so.1
+libdl.so.2      /gnu/store/m9vxv...-glibc-2.23/lib/libdl.so.2
+libpthread.so.0 /gnu/store/m9vxv...-glibc-2.23/lib/libpthread.so.0
+libz.so.1       /gnu/store/5992i...-zlib-1.2.8/lib/libz.so.1
+libm.so.6       /gnu/store/m9vxv...-glibc-2.23/lib/libm.so.6
+libstdc++.so.6  /gnu/store/9nifw...-gcc-4.9.3-lib/lib/libstdc++.so.6
+libgcc_s.so.1   /gnu/store/9nifw...-gcc-4.9.3-lib/lib/libgcc_s.so.1
+libc.so.6       /gnu/store/m9vxv...-glibc-2.23/lib/libc.so.6
+                /gnu/store/m9vxv...-glibc-2.23/lib/ld-linux-x86-64.so.2
+\end{verbatim}
+\end{frame}
+
+\begin{frame}{Relocate}
+\begin{itemize}
+\item Guix binaries have unique fingerprints for PATHs
+\item Replace these with the target prefix
+\item Only dependency is the kernel
+\end{itemize}
+\end{frame}
+
+
+\begin{frame}[fragile]{After relocation}
+  \small
+  ldd $\sim$/opt/ldc-test/ldc-1.1.0-pk9rkm4zvdp6pglam7s2/bin/ldc2
+\begin{verbatim}
+qlibconfig.so.9  ~/opt/ldc-test/libconfig-1.5-1v4anv1.../lib/libconfig.so.9
+librt.so.1      ~/opt/ldc-test/glibc-2.23-m9vxvh.../lib/librt.so.1
+libdl.so.2      ~/opt/ldc-test/glibc-2.23-m9vxvh.../lib/libdl.so.2
+libpthread.so.0 ~/opt/ldc-test/glibc-2.23-m9vxvh.../lib/libpthread.so.0
+libz.so.1       ~/opt/ldc-test/zlib-1.2.8-5992iq1.../lib/libz.so.1
+libm.so.6       ~/opt/ldc-test/glibc-2.23-m9vxvh.../lib/libm.so.6
+libstdc++.so.6  ~/opt/ldc-test/gcc-4.9.3-lib-9nifwk7.../lib/libstdc++.so.6
+libgcc_s.so.1   ~/opt/ldc-test/gcc-4.9.3-lib-9nifwk7.../lib/libgcc_s.so.1
+libc.so.6       ~/opt/ldc-test/glibc-2.23-m9vxvh.../lib/libc.so.6
+                ~/opt/ldc-test/glibc-2.23-m9vxvh.../lib/ld-linux-x86-64.so.2
+\end{verbatim}
+\end{frame}
+
+\begin{frame}{What really happened here?}
+
+  \begin{itemize}
+  \item All Guix packages are isolated in the store
+  \item Path is a fingerprint, e.g. 
\texttt{/gnu/store/m9vxvhdj691bq1f85lpflvnhcvrdilih-glibc-2.23}
+  \item Scan all files and replace fingerprints with relative path 
\texttt{$\sim$/opt/ldc-test/glibc-2.23-m9vxvhdj691bq1f85lpf}
+  \item First attempt by using Eelco Dolstra's Patchelf tool worked for shared 
libs by rewriting \texttt{RPATH} in binaries
+  \end{itemize}
+\end{frame}
+
+\begin{frame}{Other files}
+  \begin{itemize}
+  \item Text files that reference the store can be rewritten (Ruby, Perl, bash 
scripts)
+  \item Some formats are not zero-terminated (compiled Python and JVM files)
+  \item Also in ELF files there are references that are not zero-terminated
+  \item Solution: keep the file path at exactly the same length and patch all
+  \end{itemize}
+\end{frame}
+
+\begin{frame}[fragile]{Insight 2}
+  The second key insight: if a path gets rewritten with the exact same size
+  string it will always work (unless there is encryption or some CRC checking)
+
+\small
+\begin{verbatim}
+/gnu/store/m9vxvhdj691bq1f85lpflvnhcvrdilih-glibc-2.23/lib/libc.so
+/home/user/opt/ldc-test/glibc-2.23-m9vxvhdj691bq1f851p/lib/libc.so
+\end{verbatim}
+\end{frame}
+
+
+\begin{frame}{Same size patching}
+  \begin{enumerate}
+  \item start from store path, e.g.
+    \texttt{/gnu/store/m9vxvhdj691bq1f85lpflvnhcvrdilih-glibc-2.23}
+  \item reverse the contents
+    \texttt{/gnu/store/glibc-2.23-m9vxvhdj691bq1f85lpflvnhcvrdilih}
+  \item overwrite with prefix and shorten the HASH value to match the same size
+  \texttt{/home/user/opt/ldc-test/glibc-2.23-m9vxvhdj691bq1f851p}
+  \item and replace in all files
+  \end{enumerate}
+\end{frame}
+
+\begin{frame}[fragile]{Example}
+  So, store path
+  \small
+\begin{verbatim}
+    /gnu/store/m9vxvhdj691bq1f85lpflvnhcvrdilih-glibc-2.23/bin/ldc2
+
+    prefix /home/usr/opt/ldc-test/ becomes
+    /home/user/opt/ldc-test/glibc-2.23-m9vxvhdj691bq1f851p/bin/ldc2
+
+    prefix /usr/local/share/ldc-1.1.0/ becomes
+    /usr/local/share/ldc-1.1.0/glibc-2.23-m9vxvhdj691bq1f8/bin/ldc2
+\end{verbatim}
+Note: prefix can be up to $\sim 40$ letters long
+\end{frame}
+
+\begin{frame}{So far\ldots}
+  Successfully compiled and run
+\begin{itemize}
+\item ldc2 1.1.0: the LLVM D compiler
+\item ruby 2.3.0: with ssl and nokogiri
+\item sambamba: tool used in many sequencing HPCs around the world
+\item more to come, including OpenCL, R, Python and Julia
+\end{itemize}
+\end{frame}
+
+\begin{frame}{Cross compile}
+\begin{itemize}
+\item Install compilers that can cross compile binaries
+\item LLVM can output C code
+\item Provide GNU Guix packages for Intel PHI and NVIDIA TESLA
+\item GNU Guix has elegant support for different targets, including a build 
farm for ARM, ...
+\end{itemize}
+\end{frame}
diff --git a/talks/fosdem-2017/hpc/talk.tex b/talks/fosdem-2017/hpc/talk.tex
index d91e010..50eb0ae 100644
--- a/talks/fosdem-2017/hpc/talk.tex
+++ b/talks/fosdem-2017/hpc/talk.tex
@@ -486,10 +486,12 @@
 
 \setbeamercolor{normal text}{bg=guixblue2}
 \begin{frame}
-  \Huge{\textbf{Relocatable binaries (Pjotr).}}
+  \Huge{\textbf{Relocatable binaries.}}
 \end{frame}
 \setbeamercolor{normal text}{fg=white,bg=black}
 
+\input{section2.tex}
+
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \setbeamercolor{normal text}{bg=guixblue2}
 \begin{frame}[plain]
@@ -540,31 +542,54 @@
 \end{frame}
 \setbeamercolor{normal text}{fg=white,bg=black}
 
+\begin{frame}{Future}
+  Implications carry beyond HPC
+  \\
+  \begin{itemize}
+  \item Automated builds with testing for different architectures
+  \item Repository of binary packages
+  \item One-click installs: download and run \texttt{install.sh}
+  \item Ship software easily
+  \item Talking about a holy grail\ldots
+  \end{itemize}
+\end{frame}
+
 \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
+    \item relocation allows \highlight{unprivileged} Guix usage in HPC
     \end{itemize}
   }
 \end{frame}
 
+\begin{frame}{Acknowledgements}
+\small
+\begin{itemize}
+\item Roel Janssen (@roelj), Dennis Mungai (@Brainiarc7), and Frederick 
Muriithi (@fredmanglis) for helping with packaging D compilers, sambamba, Ruby 
packages, OpenCL etc.
+%\item GNU Guix project leaders Ludovic Court\`{e}s and Ricardo Wurmus
+\item The GNU and GNU Guix communities (many, many talented individuals)
+\end{itemize}
+\end{frame}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[plain]
 
 \vfill{
   \vspace{2.5cm}
   \center{\includegraphics[width=0.2\textwidth]{images/GuixSD}}\\[1.0cm]
-  address@hidden://gnu.org/software/guix/}}}
+  %% address@hidden
+  \center{\alert{\url{https://gnu.org/software/guix/}}}
+  \\
 }
-
 \end{frame}
 
 \begin{frame}{}
 
   \begin{textblock}{12}(2, 8)
     \tiny{
+      Copyright \copyright{} 2017 Pjotr Prins\\
       Copyright \copyright{} 2010, 2012--2017 Ludovic Courtès address@hidden
       GNU GuixSD logo, CC-BY-SA 4.0, \url{http://gnu.org/s/guix/graphics}