#+TITLE:  Writing a Reproducible Article
#+AUTHOR: Luka Stanisic and Arnaud Legrand 
#+LaTeX_HEADER: \institute{MESCAL team, LIG, Univ. of Grenoble}
#+DATE:   COMPAS, 22.04.2014
#+LANGUAGE:  en
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* Intro
*** Context
**** 								    :B_block:
     :PROPERTIES:
     :BEAMER_env: block
     :END:
    - HPC applications nowadays use both multi-core CPUs and GPUs
    - Managing efficiently computation execution and data transfer is extremely complex
    - Need for portable performance $\leadsto$ *Runtime* system
# based on the task programming paradigm
**** 								    :B_block:
     :PROPERTIES:
     :BEAMER_env: block
     :BEAMER_ACT: <2->
     :END:
    Many configuration parameters:
      1. Task granularity
      2. Scheduling strategies
      3. Application structure
    Emerging challenges:
      1. Finding optimal combination of parameters for a given machine
      2. Evaluate configurations on a wide variety of platforms
      3. Quickly identify performance issues (e.g., bottlenecks) 

    Possible solution: *Simulation*
*** Our proposal
**** StarPU
     Dynamic runtime for hybrid architectures. StarPU execution consists in scheduling a graph of tasks with data dependencies on the different computing resources
**** Simgrid
     Versatile simulator for distributed systems
**** Implementation:					    :B_ignoreheading:
     :PROPERTIES:
     :BEAMER_env: ignoreheading
     :END:
Implementation:
    - StarPU applications and runtime are *emulated*
    - All operations related to thread synchronization, actual computations and data transfer are *simulated*
    - Control part of StarPU is modified to dynamically inject computation and communication tasks into the simulator
    - StarPU calibration and platform description is used by Simgrid

*** Results
 #+BEGIN_LaTeX
    \begin{overlayarea}{\linewidth}{8cm}
    \begin{center}
    \only<1>{
      \vspace{.7cm}
      \includegraphics<1>[width=.95\linewidth]{figures_presentation/recap_all-crop.pdf}
    }
    \includegraphics<2>[width=.95\linewidth]{figures_presentation/comparing_paje2-crop.png}
    \end{center}
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    #+LaTeX: \only<3>{
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**** 							    :B_ignoreheading:
     :PROPERTIES:
     :BEAMER_env: ignoreheading
     :END:
     - Works fine *now*, but coming to this point was not easy
     - We had to do many iterations of:
       1. Running *complex* *beta* code on *several* not always *dedicated* machines
       2. Comparing with simulations, *debugging*, *understanding*, *remodeling* and going back to step 1 until not satisfied

\medskip

**** 							    :B_ignoreheading:
     :PROPERTIES:
     :BEAMER_env: ignoreheading
     :END:
     - With good results, we decided to make a reproducible article
       1. From outside it looks like any other pdf paper
       2. From inside ...

**** 							    :B_ignoreheading:
     :PROPERTIES:
     :BEAMER_env: ignoreheading
     :END:

\medskip
\medskip

     I will try to convince you that our article is not only *reproducible* but also *readable* and *understandable*!

     #+BEGIN_CENTER
     http://dx.doi.org/10.6084/m9.figshare.928338     
     #+END_CENTER

    #+LaTeX: }\end{overlayarea}
*** Reproducible Research
#+BEGIN_LaTeX
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\hbox{\hspace{-.1\linewidth}\includegraphics[width=1.2\linewidth,height=9cm]{iceberg/iceberg.pdf}}
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 \begin{center}
  \begin{minipage}{.75\linewidth}
  \begin{block}{}
\smallskip
    Requires a \textbf{daily usage of a labbook} (org, git/svn, ...)
\smallskip
  \end{block}
  \end{minipage}
 \end{center}
}
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* Emacs demonstration						   :noexport:
** Reproducible Article: 
- [ ] Doc structure
- [ ] Download data 
- [ ] Parse/Filter/Convert
- [ ] Load R
- [ ] Change figures
- [ ] Export to .pdf
** Reproducible Experimentation	
- [ ] Data+metadata
- [ ] Labbook