Initial commit

beamercolorthemetrex.sty

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+\mode<presentation>
+
+% Settings
+\setbeamercolor*{title page header}{fg=red!80!black}
+\setbeamercolor*{author}{fg=blue!50!cyan!80!black}
+\setbeamercolor*{institute}{fg=blue!80!cyan!50!black}
+\setbeamercolor*{date}{fg=blue!80!cyan!50!black}
+
+\setbeamercolor*{item}{fg=blue!50!cyan!80!black}
+\setbeamertemplate{items}[square]
+\setbeamertemplate{sections/subsections in toc}[square]
+
+\setbeamercolor{block title}{fg=white,bg=blue!50!cyan!80!black}
+%\setbeamercolor{block body}{bg=block title.bg!30!bg}
+
+% alertblock
+\setbeamercolor{block title alerted}{fg=white,bg=red!80!black}
+%\setbeamercolor{block body alerted}{bg=block title alerted.bg!10!bg}
+
+% exampleblock
+\setbeamercolor{block title example}{fg=white,bg=blue!50!cyan!80!black}
+%\setbeamercolor{block body example}{bg=white}
+
+\mode
+<all>

beamerfontthemetrex.sty

@@ -0,0 +1,313 @@
+%%
+%% This is file `beamerfontthemetrex.sty',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% beamerfontthemetrex.dtx  (with options: `package')
+%% ---------------------------------------------------------------------------
+%% Copyright 2015 Matthias Vogelgesang and the LaTeX community. A full list of
+%% contributors can be found at
+%% 
+%%     https://github.com/matze/mtheme/graphs/contributors
+%% 
+%% and the original template was based on the HSRM theme by Benjamin Weiss.
+%% 
+%% This work is licensed under a Creative Commons Attribution-ShareAlike 4.0
+%% International License (https://creativecommons.org/licenses/by-sa/4.0/).
+%% ---------------------------------------------------------------------------
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{beamerfontthemetrex}[2017/01/23 trex font theme]
+\RequirePackage{etoolbox}
+\RequirePackage{ifxetex}
+\RequirePackage{ifluatex}
+\RequirePackage{pgfopts}
+\ifboolexpr{bool {xetex} or bool {luatex}}{
+  \@ifpackageloaded{fontspec}{
+    \PassOptionsToPackage{no-math}{fontspec}
+  }{
+    \RequirePackage[no-math]{fontspec}
+  }
+  \newcounter{fontsnotfound}
+  \newcommand{\checkfont}[1]{%
+    \suppressfontnotfounderror=1%
+    \font\x = "#1" at 10pt
+    \selectfont
+    \ifx\x\nullfont%
+      \stepcounter{fontsnotfound}%
+    \fi%
+    \suppressfontnotfounderror=0%
+  }
+
+  \newcommand{\iffontsavailable}[3]{%
+    \setcounter{fontsnotfound}{0}%
+    \expandafter\forcsvlist\expandafter%
+    \checkfont\expandafter{#1}%
+    \ifnum\value{fontsnotfound}=0%
+      #2%
+    \else%
+      #3%
+    \fi%
+  }
+  \iffontsavailable{Fira Sans Light,%
+                    Fira Sans Light Italic,%
+                    Fira Sans,%
+                    Fira Sans Italic}%
+  {%
+    \setsansfont[ItalicFont={Fira Sans Light Italic},%
+                 BoldFont={Fira Sans},%
+                 BoldItalicFont={Fira Sans Italic}]%
+                {Fira Sans Light}%
+  }{%
+    \iffontsavailable{Fira Sans Light OT,%
+                      Fira Sans Light Italic OT,%
+                      Fira Sans OT,%
+                      Fira Sans Italic OT}%
+    {%
+      \setsansfont[ItalicFont={Fira Sans Light Italic OT},%
+                   BoldFont={Fira Sans OT},%
+                   BoldItalicFont={Fira Sans Italic OT}]%
+                  {Fira Sans Light OT}%
+    }{%
+      \PackageWarning{beamerthemetrex}{%
+        Could not find Fira Sans fonts%
+      }
+    }
+  }
+  \iffontsavailable{Fira Mono, Fira Mono Bold}{%
+    \setmonofont[BoldFont={Fira Mono Medium}]{Fira Mono}%
+  }{%
+    \iffontsavailable{Fira Mono OT, Fira Mono Bold OT}{%
+      \setmonofont[BoldFont={Fira Mono Medium OT}]{Fira Mono OT}%
+    }{%
+      \PackageWarning{beamerthemetrex}{%
+        Could not find Fira Mono fonts%
+      }
+    }
+  }
+  \AtBeginEnvironment{tabular}{%
+    \addfontfeature{Numbers={Monospaced}}%
+  }
+}{%
+  \PackageWarning{beamerthemetrex}{%
+    You need to compile with XeLaTeX or LuaLaTeX to use the Fira fonts%
+  }
+}
+\setbeamerfont{title}{size=\Large,%
+                      series=\bfseries}
+\setbeamerfont{author}{size=\small}
+\setbeamerfont{date}{size=\small}
+\setbeamerfont{section title}{size=\Large,%
+                              series=\bfseries}
+\setbeamerfont{block title}{size=\normalsize,%
+                            series=\bfseries}
+\setbeamerfont{block title alerted}{size=\normalsize,%
+                                    series=\bfseries}
+\setbeamerfont*{subtitle}{size=\large}
+\setbeamerfont{frametitle}{size=\large,%
+                           series=\bfseries}
+\setbeamerfont{caption}{size=\small}
+\setbeamerfont{caption name}{series=\bfseries}
+\setbeamerfont{description item}{series=\bfseries}
+\setbeamerfont{page number in head/foot}{size=\scriptsize}
+\setbeamerfont{bibliography entry author}{size=\normalsize,%
+                                          series=\normalfont}
+\setbeamerfont{bibliography entry title}{size=\normalsize,%
+                                         series=\bfseries}
+\setbeamerfont{bibliography entry location}{size=\normalsize,%
+                                            series=\normalfont}
+\setbeamerfont{bibliography entry note}{size=\small,%
+                                        series=\normalfont}
+\setbeamerfont{standout}{size=\Large,%
+                         series=\bfseries}
+\pgfkeys{
+  /trex/font/titleformat title/.cd,
+    .is choice,
+    regular/.code={%
+      \let\trex@titleformat\@empty%
+      \setbeamerfont{title}{shape=\normalfont}%
+    },
+    smallcaps/.code={%
+      \let\trex@titleformat\@empty%
+      \setbeamerfont{title}{shape=\scshape}%
+    },
+    allsmallcaps/.code={%
+      \let\trex@titleformat\lowercase%
+      \setbeamerfont{title}{shape=\scshape}%
+      \PackageWarning{beamerthemetrex}{%
+        Be aware that titleformat title=allsmallcaps can lead to problems%
+      }
+    },
+    allcaps/.code={%
+      \let\trex@titleformat\uppercase%
+      \setbeamerfont{title}{shape=\normalfont}
+      \PackageWarning{beamerthemetrex}{%
+        Be aware that titleformat title=allcaps can lead to problems%
+      }
+    },
+}
+\pgfkeys{
+  /trex/font/titleformat subtitle/.cd,
+    .is choice,
+    regular/.code={%
+      \let\trex@subtitleformat\@empty%
+      \setbeamerfont{subtitle}{shape=\normalfont}%
+    },
+    smallcaps/.code={%
+      \let\trex@subtitleformat\@empty%
+      \setbeamerfont{subtitle}{shape=\scshape}%
+    },
+    allsmallcaps/.code={%
+      \let\trex@subtitleformat\lowercase%
+      \setbeamerfont{subtitle}{shape=\scshape}%
+      \PackageWarning{beamerthemetrex}{%
+        Be aware that titleformat subtitle=allsmallcaps can lead to problems%
+      }
+    },
+    allcaps/.code={%
+      \let\trex@subtitleformat\uppercase%
+      \setbeamerfont{subtitle}{shape=\normalfont}%
+      \PackageWarning{beamerthemetrex}{%
+        Be aware that titleformat subtitle=allcaps can lead to problems%
+      }
+    },
+}
+\pgfkeys{
+  /trex/font/titleformat section/.cd,
+    .is choice,
+    regular/.code={%
+      \let\trex@sectiontitleformat\@empty%
+      \setbeamerfont{section title}{shape=\normalfont}%
+    },
+    smallcaps/.code={%
+      \let\trex@sectiontitleformat\@empty%
+      \setbeamerfont{section title}{shape=\scshape}%
+    },
+    allsmallcaps/.code={%
+      \let\trex@sectiontitleformat\MakeLowercase%
+      \setbeamerfont{section title}{shape=\scshape}%
+      \PackageWarning{beamerthemetrex}{%
+        Be aware that titleformat section=allsmallcaps can lead to problems%
+      }
+    },
+    allcaps/.code={%
+      \let\trex@sectiontitleformat\MakeUppercase%
+      \setbeamerfont{section title}{shape=\normalfont}%
+      \PackageWarning{beamerthemetrex}{%
+        Be aware that titleformat section=allcaps can lead to problems%
+      }
+    },
+}
+\pgfkeys{
+  /trex/font/titleformat frame/.cd,
+    .is choice,
+    regular/.code={%
+      \let\trex@frametitleformat\@empty%
+      \setbeamerfont{frametitle}{shape=\normalfont}%
+    },
+    smallcaps/.code={%
+      \let\trex@frametitleformat\@empty%
+      \setbeamerfont{frametitle}{shape=\scshape}%
+    },
+    allsmallcaps/.code={%
+      \let\trex@frametitleformat\MakeLowercase%
+      \setbeamerfont{frametitle}{shape=\scshape}%
+      \PackageWarning{beamerthemetrex}{%
+        Be aware that titleformat frame=allsmallcaps can lead to problems%
+      }
+    },
+    allcaps/.code={%
+      \let\trex@frametitleformat\MakeUppercase%
+      \setbeamerfont{frametitle}{shape=\normalfont}
+      \PackageWarning{beamerthemetrex}{%
+        Be aware that titleformat frame=allcaps can lead to problems%
+      }
+    },
+}
+\pgfkeys{
+  /trex/font/.cd,
+  titleformattitle/.code=\pgfkeysalso{titleformat title=#1},
+  titleformatsubtitle/.code=\pgfkeysalso{titleformat subtitle=#1},
+  titleformatsection/.code=\pgfkeysalso{titleformat section=#1},
+  titleformatframe/.code=\pgfkeysalso{titleformat frame=#1},
+}
+\newcommand{\trex@font@setdefaults}{
+  \pgfkeys{/trex/font/.cd,
+    titleformat title=regular,
+    titleformat subtitle=regular,
+    titleformat section=regular,
+    titleformat frame=regular,
+  }
+}
+\def\trex@titleformat#1{#1}
+\def\trex@subtitleformat#1{#1}
+\def\trex@sectiontitleformat#1{#1}
+\def\trex@frametitleformat#1{#1}
+\patchcmd{\beamer@title}%
+  {\def\inserttitle{#2}}%
+  {\def\inserttitle{\trex@titleformat{#2}}}%
+  {}%
+  {\PackageError{beamerfontthemetrex}{Patching title failed}\@ehc}
+\patchcmd{\beamer@subtitle}%
+  {\def\insertsubtitle{#2}}%
+  {\def\insertsubtitle{\trex@subtitleformat{#2}}}%
+  {}%
+  {\PackageError{beamerfontthemetrex}{Patching subtitle failed}\@ehc}
+\patchcmd{\sectionentry}
+  {\def\insertsectionhead{#2}}
+  {\def\insertsectionhead{\trex@sectiontitleformat{#2}}}
+  {}
+  {\PackageError{beamerfontthemetrex}{Patching section title failed}\@ehc}
+\@tempswafalse
+\patchcmd{\beamer@section}
+  {\def\insertsectionhead{\hyperlink{Navigation\the\c@page}{#1}}}
+  {\def\insertsectionhead{\hyperlink{Navigation\the\c@page}{%
+    \trex@sectiontitleformat{#1}}}}
+  {\@tempswatrue}
+  {}
+\patchcmd{\beamer@section}
+  {\protected@edef\insertsectionhead{\noexpand\hyperlink{Navigation\the\c@page}{#1}}}
+  {\protected@edef\insertsectionhead{\noexpand\hyperlink{Navigation\the\c@page}{%
+    \noexpand\trex@sectiontitleformat{#1}}}}
+  {\@tempswatrue}
+  {}
+\if@tempswa\else
+  \PackageError{beamerfontthemetrex}{Patching section title failed}\@ehc
+\fi
+\@tempswafalse
+\patchcmd{\beamer@subsection}
+  {\def\insertsubsectionhead{\hyperlink{Navigation\the\c@page}{#1}}}
+  {\def\insertsubsectionhead{\hyperlink{Navigation\the\c@page}{%
+    \trex@sectiontitleformat{#1}}}}
+  {\@tempswatrue}
+  {}
+\patchcmd{\beamer@subsection}
+  {\protected@edef\insertsubsectionhead{\noexpand\hyperlink{Navigation\the\c@page}{#1}}}
+  {\protected@edef\insertsubsectionhead{\noexpand\hyperlink{Navigation\the\c@page}{%
+    \noexpand\trex@sectiontitleformat{#1}}}}
+  {\@tempswatrue}
+  {}
+\if@tempswa\else
+  \PackageError{beamerfontthemetrex}{Patching section title failed}\@ehc
+\fi
+\patchcmd{\beamer@@frametitle}
+  {{%
+      \gdef\insertframetitle{{#2\ifnum\beamer@autobreakcount>0\relax{}\space%
+      \usebeamertemplate*{frametitle continuation}\fi}}%
+    \gdef\beamer@frametitle{#2}%
+    \gdef\beamer@shortframetitle{#1}%
+    }}
+  {{%
+      \gdef\insertframetitle{{\trex@frametitleformat{#2}\ifnum%
+      \beamer@autobreakcount>0\relax{}\space%
+      \usebeamertemplate*{frametitle continuation}\fi}}%
+    \gdef\beamer@frametitle{#2}%
+    \gdef\beamer@shortframetitle{#1}%
+    }}
+  {}
+  {\PackageError{beamerfontthemetrex}{Patching frame title failed}\@ehc}
+\trex@font@setdefaults
+\ProcessPgfPackageOptions{/trex/font}
+\endinput
+%%
+%% End of file `beamerfontthemetrex.sty'.

beamerinnerthemetrex.sty

@@ -0,0 +1,53 @@
+\mode<presentation>
+
+\setbeamertemplate{background}{
+\ifnum\thepage>1
+\includegraphics[height=\paperheight]{beamerbackgroundtrex.png}
+\else
+\includegraphics[height=\paperheight]{beamertitletrex.png}
+\fi
+}
+
+% Title page
+\defbeamertemplate*{title page}{trex}[1][]
+{
+   \vskip3cm%
+    \begin{beamercolorbox}[wd=6.cm,leftskip=-0.5cm,#1]{title page header}
+      \usebeamerfont{title}\inserttitle\par%
+    \end{beamercolorbox}%
+    \vskip0.2cm%
+    \begin{beamercolorbox}[wd=6.cm,leftskip=-0.5cm,#1]{author}
+      \usebeamerfont{author}\insertauthor%
+    \end{beamercolorbox}
+     \vskip0.3cm%
+    \begin{beamercolorbox}[wd=6.cm,leftskip=-0.5cm,#1]{date}
+      \usebeamerfont{author}\insertdate%
+    \end{beamercolorbox}
+     \vskip0.3cm%
+    \begin{beamercolorbox}[wd=7.cm,leftskip=-0.5cm,#1]{institute}
+      \usebeamerfont{author}{\tiny \insertinstitute}%
+    \end{beamercolorbox}
+  \vfill
+}
+
+% Section page
+\defbeamertemplate*{section page}{trex}{
+  \centering
+  \begin{minipage}{22em}
+    \raggedright
+    \usebeamercolor[fg]{section title}
+    \usebeamerfont{section title}
+    \insertsectionhead\\[-1ex]
+    \par
+    \ifx\insertsubsectionhead\@empty\else%
+      \usebeamercolor[fg]{subsection title}%
+      \usebeamerfont{subsection title}%
+      \insertsubsectionhead
+    \fi
+  \end{minipage}
+  \par
+  \vspace{\baselineskip}
+}
+
+
+\mode<all>

beamerouterthemetrex.sty

@@ -0,0 +1,20 @@
+\mode<presentation>
+
+% Frame title
+\defbeamertemplate*{frametitle}{trex}[1][]
+{
+ \begin{beamercolorbox}[wd=\paperwidth,ht=0.95cm]{frametitle} 
+ \begin{tikzpicture}
+% \useasboundingbox[fill=white](0,0) rectangle(\the\paperwidth,1.);
+%\fill[red!80!black] (0,0) rectangle(2.95,1.);
+%\fill[blue!50!cyan!80!black] (3.05,0) rectangle(\the\paperwidth,1.);
+%\fill[white!50] (3.05,0) rectangle(\the\paperwidth,1.);
+  \useasboundingbox[](0,0) rectangle(\the\paperwidth,1.);
+  \node[anchor=east, white,font=\large] at
+  (\paperwidth,0.25){\insertframetitle \phantom{m}};
+ \end{tikzpicture}
+ \end{beamercolorbox}
+}
+
+\mode<all>
+

beamerthemetrex.sty

@@ -0,0 +1,38 @@
+\mode<presentation>
+
+
+% Requirement
+\RequirePackage{tikz}
+
+% Settings
+\useinnertheme{trex}
+\useoutertheme{trex}
+\usecolortheme{trex}
+\usefonttheme{trex}
+
+
+% we remove the navigation symbols and define blocks aspect.
+\setbeamertemplate{navigation symbols}{}
+\setbeamertemplate{blocks}[rounded][shadow=true]
+
+\AtBeginSection[]{%
+    \begin{frame}[plain]
+        \usebeamertemplate{section page}
+    \end{frame}
+}
+
+\setbeamertemplate{footline}{
+    \vspace{0.6cm}
+  \hbox{%
+  \begin{beamercolorbox}[wd=.9\paperwidth,ht=2.25ex,dp=1ex,right]{date in head/foot}%
+    \usebeamercolor[fg]{block title}%
+\ifnum\thepage>1
+    \thepage / \inserttotalframenumber\hspace*{2ex} % old version
+\fi
+   %\insertframenumber{} \hspace*{2ex} % new version without total frames
+  \end{beamercolorbox}}%
+  \vskip0pt%
+}
+
+
+\mode<all>

parallelism_scemama.org

@@ -0,0 +1,148 @@
+#+TITLE: Fundamentals of parallelization
+#+DATE: 23-24/11/2021
+#+AUTHOR: Anthony Scemama
+
+#+LaTeX_HEADER: \institute{Lab. Chimie et Physique Quantiques, IRSAMC, UPS/CNRS, Toulouse (France)}
+#+LATEX_CLASS: beamer
+#+LaTeX_CLASS_OPTIONS:[aspectratio=169]
+#+BEAMER_THEME: trex
+#+LaTeX_HEADER: \usepackage{minted}
+#+LaTeX_HEADER: \usemintedstyle{emacs}
+#+LaTeX_HEADER: \newminted{f90}{fontsize=\footnotesize}
+#+LaTeX_HEADER: \usepackage[utf8]{inputenc}
+#+LaTeX_HEADER: \usepackage[T1]{fontenc}
+#+LaTeX_HEADER: \usepackage{hyperref}
+#+LaTeX_HEADER: \usepackage{mathtools}
+#+LaTeX_HEADER: \usepackage{physics}
+#+LaTeX_HEADER: \definecolor{darkgreen}{rgb}{0.,0.6,0.}
+#+LaTeX_HEADER: \definecolor{darkblue}{rgb}{0.,0.2,0.7}
+#+LaTeX_HEADER: \definecolor{darkred}{rgb}{0.6,0.1,0.1}
+#+LaTeX_HEADER: \definecolor{darkpink}{rgb}{0.7,0.0,0.7}
+#+EXPORT_EXCLUDE_TAGS: noexport
+
+#+startup: beamer
+#+options: H:2
+
+
+* Supercomputers
+
+  
+* Fundamentals of parallelization
+  
+  
+** Introduction
+   
+*** Definitions
+    - Concurrency :: Running multiple computations at the same time.
+    - Parallelism :: Running multiple computations *on different execution units*.
+
+      
+*** Multiple levels
+
+    | *Distributed*       | Multiple machines                  |
+    | *Shared memory*     | Single machine, multiple CPU cores |
+    | *Hybrid*            | With accelerators (GPUs, ...)      |
+    | *Instruction-level* | Superscalar processors             |
+    | *Bit-level*         | Vectorization                      |
+
+All levels of parallelism can be exploited in the same code,
+but every problem is not parallelizable at all levels.
+                                                                                                                              
+
+
+     
+   
+** Data movement
+
+   
+* OpenMP
+
+* Message Passing Interface (MPI)
+
+
+
+* Export                                                           :noexport:
+  #+BEGIN_SRC elisp :output none
+(setq org-latex-listings 'minted)
+(setq org-latex-custom-lang-environments
+      '(
+	(f90 "fortran")
+      ))
+(setq org-latex-minted-options
+      '(("frame" "lines")
+	("fontsize" "\\scriptsize")
+	("linenos" "")))
+(setq org-latex-to-pdf-process
+      '("pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
+	"pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
+	"pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"))
+(org-beamer-export-to-pdf)
+  #+END_SRC
+
+  #+RESULTS:
+  : /home/scemama/MEGA/TEX/Cours/TCCM/TCCM2022/Parallelism/parallelism_scemama.pdf
+
+
+  
+* Figures                                                          :noexport:
+
+  #+BEGIN_SRC dot :output file :file interfaces.png
+digraph G {
+  QP [label="Quantum Package"];
+  DM [label="Density matrices"];
+  QMCCHEM [label="QMC=Chem"];
+  Turbo   [label="TurboRVB"];
+  QP -> FCIDUMP;
+  FCIDUMP -> NECI;
+  NECI -> DM [style="dotted"];
+  NECI -> QMCCHEM [style="dotted"] ;
+  QP -> QMCCHEM;
+  QP -> CHAMP;
+  QP -> DM [style="dotted"];
+  QP -> Turbo [style="dotted"];
+  NECI -> Turbo [style="dotted"];
+  NECI -> CHAMP [style="dotted"];
+  QMCCHEM -> DM [style="dotted"];
+  CHAMP -> DM [style="dotted"];
+  Turbo -> DM [style="dotted"];
+  DM -> GammCor;
+
+  QP -> QML [style="dotted"];
+  NECI -> QML [style="dotted"];
+  QMCCHEM -> QML [style="dotted"];
+  CHAMP -> QML [style="dotted"];
+  Turbo -> QML [style="dotted"];
+  GammCor -> QML  [style="dotted"];
+  }
+  #+END_SRC
+  #+RESULTS:
+  [[file:interfaces.png]]
+
+  #+BEGIN_SRC dot :output file :file interfaces2.png
+digraph G {
+	layout=circo;
+  QP [label="Quantum Package"];
+  QMCCHEM [label="QMC=Chem"];
+  Turbo   [label="TurboRVB"];
+  TREX [label="TREX Format"];
+  CHAMP -> TREX;
+  GammCor -> TREX;
+  NECI -> TREX;
+  QMCCHEM -> TREX;
+  QML -> TREX;
+  QP -> TREX;
+  Turbo -> TREX;
+
+  TREX -> CHAMP;
+  TREX -> GammCor;
+  TREX -> NECI;
+  TREX -> QMCCHEM;
+  TREX -> QML;
+  TREX -> QP;
+  TREX -> Turbo;
+  }
+  #+END_SRC
+  #+RESULTS:
+  [[file:interfaces2.png]]
+
+