feat: new slide set covering issue #47 (#88)

* feat: new slide set covering issue #47

* fix: identation of sample code

slides/Snakemake_HPC_Users.tex

@@ -70,6 +70,9 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \include{common/using_wrappers}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\include{common/Fine_Tuning}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % \include{common/Contributing} 
 \end{document}

slides/common/Fine_Tuning.tex

@@ -0,0 +1,63 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Fine Tuning Cluster Behaviour}
+{   
+	\usebackgroundtemplate{
+		\vbox to \paperheight{\vfil\hbox to \paperwidth{\hfil\includegraphics[height=.7\paperheight]{misc/radio-am-und-fm-tuner.png}\hfil}\vfil}
+	}
+	\frame{
+		\frametitle{Fine Tuning!}
+		\begin{mdframed}[tikzsetting={draw=white,fill=white,fill opacity=0.8,
+				line width=0pt},backgroundcolor=none,leftmargin=0,
+			rightmargin=150,innertopmargin=4pt,roundcorner=10pt]
+			\tableofcontents[currentsection,sections={1-4},hideothersubsections]
+		\end{mdframed}
+	}
+}
+
+%<a href="https://www.flaticon.com/de/kostenlose-icons/radio" title="radio Icons">Radio Icons erstellt von Freepik - Flaticon</a>
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}
+	\frametitle{What is this about?}
+	\begin{question}[Questions]
+		\begin{itemize}
+			\item What if I really need to submit \textbf{\textsc many} jobs?
+	        \item Will crash the cluster?
+	        \item My admins report a slow accounting DB. How do I cope with that?
+		\end{itemize}
+	\end{question}
+	\begin{docs}[Objectives]
+		\begin{enumerate}
+			\item Learning how throttle job submission with \Snakemake{}.
+			\item Knowing how to limit the status request from \Snakemake to SLURM.
+		\end{enumerate}
+	\end{docs}
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[fragile]
+	\frametitle{Limiting Job Submission Rates}
+	\begin{docs}
+		We can limit the number of jobs submitted per second with the \altvberb{--max-jobs-per-second} flag.\newline
+		\emph{However}, this is only necessary, when dealing with an enormous load of jobs ($\gg$ 1.000 -- 10.000 jobs)\newline\pause
+		The default is 10 per second.
+	\end{docs}
+    \begin{lstlisting}[language=Bash, style=Shell]
+$ snakemake --max-job-per-second=0.1
+   \end{lstlisting}	
+   The value may be a fraction (here: 1 job per ten seconds). Or simply
+   \begin{lstlisting}[language=Bash, style=Shell]
+$ snakemake --max-job-per-second=5
+   \end{lstlisting}
+   which would half the submission rate (5 instead of 10)
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[fragile]
+	\frametitle{Limiting Job Status Queries}
+	\begin{docs}
+		The SLURM executor plugin has its own limiter and ensures that the accounting data base is not overwhelmed.\newline
+		The \altverb{--max-status-checks-per-second} flag allows us to throttle the number of status queries per second.\newline
+		The default is at 10. -- Usefull for local jobs, only.
+    \end{docs}
+\end{frame}