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Removed unneeded TeX packages. Updated URLs.
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‎presentation/linux_bash_metacentrum_course.tex‎

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\documentclass[compress, ucs, xelatex, 11pt, xcolor=svgnames, aspectratio=169,
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\documentclass[compress, xelatex, 11pt, xcolor=svgnames, aspectratio=169,
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hyperref={
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bookmarks=true,
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unicode=true,
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filecolor=NavyBlue, % Not in use?
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menucolor=DarkMagenta, % Not in use?
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urlcolor=DarkBlue, % Links with \href and \url
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pdftex},
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},
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url={hyphens, lowtilde} % Allow line breaks within URLs
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]{beamer}
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@@ -153,7 +153,7 @@ \subsection{Learning machine}
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\item If you do not have Linux installed, download and install VirtualBox from \url{https://www.virtualbox.org/}
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\item Download openSUSE Leap 15.3 Linux distribution for this course from \url{https://botany.natur.cuni.cz/zeisek/openSUSE_Leap_courses.ova} ($\sim$4.6~GB)
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\item Launch VirtualBox and go to menu \textbf{File | Import appliance\ldots} to import it. When done, launch it (\textbf{Start})
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\item See also \url{https://trapa.cz/en/node/128}
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\item See also \url{https://trapa.cz/en/vm-for-courses}
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\end{itemize}
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\includegraphics[height=6.5cm]{virtualbox.png}
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\end{multicols}
@@ -247,7 +247,7 @@ \subsection{What it is a~\enquote{UNIX}}
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\item Installation and management is for beginners usually harder than Linux, everything must be done manually, not so common as Linux anymore
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\item E.g. \href{https://www.freebsd.org/}{FreeBSD}, \href{https://www.dragonflybsd.org/}{DragonFly BSD}, \href{https://www.openbsd.org/}{OpenBSD}, \href{https://www.truenas.com/}{TrueNAS} (for storage servers),~\ldots
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\end{itemize}
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\item \href{https://en.wikipedia.org/wiki/Solaris_(operating_system)}{Solaris} --- commercial, not very common
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\item \href{https://en.wikipedia.org/wiki/Oracle_Solaris}{Solaris} --- commercial, not very common
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\begin{itemize}
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\item Mainly special servers, paid
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\item \href{https://distrowatch.com/search.php?ostype=Solaris}{Several community-based variants} freely available
@@ -391,7 +391,7 @@ \subsection{Choose one}
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\item \href{https://distrowatch.com/search.php?package=RPM}{Red Hat (RPM) based}
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\begin{itemize}
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\item \href{https://www.redhat.com/}{Red Hat} --- probably the most common commercial
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\item \href{https://getfedora.org/}{Fedora} --- \enquote{playground} for Red Hat --- very experimental
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\item \href{https://fedoraproject.org/}{Fedora} --- \enquote{playground} for Red Hat --- very experimental
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\item \href{https://www.centos.org/}{Centos} --- Clone of Red Hat
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\item \href{https://www.opensuse.org/}{openSUSE} --- SUSE is second largest Linux company, openSUSE is community distribution (free) companion of SUSE Linux Enterprise
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\item \href{https://www.mageia.org/}{Mageia}, \href{https://www.pclinuxos.com/}{PCLinuxOS},~\ldots
@@ -2634,7 +2634,7 @@ \section{Text}
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\item \href{https://www.gnu.org/software/emacs/}{GNU Emacs}
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\item \href{https://www.geany.org/}{Geany}
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\item \href{https://bluefish.openoffice.nl/}{Bluefish}
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\item \href{https://wiki.gnome.org/Apps/Gedit}{Gedit}
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\item \href{https://gedit-technology.github.io/apps/gedit/}{Gedit}
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\item \href{https://notepad-plus-plus.org/}{Notepad++}
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\item \href{https://www.sublimetext.com/}{Sublime}
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\item \href{https://code.visualstudio.com/}{VS Code}
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\end{itemize}
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\item \textbf{Emacs} use huge number of commands with \texttt{Ctrl} key (basics on next slide)
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\begin{itemize}
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\item See \url{https://www.gnu.org/software/emacs/tour/}, \url{https://tuhdo.github.io/emacs-tutor.html} and \url{http://www.jesshamrick.com/2012/09/10/absolute-beginners-guide-to-emacs/}
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\item See \url{https://www.gnu.org/software/emacs/tour/}, \url{https://tuhdo.github.io/emacs-tutor.html} and \url{https://systemcrafters.net/emacs-essentials/absolute-beginners-guide-to-emacs/}
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\end{itemize}
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\item The most common (but very complex and specific) is \textbf{Vim}
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\begin{itemize}
@@ -3953,7 +3953,7 @@ \subsection{Branching the code}
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\begin{frame}[fragile]{Selecting version of RAxML according the CPU type I} %FIXME Fix wrong syntax highlight
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\begin{itemize}
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\item \href{https://github.com/stamatak/standard-RAxML}{RAxML} can take advantage of modern CPUs to highly speed up calculations, with or without parallelization --- every version has separated binary, user must select, see \href{https://github.com/stamatak/standard-RAxML/blob/master/README}{README}
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\item \href{https://github.com/stamatak/standard-RAxML}{RAxML} can take advantage of modern CPUs to highly speed up calculations, with or without parallelization --- every version has separated binary, user must select, see \href{https://github.com/stamatak/standard-RAxML/blob/master/README.md}{README}
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\item After compilation, the script can select e.g. on remote server appropriate version
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\item RAxML binaries must be in \texttt{\$PATH}
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\item See \texttt{raxml\_if.sh} for whole script
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\begin{frame}[fragile]{Compilation of RAxML}
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\begin{itemize}
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\item Available from \url{https://github.com/stamatak/standard-RAxML}
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\item Before compilation check \href{https://github.com/stamatak/standard-RAxML/blob/master/README}{README}
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\item Before compilation check \href{https://github.com/stamatak/standard-RAxML/blob/master/README.md}{README}
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\item This example does not require to run \texttt{make install}, it does not have extra dependencies for compilation, it requires specifying of particular source file by \texttt{make~-f} (there are multiple \texttt{GCC} files, no one main)
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\end{itemize}
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\begin{bashcode}
@@ -4438,7 +4438,7 @@ \subsection{Scientific applications}
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\end{itemize}
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\item There are projects creating repositories with custom management system providing (among others) plenty of scientific applications
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\begin{itemize}
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\item Probably most known is \href{https://conda.io/}{Conda}
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\item Probably most known is \href{https://docs.conda.io/}{Conda}
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\item \href{https://docs.brew.sh/Homebrew-on-Linux}{Homebrew on Linux} is derived from macOS Homebrew, works also on WSL
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\end{itemize}
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\item Authors sometimes provide on homepages RPM/DEB/precompiled Java binaries/\ldots{ }--- check them first
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\end{itemize}
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\item Information about data storage \url{https://du.cesnet.cz/en/start} (\href{https://du.cesnet.cz/cs/start}{česky}) contains detailed usage instructions
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\item Information about MetaCentrum \url{https://www.metacentrum.cz/en/} (\href{https://www.metacentrum.cz/cs/}{česky}) and wiki \url{https://wiki.metacentrum.cz/wiki/Main_Page} (\href{https://wiki.metacentrum.cz/wiki/Hlavn\%C3\%AD_strana}{česky}) (main information for users containing all needed documentation)
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\begin{itemize}
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\item The documentation is being moved into \url{https://docs.metacentrum.cz/}
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\end{itemize}
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\item Information about MetaCloud \url{https://wiki.metacentrum.cz/wiki/Kategorie:Clouds}
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\item Also available is Galaxy \url{https://galaxy.metacentrum.cz/galaxy/} (same login as to MetaCentrum) --- web based bioinformatics framework (more information at \href{https://wiki.metacentrum.cz/wiki/Galaxy}{wiki})
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\item Also available is Galaxy \url{https://usegalaxy.cz/} (same login as to MetaCentrum) --- web based bioinformatics framework (more information at \href{https://docs.metacentrum.cz/related/galaxy/}{documentation})
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\item Current state and usage of resources is available at \url{https://metavo.metacentrum.cz/en/} (\href{https://metavo.metacentrum.cz/cs/}{česky})
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\item Manage your user account at \url{http://metavo.metacentrum.cz/en/myaccount/} (\href{https://metavo.metacentrum.cz/cs/myaccount/}{česky})
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\item Personal view on actual resources and running tasks is at \url{https://metavo.metacentrum.cz/pbsmon2/person}
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\item List of available applications \url{https://wiki.metacentrum.cz/wiki/Kategorie:Applications}
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\item MetaCentrum has 11~\href{https://wiki.metacentrum.cz/wiki/Frontend}{frontends} where users log and thousands of computers doing the calculations --- they are not accessed directly to run task
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\item List of available applications \url{https://docs.metacentrum.cz/software/}
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\item MetaCentrum has 11~\href{https://docs.metacentrum.cz/computing/frontends/}{frontends} where users log and thousands of computers doing the calculations --- they are not accessed directly to run task
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\item Most of computers are running \href{https://www.debian.org/}{Debian GNU/Linux}
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\begin{itemize}
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\item Basic usage as with any other Linux server --- SSH \& command line\ldots
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\end{center}
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\begin{itemize}
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\item Users have different quota on different arrays (depending on home organization etc.)
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\item There are 11 \href{https://wiki.metacentrum.cz/wiki/Frontend}{frontends} (\href{https://wiki.metacentrum.cz/wiki/Celni_uzel}{česky}) where user logs via SSH and prepare computing task for submission etc. (see further)
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\item There are 11 \href{https://docs.metacentrum.cz/computing/frontends/}{frontends} where user logs via SSH and prepare computing task for submission etc. (see further)
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\item Distributed topology might be bit confusing --- user has different home directory when logging to different frontends --- recommended is to use as few frontends and storages as possible
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\item Some special services (like \href{https://wiki.metacentrum.cz/wiki/OnDemand}{OnDemand}) start on particular storage (here \texttt{brno3})
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\item Some special services (like \href{https://docs.metacentrum.cz/software/ondemand/}{OnDemand}) start on particular storage (here \texttt{brno3})
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\item Generally, computing task loads data from selected storage and can start on any cluster
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\item Orientation is plenty of storages might be sometimes tricky --- ensure where you are and where your data are supposed to be
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\begin{itemize}
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\includegraphics[height=5.5cm]{grid_graphics.jpg}
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\end{center}
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\begin{flushright}
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From \href{https://wiki.metacentrum.cz/wiki/Beginners_guide}{Beginners guide} (\href{https://wiki.metacentrum.cz/wiki/Pruvodce_pro_zacatecniky}{česky})
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From \href{https://docs.metacentrum.cz/tutorials/}{Beginners guide}
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\end{flushright}
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\end{frame}
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\begin{frame}[fragile]{MetaCentrum usage}
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\begin{enumerate}
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\item Transfer data into one of \href{https://wiki.metacentrum.cz/wiki/Working_with_data}{storages} (\href{https://wiki.metacentrum.cz/wiki/Prace_s_daty}{česky}) by e.g. \texttt{scp} from command line, \href{https://winscp.net/}{WinSCP} from Windows or \href{https://filezilla-project.org/}{FileZilla} from any OS
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\item Connect via SSH to selected \href{https://wiki.metacentrum.cz/wiki/Frontend}{frontend} (\href{https://wiki.metacentrum.cz/wiki/Celni_uzel}{česky}). Same credentials are used for all frontends, for SSH login as well as file transmissions
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\item Transfer data into one of \href{https://docs.metacentrum.cz/data/}{storages} by e.g. \texttt{scp} from command line, \href{https://winscp.net/}{WinSCP} from Windows or \href{https://filezilla-project.org/}{FileZilla} from any OS
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\item Connect via SSH to selected \href{https://docs.metacentrum.cz/computing/frontends/}{frontend}. Same credentials are used for all frontends, for SSH login as well as file transmissions
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\item In home directory on the storage (accessed via frontend) prepare all needed data and non-interactive script to do the calculations
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\item Submit job using \texttt{qsub}. Tasks are not launched immediately, but submitted into queue and system decides when it will be launched
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\item Monitor job progress. Check results. Etc\ldots
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\begin{multicols}{2}
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\begin{itemize}
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\item Graphical applications: e.g. \href{https://filezilla-project.org/}{FileZilla} or most of Linux file managers
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\item Protocol is SSH/SSH2/SFTP/SCP, port 22, server is selected \href{https://wiki.metacentrum.cz/wiki/NFS4_Servery}{storage} address --- if possible, select any and keep using it
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\item Protocol is SSH/SSH2/SFTP/SCP, port 22, server is selected \href{https://docs.metacentrum.cz/snippets/storages-direct-ssh-table/}{storage} address --- if possible, select any and keep using it
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\item All servers (storages, frontends, computing nodes) are accessible under domain \texttt{*.metacentrum.cz} --- e.g. \texttt{tarkil.grid.cesnet.cz} is same as \texttt{tarkil.metacentrum.cz}
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\item See slide \ref{transfers} and following to command-line transfers of files
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\end{itemize}
@@ -4615,7 +4618,7 @@ \subsection{Tasks}
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# ...begins on previous slide; copy data - if it fails, exit
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cp -a "${DATADIR}"/"${WORKDIR}"/* "${SCRATCHDIR}"/ || exit 1
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# Prepare calculations - load required application modules
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# See https://wiki.metacentrum.cz/wiki/Kategorie:Applications
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# See https://docs.metacentrum.cz/software/
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# Every application module is loaded by "module add XXX"
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module add parallel # In this (example) case GNU Parallel and MrBayes
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module add mrbayes-3.2.6
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\begin{frame}[fragile]{Launching of tasks}
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\begin{itemize}
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\item See \href{https://wiki.metacentrum.cz/wiki/Beginners_guide}{beginners guide} (\href{https://wiki.metacentrum.cz/wiki/Pruvodce_pro_zacatecniky}{česky}) and \href{https://wiki.metacentrum.cz/wiki/Categorized_list_of_topics}{list of topics} (\href{https://wiki.metacentrum.cz/wiki/Rozcestnik}{česky})
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\item See \url{https://docs.metacentrum.cz/}
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\item Personal view \url{https://metavo.metacentrum.cz/pbsmon2/person} has nice overview of available resources and tasks and allows comfortable construction of submission command
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\end{itemize}
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\vfill
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\begin{frame}[fragile]{Key MetaCentrum commands}
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\begin{itemize}
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\item MetaCentrum is \enquote{just} normal Linux server --- work there as on any other Linux system
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\item Command \texttt{module} loads/unloads selected \href{https://wiki.metacentrum.cz/wiki/Kategorie:Applications}{application}
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\item Command \texttt{module} loads/unloads selected \href{https://docs.metacentrum.cz/software/}{application}
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\item Tasks (BASH scripts) are submitted for computing by \texttt{qsub} --- the script must copy the data into \texttt{\$SCRATCHDIR} and do all calculations there
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\begin{itemize}
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\item It has plenty of options how to specify requirements (see next slide and \href{https://wiki.metacentrum.cz/wiki/About_scheduling_system}{help})
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\item If using more physical machines, ensure correct settings of e.g. MPI (see documentation for respective software you are using)
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\end{itemize}
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\item If requesting e-mails (e.g. \texttt{-m abe} to get mail about abort, beginning and exit of the task) and submitting plenty of tasks by some script, it can result in plenty of mails\ldots
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\item Every user has certain \href{https://metavo.metacentrum.cz/pbsmon2/users/}{priority} increased by \href{https://wiki.metacentrum.cz/wiki/Usage_rules/Acknowledgement}{acknowledgments} (\textbf{it's mandatory to acknowledge MetaCentrum when using it}) in publications to MetaCentrum, and lowered by intensive usage of the service (the usage is calculated from past month)
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\item Every user has certain \href{https://metavo.metacentrum.cz/pbsmon2/users/}{priority} increased by \href{https://docs.metacentrum.cz/access/terms/\#acknowledgements-and-publications}{acknowledgments} (\textbf{it's mandatory to acknowledge MetaCentrum when using it}) in publications to MetaCentrum, and lowered by intensive usage of the service (the usage is calculated from past month)
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\item After submission of the task, check in \href{https://metavo.metacentrum.cz/pbsmon2/queues/jobsQueued}{the queue} in which state it is --- sometimes it can't start because of impossible combination of requested resources or so
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\item User can \href{https://metavo.metacentrum.cz/pbsmon2/nodes/physical}{check load of machines}
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\item For more options read \url{https://wiki.metacentrum.cz/wiki/About_scheduling_system}
@@ -4718,7 +4721,7 @@ \subsection{Tasks}
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\end{itemize}
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\item Not all required applications are correctly loaded
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\begin{itemize}
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\item Check \href{https://wiki.metacentrum.cz/wiki/Kategorie:Applications}{wiki} and load all needed applications
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\item Check \href{https://docs.metacentrum.cz/software/}{wiki} and load all needed applications
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\item Names of binaries are sometimes little bit different --- contain names of versions, etc.
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\end{itemize}
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\item Estimation of time needed to run the task
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\begin{frame}[fragile]{Graphical interactive task}
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\begin{itemize}
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\item See \url{https://wiki.metacentrum.cz/wiki/Remote_desktop}
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\item See \url{https://docs.metacentrum.cz/software/graphical-access/}
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\end{itemize}
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\begin{bashcode}
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screen # Secure we can log off in the meantime
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\begin{frame}{OnDemand}{Applications in web browser}
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\begin{itemize}
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\item It allows to run selected interactive applications in web browser
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\item See \url{https://wiki.metacentrum.cz/wiki/OnDemand} and \url{https://ondemand.cerit-sc.cz/}
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\item See \url{https://docs.metacentrum.cz/software/ondemand/} and \url{https://ondemand.cerit-sc.cz/}
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\item Applications start in \texttt{/storage/brno3-cerit/home/\$USER/} --- ensure to have everything needed there
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\end{itemize}
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\begin{center}
@@ -4902,7 +4905,7 @@ \subsection{More services}
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\begin{itemize}
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\item Data are in \texttt{/storage/brno2/home/USER/}
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\end{itemize}
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\item \href{https://wiki.metacentrum.cz/wiki/Jupyter_notebook}{Available} also as part of OnDemand (previous slide), or bit experimental \href{https://hub.cerit-sc.cz/}{CERIT hub}, which allows to select custom storage and also custom docker image (see \href{https://docs.cerit.io/docs/jupyterhub.html}{documentation})
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\item \href{https://docs.metacentrum.cz/related/jupyter/}{Available} also as part of OnDemand (previous slide), or bit experimental \href{https://hub.cerit-sc.cz/}{CERIT hub}, which allows to select custom storage and also custom docker image (see \href{https://docs.cerit.io/docs/jupyterhub.html}{documentation})
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\end{itemize}
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\begin{center}
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\includegraphics[height=6.5cm]{jupyter.png}
@@ -5295,10 +5298,10 @@ \subsection{Resources}
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\begin{frame}{Fedora}
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\begin{itemize}
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\item Homepage \url{https://getfedora.org/}
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\item Homepage \url{https://fedoraproject.org/}
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\item Communication and help overview \url{https://fedoraproject.org/wiki/Communicating_and_getting_help}
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\item Wiki \url{https://fedoraproject.org/wiki/Fedora_Project_Wiki}
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\item Official forum \url{https://ask.fedoraproject.org/}
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\item Official forum \url{https://discussion.fedoraproject.org/}
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\item Documentation \url{https://docs.fedoraproject.org/}
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\item Community forum \url{https://fedoraforum.org/}
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\end{itemize}
@@ -5313,10 +5316,10 @@ \subsection{Resources}
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\end{itemize}
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\item KDE \url{https://kde.org/}
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\begin{itemize}
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\item Forum \url{https://forum.kde.org/}
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\item Forum \url{https://discuss.kde.org/}
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\item UserBase wiki \url{https://userbase.kde.org/}
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\item Application store \url{https://store.kde.org/}
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\item KDE for education \url{https://edu.kde.org/}
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\item KDE for education \url{https://apps.kde.org/categories/education/}
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\item Blogs \url{https://planet.kde.org/}
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\end{itemize}
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\item XFCE \url{https://xfce.org/}

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