Commits July 2013

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[svn:einsteintoolkit] Workshop_Summer_2013/tutorial/ (Rev. 27)
by sbrandt＠cct.lsu.edu 26 Jul '13

26 Jul '13

User: sbrandt Date: 2013/07/26 01:09 PM Modified: /tutorial/ Cac.tex Log: A few small changes to building and syncing File Changes: Directory: /tutorial/ ===================== File [modified]: Cac.tex Delta lines: +8 -0 =================================================================== --- tutorial/Cac.tex 2013-07-26 17:50:44 UTC (rev 26) +++ tutorial/Cac.tex 2013-07-26 18:09:11 UTC (rev 27) @@ -156,6 +156,8 @@ \begin{verbatim} cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim sync zwicky \end{verbatim} +You can edit the \verb=~/simfactory/etc/defs.ini= directory if +you want to sync non-default directories. \end{itemize} } @@ -170,6 +172,12 @@ \item You can perform all the build, submit, commands on zwicky now, or you can exit and use the --remotemachine options. We'll do the latter. +\begin{verbatim} +cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim build \ + --remotemachine zwicky \ + --thornlist /home/sxs-40/Cactus/thornlists/einsteinto +olkit.th +\end{verbatim} \end{itemize} }

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[svn:einsteintoolkit] Workshop_Summer_2013/et_intro_details/ (Rev. 26)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 12:50 PM Modified: /et_intro_details/ et_intro_details.tex Log: fix typos in et_intro_details File Changes: Directory: /et_intro_details/ ============================= File [modified]: et_intro_details.tex Delta lines: +3 -5 =================================================================== --- et_intro_details/et_intro_details.tex 2013-07-26 17:04:35 UTC (rev 25) +++ et_intro_details/et_intro_details.tex 2013-07-26 17:50:44 UTC (rev 26) @@ -41,7 +41,6 @@ \item<1-> a framework for developing portable, modular applications \item<2-> focusing, although not exclusively, on high-performance simulation codes -he other modules \item<3-> separate concerns: designed to allow experts in different fields to develop modules based upon their experience and to use modules developed by experts in other fields with minimal knowledge of the internals or operation of @@ -166,7 +165,7 @@ \begin{frame} \frametitle{GetComponents -- what?} \begin{itemize} -\item (parallised) download of modules from source code repositories +\item (parallelized) download of modules from source code repositories \item access to sub-parts of repositories \item assemble directory structure \item simplify update of modules @@ -215,7 +214,6 @@ \begin{itemize} \item Captures the best practices of experienced users, ensuring repeatable and well-documented scientific results. - \item Developed by Erik Schnetter and Michael Thomas. \item Included in virtual machine: {\tt Cactus/simfactory}. \item For more, see: {\tt http://simfactory.org} \end{itemize} @@ -230,7 +228,7 @@ \item[grid scalar] single number (or set of numbers) managed by Cactus, eg. total mass \item[schedule] order in which Cactus calls user supplied routines, defined -through orderign relations ``SCHEDULE \texttt{compute\_rho} BEFORE +through ordering relations ``SCHEDULE \texttt{compute\_rho} BEFORE \texttt{compute\_mass}'' \item[parameter] user specifyable option controlling simulation. Used for example to provide central density in TOV stars, give final time of @@ -244,7 +242,7 @@ thorn} Directory structure: \begin{alltt} -GRhydro/ +GRHydro/ |-- COPYRIGHT |-- README |-- configuration.ccl

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[svn:einsteintoolkit] Workshop_Summer_2013/ (Rev. 25)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 12:04 PM Modified: /et_intro_details/ et_intro_details.tex /handson_analysis/ handson_analysis.tex Log: save state on et_intro and handson_analysis File Changes: Directory: /et_intro_details/ ============================= File [modified]: et_intro_details.tex Delta lines: +1 -1 =================================================================== --- et_intro_details/et_intro_details.tex 2013-07-26 17:04:29 UTC (rev 24) +++ et_intro_details/et_intro_details.tex 2013-07-26 17:04:35 UTC (rev 25) @@ -171,7 +171,7 @@ \item assemble directory structure \item simplify update of modules \item show local changes in all thorns -\item operates on \texttt{thornlist} describing collection of thorns +\item operates on \texttt{ThornList} describing collection of thorns \end{itemize} \end{frame} Directory: /handson_analysis/ ============================= File [modified]: handson_analysis.tex Delta lines: +16 -40 =================================================================== --- handson_analysis/handson_analysis.tex 2013-07-26 17:04:29 UTC (rev 24) +++ handson_analysis/handson_analysis.tex 2013-07-26 17:04:35 UTC (rev 25) @@ -5,7 +5,7 @@ \newcommand{\Heaviside}{\operatorname{\Theta}} \subtitle[Analysis hands-on]{{\large Einstein Toolkit -Workshop}\\*[0.3em]Hands-on exercise: tracking stars} +Workshop}\\*[0.3em]Hands-on exercise: center of mass} \author{Roland Haas} \date{Jul 26 2013} @@ -32,59 +32,35 @@ \begin{frame} \frametitle{Problem description} -\begin{block}{Requirements} - \begin{itemize} - \item be able to pick out a single neutron star, among several - \item roughly track the neutron star centre - \item be reasonably fast - \item be easy to use - \end{itemize} -\end{block} \begin{block}{Ansatz} - \begin{itemize} - \item compute centre of mass $X^i = \int \rho(x^i)\,x^i\,d^3x / \int \rho(x^i)\,d^3x$ - \item use distance from last known location to distinguish between - stars - \item use density to limit centre of mass to central region to remove - influence of outflowing tails - \end{itemize} + Compute centre of mass +\begin{equation} +X^i = \int \rho(x^i)\,x^i\,d^3x / \int \rho(x^i)\,d^3x +\end{equation} \end{block} -\end{frame} - -\begin{frame}[containsverbatim] -\frametitle{Recipe in formulae} \begin{block}{What to compute} \begin{align*} - M &= \int \Heaviside(\rho - \rho_{\text{min}}) - \Heaviside(R_{\text{max}} - |x^i - x^i_{\text{old}}|) - \rho\,d^3x \\ - X^i&= \left( - \int \Heaviside(\rho - \rho_{\text{min}}) - \Heaviside(|x^i - x^i_{\text{old}}| - R_{\text{max}}) - \rho\,x^i\,d^3x \right) / M + M &= \int \rho\,d^3x \\ + X^i&= \left(\rho\,x^i\,d^3x \right) / M \end{align*} \end{block} \begin{block}{Does this fit into code?} - Certainly. - \begin{itemize} - \item $\int$ $\rightarrow$ - \parbox{.75\linewidth}{\begin{alltt}core\_density\_x[idx] = \ldots;\\\vdots\\CCTK\_Reduce(\ldots,handle\_sum,\ldots,core\_density\_x,\ldots);\end{alltt}} - \item $\Heaviside$ $\rightarrow$ \verb|if(...)| - \end{itemize} + Certainly.\\ + $\int$ $\rightarrow$ + \parbox{.75\linewidth}{ + \begin{alltt} + comIntegrandX[idx] = \ldots;\\ + \vdots\\ + CCTK\_Reduce(\ldots,handle\_sum,\ldots,varindex,\ldots); + \end{alltt}} \end{block} \end{frame} \begin{frame} \frametitle{Entities to define} \begin{itemize} - \item<1-> \texttt{param.ccl} + \item<1-> \texttt{interface.ccl} \begin{alltt}\color{blue} - CCTK\_REAL density\_threshold\\ - CCTK\_REAL core\_radius\\ - CCTK\_REAL inital\_core\_\{x,y,z\} - \end{alltt} - \item<2-> \texttt{interface.ccl} - \begin{alltt}\color{blue} CCTK\_REAL core\_density\_gf type=gf\\ \hspace{1cm}core\_density\_\{x,y,z\}\\ \hspace{1cm}core\_density\\

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[svn:einsteintoolkit] Workshop_Summer_2013/handson_analysis/codes/ (Rev. 24)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 12:04 PM Modified: /handson_analysis/codes/ FindCoM_v1.tar, FindCoM_v2.tar, FindCoM_v3.tar, FindCoM_v4.tar, FindCoM_v5.tar Log: update analysis code to not require admbase anymore File Changes: Directory: /handson_analysis/codes/ =================================== File [modified]: FindCoM_v1.tar Delta lines: <Unavailable> File [modified]: FindCoM_v2.tar Delta lines: <Unavailable> File [modified]: FindCoM_v3.tar Delta lines: <Unavailable> File [modified]: FindCoM_v4.tar Delta lines: <Unavailable> File [modified]: FindCoM_v5.tar Delta lines: <Unavailable>

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[svn:einsteintoolkit] Workshop_Summer_2013/handson_viz/ (Rev. 23)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 12:04 PM Modified: /handson_viz/ fast_tov.par Log: update fast_tov file for hands on exercise File Changes: Directory: /handson_viz/ ======================== File [modified]: fast_tov.par Delta lines: +5 -0 =================================================================== --- handson_viz/fast_tov.par 2013-07-26 16:30:09 UTC (rev 22) +++ handson_viz/fast_tov.par 2013-07-26 17:04:22 UTC (rev 23) @@ -219,3 +219,8 @@ ADMConstraints::momentum " + +IOHDF5::out_every = 256 +IOASCII::out1D_vars = " + HydroBase::rho +"

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[svn:einsteintoolkit] Workshop_Summer_2013/ (Rev. 22)
by knarf＠cct.lsu.edu 26 Jul '13

26 Jul '13

User: knarf Date: 2013/07/26 11:30 AM Added: /pics/ Apple_Logo.pdf, Git-logo.pdf, Imperial-Metric.png, Mediawiki_logo.pdf, Mercurial_logo.pdf, Subversion-logo.pdf, Trac_logo.pdf, Tux-linux_logo.pdf, Windows_logo.pdf, Workshop.pdf, community_of_groups.pdf, community_of_groups.svg, community_only_problem.pdf, community_only_problem.svg, community_with_competition.pdf, community_with_competition.svg, community_with_computation.pdf, community_with_computation.svg, community_with_credit.pdf, community_with_credit.svg, community_with_license.pdf, community_with_license.svg, community_with_problem.pdf, community_with_problem.svg, community_with_problems.pdf, community_with_problems.svg, community_with_standards.pdf, community_with_standards.svg, community_with_tools.pdf, community_with_tools.svg, community_with_tools_examples.pdf, community_with_tools_examples.svg, crab.jpeg, email.pdf, gorilla_fight.jpg, gorilla_tablet.jpg, hdf_logo.jpg, hurricane.jpeg, irc.pdf, people.jpeg, phone.pdf, space_shuttle.jpeg, tianhe1.jpg, wind_park.jpeg, www.pdf Modified: /et_intro/ slides.tex Log: a few more slides for a little more time File Changes: Directory: /et_intro/ ===================== File [modified]: slides.tex Delta lines: <Unavailable> Directory: /pics/ ================= File [added]: Apple_Logo.pdf Delta lines: <Unavailable> File [added]: Git-logo.pdf Delta lines: <Unavailable> File [added]: Imperial-Metric.png Delta lines: <Unavailable> File [added]: Mediawiki_logo.pdf Delta lines: <Unavailable> File [added]: Mercurial_logo.pdf Delta lines: <Unavailable> File [added]: Subversion-logo.pdf Delta lines: <Unavailable> File [added]: Trac_logo.pdf Delta lines: <Unavailable> File [added]: Tux-linux_logo.pdf Delta lines: <Unavailable> File [added]: Windows_logo.pdf Delta lines: <Unavailable> File [added]: Workshop.pdf Delta lines: <Unavailable> File [added]: community_of_groups.pdf Delta lines: <Unavailable> File [added]: community_of_groups.svg Delta lines: <Unavailable> File [added]: community_only_problem.pdf Delta lines: <Unavailable> File [added]: community_only_problem.svg Delta lines: <Unavailable> File [added]: community_with_competition.pdf Delta lines: <Unavailable> File [added]: community_with_competition.svg Delta lines: <Unavailable> File [added]: community_with_computation.pdf Delta lines: <Unavailable> File [added]: community_with_computation.svg Delta lines: <Unavailable> File [added]: community_with_credit.pdf Delta lines: <Unavailable> File [added]: community_with_credit.svg Delta lines: <Unavailable> File [added]: community_with_license.pdf Delta lines: <Unavailable> File [added]: community_with_license.svg Delta lines: <Unavailable> File [added]: community_with_problem.pdf Delta lines: <Unavailable> File [added]: community_with_problem.svg Delta lines: <Unavailable> File [added]: community_with_problems.pdf Delta lines: <Unavailable> File [added]: community_with_problems.svg Delta lines: <Unavailable> File [added]: community_with_standards.pdf Delta lines: <Unavailable> File [added]: community_with_standards.svg Delta lines: <Unavailable> File [added]: community_with_tools.pdf Delta lines: <Unavailable> File [added]: community_with_tools.svg Delta lines: <Unavailable> File [added]: community_with_tools_examples.pdf Delta lines: <Unavailable> File [added]: community_with_tools_examples.svg Delta lines: <Unavailable> File [added]: crab.jpeg Delta lines: <Unavailable> File [added]: email.pdf Delta lines: <Unavailable> File [added]: gorilla_fight.jpg Delta lines: <Unavailable> File [added]: gorilla_tablet.jpg Delta lines: <Unavailable> File [added]: hdf_logo.jpg Delta lines: <Unavailable> File [added]: hurricane.jpeg Delta lines: <Unavailable> File [added]: irc.pdf Delta lines: <Unavailable> File [added]: people.jpeg Delta lines: <Unavailable> File [added]: phone.pdf Delta lines: <Unavailable> File [added]: space_shuttle.jpeg Delta lines: <Unavailable> File [added]: tianhe1.jpg Delta lines: <Unavailable> File [added]: wind_park.jpeg Delta lines: <Unavailable> File [added]: www.pdf Delta lines: <Unavailable>

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[svn:einsteintoolkit] Workshop_Summer_2013/et_intro_details/ (Rev. 21)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 10:53 AM Modified: /et_intro_details/ et_intro_details.tex Log: work on et intro details File Changes: Directory: /et_intro_details/ ============================= File [modified]: et_intro_details.tex Delta lines: +194 -3 =================================================================== --- et_intro_details/et_intro_details.tex 2013-07-26 15:52:55 UTC (rev 20) +++ et_intro_details/et_intro_details.tex 2013-07-26 15:53:04 UTC (rev 21) @@ -222,7 +222,197 @@ More on \texttt{Simfactory} in the hands-on session. \end{frame} -\begin{frame} \frametitle{Example: solving scalar wave equation} +\begin{frame} \frametitle{Cactus thorn writing: Cactus concepts} +\begin{description} +\item[thorn] Cactus module providing physics or infrastructure capabilities +\item[grid function] discrete representation of function eg. density +$\rho(x,y,z)$ on the numerical grid, eg. $\mathtt{rho}_{i,j,k}$ +\item[grid scalar] single number (or set of numbers) managed by Cactus, eg. +total mass +\item[schedule] order in which Cactus calls user supplied routines, defined +through orderign relations ``SCHEDULE \texttt{compute\_rho} BEFORE +\texttt{compute\_mass}'' +\item[parameter] user specifyable option controlling simulation. Used for +example to provide central density in TOV stars, give final time of +simulation, specify type of equation of state +\item[parameter file] set of parameter values used in a single simulation run, +key---value pairs +\end{description} +\end{frame} + +\begin{frame}[containsverbatim] \frametitle{Cactus thorn writing: anatomy of a +thorn} + Directory structure: + \begin{alltt} +GRhydro/ +|-- COPYRIGHT +|-- README +|-- configuration.ccl +|-- doc +| `-- documentation.tex +|-- interface.ccl +|-- schedule.ccl +|-- param.ccl +`-- src + |-- GRHydro\_Startup.F90, \ldots + `-- make.code.defn +\end{alltt} +\end{frame} + +\frame[containsverbatim]{\frametitle{configuration.ccl} +\begin{block}{configuration.ccl} +\small\begin{alltt} +# Configuration definition for thorn GRHydro + +REQUIRES EOS_Omni Boundary CartGrid3D SpaceMask ADMMacros + +OPTIONAL_IFACTIVE Carpet +\{ +\} +\end{alltt} +\end{block} +%\includegraphics[width=6in]{config} + +List the thorns without which yours will not compile. Popular choices include +external libraries ({\tt GSL/LAPACK/LORENE/HDF5}, etc.), {\tt EOS\_Omni} for +matter. +} + +\frame[containsverbatim]{\frametitle{interface.ccl} +\begin{block}{interface.ccl} +\small\begin{alltt} +implements: GRHydro +inherits: ADMBase, SpaceMask, Tmunubase, HydroBase + +USES INCLUDE HEADER: carpet.hh + +void FUNCTION SpatialDet(CCTK_REAL IN gxx, CCTK_REAL IN gxy, \textbackslash + CCTK_REAL IN gxz, CCTK_REAL IN gyy, \textbackslash + CCTK_REAL IN gyz, CCTK_REAL IN gzz, \textbackslash + CCTK_REAL OUT det) +PROVIDES FUNCTION SpatialDet WITH SpatialDeterminant LANG Fortran + +public: +real dens type = GF Timelevels = 3 \textbackslash + tensortypealias="Scalar" interpolator="matter"' \textbackslash + "generalized particle number" +\end{alltt} +\end{block} +} + +\frame[containsverbatim]{\frametitle{param.ccl} +\begin{block}{param.ccl} +\begin{alltt} +REAL rho\_abs\_min "A minimum rho below which evolution is \textbackslash + turned off (atmosphere)." STEERABLE=recover +\{ + -1.0 :: "use relative minimum" + 0.0:* :: "reset rho when it falls below" +\} -1.0 + +SHARES: HydroBase +USES CCTK\_INT timelevels +EXTENDS KEYWORD evolution\_method +\{ + "GRHydro" :: "Use GRHydro to evolve the hydro variables" +\} +\end{alltt} +\end{block} +Parameters are typically set at startup, not during execution. + +%\includegraphics[width=5.5in]{param1} +} + +\frame[containsverbatim]{\frametitle{schedule.ccl} +\begin{block}{schedule.ccl---storage} +\begin{alltt} +STORAGE: dens[timelevels] + +if(CCTK\_Equals(Bvec\_evolution\_method,"GRHydro")) +\{ + STORAGE: HydroBase::Bvec[timelevels] + STORAGE: GRHydro::Bcons[timelevels] + STORAGE: Bconsrhs +\} +\end{alltt} +\end{block} +{\tt schedule.ccl} handles global storage control. +} + +\frame[containsverbatim]{\frametitle{schedule.ccl} +\begin{block}{schedule.ccl---scheduling} +\begin{alltt} +schedule Conservative2Primitive IN HydroBase\_Con2Prim +\{ + LANG: Fortran +\} "Convert back to primitive variables (general)" + +schedule GRHydro\_Boundaries IN HydroBase\_Select\_Boundaries \textbackslash + AS GRHydro\_Bound +\{ + LANG: Fortran + OPTIONS: LEVEL + SYNC: dens + SYNC: HydroBase::Bvec +\} "Select GRHydro boundary conditions" +\end{alltt} +\end{block} +{\tt schedule.ccl} handles subroutine scheduling. +} + +\frame[containsverbatim]{\frametitle{schedule.ccl cont'd} +\begin{block}{schedule.ccl---scheduling} +\begin{alltt} +schedule group GRHydroRHS IN HydroBase\_RHS +\{ + STORAGE: GRHydro\_scalars +\} "Calculate the update terms" + +schedule SourceTerms IN GRHydroRHS BEFORE FluxTerms +\{ + LANG: Fortran +\} "Source term calculation" + +schedule UpdateAtmosphereMask IN GRHydroRHS AFTER FluxTerms +\{ + LANG: Fortran +\} "Alter the update terms if inside the atmosphere region" + +\end{alltt} +\end{block} +group routines so that group can be reused +} + +\frame[containsverbatim]{\frametitle{make.code.defn} +\begin{block}{files to compile} +\begin{alltt} +# Source files in this directory + +SRCS = GRHydro_Source.F90 \textbackslash + GRHydro_UpdateMask.F90 \textbackslash + GRHydro_Prim2Con.c \textbackslash + GRHydro_Boundaries.F90 + +SUBDIRS = +\end{alltt} +\end{block} +{\tt make.code.defn} +} + +\frame{\frametitle{Final tips} +\begin{itemize} +\item \emph{Plagiarize and copy liberally, especially at first!!!} + +\item Consider compilation time when you write your thorn. You want a +thornlist that is as small as possible, but not smaller. + +\item Get version control running first! + +\item Learn how to output. It is a huge timesaver for debugging/running. +\end{itemize} +} + +\begin{frame} \frametitle{Worked out example: solving scalar wave equation} For a given source function $S(x,y,t)$ find a scalar wave field $\varphi(x,y,t)$ inside the domain $\mathcal{D}$ with a boundary condition: @@ -502,6 +692,7 @@ (0,0) grid (3.0cm,2.6cm); \draw[xstep=.6cm,ystep=.4cm,gray,dashed,xshift=0.05cm,yshift=0.05cm] (2.4,0) grid (5.4cm,2.6cm); + \draw[above=2pt] (5.9,0.7) node {\small $t=0$}; }% \uncover<5>{ \scope[color=red,thick,fill=white] @@ -520,8 +711,8 @@ \draw[xshift=2.45cm,yshift=0.05cm] (0cm,-1pt) grid (3.0cm,1pt); \draw[xshift=0cm,yshift=0.4cm] (0cm,-1pt) grid (3.0cm,1pt); \draw[xshift=2.45cm,yshift=0.45cm] (0cm,-1pt) grid (3.0cm,1pt); - \draw[xshift=0cm,yshift=0.8cm,color=black] (0cm,-1pt) grid (3.0cm,1pt); - \draw[xshift=2.45cm,yshift=0.85cm,color=black] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=0cm,yshift=0.8cm] (0cm,-1pt) grid (3.0cm,1pt); + \draw[xshift=2.45cm,yshift=0.85cm] (0cm,-1pt) grid (3.0cm,1pt); \endscope \scope[color=blue] \draw (-0.5,0.4) node[anchor=east] {\small phi\_p};

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[svn:einsteintoolkit] Workshop_Summer_2013/et_intro_details/ (Rev. 20)
by rhaas＠tapir.caltech.edu 26 Jul '13

26 Jul '13

User: rhaas Date: 2013/07/26 10:52 AM Added: /et_intro_details/ WaveToy.tar.gz Modified: /et_intro_details/ et_intro_details.tex Log: revert WaveToy example to old non-MoL method File Changes: Directory: /et_intro_details/ ============================= File [added]: WaveToy.tar.gz Delta lines: +45 -0 =================================================================== --- et_intro_details/WaveToy.tar.gz (rev 0) +++ et_intro_details/WaveToy.tar.gz 2013-07-26 15:52:55 UTC (rev 20) @@ -0,0 +1,83 @@ +-{òQì[YsGÖëTì¨Ð>Ü!Ö1¶66$A 3$H d=6ÐV£Û)üûùò¨îjòÌ½;ñDWgeåùeVâSôè&ÙöÅ³?ðç%~Þ¾~Iÿíüë½}õ +ãó³³WçoÙ×$Sþ§*Ê(·öY¾¢âë~ëùÿÑOªÿY.âeGe¥ÝÙ,ù÷ ¿yu\ÿggoá¿^½zõúÍË·Ðÿ«·oÏÙ¿#Gþëÿ_íe¨y;w8ù×EÛrå©¤eÍ«}üB-ÆQÿçÁ¨?¶Q^¾ÏãùWæû8ÿüù¼ÿ_ÞÝ +Þü{|Ûÿ_ýðæõùÿ¿}õæþÿ?ñcÌdêçøådv°ÙæñrUâcg£6ÒÍmò§EVå3WØE¸¢k©Ì±4§¯Ò¹Ëù÷ÃûþþÆ>ÅåJhlÜ,^Ä3ë¾ÎÜcN¹J.gØ$ÍJ»QÎesvÒ/qº¤¿§ª~ÓEakDª*wfgkPôÇëó=uWx^ØÖößgüÇ:Óò?åw"ßÍòåóo¿Û1úÅ«?ìz7öþáâfpiñ_8îëü|tyAÂ8ïØ¿T©³g?þxfL ËS|øç;üÈ^çÎÙq¶(¢ÜÙë"ç`ÞAàu=úóæík{í=ºÄ²"/ñëmÏ¾<?û<{Æö]¾ÍÀ D¹qù:.I³¬ÍÖFé<Ð¸ÅÚ)¶_ÓÃØÆfQBÏ\Z8¨tV]Zv,ÖÛÙ*J¬¼Èª£$ÉÜ¼K2cÜçPÕ4q+P)¢ÖYQÂõôôßÜñ2Ëè>|¶vI87'«Èl±âõ`YÀáÊ®µ[ðt3ê4VëRG½¯¦ØÚÜèAÀ.¬ÆÁÀy«eåþv¼ýÖVôÌx¿ÿKÖÄg«UïÒã`ZËXÀc[}tø\5ëY6Â§ÍY>¬×¶ÓXÊwE ÁO¥[áÜnò®·¶O«¬hÂÁ,[Ã°Ò¨ïôNÆÙÚékÇ¬²u¸Ysø¦ÛÚëoâiå[{ädq0Í»§Ö~Î*;R>ìÖ +3,zå¸³¬KVóiåRûÄ!'úBÒ`©zN:ô8ÊÝÂå¹U`lÒlrìÞüaÎ=ÛudftË¬#ðq=þìÚN¾dS0ìO0GlmãFX-V§z+eæâG©%hÂH`K_+F?WiZjË9Ð:gÂ%Imê_/÷wbDÜ4{ªéÎ3¢YeÈ¹`íL2zµt³R\£\ÁZI] ËÜ¤BÂÆsc¥ðDÂt)»ºn"q2éâ<ÊH+¹«3¬ê"ò;]àÒEâËK$ +Z±ÁÃx'Ê²HÔÔh(Éq¤â_góxAæË¢¸Æ÷5Zo,ÒÉÕle#/rÈjåÈíeÉOÌ1Ã.ñ>@:v«ýÁ:bJ!+$Ód«]ñ2~wÇñÊ¬SZ`^xjËL¢æ£XÁ$°fíYbSÁoqn¼jÈÝ!+Q8ñnSüdOÎN9/5¦:ÌÒB~ðs5 3=bdTðÃÄ-áæñ +ÎÈò:¡Aó§!Vc¸sÝK +Htá"ÒOÄ[= +Q%gÁÄàÙ½Á«Á¸óY!`k:/jUH8M3¼SÚjù¦ ¤N6PÄ`±cùã0>_;ÚÅ%$ +xrF£EZØU'ol@>§ÓT§QÒÁr$J2Rûs)WÂ'Ò.¬ 4'¤ú,mÑ2¾ÃMUrs¹¦ÇÉ¶ÃáÉ2 ¤@êÆ^H÷$Ë)O¯ÉqCKÊ³°;A³xÎûÏ):ærb$0oá½Ît8Çñ¼"¦l6å@"Ôx¦CèÚÁ6gìmV +ü4äP¯l»4ad.P3K|Í ÌØYâ"å"ÐûMk5ÓTÓúNáEy|Lr¯×EÌºmHÿµçr~ÊpBD'è4áKmÝµÍ"í2Úëùm§þèvl{Ã+{y7¼LwÃ±½¾Yª_Ã÷{5OFzÄoï®×Ë}@Ì¿jåTRsdaãc²üFBP[a" +åÞM©½Q4ag%\h«Ðv + +©i*#¡ÇÉáEWÄþü^ø{ôì ¸aÌR³Ïi!8qÏq6ù2ÄygOÍ¬òu19xB4.X¡1ØSæ'ÑÓOâÓ1óc[Y«bSsnQ¶,g3`0Ñ1Ê@]CÐ (¾&Sø[çfªJùü¬1À7«hI";ùÈ@°;õ´!÷YRx§-²lV§ÆkÆ>wNÈ³O¡\=C\4°ö9rÇs8JáýQB¦r%`uÌ/Zd0IÀ³AÈbjï$Ä2*«Ê"fGuo*EËÉ«tOô=Òqó"6¦8jµv®_1XÏRÛÞtË9Ãh\rF´{füÎ'nCÐ+åª:às\8çO»æ[Y^Ü&ZíâóN}Hjp¸:ë +¶OÁê±ù®q©7×ã=d,PÁùæ] +fÏª¬*Ù1c9llÈÑ`pÆÊd¸Ê4¦G1K¢x +©iùßÙ/ÎmÈ%ÈÝyððÇH(7}¦K±å2&mh +È¦>@[t0>lºÚÛ@ºªªµ$WÅ1µ«mçHÔ®Å}¹&; 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- \draw (-1,1) -- (1,1); - \draw (-1,-1) -- (1,-1); + \draw (0,-1) -- (0,1); \scope[fill=green!50!blue, draw=black] \filldraw (0,0) circle (0.07cm); \filldraw (1,0) circle (0.07cm); + \filldraw (0,1) circle (0.07cm); \filldraw (-1,0) circle (0.07cm); - \filldraw (0,1) circle (0.07cm); - \filldraw (1,1) circle (0.07cm); - \filldraw (-1,1) circle (0.07cm); \filldraw (0,-1) circle (0.07cm); - \filldraw (1,-1) circle (0.07cm); - \filldraw (-1,-1) circle (0.07cm); \endscope \scope[xshift=0.45cm,yshift=0.25cm] \draw (0,0) node {{\tiny $\varphi^{(n)}_{i}$}}; \draw (1,0) node {{\tiny $\varphi^{(n)}_{i+1}$}}; - \draw (-1,0) node {{\tiny $\varphi^{(n)}_{i}$}}; \draw (0,1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; - \draw (1,1) node {{\tiny $\varphi^{(n+1)}_{i+1}$}}; - \draw (-1,1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; - \draw (0,-1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; - \draw (1,-1) node {{\tiny $\varphi^{(n+1)}_{i+1}$}}; - \draw (-1,-1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; + \draw (-1,0) node {{\tiny $\varphi^{(n)}_{i-1}$}}; + \draw (0,-1) node {{\tiny $\varphi^{(n-1)}_{i}$}}; \endscope \end{tikzpicture} \end{center} @@ -299,19 +290,75 @@ c^2 (\partial_x^2\varphi + \partial_y^2\varphi) + S \\ \Downarrow (c\equiv1)\\ - \begin{aligned} - %\text{\makebox[0pt][l]{\framebox{\parbox{4cm}{Semi-descretization for Method of Lines}}}} - \frac{\partial \phi_{i,j}}{\partial t} = & \psi_{i,j} \\ - \frac{\partial \psi_{i,j}}{\partial t} = & - \frac{\varphi_{i+1,j} - 2\varphi_{i,j}+\varphi_{i-1,j}} + \begin{split} + \frac{\varphi^{(n+1)}_{i,j} - 2\varphi^{(n)}_{i,j}+\varphi^{(n-1)}_{i,j}} + {2\Delta t^2} = & + \frac{\varphi^{(n)}_{i+1,j} - 2\varphi^{(n)}_{i,j}+\varphi^{(n)}_{i-1,j}} {2\Delta x^2} + \\ - & \frac{\varphi_{i,j+1} - 2\varphi_{i,j}+\varphi_{i,j-1}} - {2\Delta y^2} + S_{i,j} - \end{aligned} + & \frac{\varphi^{(n)}_{i,j+1} - 2\varphi^{(n)}_{i,j}+\varphi^{(n)}_{i,j-1}} + {2\Delta y^2} + S^{(n)}_{i,j} + \end{split} \end{gather*} \end{columns} } +%\frame{ \frametitle{WaveToy Thorn: Discretization} +% Discretization: \\ +% approximating continuous function $\varphi(x,y,t)$ +% with a grid function $\varphi^{(n)}_{i,j}$: +% \begin{columns}[t] +% \column{.2\textwidth} +% \begin{figure}[!htp] +% \begin{center} +% \begin{tikzpicture}[scale=1.1] +% \draw (-1,0) -- (1,0); +% \draw (-1,1) -- (1,1); +% \draw (-1,-1) -- (1,-1); +% \scope[fill=green!50!blue, draw=black] +% \filldraw (0,0) circle (0.07cm); +% \filldraw (1,0) circle (0.07cm); +% \filldraw (-1,0) circle (0.07cm); +% \filldraw (0,1) circle (0.07cm); +% \filldraw (1,1) circle (0.07cm); +% \filldraw (-1,1) circle (0.07cm); +% \filldraw (0,-1) circle (0.07cm); +% \filldraw (1,-1) circle (0.07cm); +% \filldraw (-1,-1) circle (0.07cm); +% \endscope +% \scope[xshift=0.45cm,yshift=0.25cm] +% \draw (0,0) node {{\tiny $\varphi^{(n)}_{i}$}}; +% \draw (1,0) node {{\tiny $\varphi^{(n)}_{i+1}$}}; +% \draw (-1,0) node {{\tiny $\varphi^{(n)}_{i}$}}; +% \draw (0,1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; +% \draw (1,1) node {{\tiny $\varphi^{(n+1)}_{i+1}$}}; +% \draw (-1,1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; +% \draw (0,-1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; +% \draw (1,-1) node {{\tiny $\varphi^{(n+1)}_{i+1}$}}; +% \draw (-1,-1) node {{\tiny $\varphi^{(n+1)}_{i}$}}; +% \endscope +% \end{tikzpicture} +% \end{center} +% \end{figure} +% +% \column{.8\textwidth} +% \begin{gather*} +% \\ +% \frac{\partial^2\varphi}{\partial t^2} = +% c^2 (\partial_x^2\varphi + \partial_y^2\varphi) +% + S \\ +% \Downarrow (c\equiv1)\\ +% \begin{aligned} +% \frac{\partial \phi_{i,j}}{\partial t} = & \psi_{i,j} \\ +% \frac{\partial \psi_{i,j}}{\partial t} = & +% \frac{\varphi_{i+1,j} - 2\varphi_{i,j}+\varphi_{i-1,j}} +% {2\Delta x^2} + \\ +% & \frac{\varphi_{i,j+1} - 2\varphi_{i,j}+\varphi_{i,j-1}} +% {2\Delta y^2} + S_{i,j} +% \end{aligned} +% \end{gather*} +% \end{columns} +%} + \frame{ \frametitle{WaveToyMoL Thorn} Thorn structure:

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[svn:einsteintoolkit] Workshop_Summer_2013/tutorial/ (Rev. 19)
by sbrandt＠cct.lsu.edu 26 Jul '13

26 Jul '13

User: sbrandt Date: 2013/07/26 09:39 AM Modified: /tutorial/ Cac.tex Log: Added Frank's suggestions. File Changes: Directory: /tutorial/ ===================== File [modified]: Cac.tex Delta lines: +20 -6 =================================================================== --- tutorial/Cac.tex 2013-07-26 14:31:34 UTC (rev 18) +++ tutorial/Cac.tex 2013-07-26 14:39:05 UTC (rev 19) @@ -37,7 +37,8 @@ \begin{verbatim} cgwas@cgwas:~$ cd Cactus -cgaws@cgwas:~/Cactus$ ./simfactory/bin/sim build +cgaws@cgwas:~/Cactus$ ./simfactory/bin/sim build \ +--thornlist ~/einsteintoolkit.th Building sim Cactus - version: 4.2.0 Building configuration sim @@ -153,26 +154,39 @@ \item Copy local changes to the remote machine using the synchronize command: \begin{verbatim} -cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim sync \ - zwicky.cacr.caltech.edu +cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim sync zwicky \end{verbatim} \end{itemize} } \frame[containsverbatim]{ \frametitle{Running Remotely} \begin{itemize} +\item You'll need to create the simulations directory +on zwicky. +\begin{verbatim} +cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim login zwicky +sxs-39@zwicky:~/$ mkdir ~/simulations +\end{verbatim} +\item You can perform all the build, submit, commands +on zwicky now, or you can exit and use the --remotemachine +options. We'll do the latter. +\end{itemize} +} + +\frame[containsverbatim]{ \frametitle{Running Remotely} +\begin{itemize} \item Submit the job on the remote machine (after creating an appropriately named simulation): \begin{verbatim} cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim submit \ --procs 12 \ - --remotemachine zwicky.cacr.caltech.edu \ + --remotemachine zwicky \ s2 \end{verbatim} \item Monitor the simulations: \begin{verbatim} -cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim list-simulations \ - --remotemachine zwicky.cacr.caltech.edu +cgwas@cgwas:~/Cactus$ ./simfactory/bin/sim \ + list-simulations --remotemachine zwicky s1 [ACTIVE (FINISHED), restart 0001, job id -1] \end{verbatim} \end{itemize}

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[svn:einsteintoolkit] Workshop_Summer_2013/tutorial/ (Rev. 18)
by sbrandt＠cct.lsu.edu 26 Jul '13

26 Jul '13

User: sbrandt Date: 2013/07/26 09:31 AM Modified: /tutorial/ Cac.tex Log: Make the ~ display File Changes: Directory: /tutorial/ ===================== File [modified]: Cac.tex Delta lines: +1 -1 =================================================================== --- tutorial/Cac.tex 2013-07-26 13:27:46 UTC (rev 17) +++ tutorial/Cac.tex 2013-07-26 14:31:34 UTC (rev 18) @@ -123,7 +123,7 @@ \frame[containsverbatim]{ \frametitle{Running} \begin{itemize} -\item Your simulation will be stored in the ~/simulations directory. +\item Your simulation will be stored in the \verb=~/simulations= directory. \begin{verbatim} cgwas@cgwas:~/Cactus$ ls ~/simulations CACHE s1

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