Commits April 2012

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167 discussions

[svn:einsteintoolkit] AHFinder/trunk/src/ (Rev. 409)
by knarf＠cct.lsu.edu 11 Apr '12

11 Apr '12

User: knarf Date: 2012/04/11 02:36 PM Modified: /trunk/src/ AHFinder_int.F Log: fix tab -> space issue which prevented compilation of F77 code File Changes: Directory: /trunk/src/ ====================== File [modified]: AHFinder_int.F Delta lines: +1 -1 =================================================================== --- trunk/src/AHFinder_int.F 2011-10-25 18:44:51 UTC (rev 408) +++ trunk/src/AHFinder_int.F 2012-04-11 19:36:38 UTC (rev 409) @@ -981,7 +981,7 @@ . 1, input_array,0, 0, input_array_type, 1, . input_array_type, reduction_value) - intarea=aux + intarea=aux input_array_type(1) = CCTK_VARIABLE_REAL reduction_value(1)= CCTK_PointerTo(aux)

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[svn:einsteintoolkit] Paper_EinsteinToolkit_2010/ (Rev. 316)
by knarf＠cct.lsu.edu 11 Apr '12

11 Apr '12

User: knarf Date: 2012/04/11 01:51 PM Added: / iop_revised2.pdf, iop_revised2.tar.gz Log: version to be submitted to IOP Directory Changes: Directory: /svn:mime-type/ ========================== + application/octet-stream File Changes: Directory: / ============ File [added]: iop_revised2.pdf Delta lines: +0 -0 =================================================================== (Binary files differ) Property changes on: iop_revised2.pdf ___________________________________________________________________ File [added]: iop_revised2.tar.gz Delta lines: +0 -0 =================================================================== (Binary files differ) Property changes on: iop_revised2.tar.gz ___________________________________________________________________

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New changesets in Carpet Mercurial
by Carpet mercurial repositories 10 Apr '12

10 Apr '12

changeset: 3511:e1358b72c543 user: Roland Haas <rhaas(a)caltech.edu> date: Mon Apr 09 16:21:38 2012 -0700 summary: CarpetLib: store OpenMP thread number in dist object changeset: 3512:9a68366f3426 tag: tip user: Roland Haas <rhaas(a)caltech.edu> date: Mon Apr 09 16:22:00 2012 -0700 summary: Carpet: get thread number from CarpetLib's dist object

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[svn:einsteintoolkit] Workshop_Spring_2012/ (Rev. 90)
by tanja.bode＠physics.gatech.edu 10 Apr '12

10 Apr '12

User: tbode Date: 2012/04/10 06:50 AM Added: /et-tour/ et_tour.pdf Modified: /scientific_viz/ scientific_viz.pdf, scientific_viz.tex Log: Add ET tour pdf so workshop website link exists. File Changes: Directory: /et-tour/ ==================== File [added]: et_tour.pdf Delta lines: <Unavailable> Directory: /scientific_viz/ =========================== File [modified]: scientific_viz.pdf Delta lines: <Unavailable> File [modified]: scientific_viz.tex Delta lines: <Unavailable>

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[svn:einsteintoolkit] Workshop_Spring_2012/ (Rev. 89)
by tanja.bode＠physics.gatech.edu 09 Apr '12

09 Apr '12

User: tbode Date: 2012/04/09 03:58 PM Added: / John_Wise_EnzoAlgorithmsMod.pdf Log: Add John Wise's talk. Directory Changes: Directory: /svn:mime-type/ ========================== + application/octet-stream File Changes: Directory: / ============ File [added]: John_Wise_EnzoAlgorithmsMod.pdf Delta lines: +0 -0 =================================================================== (Binary files differ) Property changes on: John_Wise_EnzoAlgorithmsMod.pdf ___________________________________________________________________

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[svn:einsteintoolkit] www/about/members/ (Rev. 787)
by knarf＠cct.lsu.edu 08 Apr '12

08 Apr '12

User: knarf Date: 2012/04/08 10:02 PM Modified: /about/members/ members.txt Log: new member :) File Changes: Directory: /about/members/ ========================== File [modified]: members.txt Delta lines: +3 -0 =================================================================== --- about/members/members.txt 2012-03-31 14:00:35 UTC (rev 786) +++ about/members/members.txt 2012-04-09 03:02:29 UTC (rev 787) @@ -66,6 +66,9 @@ Bernard Kelly Jennifer Seiler +http://www.northwestern.edu/ Northwestern University + Carl Rodriguez + http://www.osaka-u.ac.jp/en Osaka University Luca Baiotti

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[svn:einsteintoolkit] Workshop_Spring_2012/supercomputing/ (Rev. 88)
by diener＠cct.lsu.edu 06 Apr '12

06 Apr '12

User: diener Date: 2012/04/06 07:33 AM Modified: /supercomputing/ supercomputing.tex Log: A few tweaks. File Changes: Directory: /supercomputing/ =========================== File [modified]: supercomputing.tex Delta lines: +6 -3 =================================================================== --- supercomputing/supercomputing.tex 2012-04-06 12:07:18 UTC (rev 87) +++ supercomputing/supercomputing.tex 2012-04-06 12:33:27 UTC (rev 88) @@ -36,21 +36,24 @@ {\em An abstract with a general description of the work may be sufficient, but additional information that will enhance your request may include explanations for why the project needs access to XSEDE resources, how the estimate of resources request was reached, and how the resources requested were selected.} You'll need to submit CV's for PI/co-PI's, and then your request will be considered within a few weeks. On Kraken and Ranger, you can ask for up to 200kSUs, or roughly 20 CPU-years of time. + +The PI can be a post-doc, research staff or a faculty member so you might +have to twist the arm of your advisor. } \frame{\frametitle{Your initial proposal} The recommended format for an initial proposal goes something like this: One paragraph that reads like a scientific abstract. Lay out reasonable goals, and motivate the interesting nature of your proposed research. -In the second paragraph, delve into your code in more detail. Describe how it currently runs, mention any scaling results you have, whether it is built on commonly used packages, how you have modified it, etc. Try to demonstrate that it should be running on a parallel architecture and will do so efficently. +In the second paragraph, delve into your code in more detail. Describe how it currently runs, the numerical methods used, mention any scaling results you have, whether it is built on commonly used packages, how you have modified it, etc. Try to demonstrate that it should be running on a parallel architecture and will do so efficently. } \frame{\frametitle{Your research proposal} Try to remember the following when submitting a larger-scale Research proposal: \begin{itemize} -\item There are numerical relativists on the XSede Resource Allocation Committee (XRAC). Don't spend page after page justifying why the BSSN formalism is a tremendous breakthrough, or why the Einstein Toolkit ior some other software package s well-suited to use on Ranger/Kraken... they already believe it! -\item You do want to demonstrate you understand how to show that codes scale well to the run sizes you propose. Plot scaling results for +\item There are numerical relativists on the XSede Resource Allocation Committee (XRAC). Don't spend page after page justifying why the BSSN formalism is a tremendous breakthrough, or why the Einstein Toolkit or some other software package is well-suited to use on Ranger/Kraken... they already believe it! +\item You do want to demonstrate that you understand how to show that codes scale well to the run sizes you propose. Plot scaling results for cases that are as close as you can reasonably get to the real runs you want to do. This is especially true if you've modified an existing code, even if it is in wide use in its released form. \end{itemize} }

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[svn:einsteintoolkit] Workshop_Spring_2012/et-tour/ (Rev. 87)
by diener＠cct.lsu.edu 06 Apr '12

06 Apr '12

User: diener Date: 2012/04/06 07:07 AM Modified: /et-tour/ et_tour.tex Log: Some final changes. File Changes: Directory: /et-tour/ ==================== File [modified]: et_tour.tex Delta lines: +4 -20 =================================================================== --- et-tour/et_tour.tex 2012-04-06 04:39:59 UTC (rev 86) +++ et-tour/et_tour.tex 2012-04-06 12:07:18 UTC (rev 87) @@ -17,7 +17,7 @@ \item EinsteinBase. \item EinsteinInitial. \item EinsteinEvolve - \item Einsteinanalysis. + \item EinsteinAnalysis. \item Miscellaneous. \end{itemize} } @@ -47,8 +47,6 @@ The script can also check the status of each component, create diffs or check out from a specific date. - -GetComponents was written by Eric Seidel. } \frame{\frametitle{SimFactory} @@ -74,8 +72,6 @@ check the status of simulations, stop simulations and delete simulations. Simfactory guards against common human errors when managing simulations. - -Simfactory was written by Erik Schnetter and Michael Thomas. } \frame{\frametitle{Computational Infrastructure} @@ -109,8 +105,6 @@ Carpet is the Adaptive Mesh Refinement (AMR) driver used by most (if not all) of the numerical relativity groups that uses Cactus. -It's developed primarily by Erik Schnetter. - The code is continuously being developed and upgraded for efficiency and scalability on modern supercomputer architectures. @@ -122,7 +116,7 @@ \item Splitting grid functions and grid arrays among the MPI processes and to allocate memory for them. \item Setup the mesh refinement grid hierarchy. - \item Communicate ghost cell information between neighbouring MPI processes + \item Communicate ghost cell information between neighboring MPI processes when needed. \item Communicate between different refinement levels by prolongation and restriction when necessary. @@ -212,7 +206,7 @@ \begin{description} \item[TwoPunctures] Puncture binary black hole initial data. \item[Meudon\_Bin\_BH] Meudon binary black hole initial data. - \item[Noexcision] Turduckening. + \item[NoExcision] Turduckening. \item[Exact] A bunch of exact solutions to the Einstein equations. \item[TOVSolver] Single TOV star. \item[Meudon\_Bin\_NS] Meudon binary neutron star initial data. @@ -225,7 +219,7 @@ } \frame{\frametitle{EinsteinEvolve} -The EinsteinToolkit provides McLachlan for spacetime evolution and GRHydro +The Einstein Toolkit provides McLachlan for spacetime evolution and GRHydro for GRMHD matter evolution. The codes are designed to interoperate through the ADMBase and TmunuBase @@ -264,18 +258,8 @@ \frame{\frametitle{Miscellaneous} \begin{description} - \item[HTTPD] A thorn that turns your simulation into a web server. \item[Cartoon2D] A thorn that allows you to perform 2D simulations with a 3D code. - \item[Dissipation] A thorn that allows you to add Kreiss-Oliger dissipation - to any evolved variable. - \item[Formaline] A thorn that stores the complete source tree in the - executable. - \item[NaNChecker] A thorn that checks for NaN's. - \item[TerminationTrigger] A thorn that triggers checkpointing and - termination. - \item[TimerReport] A thorn that reports the time spent in scheduled routines. - \item[SphericalSurface] A thorn that stores surfaces of spherical topology. \item[SummationByParts] A thorn that provides summation by parts finite difference operators and compatible dissipation operators. \end{description}

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[svn:einsteintoolkit] Workshop_Spring_2012/ (Rev. 86)
by knarf＠cct.lsu.edu 05 Apr '12

05 Apr '12

User: knarf Date: 2012/04/05 11:40 PM Added: /future/ future.pdf, future.tex, recompile /pics/ arrow.jpeg, logo.png, multipatch1.pdf, multipatch2.pdf, non_rectangular_grid.jpg Log: some slides for the future of the ET Directory Changes: Directory: /svn:executable/ =========================== + * Directory: /svn:mime-type/ ========================== + application/octet-stream File Changes: Directory: /future/ =================== File [added]: future.pdf Delta lines: +0 -0 =================================================================== (Binary files differ) Property changes on: future/future.pdf ___________________________________________________________________ File [added]: future.tex Delta lines: +119 -0 =================================================================== --- future/future.tex (rev 0) +++ future/future.tex 2012-04-06 04:39:59 UTC (rev 86) @@ -0,0 +1,119 @@ +\input{../preamble} +\usepackage{ragged2e} +\usecolortheme[RGB={200,200,200}]{structure} + +\subtitle[Future of the ET]{{\large Einstein Toolkit Workshop}\\*[0.3em]The Future of the Einstein Toolkit} +\author[\mbox{\includegraphics[height=0.6em]{fl_300}\hspace{0.5em}Frank LÃ¶ffler}]{Dr Frank LÃ¶ffler} +\date{Apr 06 2012} +\titlegraphic{\includegraphics[height=3cm]{einstein_flip}\includegraphics[height=2cm]{logo}\\ + \tiny Supported by NFS grants 0903973/0903782/0904015 (CIGR)} + +\begin{document} + +\frame{\titlepage} + +\frame{\frametitle{Future} + \begin{centering} + \includegraphics[height=2cm]{arrow}\\ + \end{centering} + In general: + \begin{itemize} + \item Inviting users and contributions + \item Currently Cactus-centric, does not need to be + \item Also looking for analysis tools / scripts\\ + (e.g. gravitational wave postprocessing tools, visualization networks) + \end{itemize} + In particular: + \begin{itemize} + \item Multipatch techniques, GPU support + \item MHD improvements, more EOSs, neutrino transport, ... + \end{itemize} +} + +\frame{\frametitle{Inviting users and contributions} + Requirements: + \begin{itemize} + \item Open Source: free software license + \item High product of + \begin{itemize} + \item Usefulness + \item Usability + \item Readability / Maintainability + \end{itemize} + \item Availability to public through revision control + \item At least one ET maintainer with write permissions + \end{itemize} +} + +\frame{\frametitle{Also looking for analysis tools / scripts} + \begin{itemize} + \item Postprocessing tools + \begin{itemize} + \item gravitational wave data processing + \item data format conversion + \item physics-analysis + \end{itemize} + \item Visualization networks + \item Data format import and export plugins + \item Usability scripts + \item Cactus syntax highlighting for common editors + \item Cactus plugin for Eclipse (Mojave: \texttt{http://mojave.cct.lsu.edu/}) + \end{itemize} +} + +\frame{\frametitle{New Physics / Models: Non-rectangular grids} +\begin{centering} + \includegraphics[height=7.5cm]{non_rectangular_grid}\\ +\end{centering} +} +\frame{\frametitle{New Physics / Models: Multipatch} +\includegraphics[height=4cm]{multipatch1}\hspace{1cm} +\includegraphics[height=5cm]{multipatch2}\\ +} + +\frame{\frametitle{New Physics / Models: GPU support} + \begin{itemize} + \item Support for + \begin{itemize} + \item OpenCL + \item CUDA + \end{itemize} + \item Automatic tranfer of data between CPU \& GPU + \item Automatic domain-decomposition/syncs between multiple GPGPUs + \item Simultanous computation on CPU \& GPU + \item Dynamic load-balancing + \end{itemize} +} + +\frame{\frametitle{New Physics / Models: MHD improvements} + \begin{itemize} + \item Constraint transport + \item Vector potential + \begin{itemize} + \item at cell centers + \item at cell faces + \end{itemize} + \item Non-ideal MHD + \end{itemize} +} + +\frame{\frametitle{New Physics / Models: radiation transport} + \begin{itemize} + \item Very important for a number of ``hot'' topics + \item 7D problem + \begin{itemize} + \item 3D: position (space) + \item 3D: direction + \item 1D: energy / frequency + \end{itemize} + \item Neutrinos / EM + \item Best methods still unclear + \begin{itemize} + \item Monte Carlo? + \item Deterministic methods in 3D? + \item Various approximations of full 7D problem + \end{itemize} + \end{itemize} +} + +\end{document} File [added]: recompile Delta lines: +14 -0 =================================================================== --- future/recompile (rev 0) +++ future/recompile 2012-04-06 04:39:59 UTC (rev 86) @@ -0,0 +1,14 @@ +#!/bin/bash + +function pdf { + NAME=$1 + pdflatex $NAME.tex + pgrep -f "xpdf -remote 127.0.0.1 $NAME.pdf" 2>&1 > /dev/null + if [ $? == 0 ]; then + xpdf -remote 127.0.0.1 -reload -raise + else + xpdf -remote 127.0.0.1 $NAME.pdf & + fi +} + +pdf future Property changes on: future/recompile ___________________________________________________________________ Directory: /pics/ ================= File [added]: arrow.jpeg Delta lines: +0 -0 =================================================================== (Binary files differ) Property changes on: pics/arrow.jpeg ___________________________________________________________________ File [added]: logo.png Delta lines: +0 -0 =================================================================== (Binary files differ) Property changes on: pics/logo.png ___________________________________________________________________ File [added]: multipatch1.pdf Delta lines: +0 -0 =================================================================== (Binary files differ) Property changes on: pics/multipatch1.pdf ___________________________________________________________________ File [added]: multipatch2.pdf Delta lines: +0 -0 =================================================================== (Binary files differ) Property changes on: pics/multipatch2.pdf ___________________________________________________________________ File [added]: non_rectangular_grid.jpg Delta lines: +0 -0 =================================================================== (Binary files differ) Property changes on: pics/non_rectangular_grid.jpg ___________________________________________________________________

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[svn:einsteintoolkit] Workshop_Spring_2012/et-tour/ (Rev. 85)
by diener＠cct.lsu.edu 05 Apr '12

05 Apr '12

User: diener Date: 2012/04/05 04:09 PM Modified: /et-tour/ et_tour.tex Log: More slides for tour of ET. File Changes: Directory: /et-tour/ ==================== File [modified]: et_tour.tex Delta lines: +129 -5 =================================================================== --- et-tour/et_tour.tex 2012-04-05 20:14:36 UTC (rev 84) +++ et-tour/et_tour.tex 2012-04-05 21:09:35 UTC (rev 85) @@ -15,10 +15,10 @@ \item Support Tools. \item Computational Infrastructure. \item EinsteinBase. - \item Spacetime evolution. - \item Spacetime analysis. - \item Matter evolution. - \item Matter analysis. + \item EinsteinInitial. + \item EinsteinEvolve + \item Einsteinanalysis. + \item Miscellaneous. \end{itemize} } @@ -147,13 +147,137 @@ \item TmunuBase (basic stress-energy variables). \item EOS\_Base (EOS registration). \item EOSG\_Base (interface to generic EOS'). + \item Constants (Provides $c$, $G$ and $M_{\odot}$ in various units). \item CoordGauge (not used by many thorns anymore). \item ADMCoupling (not used by many thorns anymore). \item ADMMacros (Macros for calculating various quantities based on the ADM variables). - \item Constants (Provides $c$, $G$ and $M_{\odot}$ in various units). \item StaticConformal (variables for a static conformal factor; not used anymore). \end{itemize} } + +\frame{\frametitle{ADMBase} +ADMBase is the glue that holds the Einstein Toolkit together. It serves 3 main +functions. +\begin{enumerate} + \item It defines groups of grid functions for the basic variables: + metric (gxx, gxy, gxz, gyy, gyz, gzz), + extrinsic curvature (kxx, kxy, kxz, kyy, kyz, kzz), + lapse (alp), shift (betax, betay, betaz), + time derivative of the lapse (dtalp) and time derivative of the + shift (dtbetax, dtbetay, dtbetaz) along with their symmetry information. + \item Defines basic parameters to choose the initial data, evolution + method and number of active timelevels that other thorns can use or + extend where appropriate. Ensures that only one initial data or + evolution method can be chosen at a time. + \item Defines a schedule group for other thorns to schedule their + routines modifying the ADMBase variables. Used correctly, + ensures that the ADMBase variables gets modified at the right time in + the Cactus schedule so they are available when needed by other thorns. +\end{enumerate} +Also contains routines for Minkowski initial data and `static' evolutions. +} + +\frame{\frametitle{HydroBase} +Provides the basic variables for matter evolution. +\begin{itemize} + \item {\tt rho}: rest mass density $\rho$ + \item {\tt press}: pressure $P$ + \item {\tt eps}: Specific internal energy $\epsilon$ + \item {\tt vel[3]}: contravariant fluid three velocity $v^i$ + \item {\tt w\_lorentz}: Lorentz factor $\gamma$ + \item {\tt Y\_e}: electron fraction $Y_e$ + \item {\tt temperature}: temperature $T$ + \item {\tt entropy}: specific entropy per particle $s$ + \item {\tt Bvec[3]}: contravariant magnetic field vector $B^i$ +\end{itemize} +Also sets up scheduling groups for recommended interaction with the fluid variables. +} + +\frame{\frametitle{TmunuBase} +Defines the grid functions for the stress-energy tensor. +\begin{itemize} + \item The time component $T_{00}$: {\tt eTtt} + \item The mixed components $T_{0i}$: {\tt eTtx}, {\tt eTty}, {\tt eTtz} + \item The spatial components $T_{ij}$: {\tt eTxx}, {\tt eTxy}, {\tt eTxz}, + {\tt eTyy}, {\tt eTyz}, {\tt eTzz} +\end{itemize} +Also sets up scheduling groups for other thorns to schedule routines that adds +to the stress-energy tensor. +} + +\frame{\frametitle{EinsteinInitial} +Many kinds of initial data are available in the Einstein Toolkit +\begin{description} + \item[TwoPunctures] Puncture binary black hole initial data. + \item[Meudon\_Bin\_BH] Meudon binary black hole initial data. + \item[Noexcision] Turduckening. + \item[Exact] A bunch of exact solutions to the Einstein equations. + \item[TOVSolver] Single TOV star. + \item[Meudon\_Bin\_NS] Meudon binary neutron star initial data. + \item[Meudon\_Mag\_NS] Meudon binary magnetized neutron star initial data. + \item[GRHydro\_InitData] Test initial data for hydro evolutions. + \item[Other] Many other less used (i.e.\ old and less accurate) initial + data thorns. +\end{description} +More are welcome. +} + +\frame{\frametitle{EinsteinEvolve} +The EinsteinToolkit provides McLachlan for spacetime evolution and GRHydro +for GRMHD matter evolution. + +The codes are designed to interoperate through the ADMBase and TmunuBase +interface. + +For black hole simulations we have PunctureTracker that allow us to track the +black holes and move the refined grids accordingly. + +You have been working on a similar thorn for neutron star simulations during +the hands on session at this workshop. + +NewRad is a radiative boundary condition thorn and LegoExcision provides +excision (not used very often anymore). +} + +\frame{\frametitle{EinsteinAnalysis} +Several thorns in the Einstein Toolkit can be used to analyze numerical +spacetimes +\begin{description} + \item[AHFinderDirect] Find black hole apparent horizons quickly. + \item[AHfinder] Find black hole apparent horizons slowly. + \item[QuasiLocalMeasures] Calculate spins of surfaces with spherical topology. + \item[WeylScal4] Calculate the Newman-Penrose scalar $\Psi_4$. + \item[Multipole] Decompose arbitrary grid functions into spin-weighted + spherical harmonics. + \item[Extract] Perform Regge-Wheeler-Zerilli 1st order gauge invariant + gravitational wave extraction. + \item[PITTNullCode] Cauchy extraction of gravitational waves. + \item[ADMAnalysis] Calculate several quantitites from the ADM variables. + \item[EHFinder] Find event horizons in numerical spacetimes. + \item[ADMConstraints] Calculate the ADM constraints from the ADM variables. + \item[Hydro\_Analysis] Calculate various quantities related to the + density maximum of matter evolutions. +\end{description} +} + +\frame{\frametitle{Miscellaneous} +\begin{description} + \item[HTTPD] A thorn that turns your simulation into a web server. + \item[Cartoon2D] A thorn that allows you to perform 2D simulations with a 3D + code. + \item[Dissipation] A thorn that allows you to add Kreiss-Oliger dissipation + to any evolved variable. + \item[Formaline] A thorn that stores the complete source tree in the + executable. + \item[NaNChecker] A thorn that checks for NaN's. + \item[TerminationTrigger] A thorn that triggers checkpointing and + termination. + \item[TimerReport] A thorn that reports the time spent in scheduled routines. + \item[SphericalSurface] A thorn that stores surfaces of spherical topology. + \item[SummationByParts] A thorn that provides summation by parts finite + difference operators and compatible dissipation operators. +\end{description} +} \end{document}

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Commits April 2012