Users October 2010

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15 participants
33 discussions

Meeting minutes
by Roland Haas 25 Oct '10

25 Oct '10

Meeting minutes: Present were: Frank, Tanja, Roland, Bruno, Ian, Peter * MHD: testing is taking place, all are encouraged to try and run the hydro-tests in GRHydro using the MHD codebase and Bvec=0 * we originally wanted to release a new version of the toolkit this week. We will start the process be running the testsuites using the current codebase to see where we might have to fix things. * TS assignments (results to be posted on the website/wiki. Frank will send around a reminder email with more details): ** Ranger: Tanja ** Queenbee: Peter ** Damiana, Kraken: Ian ** Bluedrop: Bruno * no news on citation policy Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net.

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Meeting minutes
by Roland Haas 25 Oct '10

25 Oct '10

Meeting minutes: Present were: Erik, Gabrielle, Chrisitna, Frank, Peter, Ian, Yosef, Tanja, Roland Citation policy: * see attached draft * will put list of requested citations on the wiki * will create a "cheat sheet" for maintainers for releases * will announce trac bug tracker (http://trac.einsteintoolkit.org) on the users mailing list Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net.

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Reminder weekly call, Monday Oct 25
by Frank Loeffler 25 Oct '10

25 Oct '10

Hi, The next weekly Einstein Toolkit telecon will be today: Monday, Oct 25th, 10am central US time. We will mainly catch up with everything that has been done during the last week: - MHD progress - new EOS - ...? As usual, find the instructions for the call on the ET web pages [1]. Frank Loeffler [1] http://einsteintoolkit.org/info/support/

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Re: [Users] using WeylScal4 and Multipole for WF output -- scheduling issues
by Ian Hinder 23 Oct '10

23 Oct '10

On 21 Oct 2010, at 20:58, Bernard Kelly wrote: > Hi all. > > I'm trying some GW extraction from a Carpet/McLachlan black-hole > binary evolution. I thought the combination of thorns WeylScal4 and > Multipole would give me something reasonable, but I'm having trouble > with it. > > I'm attaching a parameter file for my run. As you can see, the > extraction is supposed to be over a set of coordinate spheres at > radii 45, 50 55, 60 65, & 70. > > What I get is NaN in the WFs at all timesteps after t=0. I'm also > outputting 2D data (though not as frequently), and Psi4 seems well- > behaved. So what's going wrong? > > I have noted that though the routine "Multipole_Calc" should happen > after "calc_np" according to its schedule.ccl, it appears -before- > GROUP WeylScal4_Calculate in the run's initial printing of scheduled > routines. Could you post the schedule output? According to the copy of the code that I have from the release version, Multipole_Calc is called in ANALYSIS and WeylScal4_Calculate is called in MoL_PseudoEvolution, which is called in EVOL (and some other places). The calc_np is a relic from when both were called in ANALYSIS. > Suggestions appreciated, I tried to run your parameter file to test, but unfortunately I have some work-in-progress hacks to my local copy of WeylScal4, so it didn't run. Nevertheless, I think I know what the problem is. The spatial triad used by WeylScal4 is a coordinate triad (d/dph, d/dr, d/ dth), suitably orthonormalised. This triad is singular on the z axis, and the way it is computed there leads to a NaN. When you compute spherical harmonic modes, points on the z axis (th = 0) are multiplied by sin(th) = 0, so the value on the axis is never used, but numerically the NaN still causes problems. There are several approaches to this: 1. Replace the triad at that point with a different one. This way, Psi4 on th = 0 is still "Psi4", just with respect to a different tetrad at that point. This is probably the best approach, and I have it implemented in my local copy. I can commit this to the development version. 2. Use an open integration formula on (0,Pi) on the 2-sphere when doing the mode decomposition. This means that the point at th = 0 is not used. Multipole does not do this, but it wouldn't be too hard to modify it. 3. Do a numerical trick to make sure that the point at th = 0 doesn't have a NaN. The particular trick I usually use is to offset the coordinates used to construct the spatial triad by 10^-15 in one direction. WeylScal4::offset = 1e-15 This is what I did before I implemented the triad change on the axis. What do other people do to get around this problem? Would some more physical tetrad (e.g. quasi-Kinnersley?) help? > P.S. Is this appropriate to einsteintoolkit, or Cactus at large? I'm > using the ET_2010_06 release ... WeylScal4 and Multipole are both part of the Einstein Toolkit (in the EinsteinAnalysis arrangement), so discussion is probably best on the ET list. I have CC'd this message to that list. Other comments about your parameter file: * You have asked for the mode decomposition of Psi4r and Psi4i individually, and you have not set the spin weight parameter, so it will default to 0, which is not what you want. Try Multipole::variables = "WeylScal4::Psi4r{sw=-2 cmplx='WeylScal4::Psi4i' name='Psi4'}" instead. This tells Multipole to use spin weight -2 for Psi4, and to treat Psi4r and Psi4i as the real and imaginary parts of a complex number. This means you don't have to recombine the modes of the real and imaginary parts by hand. WeylScal4 and Multipole could be modified to work with Cactus complex grid functions, but I don't have any experience with using them, and Kranc does not currently support them. * Your time_refinement_factors parameter is quite aggressive - you are using time refinement only for finest four levels. You can probably get away with time refinement for the last 6, or more depending on your finite differencing order and value of eta. * I recommend using the parameters TimerReport::out_every = 32 TimerReport::n_top_timers = 40 which will give you a quick overview of the parts of the code which are taking the most time. Apart from those points, the parameter file looks fine. -- Ian Hinder ian.hinder(a)aei.mpg.de

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commits mailing list and trac
by Frank Loeffler 19 Oct '10

19 Oct '10

Hi, we are currently testing a bug tracker for the Einstein Toolkit. This can send email notifications if a new ticket is issued or an existing is changed, e.g. closed. In addition to sending that to the reporter/assigned person, it can also send those emails to a general address. At the moment this is the commits email list. I don't think that this is the best option. There could be another email list e.g. trac(a)einsteintoolkit.org. The advantage would be that there would be less traffic on the commits mailing list, but the disadvantage is that there would be yet another mailing list where people could/would have to subscribe. Please discuss which of the options would serve more people, e.g you. Frank

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Git problem: "git pull" vs. "git pull -a"?
by Erik Schnetter 18 Oct '10

18 Oct '10

I notice that GetComponents uses the command "git pull -a" instead of "git pull" to update existing repositories. I also notice that many of my git repositories which I updated via GetComponents have spurious merge patches in there, apparently automatically committed by myself, merging many versions of "master": commit 2db16f219702be9b9bbdbe3290cd4ec67f514dbd Author: Erik Schnetter <schnetter(a)cct.lsu.edu> Date: Tue Sep 14 21:54:25 2010 -0500 Merge branches 'master', 'master', 'master', 'master', 'master' and 'master' Another problem is that the checked out version of my source tree does not change. In addition, the additional patches that have been pulled in are marked as "undone" in the staging area, so that my next "git commit" would create a patch that undoes them. What does "git pull -a" do? Is that a bad option? I don't understand the description of the git-pull man page; it says: -a, --append Append ref names and object names of fetched refs to the existing contents of .git/FETCH_HEAD. Without this option old data in .git/FETCH_HEAD will be overwritten. Do we need to leave out the "-a" option? Or are my spurious merge commits caused by something else? I didn't have any local changes to start with. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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Thorn References
by Frank Loeffler 18 Oct '10

18 Oct '10

Hi, this is a (known to be incomplete) short list of papers which are requested to be cited when the relevant thorns are used - to have an idea what kind of papers we talk about. This is to be discussed in todays phone call. Frank EinsteinAnalysis/AHFinderDirect: @Article{Thornburg:2003sf, author = "Thornburg, Jonathan", title = "{A Fast Apparent-Horizon Finder for 3-Dimensional Cartesian Grids in Numerical Relativity}", journal = "Class. Quant. Grav.", volume = "21", year = "2004", pages = "743-766", eprint = "gr-qc/0306056", archivePrefix = "arXiv", doi = "10.1088/0264-9381/21/2/026", SLACcitation = "%%CITATION = GR-QC/0306056;%%" } EinsteinAnalysis/EHFinder: @Article{Diener:2003jc, author = "Diener, Peter", title = "{A new general purpose event horizon finder for 3D numerical spacetimes}", journal = "Class. Quant. Grav.", volume = "20", year = "2003", pages = "4901-4918", eprint = "gr-qc/0305039", archivePrefix = "arXiv", doi = "10.1088/0264-9381/20/22/014", SLACcitation = "%%CITATION = GR-QC/0305039;%%" } EinsteinAnalysis/NoExcision: @Article{Brown:2007pg, author = "Brown, J. David and others", title = "{Excision without excision: the relativistic turducken}", journal = "Phys. Rev.", volume = "D76", year = "2007", pages = "081503", eprint = "0707.3101", archivePrefix = "arXiv", primaryClass = "gr-qc", doi = "10.1103/PhysRevD.76.081503", SLACcitation = "%%CITATION = 0707.3101;%%" } @Article{Brown:2008sb, author = "Brown, J. David and Diener, Peter and Sarbach, Olivier and Schnetter, Erik and Tiglio, Manuel", title = "{Turduckening black holes: an analytical and computational study}", journal = "Phys. Rev.", volume = "D79", year = "2009", pages = "044023", eprint = "0809.3533", archivePrefix = "arXiv", primaryClass = "gr-qc", doi = "10.1103/PhysRevD.79.044023", SLACcitation = "%%CITATION = 0809.3533;%%" } EinsteinAnalysis/TwoPunctures: @Article{Ansorg:2004ds, author = "Ansorg, Marcus and Bruegmann, Bernd and Tichy, Wolfgang", title = "{A single-domain spectral method for black hole puncture data}", journal = "Phys. Rev.", volume = "D70", year = "2004", pages = "064011", eprint = "gr-qc/0404056", archivePrefix = "arXiv", doi = "10.1103/PhysRevD.70.064011", SLACcitation = "%%CITATION = GR-QC/0404056;%%" } EinsteinEvolve/LegoExcision @unpublished{Alcubierre2003:BBH0-excision, author = {Miguel Alcubierre and Bernd Br{\"u}gmann and Peter Diener and Frank Herrmann and Denis Pollney and Edward Seidel and Ryoji Takahashi}, title = "Testing excision techniques for dynamical {3D} black hole evolutions", X-note = "submitted to Phys. Rev. D", year = 2004, eprint = {gr-qc/0411137}, } "Should we keep this? It is unpublished. EinsteinEvolve/GRHydro @Article{Baiotti:2010zf, author = "Baiotti, Luca and Hawke, Ian and Montero, Pedro J. and Rezzolla, Luciano", title = "{A new three-dimensional general-relativistic hydrodynamics code}", journal = "Mem. Soc. Ast. It.", volume = "74", year = "2003", pages = "S210", eprint = "1004.3849", archivePrefix = "arXiv", primaryClass = "gr-qc", SLACcitation = "%%CITATION = 1004.3849;%%" } EinsteinInitialData/Meudon_Bin_BH @Article{Gourgoulhon:2001ec, author = "Gourgoulhon, Eric and Grandclement, Philippe and Bonazzola, Silvano", title = "{Binary black holes in circular orbits. I. A global spacetime approach}", journal = "Phys. Rev.", volume = "D65", year = "2002", pages = "044020", eprint = "gr-qc/0106015", archivePrefix = "arXiv", doi = "10.1103/PhysRevD.65.044020", SLACcitation = "%%CITATION = GR-QC/0106015;%%" } @Article{Grandclement:2001ed, author = "Grandclement, Philippe and Gourgoulhon, Eric and Bonazzola, Silvano", title = "{Binary black holes in circular orbits. II. Numerical methods and first results}", journal = "Phys. Rev.", volume = "D65", year = "2002", pages = "044021", eprint = "gr-qc/0106016", archivePrefix = "arXiv", doi = "10.1103/PhysRevD.65.044021", SLACcitation = "%%CITATION = GR-QC/0106016;%%" } EinsteinInitialData/Meudon_Bin_NS @Article{Gourgoulhon:2000nn, author = "Gourgoulhon, Eric and Grandclement, Philippe and Taniguchi, Keisuke and Marck, Jean-Alain and Bonazzola, Silvano", title = "{Quasiequilibrium sequences of synchronized and irrotational binary neutron stars in general relativity. I. Method and tests}", journal = "Phys. Rev.", volume = "D63", year = "2001", pages = "064029", eprint = "gr-qc/0007028", archivePrefix = "arXiv", doi = "10.1103/PhysRevD.63.064029", SLACcitation = "%%CITATION = GR-QC/0007028;%%" } LSUThorns/SummationByParts @Article{Diener:2005tn, author = "Diener, Peter and Dorband, Ernst Nils and Schnetter, Erik and Tiglio, Manuel", title = "{New, efficient, and accurate high order derivative and dissipation operators satisfying summation by parts, and applications in three-dimensional multi-block evolutions}", journal = "J. Sci. Comput.", volume = "32", year = "2007", pages = "109-145", eprint = "gr-qc/0512001", archivePrefix = "arXiv", doi = "10.1007/s10915-006-9123-7", SLACcitation = "%%CITATION = GR-QC/0512001;%%" } LSUThorns/QuasiLocalMeasures @Article{Schnetter:2006yt, author = "Schnetter, Erik and Krishnan, Badri and Beyer, Florian", title = "{Introduction to dynamical horizons in numerical relativity}", journal = "Phys. Rev.", volume = "D74", year = "2006", pages = "024028", eprint = "gr-qc/0604015", archivePrefix = "arXiv", doi = "10.1103/PhysRevD.74.024028", SLACcitation = "%%CITATION = GR-QC/0604015;%%" } Carpet/Carpet @Article{Schnetter:2003rb, author = "Schnetter, Erik and Hawley, Scott H. and Hawke, Ian", title = "{Evolutions in 3D numerical relativity using fixed mesh refinement}", journal = "Class. Quant. Grav.", volume = "21", year = "2004", pages = "1465-1488", eprint = "gr-qc/0310042", archivePrefix = "arXiv", doi = "10.1088/0264-9381/21/6/014", SLACcitation = "%%CITATION = GR-QC/0310042;%%" } McLachlan/ML_BSSN This is the first paper published using McLachlan, but doesn't really fit the mold of af method description paper. Should we keep it? @Article{Brown:2008sb, author = "Brown, J. David and Diener, Peter and Sarbach, Olivier and Schnetter, Erik and Tiglio, Manuel", title = "{Turduckening black holes: an analytical and computational study}", journal = "Phys. Rev.", volume = "D79", year = "2009", pages = "044023", eprint = "0809.3533", archivePrefix = "arXiv", primaryClass = "gr-qc", doi = "10.1103/PhysRevD.79.044023", SLACcitation = "%%CITATION = 0809.3533;%%" }

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For discussion today.
by Allen Gabrielle 18 Oct '10

18 Oct '10

Here are the two policies we plan to discuss on the call today.

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Reminder weekly call, Monday Oct 17
by Frank Loeffler 17 Oct '10

17 Oct '10

Hi, Please be reminded of the weekly Einstein Toolkit phone call tomorrow, Monday October 17th at 10am central US time. One of the topics will (again) be to finalize the citation policy, along with a first list of papers and thorns. Have a look at the following link for help regarding the phone call: http://einsteintoolkit.org/info/support/ Frank Loeffler

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Re: [Users] simulationfactory issue?
by Erik Schnetter 17 Oct '10

17 Oct '10

Richard You created a configuration with the non-default name "static_tov". (The default name would be "sim"). Therefore you need to specify this configuration name when you create and submit a simulation: ./simfactory/sim create-submit static_tov --configuration=static_tov --parfile=... You will then have a configuration and a simulation with the same name; this does not matter. I usually have a single configuration "sim", and use this configuration for all my simulations. -erik On Fri, Oct 15, 2010 at 1:16 PM, Richard O'Shaughnessy <oshaughn(a)gravity.phys.uwm.edu> wrote: > Hi Erik > > > After a seemingly successful compile, I tried a simple single-cpu run (using > > generic.sh submission) on my cluster head node. I believe this > > installation is the release version; the only changes have been to the > > optionlist and udb.pm. A similar configuration works on other machines > > (i.e, my laptop, albeit with svn rather than release versions), but for some > > reason not here. It's not creating the simulations directory at all. > > Thoughts? > > --- command-line > > [oshaughn@hydra Cactus]$ ./simfactory/sim create-submit static_tov > > --parfile=par/static_tov.par --procs=1 --walltime=8:0:0 > > Simulation Factory: > > Configuration name(s) not specified -- using default configuration "sim" > > Uncaught exception from user code: > > Configuration "sim" contains no executable at ./simfactory/sim line > > 5216. > > at ./simfactory/sim line 5216 > > main::get_executable() called at ./simfactory/sim line 1883 > > main::command_create('static_tov') called at ./simfactory/sim line > > 2955 > > main::command_create_submit('static_tov') called at ./simfactory/sim > > line 452 > > Richard > > The error message "no executable" indicates that your build didn't > complete. There are probably problems with your compiler or linker > options. > > - All Cactus executables are stored in Cactus's "exe" directories. > What does "ls exe" say? > - Did you specify a different name for your configuration while > building? If so, you need to use the --configuration=... option when > submitting the simulation. > - If you use the --debug or --profile flag while building, you also > need to specify it while submitting a simulation, since you'll need to > use the debugging or profiling executable. > > > Ok. I'm simply trying to follow the EinsteinToolkit new user instructions > on a new machine, as a test case, with one CPU. > 1) executables are made > [oshaughn@hydra Cactus]$ ls exe > cactus_static_tov static_tov > 2) I just changed udb.pm (see original email) The build command (which > says it completed successfully) is > [oshaughn@hydra Cactus]$ ./simfactory/sim build static_tov > --thornlist=manifest/einsteintoolkit.th > 3) I didn't specify any debugging options. > > -erik > > -- > Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/ > > Richard O'Shaughnessy oshaughn(a)gravity.phys.uwm.edu > 462 Physics Building Phone: 414 229 6674 > Center for Gravitation and Cosmology > University of Wisconsin, Milwaukee 53211 > -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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