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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.

1 0

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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Fwd: Problems when opening Visit
by Erik Schnetter 16 Oct '10

16 Oct '10

Stephen There are two slightly different Cactus output formats, depending on which driver you are using, PUGH or Carpet. The VisIt Cactus reader works with Carpet, which is what we use for production runs. The WaveToy demo may be using PUGH as driver, and these files may then not be readable. Which driver did you use? You can see in the parameter file which thorns are activated, and you are probably activating either PUGH or Carpet. VisIt is not very clever about detecting file formats. It may become confused and assume that this is a Pixie file, even though it is actually a Cactus file. -erik On Fri, Oct 15, 2010 at 2:27 PM, Sheler, Stephen Andrew <sheler1(a)live.marshall.edu> wrote: > Hello, > I have a question concerning the opening of Visit and trying to visualize > the wave toy demo there. I am following the instructions on configuring Mac > OS X for Cactus. After compiling HDF5, I opened Visit and ran the file > phi.h5 and this warning was shown... > If this is not a Pixie file, you can manually select the correct file format > reader when opening the file, set the correct reader as a preferred plugin, > disable the Pixie plugin, or request that the developers of the Pixie plugin > add code to distinguish your file from one of theirs. > how do set the correct reader? > one more thing, if I ignore the warning i can visualize but i have the > following error > HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0: > #000: H5G.c line 397 in H5Gopen2(): unable to open group > major: Symbol table > minor: Can't open object > > I would appreciate your help with these problems, > Stephen Sheler > _______________________________________________ > Users mailing list > Users(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users > > -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

1 0

Problems when opening Visit
by Sheler, Stephen Andrew 15 Oct '10

15 Oct '10

Hello, I have a question concerning the opening of Visit and trying to visualize the wave toy demo there. I am following the instructions on configuring Mac OS X for Cactus. After compiling HDF5, I opened Visit and ran the file phi.h5 and this warning was shown... If this is not a Pixie file, you can manually select the correct file format reader when opening the file, set the correct reader as a preferred plugin, disable the Pixie plugin, or request that the developers of the Pixie plugin add code to distinguish your file from one of theirs. how do set the correct reader? one more thing, if I ignore the warning i can visualize but i have the following error HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0: #000: H5G.c line 397 in H5Gopen2(): unable to open group major: Symbol table minor: Can't open object I would appreciate your help with these problems, Stephen Sheler

1 0

simulationfactory issue?
by Richard O'Shaughnessy 15 Oct '10

15 Oct '10

Helloall, 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 ---- udb.pm # What you will refer to the machine as in simfactory commands set_option 'hydra', 'nickname', 'hydra'; set_option 'hydra', 'hostname', 'hydra.phys.uwm.edu'; set_option 'hydra', 'aliaspattern', '^hydra(\.phys\.uwm\.edu)?$'; set_option 'hydra', 'user', 'oshaughn'; set_option 'hydra', 'sourcebasedir', '/home/oshaughn/Numerical/EinsteinToolkit'; set_option 'hydra', 'basedir', '/home/oshaughn/Numerical/simulations'; set_option 'hydra', 'optionlist', 'hydra.cfg'; 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

2 1

Question: odd compilation failure
by Richard O'Shaughnessy 15 Oct '10

15 Oct '10

Hello, While setting up a local cluster, I've run into a problem I just don't understand when compiling. It seems that the compiler's not finding <math.h>! (for one program, at least) To this point, the compilation procedure has proceeded without trouble; I've successfully compiled on other machines. Thoughts? Thanks, -Richard PS: for reference, the compilation is below [oshaughn@hydra Cactus]$ ./simfactory/sim build --thornlist=manifest/einsteintoolkit.th --optionlist=simfactory/optionlists/hydra.cfg </cut> Checking status of thorn LoopControl ________________________________________________________________________ Preprocessing /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c Compiling /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c: In function 'lc_demo': /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c:183: error: 'M_PI' undeclared (first use in this function) /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c:183: error: (Each undeclared identifier is reported only once /home/oshaughn/Numerical/EinsteinToolkit/Cactus/arrangements/Carpet/LoopControl/src/wavetoy-loopcontrol.c:183: error: for each function it appears in.) 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

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