Users July 2013

users@lists.einsteintoolkit.org

16 participants
22 discussions

New Thorn: LlamaWaveHyperboloidal
by Michael Jasiulek 17 Jul '13

17 Jul '13

Hello all, here is a new thorn: https://bitbucket.org/mjasiulek/llamawavehyperboloidal =============================================================================== LlamaWaveHyperboloidal =============================================================================== This thorn allows to evolve the scalar wave equation in 3D in Kerr spacetimes using Kerr-Schild coordinates which are horizon penetrating. At some transition radius the user can specify where the Kerr-Schild slicing becomes hyperboloidal, thus, 'bends up' to scri (future null infinity). Therefore, no outer (and inner) boundary conditions have to be set, radiation leaves the spacetime 'naturally' through the inner horizon and scri. The waveform at scri is readily computed during the evolution. It uses Llama's spherical 6-patch coordinates (r,u,v), the method-of-lines with 4th-order Runge-Kutta and 4th-,6th- or 8th-order spatial finite-differencing and matching Kreiss-Oliger dissipation. In http://arxiv.org/abs/1109.2513 <http://arxiv.org/abs/1109.2513> (or http://iopscience.iop.org/0264-9381/29/1/015008/ <http://iopscience.iop.org/0264-9381/29/1/015008/>) I used this code to study QNMs, late-time tails in Kerr at scri and to test the novel hyperboloidal transformation used to smoothly attach the hyperboloidal slice. If you find this code useful, please cite the paper Class. Quantum Grav. 29 015008 (2012). =============================================================================== Enjoy, Michael Jasiulek .

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Einstein Toolkit: Minutes for 8 July
by Joshua Faber 15 Jul '13

15 Jul '13

Present: Josh, Vassileos, Frank, Ian, Erik, Philipp, (Peter?) McLachlan: *Erik and Ian want to make several changes to the code: -Allow arguments to be passed via scripts to generate multiple thorns in parallel, rather than sequentially - Design of more high level APIs to streamline declaration of new objects, e.g. tensors - Introduce master calculation for BSSN variables, and use filtering to isolate necessary code to be called in a specific run - Enable making parameters available at either runtime or Kranctime for greater flexibility - Additional Optimizations Carpet: Users are welcome to create their own branches to work on new features, but please use subdirectories as needed to keep the codebase clean. Incoming Thorns: *README has been updated with current status of several thorns and primary maintainer/developer, but some updates are needed from developers * MemSpeed likely moving to ET, but needs a testsuite * CartesianCoordinates requires use of Llama, which is not available in the ET yet

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simulation time
by Udayaraj Khanal 14 Jul '13

14 Jul '13

Dear allI have created a batch queue script and submitted it to queue an example simulation static_tov as in tutorial for new user. Then I checked the status by ./simfactory/bin/sim list-simulations. I got static_tov [ACTIVE (FINISHED), restart 0000, job id -1]. Does this signifies the completion of the simulation?When I logged in by ssh -Y qb.loni.org and give command cd /scratch/ettest52/simulations/static_tov/output-0000/static_tovNo such file or directory. Is it due to not completion of the simulation?How much time does it take to complete a simulation? I have submitted it almost a week before. Udayaraj KhanalProfessorCentral Department of PhysicsTribhuvan UniversityKirtipur, Nepal

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 14 Jul '13

14 Jul '13

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ In short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. In addition to anything that might be brought up at the meeting I would like to discuss the following points: - incoming Currently we do have quite a collection piling up in incoming. This is good. However, now it the best time to work on these, deciding about the faith of these contributions. Doing so means that they should get tested by someone else than someone from the contributing group, ideally multiple maintainers. If we could do so at least for some until Monday this would be great, but realistically we first probably need to remind everyone what these are actually about. So: I would like each author/contributor of the new modules to say just a few words about each of these. Also, please mention how well tested they are from the contributor's side (have they been built on a larger number of machines, or only on very few / are they used in production runs, ect) , and whether there exists sufficient documentation and testsuites to be able to include them as is. I created a README in the root of incoming where I would like to have a very short status indication of each of the contributions. We currently have in incoming: ADMDerivatives CartesianCoordinates CoreCollapseControl IDFileHydro MemSpeed PITTNullCode SphericalSlice Symmetry TOVSolverHot ZelmaniQuadWaveExtract In addition, there are tickets for inclusion of ZelmaniQuadWaveExtract [1], CartesianCoordiantes [2] and CoreCollapseControl [3], which each live in Zelmani [4]. Same goes here: please describe their current status (just very briefly). Please let me know if there is something else I missed for inclusion. - issues up for review There are currently 14 issues up for review, which is a rather high number. Issues up for review mean that someone already has put in enough time and work to come up with a solution that she/he thinks is worthy being considered as fix. What is not needed is a second pair of eyes to decide if this is ok, or should be changed in some way. Please consider going through that list [5] and help a few of these to finally pass. Frank Löffler [1] https://trac.einsteintoolkit.org/ticket/1356 [2] https://trac.einsteintoolkit.org/ticket/1357 [3] https://trac.einsteintoolkit.org/ticket/1358 [4] git://carpetcode.org/Zelmani.git [5] https://trac.einsteintoolkit.org/query?status=review&col=id&col=summary&col…

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Re: [Users] [Commits] [svn:einsteintoolkit] TOVSolver/trunk/ (Rev. 137)
by Roland Haas 11 Jul '13

11 Jul '13

Hello all, > Log: > * remove option to have different gamma and K for different > stars. That's physically impossible. > * adjust test par files (will do so with GRHydro next) > * modify the way solutions are added so that atmosphere cuts > are applied after solutions are added. Otherwise one of the > stars will have the atmosphere added to it. This breaks symmetry. This commit (and the following ones) make the tests fail, at least in subversion (Zelmani is ok since the author *does* provide updated tests, just not in GRHydr/svn, so I could port over the change). I am personally generally unhappy about commits that require everybody to change/update their paramater files unless the change is required to prevent a bug from manifesting. Removing "[0]" from ones parameter file is not hard, but will break each and every single one of them. One of the nice things about Cactus has been that (some parts of it) are fairly stable and developers take care to not introduce changes that require each user to update their parameter files (unless the user wants/needs new features). I am also not sure I agree with the statement that one cannot have different Gama or K for different stars. Even if the same Gamma and K would be needed for all neutron stars (which I also don't fully understand, why should not a different Gamam or K be a better approximiation to NS of different massses?) there is still the possiblilty of setting up two different sorts of stars and evolve those. Note that I make no statement how to proceed with such an evolution past the point where the stars would touch. To my knowledge only Ian Hawke did such simulations in the past, and Ian effective advected the EOS parameters with the fluid if I remember correctly. If someone with more expterise would comment that would be helpful. I would like to revert parts of this patch (keeping the atmosphere treatment that prevents asymetries in the data setup and seems to be currently buggy) and restore the possibility to have different K and Gamma (indep of whether this is physical I don't see a point in removing this functionality). Please comment (in private or on the mailing list). Yours, Roland

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Simfactory/Mojave: machine name error
by Scott Hawley 10 Jul '13

10 Jul '13

Ok, this is pretty low-priority. Working around it no big deal, but it would be nice to have things configured so this didn't come up: I'm at a coffee shop and for some reason simfactory is pulling a weird machine name based on the local subnet. Never seen this before. I'm building from within Eclipse using Mojave. Here's the console log from Mojave->Build... /usr/bin/python simfactory/lib/sim.py build --mdbkey=make -j 1 --verbose bruiser --thornlist /Users/shawley/ThornLists/ThornListBruiser --optionlist /Users/shawley/options.bruiser.mac IN DIRECTORY: /Users/shawley/Cactus Unknown machine name provision.forbidden.wifi-zones.com<http://provision.forbidden.wifi-zones.com> Error: Unknown local machine provision.forbidden.wifi-zones.com<http://provision.forbidden.wifi-zones.com>. Please use 'sim setup' to create a local machine entry from the generic template. Aborting Simfactory. But when I check my environment I can't find any reference to said machine. Mojave->Env yields % env ... HOST=provision In fact there's no reference to that domain... % env | grep wifi % ?? And my machine name file is there % ls ~/Cactus/simfactory/mdb/machines/provision.ini /Users/shawley/Cactus/simfactory/mdb/machines/provision.ini Any suggestions for a solution that works automatically, all the time? For now I just turned my wifi off and it works fine... Thanks, Scott

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Re: [Users] [Einstein Toolkit] #1402: adapt admmass test to rev 137 of tovsolver
by Roland Haas 08 Jul '13

08 Jul '13

Hello all, > The patch is fine - but I was under the impression that there isn't > a final decision about that change in TOVSolver in the first place? > Anyway - committed in r56 because currently it's broken and it would > be easy to revert. yes, that (test is currently broken) was my motivation. I'd rather revert some patches (though having to do so by hand is also annoying) then miss an actual change in data and then have to backtrack where it was introduced (happened in the past). Yours, Roland

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Re: [Users] Visit & CarpetHDF5
by Scott Hawley 05 Jul '13

05 Jul '13

Maria, After seeing Frank's email that CarpetHDF5 reading is now integrated into Visit 2.6, I downloaded the Mac binary for 2.6 and found that it works -- I can read Carpet HDF5 data without doing anything special. And no need to compile Visit from source. :-) I still, however, find it necessary to start VisIt from the command line with the "-noconfig" flag, because I can't seem to get it to properly use "localhost" as a host on the Mac. e.g. I run this... % /Applications/VisIt.app/Contents/Resources/bin/visit -noconfig ...and I haven't bothered trying to get parallel-rendering working yet. Cheers, Scott

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problem installing einsteintoolkit
by Udayaraj Khanal 05 Jul '13

05 Jul '13

Dear All, I am a new user of einsteintoolkit. I follow the Tutorial for New User to install but encountered a problem. First I login to the queenbee machine by using code ubuntu$ ssh -X ettest52(a)qb.loni.org -sh-3.00$ Then i did as in prepare tools and then download, configure and build. This downloads many thorns but checking out module:PITTNullCode/SphericalHarmonicRecon from repository:http://svn.einsteintoolkit.org/Cactus/PITTNullCode/SphericalHarm… branches/ET_2013_05 into: cactus/arrangements use of uninitialized value in contenation(.) or string at/GetComponents line 1440 Warning: could not checkout EinsteinAnalysis/Outflow, unable to switch to tag. Any existing symlinks to EinsteinAnalysis/Outflow will be broken. ----------------------------------------------------------------------- > checking out module: EinsteinExact/doc > from repository: git://github.com/barrywardell/EinsteinExact > then same error as above > ------------------------------------------------------------------- > Then nothing happens for a long time. > Then I closed terminal(massage: still a process running, closing the > terminal will kill it). > Again I opened terminal and login to queenbee as above. > -sh-3.00$ ./GetComponents --parallel > http://svn.einsteintoolkit.org/manifest/branches/ET_2013_05/einsteintoolkit… > update all existing components : no > Again I encountered the same problem as above. And nothing happens for > a long time then I closed terminal. > Again I opened terminal and login to queenbee > I did as stated in configure the simulation factory > ___________________________________- > edit simfactory/etc/defs.local.ini > Defaults for all machines > user=ettest52 > email=urkhanal(a)tucdp.edu.np > allocation=loni_cactus08 > thornlist=manifest/einsteintoolkit.th > Customize user name for each machine > [queenbee] > user=ettest52 > sourcebasedir=/home/ettest52/ > writeout > __________________________________ > -sh-3.00$ ./simfactory/bin/sim build > > After many processes > --------------------------------------------------- > There were 84 errors during execution of CST > These must be corrected before compilation can proceed > -------------------------------------------------------- > -------------------------------------------------- > warnings were generated during execution of the CST > --------------------------------------------------------- > CST error 1 > Missing thorn EinsteinAnalysis/Outflow > > Similarly there are 84 errors > make[1]:***[/home/ettest52/cactus/configs/sim/config-data/make.thornlist]Error 1 > make:*** [sim] Error 2 > -sh-3.00:ls exe > ls: exe: No such file or directory Udayaraj KhanalProfessorCentral Department of PhysicsTribhuvan UniversityKirtipur, Nepal

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CarpetHDF5 compilation error
by Babiuc-Hamilton, Maria 02 Jul '13

02 Jul '13

Hi, I'm getting this error when compiling the CarpetHDF5 plugging for Visit: clang: warning: argument unused during compilation: ----------------------------------------------------------------- Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 Attribute: () -- The C compiler identification is Clang 4.2.0 -- The CXX compiler identification is Clang 4.2.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Configuring done -- Generating done -- Build files have been written to: /Users/maria/GaussCactus/CarpetHDF5 Scanning dependencies of target ECarpetHDF5Database_par [ 6%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5EnginePluginInfo.C.o clang: warning: argument unused during compilation: '-L/Users/maria/Desktop/VisIt.app/Contents/Resources/2.6.2/darwin-x86_64/include/hdf5/include' [ 12%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5PluginInfo.C.o clang: warning: argument unused during compilation: '-L/Users/maria/Desktop/VisIt.app/Contents/Resources/2.6.2/darwin-x86_64/include/hdf5/include' [ 18%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5CommonPluginInfo.C.o clang: warning: argument unused during compilation: '-L/Users/maria/Desktop/VisIt.app/Contents/Resources/2.6.2/darwin-x86_64/include/hdf5/include' In file included from /Users/maria/GaussCactus/CarpetHDF5/CarpetHDF5CommonPluginInfo.C:40: /Users/maria/GaussCactus/CarpetHDF5/avtCarpetHDF5FileFormat.h:59:10: fatal error: 'hdf5.h' file not found #include "hdf5.h" ^ 1 error generated. make[2]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5CommonPluginInfo.C.o] Error 1 make[1]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/all] Error 2 make: *** [all] Error 2 Maria

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Users July 2013