Users January 2012

users@lists.einsteintoolkit.org

14 participants
28 discussions

Einstein Toolkit Meeting Reminder
by Frank Loeffler 14 May '15

14 May '15

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/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. My agenda contains: - Fall workshop - PLEASE let us know if you come [1]! - Hotel booking - Release planning - release date: Mon Oct 24 2011 - freeze date: Mon Sep 26 - the day of the call! - branch name: ET_2011_10 - List of release-concerning bugs [2] - ET paper: proposed "freeze" by Oct 3rd (Mon after this call) As always: feel free to add to this list. Frank Loeffler [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Fall_2011#Fall_Einstei… [2] https://trac.einsteintoolkit.org/query?status=!closed&milestone=ET_2011_11&…

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Simulation domain volume and reduction weight sum differ
by Jakob Hansen 25 Sep '12

25 Sep '12

Hi, Using mercurial, I get this warning during simulations : INFO (CarpetReduce): Simulation domain volume: 170368000 INFO (CarpetReduce): Reduction weight sum: 170367999.880642 WARNING level 1 in thorn CarpetReduce processor 0 host tachyon2974 (line 120 of /home01/r632kgw/jakob/CactusP/arrangements/Carpet/CarpetReduce/src/mask_test.c): -> Simulation domain volume and reduction weight sum differ Simulations seem to run okay though. What is causing this warning and is it serious or can I just ignore it? Cheers, Jakob

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support_old_CalcTmunu_mechanism
by Frank Loeffler 23 Sep '12

23 Sep '12

Hi, Are there objections to change the default of TmunuBase::support_old_CalcTmunu_mechanism from "yes" to "no"? Frank

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Propose thorns for inclusion in the EinsteinToolkit
by Barry Wardell 26 Apr '12

26 Apr '12

Hi, Recently Ian Hinder and I have created an arrangement of thorns called EinsteinExact which provide some exact solutions for use in Cactus. The scope of these thorns is similar to that of the Exact thorn but with some notable improvements: * The extrinsic curvature is computed symbolically rather than using finite differencing so it should be accurate to within roundoff. This means that EinsteinExact is more exact than Exact. * The solutions used in EinsteinExact come from a database of metrics which have been correctness-tested, e.g., by checking symbolically that they are a solution of the Einstein equation. * EinsteinExact is written in Mathematica and uses Kranc, so the raw source is very small (~250 lines) and easy to understand. * Adding a spacetime is as simple as typing the components of the metric into Mathematica. So far, the spacetimes included are Minkowski, Kerr-Schild, gauge wave and shifted gauge wave, but the list can easily be extended in the future. There is also support for arbitrary rotations, using the same conventions as the Exact thorn uses. We have not yet included the other transformations supported by Exact, but they shouldn't be difficult to add. We have checked that for these spacetimes the Exact solutions converge to the EinsteinExact solutions at the correct finite differencing order used by Exact. We would like to propose the EinsteinExact arrangement for inclusion in the EinsteinToolkit. If you would like to try it out, you can get it using: git clone --recursive git://github.com/barrywardell/EinsteinExact Any comments or suggestions are welcome. Regards, Barry

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changing CarpetRegrid2 parameters for ETK Maxwell + mercurial Carpet?
by Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] 01 Mar '12

01 Mar '12

Hi all. At Erik's suggestion (off-list), I resolved some checkpoint recovery issues by moving from "Curie" to the new ETK release. However, my old grid specifications seem no longer to work. The parameters are for a 2:1 mass-ratio BHB evolution. I've used three "centres" -- one each for the punctures, and one centred at the origin. Below is what I used to have in CarpetRegrid2, which worked with the last "Curie" release of ETK (the full grid is [-2048,2048] in size). ------------------------------------------------------------------- # Parameters of thorn CarpetRegrid2 (implementing CarpetRegrid2) CarpetRegrid2::freeze_unaligned_levels = "yes" CarpetRegrid2::num_centres = 3 CarpetRegrid2::num_levels_1 = 12 CarpetRegrid2::position_x_1 = -3.3333333333333333333 CarpetRegrid2::movement_threshold_1 = 0.10 CarpetRegrid2::radius_1[5] = 40 CarpetRegrid2::radius_1[6] = 20 CarpetRegrid2::radius_1[7] = 10 CarpetRegrid2::radius_1[8] = 5 CarpetRegrid2::radius_1[9] = 2.5 CarpetRegrid2::radius_1[10] = 1.25 CarpetRegrid2::radius_1[11] = 0.625 CarpetRegrid2::num_levels_2 = 13 CarpetRegrid2::position_x_2 = 6.6666666666666666667 CarpetRegrid2::movement_threshold_2 = 0.05 CarpetRegrid2::radius_2[5] = 40 CarpetRegrid2::radius_2[6] = 20 CarpetRegrid2::radius_2[7] = 10 CarpetRegrid2::radius_2[8] = 5 CarpetRegrid2::radius_2[9] = 2.5 CarpetRegrid2::radius_2[10] = 1.25 CarpetRegrid2::radius_2[11] = 0.625 CarpetRegrid2::radius_2[12] = 0.3125 CarpetRegrid2::num_levels_3 = 6 CarpetRegrid2::radius_3[1] = 1024 CarpetRegrid2::radius_3[2] = 512 CarpetRegrid2::radius_3[3] = 256 CarpetRegrid2::radius_3[4] = 160 CarpetRegrid2::radius_3[5] = 96 CarpetRegrid2::regrid_every = 60 CarpetRegrid2::verbose = "yes" ------------------------------------------------------------------- This doesn't work now, however. Current ETK complains that some entries in radius_1 and radius_2 are unspecified, and it sets them to zero with catastrophic results. To resolve this, I am now explicitly setting the missing levels: CarpetRegrid2::radius_1[1] = 1024 CarpetRegrid2::radius_1[2] = 512 CarpetRegrid2::radius_1[3] = 256 CarpetRegrid2::radius_1[4] = 160 CarpetRegrid2::radius_2[1] = 1024 CarpetRegrid2::radius_2[2] = 512 CarpetRegrid2::radius_2[3] = 256 CarpetRegrid2::radius_2[4] = 160 This runs, but complains every time step about mismatched "simulated domain volume" and "reduction weight sum": ---------------------------------------------------------------------------------- INFO (CarpetReduce): Simulation domain volume: 442368 INFO (CarpetReduce): Reduction weight sum: 442367.999999072 WARNING level 1 in thorn CarpetReduce processor 0 host r186i2n12.p4.nas.nasa.gov (line 120 of /home1/bjkelly1/CODES/Cactus/configs/hahndol/build/CarpetReduce/mask_test.c): -> Simulation domain volume and reduction weight sum differ ---------------------------------------------------------------------------------- After a short evolution time (7.25 M, or more than 1700 time steps), the run crashes. First there are several messages of the form: ---------------------------------------------------------------------------------- INFO (CarpetReduce): Simulation domain volume: 442368 INFO (CarpetReduce): Reduction weight sum: 442367.999991311 INFO (CarpetRegrid2): Centre 1 is at position [-3.29831,-0.331478,7.81462e-15] with 12 levels INFO (CarpetRegrid2): Centre 2 is at position [6.58787,0.867484,8.98107e-15] with 13 levels INFO (CarpetRegrid2): Centre 3 is not active INFO (CarpetRegrid2): Regridding INFO (CarpetRegrid2): Regridding levels 10 and up WARNING level 1 in thorn CarpetLib processor 58 host r186i3n7.p4.nas.nasa.gov (line 182 of /home1/bjkelly1/CODES/Cactus/configs/hahndol/build/CarpetLib/dh.cc): [...] -> /home1/bjkelly1/CODES/Cactus/configs/hahndol/build/CarpetLib/dh.cc:948: [ml=0 rl=10 c=59] The following grid structure consistency check failed: Synchronisation and boundary prolongation: All points must have been received needrecv.empty() [...] WARNING level 0 in thorn CarpetLib processor 94 host r186i3n12.p4.nas.nasa.gov 12676 (line 1973 of /home1/bjkelly1/CODES/Cactus/configs/hahndol/build/CarpetLib/dh.cc): 12677 -> The grid structure is inconsistent. It is impossible to continue. -------------------------------------- I'm attaching my current parameter file in full. I'm reluctant to post the entire STDOUT/STDERR, since it's around a MB in size. Any ideas would be appreciated. I would turn to the copious documentation on CarpetRegrid2, but as noted before, there is none. Thanks, Bernard ----------------------------------------------------------------------------- Bernard Kelly -- CRESST Research Associate, NASA/GSFC Phone: +1 (301) 286-7243 E-Mail: bernard.j.kelly(a)nasa.gov<mailto:bernard.j.kelly@nasa.gov> Web: http://science.gsfc.nasa.gov/sed/index.cfm?fuseAction=people.jumpBio&iphone… -----------------------------------------------------------------------------

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Meeting minutes
by Roland Haas 30 Jan '12

30 Jan '12

Hello all, present were: Frank, Roland, Bruno, Tanja, Erik, Steve, Yosef, Josh, Ian, Peter ET seminars: * please add seminar proposals to the list, we'd rather have too many than not enough Spring workshop in Atlanta: * information (incl. proposed hotel) available at https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Spring_2012 * we have not definitive answer on funding but are hopeful * will discuss and invite invited speakers off-line * mailing list: workshop(a)einsteintoolkit.org for participants to register. Currently subscribed: Josh, Pablo, Tanja, Frank * Frank will create and send around flyers to be hung in public place * possible topics: ** introduction to NR ** introduction to Cactus ** Visualization using VisIt, gnuplot/grace/matplotlib ** possibly Ian's Mathematica based postprocessing/visualization package * hands on cluster: ** will use QueenBee (Steve) ** reserve block of nodes (Steve), arrange with LONI to pay for this ** use gcc compilers (Intel licenses are scarce) ** virtualbox linux image for participant's computers Next week's host will be Peter. 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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Einstein Toolkit Meeting Reminder
by Frank Loeffler 29 Jan '12

29 Jan '12

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/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Some of the things that will be discussed are: - Einstein Toolkit workshop in Atlanta [1] - Remind ourselves of submitting Einstein Seminar proposals [2] Frank Loeffler [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Spring_2012 [2] https://docs.einsteintoolkit.org/et-docs/Einstein_Toolkit_Seminar_Proposals

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using WeylScal4 and Multipole thorns in McLachlan
by Jose Fiestas Iquira 25 Jan '12

25 Jan '12

Hello, I am using WeylScal4 and Multipole thorns in McLachlan, and started a run using simfactory. It started well but stops after an MPI error. Before I get some warnings related to the parameters m_mode and l_mode. I am attaching the error file. It runs only for the initial time step zero. Does somebody have probably a hint what is the best parameter setting? I am using following: ActiveThorns = "WeylScal4 Multipole" WeylScal4::offset = 1e-8 WeylScal4::fd_order = "4th" WeylScal4::verbose = 0 Multipole::nradii = 8 Multipole::out_every = 128 Multipole::radius[0] = 15 Multipole::radius[1] = 30 Multipole::radius[2] = 40 Multipole::radius[3] = 50 Multipole::radius[4] = 60 Multipole::radius[5] = 70 Multipole::radius[6] = 80 Multipole::radius[7] = 90 Multipole::variables = "WeylScal4::Psi4r{sw=-2 cmplx='WeylScal4::Psi4i' name='Psi4'}" Multipole::l_mode = 4 Multipole::m_mode = 4 Thanks, Jose

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Hydro_Analysis problems
by Petr Tsatsin 23 Jan '12

23 Jan '12

I'm running the one from the repository from the official wiki page. I'm not sure if its "plain vanilla" ET checkout. >Hello Petr, Erik, >> I just added Hydro_Analysis thorn to static_tov.par and the run just >> crushes at the very beginning right after this warnings. I attached the >> full out file. >There was a bug in Hydro_Analysis_Init causing a segfault. It's fixed >now )in rev 119). Not sure where the L6 warnings came from though. Are >you running a plain vanilla ET checkout, Petr? Or a LSU/AEI version that >contains Multipatch code? > >Yours, >Roland -- Petr Tsatsin Graduate Student - Department of Physics Charles E. Schmidt College of Science Florida Atlantic University (561)-297-3386 cell: 561-692-2040 ptsatin(a)fau.edu, ptsatsin(a)gmail.com

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Re: [Users] problem with first example simulation with ETK
by Ian Hinder 23 Jan '12

23 Jan '12

On 16 Jan 2012, at 23:21, Jose Fiestas Iquira wrote: > Thanks, I am attaching the output file. The output file looks fine - I can't see any problem with the simulation. According to the output file, it reached t = 100 M, and in the parameter file that is listed as cctk_final_time, so all looks well! > I did copy the development version. As I can see, it was already > fixed, so I should not get this warning, since I copied the > development version. Yes, if you are using the current development version, then I don't know why you get the warning. Can you check which version of Carpet you have by doing cd repos/carpet hg tip to be sure you are using the development version? > Is the puncture tracker not a better way to plot BH trajectories. It's cheaper to use the puncture tracker, because computing the horizon centroid is more expensive, but it has to be done every iteration, whereas the horizon can be found less frequently. For comparison with point-particle results, I don't think it makes much difference; the results are gauge dependent anyway so differences on the order of the horizon size cannot be interpreted physically. Since the parameter file already has horizon-finding built in, it is easier for you to use that. If you want to figure out how to add the puncture tracker to the simulation, you can start with these parameters: ActiveThorns = "PunctureTracker" PunctureTracker::track [0] = yes PunctureTracker::initial_x [0] = $xp PunctureTracker::which_surface_to_store_info[0] = 0 PunctureTracker::track [1] = yes PunctureTracker::initial_x [1] = $xm PunctureTracker::which_surface_to_store_info[1] = 1 IOASCII::out0D_vars = "PunctureTracker::pt_loc" Replace $xp and $xm with the initial x coordinates of the +x and -x punctures (this will be \pm TwoPunctures::par_b). You then need to choose two spherical surfaces (https://docs.einsteintoolkit.org/et-docs/Einstein_Toolkit_standards) which are not being used currently to store the puncture locations in. If there is already 0D output, just add the puncturetracker variable separated with a space. > I > did some plots, what are really the combinations xx, xy, xz, yy, zz ? > Are they related to the trajectories of one BH (projections)? What > about the second BH? You should have BH_diagnostics.ah1.gp and BH_diagnostics.ah2.gp. These correspond to the first and second BHs. If you look at the top of these files, you will see an explanation of the columns. More information about each column is available in the AHFinderDirect documentation (http://einsteintoolkit.org/documentation/ThornGuide/ThornGuidech128.html#x1…). Specifically, information about the BH_diagnostics output files is at http://einsteintoolkit.org/documentation/ThornGuide/ThornGuidech128.html#x1… To plot the trajectory of one of the BHs, you want to plot column 3 and column 4 in a parametric plot. > Cheers, > Jose > > On Mon, Jan 16, 2012 at 4:39 AM, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: >> >> On 14 Jan 2012, at 00:41, Jose Fiestas Iquira wrote: >> >> Hi Ian, >> I did the changes but it started and finished early. I am attaching >> the qc0-mclachlan.err file. At the end there is a warning in one of >> the Carpet files (mask_test.c) >> >> >> The warning you see, >> >> WARNING level 1 in thorn CarpetReduce processor 0 host qb517 >> (line 120 of >> /home/ettest24/Cactus/arrangements/Carpet/CarpetReduce/src/mask_test.c): >> -> Simulation domain volume and reduction weight sum differ >> >> is a known issue (https://trac.einsteintoolkit.org/ticket/434) which was >> fixed after the last release and the fix is only available in the >> development version. I believe that the warning is not fatal, and it should >> not have terminated the simulation. Can you also post the qc0-mclachlan.out >> file? >> >> Where can I find the puncture tracker? >> >> >> The PunctureTracker thorn is part of the Einstein Toolkit thornlist, so you >> should have it already. However, I think the best thing for you to do >> initially would be to look at the BH_diagnostics files for the apparent >> horizon centroid locations for tracking the locations of the BHs. >> >> >> >> >> Thanks, >> Jose >> >> On Fri, Jan 13, 2012 at 4:38 AM, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: >> >> >> On 13 Jan 2012, at 12:32, Jose Fiestas Iquira wrote: >> >> >> Yes, trajectories and wave forms would be enough for now. Which are >> >> the names of this files? Many of the .asc files have data like kxx, >> >> kxy, kxz, etc. Is there any description of them? >> >> >> Not that I am aware of. Files with extension .x.asc are 1D ascii output of >> grid functions from CarpetIOASCII. kxy is the variable name for the x,y >> component of the extrinsic curvature tensor K. The waveform file should be >> in mp_psi4_l2_m2_r*.asc where * corresponds to the radius of the extraction >> sphere. However, looking at the qc0-mclachlan.par file, I see that there is >> no wave extraction switched on. You should be able to enable wave >> extraction by adding something like the following to the parameter file: >> >> >> ActiveThorns = "WeylScal4 CarpetInterp AEILocalInterp Multipole" >> >> >> Multipole::nradii = 3 >> >> Multipole::radius[0] = 30 >> >> Multipole::radius[1] = 40 >> >> Multipole::radius[2] = 50 >> >> Multipole::variables = "WeylScal4::Psi4r{sw=-2 cmplx=’WeylScal4::Psi4i’}" >> >> Multipole::l_max = 4 >> >> WeylScal4::fdOrder = 4 >> >> >> (I haven't tested this, so let me know if it doesn't work) >> >> >> I've just found that the usual PunctureTracker thorn is not enabled in this >> example parameter file. So to look at trajectories you will have to use the >> apparent horizon centroids. These are in the files BH_diagnostics.ah*.gp. >> The meanings of the columns are at the top of the files. You want the >> centroid x and y columns to plot in GnuPlot. >> >> >> >> >> >> >> Thanks, >> >> Jose >> >> >> On Fri, Jan 13, 2012 at 12:41 AM, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: >> >> >> On 12 Jan 2012, at 23:46, Jose Fiestas Iquira wrote: >> >> >> Dear all, >> >> >> I run the tutorial and found other interesting examples like the >> >> McLachlan tool for Binary Black Holes. >> >> >> Regarding the McLachlan tool, >> >> Could somebody help me finding a description of the output? Is all >> >> contained in the .asc files? I would like to visualize it. >> >> >> >> Hi Jose, >> >> >> What sort of output do you want to visualise? Cactus thorns typically >> >> output "lightweight" information such as BH trajectories and waveforms as >> >> ASCII, and more heavyweight data -- like gridfunctions -- as HDF5. For the >> >> trajectories (from thorn Puncture Tracker) and waveforms (from Multipole) >> >> you can use gnuplot or anything that can read standard ASCII output to >> >> visualise them. For gridfunctions in HDF5 format, I think the easiest way >> >> to get started is to use VisIt, for which there is a Carpet plugin (though >> >> installing VisIt is sometimes not so easy!). >> >> >> Does anyone know if the Carpet plugin is distributed with VisIt yet? I >> >> believe that was the intention. >> >> >> >> >> Cheers, >> >> Jose >> >> >> >> On Wed, Jan 11, 2012 at 7:06 PM, Jose Fiestas Iquira <jafiestas(a)lbl.gov> >> >> wrote: >> >> >> Thanks to Erik for advise. ETK example simulation run successfully. >> >> >> >> >> On Wed, Jan 11, 2012 at 11:49 AM, Jose Fiestas Iquira <jafiestas(a)lbl.gov> >> >> wrote: >> >> >> Right, it looks good now: >> >> >> >> ./simfactory/bin/sim list-simulations >> >> >> static_tov [ACTIVE (RUNNING), restart 0000, job id 595490] >> >> >> >> Let see how it looks when it finishes. The example was set to 8 hours. >> >> >> >> Thanks, >> >> >> Jose >> >> >> >> >> On Wed, Jan 11, 2012 at 11:45 AM, Erik Schnetter <schnetter(a)cct.lsu.edu> >> >> wrote: >> >> >> On Wed, Jan 11, 2012 at 2:42 PM, Jose Fiestas Iquira <jafiestas(a)lbl.gov> >> >> wrote: >> >> >> >> The only thing is that now >> >> >> $ ./simfactory/bin/sim list-simulations >> >> >> returns >> >> >> >> Error: unknown command list-simulation >> >> >> Aborting Simfactory. >> >> >> >> Did you really type "list-simulations", and the error message says >> >> >> "list-simulation" (without the final "s")? >> >> >> >> -erik >> >> >> >> -- >> >> >> Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/ >> >> >> _______________________________________________ >> >> >> Users mailing list >> >> Users(a)einsteintoolkit.org >> >> http://lists.einsteintoolkit.org/mailman/listinfo/users >> >> >> >> -- >> >> Ian Hinder >> >> http://numrel.aei.mpg.de/people/hinder >> >> >> >> -- >> >> Ian Hinder >> >> http://numrel.aei.mpg.de/people/hinder >> >> >> <qc0-mclachlan.err> >> >> >> -- >> Ian Hinder >> http://numrel.aei.mpg.de/people/hinder >> > <qc0-mclachlan.out> -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Users January 2012