[Users] problem with first example simulation with ETK
Jose Fiestas Iquira
jafiestas at lbl.gov
Wed Feb 8 14:05:16 CST 2012
Hi,
The first problem was solved as I reported, by disabling the
QuasiLocalMeasures. Some MPI problem. Btw, which information am I missing
without QuasiLocalMeasures? (the output file was the wrong one, of a
successful simulation without WeyScal4)
About the .par file. I found out (please correct me if necessary) that I
need to change the name of the run by the simfactory submission (here
static_tov):
./simfactory/bin/sim submit *static_tov* --parfile=par/static_tov.par
--procs=32 --walltime=8:0:0
Otherwise the run works with the original .par (first used with this run) ,
and not to the newly specified .par file. So, it worked by doing
./simfactory/bin/sim submit *static_tov01* --parfile=par/*static_tov_new.par
* --procs=32 --walltime=8:0:0
Best,
Jose
On Wed, Feb 8, 2012 at 10:05 AM, Ian Hinder <ian.hinder at aei.mpg.de> wrote:
>
> On 23 Jan 2012, at 22:36, Jose Fiestas Iquira wrote:
>
> Hi,
>
> In order to use the wave generator, I am probably not submitting the
> job properly.
>
> I had modified the .par file located at:
> /home/ettest24/Cactus/par/qc0-mclachlan.par
> since I run the example like this:
> ./simfactory/bin/sim submit qc0-mclachlan
> --parfile=par/qc0-mclachlan.par --procs=32 --walltime=8:0:0
>
> Here the run stopped with errors, as previously reported.
>
>
> Hi Jose,
>
> Could you update me on your status? Did you solve this problem? In the
> standard output file that you sent to the ET mailing list on 16-Jan-2012, I
> do not see any problem. The run reached 100 M of evolution time. The only
> problem is a non-fatal warning message which is caused by some problem with
> the way that Carpet keeps track of points which should or should not be
> included in norm operations. You can ignore this warning.
>
> Could be possible that the proper .par is located somewhere else? I
> found it also here:
>
> /home/ettest24/Cactus/simfactory/etc/par/qc0-mclachlan.par
> /home/ettest24/Cactus/arrangements/McLachlan/par/qc0-mclachlan.par
>
> Btw, in the last one WeylScal4 is activated, in a similar way as you told
> me.
>
>
> SimFactory takes the parameter file that you specify on the command line -
> it does not look anywhere else. Can you be more specific about the problem
> you are having?
>
> PS: if you ask these questions on the mailing list, other people can help
> and benefit from the discussion.
>
>
>
> Best,
> Jose
>
>
>
> On Mon, Jan 23, 2012 at 1:11 PM, Ian Hinder <ian.hinder at aei.mpg.de> wrote:
>
>
> On 23 Jan 2012, at 14:57, Jose Fiestas Iquira wrote:
>
>
> Hello,
>
>
> Regarding the Binary Black Hole coalescence example from the ETK.
>
>
> In the BH diagnostics files are columns with quadrupole terms, which
>
> are not constant. Do you know of some tool in ETK to calculate the GW
>
> emission from these terms?
>
>
>
> No, not that I am aware of. These are the quadrupole moments of the
>
> individual apparent horizons, rather than the quadrupole moment of the
>
> system as a whole. The gravitational wave emission can be computed by
> using
>
> the WeylScal4 and Multipole thorns. These give you the spherical harmonic
>
> multipoles of Psi4 (e.g. l = 2, m = 2 is the dominant one), which can then
>
> be converted to strain by "two integrations in time" [this is actually
> quite
>
> subtle and hard to get right - see Reisswig and Pollney, arXiv:1006.1632,
>
> for an overview and solution).
>
>
>
>
> Thanks,
>
> Jose
>
>
> On Tue, Jan 17, 2012 at 5:18 AM, Ian Hinder <ian.hinder at aei.mpg.de> wrote:
>
>
>
> On 17 Jan 2012, at 13:37, Jose Fiestas Iquira wrote:
>
>
>
> The Einstein Analysis guide is very useful. I found here
>
>
>
> http://einsteintoolkit.org/documentation/ThornGuide/ThornGuidech142.html#x159-2520000P8.4
>
>
> the units used in 'Hydrobase'.
>
>
>
> If I assume these are the units for all thorns, I obtain from data in
>
>
> BH_diagnostics.ah1.gp a unit of distance of about 1 Km. To estimate
>
>
> the time I am using a mass of ~0.5 M_sun for both BHs (m_irreducible
>
>
> ?) , and I read a final time (cctk_time) ~ 1microsec. Are these
>
>
> quantities in the usual range?
>
>
>
>
> The length unit is G M / c^2 and the time unit is G M / c^3. For M =
> M_sun,
>
>
> I get the length unit as 1.5 km and the time unit as 4.9 us. The final
> time
>
>
> in the simulation is 100 M (i.e. 100 G M / c^3), which would be 0.5 ms.
>
>
>
>
>
>
>
>
> Jose
>
>
>
>
> On Tue, Jan 17, 2012 at 4:04 AM, Jose Fiestas Iquira <jafiestas at lbl.gov>
>
>
> wrote:
>
>
>
> I sent the wrong file, here is the right one.
>
>
>
>
> $ hg tip
>
>
>
> gives me:
>
>
>
> -----------------------------------------------------
>
>
>
> changeset: 3421:dff4df2b3687
>
>
>
> tag: tip
>
>
>
> user: Erik Schnetter <schnetter at cct.lsu.edu>
>
>
>
> date: Thu Jan 12 14:11:27 2012 -0500
>
>
>
> summary: CarpetLib: Allocate space for dstbox before
>
>
>
> restricting/prolongating
>
>
>
>
> [40514 refs]
>
>
>
> -----------------------------------------------------
>
>
>
>
> I copied this version from:
>
>
>
>
> ./GetComponents -a
>
>
>
> http://svn.einsteintoolkit.org/manifest/trunk/einsteintoolkit.th
>
>
>
>
> Thanks,
>
>
>
> Jose
>
>
>
>
>
>
>
> On Tue, Jan 17, 2012 at 1:13 AM, Ian Hinder <ian.hinder at aei.mpg.de> wrote:
>
>
>
>
> 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#x144-2264000O4
> ).
>
>
>
> Specifically, information about the BH_diagnostics output files is
>
>
>
> at
> http://einsteintoolkit.org/documentation/ThornGuide/ThornGuidech128.html#x144-2274000O4.5.5
>
>
>
>
> 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 at 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 at 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 at 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 at 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 at 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 at cct.lsu.edu>
>
>
>
>
>
> wrote:
>
>
>
>
>
>
> On Wed, Jan 11, 2012 at 2:42 PM, Jose Fiestas Iquira <jafiestas at 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 at cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/
>
>
>
>
>
>
> _______________________________________________
>
>
>
>
>
>
> Users mailing list
>
>
>
>
>
> Users at 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
>
>
>
>
>
> --
>
>
> Ian Hinder
>
>
> http://numrel.aei.mpg.de/people/hinder
>
>
>
>
> --
>
> Ian Hinder
>
> http://numrel.aei.mpg.de/people/hinder
>
>
>
> --
> Ian Hinder
> http://numrel.aei.mpg.de/people/hinder
>
>
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