Users March 2023

users@lists.einsteintoolkit.org

14 participants
27 discussions

Re: [Users] An error occurred in make Lorene/Codes/Bin_star
by Leonardo Rosa Werneck 01 Apr '23

01 Apr '23

Dear Jimmy, Have the Lorene libraries been compiled (i.e., running make at Lorene’s home directory) before going in Lorene/Codes/Bin_star and running make? Could you please share the contents of your local_settings? Best, Leo ------ Leonardo R. Werneck, Ph.D. Postdoctoral researcher Office EP 314 | Department of Physics | University of Idaho 875 Perimeter Dr. MS 0903 Moscow, ID 83844-0903, USA leonardo(a)uidaho.edu <mailto:leonardo@uidaho.edu> https://leowerneck.github.io <https://leowerneck.github.io/> > On Mar 24, 2023, at 10:00 AM, users-request(a)einsteintoolkit.org wrote: > > An error occurred in make Lorene/Codes/Bin_star

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meeting minutes for 2023-03-30
by Roland Haas 30 Mar '23

30 Mar '23

Present: Roland, Peter, Alireza, Beyhan, Johnny, Keith, Leo, Sam, Zach Elliptica inclusion: * discussed progress of review, including code quality review * asking for a comparison of new ET reader module generated simulation with published work using BAM, "by eye trajectory agreement" would be acceptable to all FUKA reader: * review completed * currently depends on Boost, can only be included as a DISABLED thorn ** not easy to extract needed parts of Boost and include according to author * had a larger scale discussion on what including Boost would involve ** Zach would like to avoid including Boost since it is quite large and slow to compile particleTracer_ET: * included in master branch * needs updates to test tolerances to avoid breaking on different systems TwoPuncturesBBH_EF: * review concluded * look for pull request kuibit: * Gabriele managed to remove the requirement for Python 3.8 * Sam will contact Gabriele about any changes required to ThornList ET Release: * Leo asked about steps to regenerate MMA codes, Roland referred to the release process wiki page which should list the steps, essentially runing "make" * Peter offered help generating them in case a MMA license is not available at UIdaho Unanswered questions: * LORENE build errors http://lists.einsteintoolkit.org/pipermail/users/2023-March/008890.html had some discussion. Leo mentioned that even with modules loaded one still needs to set up correct localsettings files. Leo will respond. Open tickets: * https://bitbucket.org/einsteintoolkit/tickets/issues/2700 Peter will review, faced git issues * no other new tickets chair next week: Leo minute taker next week: Johnny 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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Re: [Users] Help with Einstein Toolkit Tutorial
by Steven R. Brandt 30 Mar '23

30 Mar '23

If the plots work for you, then I guess it must be unimportant. I will take a look. Thanks. --Steve On 3/29/2023 5:03 PM, Enzo Iubini wrote: > Hello again, I fixed it just commenting that specific line of code, I > hope it changes nothing important. > Either way I guess it's better I tell you about the problems in the > tutorial. > Thank you for your help! > > - Enzo > > Enviado desde mi iPhone > >> El 29-03-2023, a la(s) 16:48, Enzo Iubini <egic.enzo(a)gmail.com> escribió: >> >> >> Hello Steve! >> I was planning to work on the HeatEquation and WaveEquation notebook >> tutorials, but in the last section "Plot using >> matplotlib's plot_surface()", there seems to be a problem with the " >> plt.close()" function. >> I have restarted the notebook several times but I can't figure out >> how to solve the problem. >> Could you see if the notebook runs well for you? >> The cell I'm having problems with starts with "## set graphics >> backend", it's the one that generates the animation. >> >> Thanks for your help! >> >> pd: I'm having the same issue with the other notebook. >> maybe I have to copy again the notebook from the tutorial server? >> I remember using the cp command, to retrieve the notebook from >> "HOME", but i can't remember the whole command. >> I would appreciate it if you could repeat it for me. >> Thank you ! >> >> -Enzo >> >> El jue, 23 mar 2023 a las 14:34, Enzo Iubini (<egic.enzo(a)gmail.com>) >> escribió: >> >> ok give me just 5 minutes, thank you! >> >> Enviado desde mi iPhone >> >> > El 23-03-2023, a la(s) 14:32, Steven R. Brandt >> <sbrandt(a)cct.lsu.edu> escribió: >> > >> > If you're around now: https://lsu.zoom.us/my/steverbrandt >> > >> > --Steve >> > >> >> On 3/23/2023 12:28 PM, Enzo Iubini wrote: >> >> it's 14:30 right now here in Chile. I have time until 18:00, >> or other day, so you just tell me when. >> >> I'm running everything in the tutorial server ! >> >> >> >> - enzo >> >> :) >> >> >> >>> El 23-03-2023, a la(s) 14:06, Steven R. Brandt >> <sbrandt(a)cct.lsu.edu> escribió: >> >>> >> >>> Those options would work. What time for zoom would work for you? >> >>> >> >>> Question: Are you running in the tutorial server, in a docker >> image, or just running the notebook on your laptop? >> >>> >> >>> Thanks. >> >>> >> >>> --Steve >> >>> >> >>>> On 3/23/2023 12:03 PM, Enzo Iubini wrote: >> >>>> Hello Steve :) >> >>>> It's me again asking for some help. Your feedback was very >> helpful the last time, but I'm having some trouble with the >> "Creating a new thorn tutorial" for both the Heat Equation and >> the Wave equation. >> >>>> >> >>>> The last time we talked, you told me the notebooks were >> running just fine, but I can't seem to make them work for me. >> Maybe I could send you a video of what the cells are and maybe >> you can help me spot the problem? Is there any way we could add >> each other on Telegram so I can show you? I hope I'm not >> bothering you too much, but I want to do the exercises proposed >> at the end of these notebooks, and if the original doesn't work, >> I don't think it's very wise to continue. >> >>>> >> >>>> Thank you so much for all your help. >> >>>> >> >>>> - Enzo >>

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Einstein Toolkit Meeting Reminder
by reminders＠einsteintoolkit.org 29 Mar '23

29 Mar '23

Hello, Please consider joining the weekly Einstein Toolkit phone call at 9:00 am US central time on Thursdays. For details on how to connect and what agenda items are to be discussed, use the link below. https://docs.einsteintoolkit.org/et-docs/Main_Page#Weekly_Users_Call --The Maintainers

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Workshop "Infinity on a Gridshell", Copenhagen, Denmark, July 10-13 2023
by Alex Vañó Viñuales 29 Mar '23

29 Mar '23

Dear Einstein Toolkit users, We are excited to announce the upcoming workshop "Infinity on a Gridshell" <https://hyperboloid.al/event/copenhagen-23/>, which will take place from *July 10 to July 13, 2023, at the Niels Bohr Institute, University of Copenhagen*. The workshop will focus on the progress made in *hyperboloidal methods*, which have emerged as a crucial tool in black-hole perturbation theory and other diverse applications. The workshop aims to bring together leading experts to review and summarize the current *state-of-the-art of hyperboloidal methods* in a wide range of applications, including the computation of wave equations, quasi-normal modes, effective-one-body formalism, and self-force. The focus will be on exploring ideas to solve the full Einstein equations for astrophysically relevant scenarios. We have a *limited number of seats* for researchers to attend the conference in person. Participants will have the opportunity to present their work using hyperboloidal methods, exchange ideas, and discuss the challenges and opportunities in the field. We aim to foster new collaborations and build a community of researchers to connect and engage in productive discussions. We encourage researchers and graduate students with an interest in hyperboloidal methods to apply for this exciting event. The workshop will provide an excellent opportunity to learn about the latest developments, contribute to the advancement of the field, and to *join the hyperboloidal community*. For more information about the workshop, please visit our website <https://hyperboloid.al/event/copenhagen-23/>. A poster is available here <https://hyperboloid.al/event/copenhagen-23/poster.webp>. You can apply to participate by filling the form at the strong GR website <https://strong-gr.com/infinity-on-a-grid-shell/registration/> before the *deadline April 30, 2023*. We look forward to welcoming you to Copenhagen. *Scientific Organizing Committee*: David Hilditch, Rodrigo Panosso Macedo, Alex Vañó-Viñuales, and Anıl Zenginoğlu *Local Organizing Committee*: Vitor Cardoso, Rodrigo Panosso Macedo, Julie de Molade, Rita Sousa -- Alex Vano-Vinuales Instituto Superior Técnico Departamento de Física/CENTRA Gabinete 2-8.8 Av. Rovisco Pais 1 1049-001 Lisboa PORTUGAL

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Agenda for Thursday's Meeting
by reminders＠einsteintoolkit.org 27 Mar '23

27 Mar '23

Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers

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question about Thornburg04nc on Llama
by Luciano Combi 24 Mar '23

24 Mar '23

Hi everyone, I started testing the Thornburg04nc coordinates (spherical patches without Cartesian box) from Llama with (a modified version) of GRHydro. I started with just an atmosphere around a Kerr-Schild metric evolving only hydro. I'm seeing instabilities near the origin, so I was wondering if someone already encountered this issue. In particular, I wanted to know if someone has a good idea of how to treat the inner boundary. Right now, I'm putting the inner boundary inside the horizon, above the ring singularity, and applying hydro excision. I've tried a combination of things playing with those parameters but without success. Has anyone tried a similar thing evolving hydro? Just want to double check if there's something obvious in the grid setup I'm missing. Below I attach the relevant part of the par file I'm using. Main difference with the public version of GRHydro is that I'm using Siegel+2017 c2p which works just fine with the same setup in Cartesian coordinates. Thanks a lot!! ###### ActiveThorns = "Time MoL" ActiveThorns = "Coordbase CartGrid3d Boundary StaticConformal" ActiveThorns = "SymBase ADMBase TmunuBase HydroBase InitBase ADMCoupling ADMMacros" ActiveThorns = "IOUtil Formaline" ActiveThorns = "SpaceMask CoordGauge Constants LocalReduce aeilocalinterp LoopControl" ActiveThorns = "Carpet CarpetLib CarpetReduce CarpetRegrid2 " ActiveThorns = "Coordinates GenericFD Interpolate2 CarpetInterp2 CarpetInterp" ActiveThorns = "CarpetIOASCII CarpetIOScalar CarpetIOHDF5 CarpetIOBasic" ################################################################################ # Grid setup and general parameters ################################################################################ # Grid CartGrid3D::type = "multipatch" Coordinates::coordinate_system = "Thornburg04nc" CartGrid3D::set_coordinate_ranges_on = "all maps" Coordinates::h_radial = 0.35 Coordinates::sphere_inner_radius = 3.0 Coordinates::sphere_outer_radius = 90.0 Coordinates::n_angular = 25 #Coordinates::radial_stretch = yes #Coordinates::stretch_rmin_1 = 10.0 #Coordinates::stretch_rmax_1 = 90.0 Coordinates::stagger_patch_boundaries = "no" Coordinates::stagger_outer_boundaries = "no" Interpolate::interpolator_order = 4 Interpolate2::shift_edges = no Coordinates::store_jacobian = yes # I need to Coordinates::store_inverse_jacobian = yes # Check for runtime errors #Coordinates::store_jacobian_derivative = yes Coordinates::store_volume_form = yes #GenericFD::jacobian_group = "Coordinates::jacobian" #GenericFD::jacobian_derivative_group = "Coordinates::jacobian2" # General Carpet parameters: Carpet::enable_all_storage = "no" Carpet::use_buffer_zones = "yes" Carpet::use_overlap_zones = "no" Carpet::schedule_barriers = "no" #Carpet::processor_topology = "recursive" # recursive breaks multipatch Carpet::check_for_poison = "no" Carpet::init_3_timelevels = "no" Carpet::init_fill_timelevels = "yes" CarpetLib::poison_new_memory = "yes" CarpetLib::poison_value = 114 CarpetLib::check_bboxes = "no" CarpetLib::interleave_communications = "yes" CarpetLib::combine_sends = "no" # Erik says this is faster and does not use more memory than yes CarpetLib::combine_recompose = "no" # yes is the default, set to no if we run out of memory during recomposing #CarpetLib::restriction_order_space = 0 CarpetInterp::tree_search = "yes" CarpetInterp::check_tree_search = "no" # OVERLAP Coordinates::additional_overlap_size = 3 # BOUNDARY ZONES (needs to be set to three) Coordinates::patch_boundary_size = 3 Coordinates::outer_boundary_size = 3 #Carpet::prolongation_order_space = 5 #Carpet::prolongation_order_time = 2 Carpet::refinement_centering = "vertex" #==================================== # TmunuBase & HydroBase #==================================== TmunuBase::stress_energy_storage = yes TmunuBase::stress_energy_at_RHS = yes TmunuBase::timelevels = 1 TmunuBase::prolongation_type = none HydroBase::timelevels = 3 ############################################################# # Carpet ############################################################# Carpet::domain_from_multipatch = yes Carpet::ghost_size = 3 # not for FD #Carpet::granularity = 5 # (order+1)*m #Carpet::granularity_boundary = 1 #Carpet::poison_new_timelevels = "yes" # does not work with persistent RHS #--------CarpetMask-------------------------- ActiveThorns = "CarpetMask" CarpetMask::excluded_surface [0] = 1 CarpetMask::excluded_surface_factor[0] = 1.0 # ############################################################# # Time integration ############################################################# Cactus::terminate = "time" Cactus::cctk_final_time = 2000000000000 #Cactus::cctk_itlast = 1 Time::timestep_method = "given" Time::timestep = 0.10 MethodOfLines::ODE_method = "RK4" MethodOfLines::MoL_Intermediate_Steps = 4 MethodOfLines::MoL_Num_Scratch_Levels = 1 MethodOfLines::MoL_NaN_Check = no ################################################################################ # Hydro evolution ################################################################################ SpaceMask::use_mask = "yes" #==================================== # GRHydro #==================================== ActiveThorns = "EOS_Omni" ActiveThorns = "GRHydro" HydroBase::evolution_method = "GRHydro" HydroBase::Bvec_evolution_method = "GRHydro" # use c++ version of GRHydro GRHydro::use_cxx_code = "yes" GRHydro::method_type = "RSA FV" GRHydro::riemann_solver = "HLLE" GRHydro::recon_method = "ppm" GRHydro::recon_vars = "primitive" GRHydro::GRHydro_stencil = 3 GRHydro::bound = "flat" #also tried none GRHydro::rho_abs_min = 1e-15 GRHydro::initial_rho_abs_min = 5e-14 GRHydro::GRHydro_atmo_tolerance = 0.01 # -- settings for 3-param (tabulated) EOS -- grhydro::grhydro_eos_type = "General" grhydro::grhydro_eos_table = "nuc_eos" EOS_Omni::nuceos_read_table = "yes" EOS_Omni::nuceos_table_name = "/home/d/dsiegel/lcombi/repository/EOS_tables/etk_bns_evolution/sfho/Hempel_SFHoEOS_rho222_temp180_ye60_version_1.1_20120817.h5" GRHydro::GRHydro_eos_rf_prec = 1e-10 hydrobase::Y_e_evolution_method = "GRHydro" hydrobase::temperature_evolution_method = "GRHydro" GRHydro::reconstruct_temper = "yes" # more robust for reconstruction GRHydro::GRHydro_hot_atmo_temp = 0.012 #8.62e-06=1e5K GRHydro::GRHydro_hot_atmo_Y_e = 0.5 grhydro::grhydro_y_e_min = 0.012 grhydro::grhydro_y_e_max = 0.599 GRHydro::Grhydro_MaxNumConstrainedVars = 34 #33 GRHydro::GRHydro_MaxNumEvolvedVars = 10 # -- settings for con2prim -- GRHydro::GRHydro_c2pMHD_method = 1 GRHydro::GRHydro_c2pMHD_method_backup = 5 GRHydro::GRHydro_use_c2pMHD_method_backup = "yes" GRHydro::GRHydro_c2p_grace_radius = 7.5 grhydro::grhydro_c2p_warnlevel = 1 #1 grhydro::grhydro_c2p_warn_from_reflevel = 5 #5 # 6 # --- EOS Omni --- eos_omni::poly_gamma = 1.33333333 #eos_omni::poly_gamma_initial = 1.333333333 eos_omni::poly_k = 0.3605 #145.877704 #100 eos_omni::gl_gamma = 1.33333333 eos_omni::gl_k = 0.3605 #145.877704 #100 ################################################################################ # Spacetime evolution ################################################################################ ADMBase::metric_type = "physical" ADMBase::evolution_method = "static" ADMBase::lapse_evolution_method = "static" ADMBase::shift_evolution_method = "static" ADMBase::dtlapse_evolution_method= "static" ADMBase::dtshift_evolution_method= "static" ADMBase::metric_timelevels = 3 ADMBase::lapse_timelevels = 3 ADMBase::shift_timelevels = 3 ADMMacros::spatial_order = 4 #==================================== # Apparent horizon & excision #==================================== ActiveThorns = "hydro_initexcision" hydro_initexcision::hydro_initexcision = "yes" hydro_initexcision::hydro_initexcision_type = "sphere" hydro_initexcision::hydro_initexcision_coordinate_length = 4.2 # should be slightly larger than a_BH = spin_BH*mass_BH # --- Settings for apparent horizon --- ActiveThorns = "AHFinderDirect SetMask_SphericalSurface" AHFinderDirect::N_horizons = 1 AHFinderDirect::find_after_individual_time[1] = 0 AHFinderDirect::find_every = 20000 AHFinderDirect::output_h_every = 20000 AHFinderDirect::initial_guess_method[1] = "Kerr/Kerr-Schild" AHFinderDirect::initial_guess__Kerr_KerrSchild__x_posn[1] = 0.0 AHFinderDirect::initial_guess__Kerr_KerrSchild__y_posn[1] = 0.0 AHFinderDirect::initial_guess__Kerr_KerrSchild__z_posn[1] = 0.0 AHFinderDirect::initial_guess__Kerr_KerrSchild__mass[1] = 3.0 # adjust to settings for TorusID AHFinderDirect::initial_guess__Kerr_KerrSchild__spin[1] = 0.8 # adjust to settings for TorusID AHFinderDirect::geometry_interpolator_name = "Lagrange polynomial interpolation" AHFinderDirect::geometry_interpolator_pars = "order=4" AHFinderDirect::surface_interpolator_name = "Lagrange polynomial interpolation" AHFinderDirect::surface_interpolator_pars = "order=4" AHFinderDirect::mask_buffer_thickness = 0 AHFinderDirect::mask_radius_multiplier = 0.8 AHFinderDirect::mask_radius_offset = 0 AHFinderDirect::max_allowable_horizon_radius[1] = 10 AHFinderDirect::max_allowable_Theta_growth_iterations = 10 AHFinderDirect::max_allowable_Theta_nonshrink_iterations = 10 AHFinderDirect::max_Newton_iterations__initial = 50 AHFinderDirect::max_Newton_iterations__subsequent = 50 AHFinderDirect::which_surface_to_store_info_by_name [1] = "apparent horizon" ################################################################################ # Initial data ################################################################################ InitBase::initial_data_setup_method = "init_some_levels" ADMBase::initial_data = "exact" #TorusID" ADMBase::initial_lapse = "exact" #TorusID" ADMBase::initial_shift = "exact" #TorusID" ADMBase::initial_dtlapse = "zero" ADMBase::initial_dtshift = "zero" ActiveThorns = "Exact" Exact::exact_model = "Kerr/Kerr-Schild" Exact::Kerr_KerrSchild__mass = 3.0 Exact::Kerr_KerrSchild__parabolic = "yes" --- *Dr. Luciano Combi* Postdoctoral Researcher Perimeter Institute for Theoretical Physics CITA National Fellow (U. of Guelph) ---

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An error occurred in make Lorene/Codes/Bin_star
by 白济民 24 Mar '23

24 Mar '23

Hi all, when I trying to type make in Lorene/Codes/Bin_star, I got the following error: /lustre/home/acct-phyyzd/phyyzd-jjj/Lorene/Lib/liblorenef77_g.a(gr2p3s.o): In function `gr2p3s_': /lustre/home/acct-phyyzd/phyyzd-jjj/Lorene/F77/Source/Poisson2d/gr2p3s.f:642: undefined reference to `extm2s_' /lustre/home/acct-phyyzd/phyyzd-jjj/Lorene/F77/Source/Poisson2d/gr2p3s.f:643: undefined reference to `extm2s_' /lustre/home/acct-phyyzd/phyyzd-jjj/Lorene/F77/Source/Poisson2d/gr2p3s.f:653: undefined reference to `extm2s_' /lustre/home/acct-phyyzd/phyyzd-jjj/Lorene/F77/Source/Poisson2d/gr2p3s.f:654: undefined reference to `extm2s_' /lustre/home/acct-phyyzd/phyyzd-jjj/Lorene/F77/Source/Poisson2d/gr2p3s.f:752: undefined reference to `extm2s_' /lustre/home/acct-phyyzd/phyyzd-jjj/Lorene/Lib/liblorenef77_g.a(gr2p3s.o):/lustre/home/acct-phyyzd/phyyzd-jjj/Lorene/F77/Source/Poisson2d/gr2p3s.f:753: more undefined references to `extm2s_' follow collect2: error: ld returned 1 exit status I wonder why it happens and how to fix it. Specifically, I load these modules: module purge module load intel module load gcc/8.3.0 module load fftw/3.3.8-gcc-8.3.0 module load pgplot/5.2.2-gcc-4.8.5 module load netlib-lapack/3.8.0-gcc-8.3.0 module load gsl/2.5-gcc-8.3.0 Does anyone has met these kinds of problems before? I'm looking forward to your help! Yours sincerely, Jimmy

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Mar 23, 2023 ET Telecon Minutes
by Zach Etienne 23 Mar '23

23 Mar '23

Hello all, As an experiment, I fed Zoom transcripts from our meeting into ChatGPT to create meeting minutes. The following is an edited version of what it spit out. My conclusion is that we're not ready for humans to be replaced by bots for this task. Attendees: Beyhan, Zachariah, Roland, Samuel, Leo, Steve, Yosef Topic: Upcoming ET Release Summary of discussion: During the Einstein Toolkit telecon, the group discussed release issues, with particular emphasis on the Elliptica reader. Beyhan asked about the validation test required for the reader, which has not been used in any publication. Roland emphasized the need for a validation test to ensure the reader works for the Einstein Toolkit, and suggested a low-resolution simulation test. Samuel suggested that the person proposing the inclusion should do the validation test. Leo suggested completing the test Roland mentioned before including the reader. The deadline for reviews is next week. Topic: Progress on Various Thorns Summary of discussion: We discussed the FUKA reader, particle_tracer updates, and new features for the TwoPunctures thorn. We also discussed compatibility issues with Kuibit on Python 3.8 seem to be resolved. Topic: Achieving Compatibility and Support for Ancient Clusters Summary of discussion: During the Einstein Toolkit telecon discussion, Roland Haas mentioned the challenges of achieving compatibility and support for ancient clusters, and the need to accept different versions of quibet on different supported clusters. Leo discussed issues with the NRPyElliptic unit test and modified the test file to improve tolerances, but faced difficulties with the test suite ignoring the updated values. Topic: Release name: The group also discussed candidates for the upcoming release name, including Feynman for future quantum computing in the toolkit and Schwarzschild for a solution to the Einstein equations. No decision was made on this topic. Topic: Next meeting. Peter will be Chair. -Zach * * * Zachariah Etienne Assoc. Prof. of Physics, U. of Idaho Adjunct Assoc. Prof. of Physics & Astronomy, West Virginia U. https://etienneresearch.com https://blackholesathome.net

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Re: [Users] Help with Einstein Toolkit Tutorial
by Steven R. Brandt 23 Mar '23

23 Mar '23

Those options would work. What time for zoom would work for you? Question: Are you running in the tutorial server, in a docker image, or just running the notebook on your laptop? Thanks. --Steve On 3/23/2023 12:03 PM, Enzo Iubini wrote: > Hello Steve :) > It's me again asking for some help. Your feedback was very helpful the > last time, but I'm having some trouble with the "Creating a new thorn > tutorial" for both the Heat Equation and the Wave equation. > > The last time we talked, you told me the notebooks were running just > fine, but I can't seem to make them work for me. Maybe I could send > you a video of what the cells are and maybe you can help me spot the > problem? Is there any way we could add each other on Telegram so I can > show you? I hope I'm not bothering you too much, but I want to do the > exercises proposed at the end of these notebooks, and if the original > doesn't work, I don't think it's very wise to continue. > > Thank you so much for all your help. > > - Enzo

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