Users March 2011

users@lists.einsteintoolkit.org

15 participants
25 discussions

Re: [Users] [ET Trac] [Einstein Toolkit] #344: Checkpointing + new cleanup procedure
by Erik Schnetter 14 Mar '11

14 Mar '11

On Mon, Mar 14, 2011 at 5:40 PM, Einstein Toolkit <trac-noreply(a)einsteintoolkit.org> wrote: > #344: Checkpointing + new cleanup procedure > -------------------------+-------------------------------------------------- > Reporter: mthomas | Owner: mthomas > Type: enhancement | Status: new > Priority: blocker | Milestone: > Component: SimFactory | Version: > Keywords: | > -------------------------+-------------------------------------------------- > Attached to this ticket is the patch to fix checkpointing (which Ian has > already reviewed) plus code implementing the new cleanup procedure. Michael You can commit the original patch that you proposed. For this, you could have a fresh checkout of Simfactory around (which is a good idea anyway), apply the patch there, and then commit. Since the patch is fresh, this should work without much trouble. If you then update your other working tree (with the additional changes), you should be able to distill a new patch with just the cleanup changes. This works out of the box many times; if the changes are intertwined, this requires some manual work. -erik > The new cleanup procedure is thus: > > 1. Automatic cleanup of every simulation is now gone. > 2. Any command that creates a new restart (submit, user initiated run) > calls restartlib.CleanupSimulation on that specific simulation, and > CleanupSimulation will only attempt to do cleanup if it finds an active > restart for that given simulation > 3. sim cleanup without any arguments will cleanup all simulations. If you > specify a specific simulation, it will only clean up that one. > > Still needing to be implemented are the times when cleanup of all > simulations should happen, or the cleanup when a simulation finishes. > These need to be done via cronjobs or some other method that hasn't quite > been figured out yet. Please svn up to get the latest revision (I > committed a bunch of very trivial code changes) then apply this patch and > add comments to this ticket related to this patch. > > -- > Ticket URL: <https://trac.einsteintoolkit.org/ticket/344> > Einstein Toolkit <http://einsteintoolkit.org> > The Einstein Toolkit > _______________________________________________ > Trac mailing list > Trac(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/trac > -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.cct.lsu.edu/~eschnett/

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Meeting minutes
by Roland Haas 14 Mar '11

14 Mar '11

Meeting minutes: Present were: Frank, Peter, Tanja, Roland, Erik, Josh, Gabe ET paper: * Frank has run a TOV test run, using the numerical noise as a perturbation: ** would like "nicer/stronger" perturbation to observe a longer ringdown phase * Peter has run some of Eloisa's cosmology testcases (Kasner and Gowdy), will work with Eloisa on some NaNs that are found * Peter has some text written for the Relativity Tools, will polish it before committing * publish in "Living Review in Relativity": ** will write a proposal to send to LRR board (PDF file), Ian will write a draft, please contact him if interested ** content will (have to) focus on methods and techniques, not a manual to use our thorns ** author lists tend to be short (three -- five authors) ET spring workshop: * what worked well for the Carpet workshops: ** have users give a short (!) presentation on topics that they are interested in ** keep schedule flexible (but have one) ** include time for breakfast/email at start of sessions * schedule: MHD first, then EOS_Omni (flexible) * interest exists in an tutorial on how to add MHD to an existing HD parameter file/simulation * interest exists in information as to what works with MHD and where it currently fails (eg. which test problems fail) ET fall workshop (at GT?): * Eloisa would prefer end of October over beginning of October 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 14 Mar '11

14 Mar '11

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/info/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Some points of tomorrows discussion will be: 1) ET paper status 2) A short Einstein Toolkit workshop, targeted at core developers, is planned at CalTech from noon April 26th to noon April 29th. If you plan to come, take a look at https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Spring_2011 Register by emailing Christian Reisswig: reisswig(a)tapir.caltech.edu, and note that you have to arrange accommodation on your own (see wiki). We should also formulate a (loose) plan on which particular topics to talk address (and, as far as possible, when). The two primary topics of the workshop will be the remaining work on a) MHD b) EOS_Omni Frank Löffler

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Re: [Users] [Einstein Toolkit] #315: Cannot cleanup simulations
by Ian Hinder 11 Mar '11

11 Mar '11

On 11 Mar 2011, at 16:16, Einstein Toolkit wrote: > #315: Cannot cleanup simulations > -------------------------+-------------------------------------------------- > Reporter: hinder | Owner: mthomas > Type: defect | Status: closed > Priority: major | Milestone: > Component: SimFactory | Version: > Resolution: fixed | Keywords: > -------------------------+-------------------------------------------------- > Changes (by mthomas): > > * status: reopened => closed > * resolution: => fixed > > > Comment: > > okay. I've finally corrected this (and fully tested it). > > r1282. This now seems to be working correctly. Thanks! Can I make a request that in future, we wait for confirmation from the original reporter that the problem is fixed before closing the ticket in TRAC? There have been several cases recently where the ticket had to be reopened, perhaps because the problem which was fixed was not exactly the cause of the problem that was reported. If the ticket is closed, it is very easy to lose track of the issue, and the original reporter might not remember to test the issue and reopen the ticket in that case. -- Ian Hinder ian.hinder(a)aei.mpg.de

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Fwd: Einstein Toolkit Spring workshop
by Christian Reisswig 08 Mar '11

08 Mar '11

Dear Einstein Toolkit users, to avoid confusion: the announced ET Spring workshop will focus on the improvement of GRHydro, i.e., the hydrodynamics part of the ET. cheers, Christian ---------- Forwarded Message ---------- Subject: Einstein Toolkit Spring workshop Date: Monday, March 07, 2011, 11:55:04 am From: Christian Reisswig <reisswig(a)tapir.caltech.edu> To: Einstein Toolkit Users <users(a)einsteintoolkit.org> Dear Einstein Toolkit users, the Einstein Toolkit Spring workshop https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Spring_2011 will be held from Tue, 04/26/11 - Fri, 04/29/11 at the Cahill Center for Astronomy and Astrophysics at Caltech. Registration can be done by replying to this email. For further information, please refer to the website above. cheers, Christian -- ----------------------------------------------------------------- Christian Reisswig Cahill Center for Astronomy and Astrophysics California Institute of Technology ----------------------------------------------------------------- ----------------------------------------- -- ----------------------------------------------------------------- Dr. Christian Reisswig Cahill Center for Astronomy and Astrophysics California Institute of Technology -----------------------------------------------------------------

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Cell centered and Refluxing
by Yosef Zlochower 07 Mar '11

07 Mar '11

Hi, I would like to try using cell-centered refinement and Refluxing. I have a parfile (attached) with the grid setup for vertex-centered refinement. What parameters do I need the change to make the parfile work for cell-centered? Based on the error messages when trying cell-centered I made following changes to the parfile CoordBase::domainsize = "minmax" CoordBase::xmin = -200.00 CoordBase::ymin = -200.00 CoordBase::zmin = 0 CoordBase::xmax = 200 CoordBase::ymax = 200 CoordBase::zmax = 200 CoordBase::spacing = "numcells" CoordBase::ncells_x = 201 CoordBase::ncells_y = 201 CoordBase::ncells_z = 101 CartGrid3D::type = "coordbase" CartGrid3D::domain = "full" CartGrid3D::bitant_plane = "xy" CartGrid3D::avoid_originx = yes CartGrid3D::avoid_originy = yes CartGrid3D::avoid_originz = yes CoordBase::boundary_size_x_lower = 1 CoordBase::boundary_size_y_lower = 1 CoordBase::boundary_size_z_lower = 4 CoordBase::boundary_shiftout_x_lower = 0 CoordBase::boundary_shiftout_y_lower = 0 CoordBase::boundary_shiftout_z_lower = 0 CoordBase::boundary_size_x_upper = 1 CoordBase::boundary_size_y_upper = 1 CoordBase::boundary_size_z_upper = 1 CoordBase::boundary_staggered_x_lower = "yes" CoordBase::boundary_staggered_x_upper = "yes" CoordBase::boundary_staggered_y_lower = "yes" CoordBase::boundary_staggered_y_upper = "yes" CoordBase::boundary_staggered_z_lower = "yes" CoordBase::boundary_staggered_z_upper = "yes" ReflectionSymmetry::reflection_x="no" ReflectionSymmetry::reflection_y="no" ReflectionSymmetry::reflection_z="yes" ReflectionSymmetry::avoid_origin_x="yes" ReflectionSymmetry::avoid_origin_y="yes" ReflectionSymmetry::avoid_origin_z="yes" ReflectionSymmetry::avoid_origin_upper_x="yes" ReflectionSymmetry::avoid_origin_upper_y="yes" ReflectionSymmetry::avoid_origin_upper_z="yes" Carpet::refinement_centering = "cell" but I then get the error message (line 136 of prolongate_3d_real8_eno.F90): -> Internal error: array origins are not integer multiples of the strides WARNING level 0 in thorn CarpetLib processor 12 host i182-302.ranger.tacc.utexas.edu If I further change the HydroBase prolongation operator to Lagrange I get errors of the form WARNING[L1,P2] (AEILocalInterp): CCTK_InterpLocalUniform(): interpolation point is either outside the grid, or inside but too close to the grid boundary! (this may be caused by a global interpolation with driver::ghost_size too small) 0-origin interpolation point number pt=0 of N_interp_points=81 interpolation point (x,y,z)=(6.09375e-17,0.995185,0.0980171) grid x_min(delta_x)x_max = -200.995(1.99005)-93.5323 grid y_min(delta_y)y_max = -107.463(1.99005)7.9602 grid z_min(delta_z)z_max = -6.93069(1.9802)103.96 which is due to an analysis interpolation (an interpolation over spheres centered on the origin in global mode) I tried a parfile with no symmetries with similar results. -- Dr. Yosef Zlochower Center for Computational Relativity and Gravitation Assistant Professor School of Mathematical Sciences Rochester Institute of Technology 85 Lomb Memorial Drive Rochester, NY 14623 Office:74-2067 Phone: +1 585-475-6103 yosef(a)astro.rit.edu CONFIDENTIALITY NOTE: The information transmitted, including attachments, is intended only for the person(s) or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and destroy any copies of this information. #============================================================================== ActiveThorns = "admanalysis admbase admcoupling admmacros coordgauge spacemask StaticConformal boundary time cartgrid3d ioutil iobasic nanchecker CoordBase aeilocalinterp Slab SphericalSurface LocalReduce MoL Carpet CarpetInterp CarpetIOASCII CarpetLib CarpetReduce CarpetSlab CarpetRegrid2 AHFinderDirect CarpetIOHDF5 CarpetIOScalar InitBase SymBase LoopControl GSL ReflectionSymmetry TmunuBase HydroBase" ActiveThorns = "TimerReport" TimerReport::out_every = 512 TimerReport::out_filename = "TimerReport" TimerReport::n_top_timers = 20 TimerReport::output_all_timers = yes Carpet::output_timers_every = 512 CarpetLib::print_memstats_every = 1024 #------------------------------------------------------------------------------ # Run parameters #------------------------------------------------------------------------------ # Grid mol::ode_method = "RK4" mol::mol_intermediate_steps = 4 mol::mol_num_scratch_levels = 1 #mol::initial_data_is_crap = true CoordBase::domainsize = "minmax" CoordBase::xmin = -200.001 CoordBase::ymin = -200.001 CoordBase::zmin = 0 CoordBase::xmax = 200 CoordBase::ymax = 200 CoordBase::zmax = 200 CoordBase::spacing = "numcells" CoordBase::ncells_x = 200 CoordBase::ncells_y = 200 CoordBase::ncells_z = 100 CartGrid3D::type = "coordbase" CartGrid3D::domain = "full" CartGrid3D::bitant_plane = "xy" CartGrid3D::avoid_originx = no CartGrid3D::avoid_originy = no CartGrid3D::avoid_originz = no CoordBase::boundary_size_x_lower = 1 CoordBase::boundary_size_y_lower = 1 CoordBase::boundary_size_z_lower = 4 CoordBase::boundary_shiftout_x_lower = 0 CoordBase::boundary_shiftout_y_lower = 0 CoordBase::boundary_shiftout_z_lower = 1 CoordBase::boundary_size_x_upper = 1 CoordBase::boundary_size_y_upper = 1 CoordBase::boundary_size_z_upper = 1 ReflectionSymmetry::reflection_x="no" ReflectionSymmetry::reflection_y="no" ReflectionSymmetry::reflection_z="yes" ReflectionSymmetry::avoid_origin_x="no" ReflectionSymmetry::avoid_origin_y="no" ReflectionSymmetry::avoid_origin_z="no" ReflectionSymmetry::avoid_origin_upper_x="no" ReflectionSymmetry::avoid_origin_upper_y="no" ReflectionSymmetry::avoid_origin_upper_z="no" driver::ghost_size = 4 #--------------------------------------------------------------------------- cactus::cctk_itlast = 12800000 time::dtfac = .1 Carpet::domain_from_coordbase = yes Carpet::prolongation_order_space = 5 Carpet::prolongation_order_time = 2 Carpet::max_refinement_levels = 8 Carpet::use_buffer_zones = yes Carpet::num_integrator_substeps = 1 Carpet::additional_buffer_zones = 2 Carpet::verbose = no Carpet::schedule_barriers = no Carpet::veryverbose = no CarpetLib::output_bboxes = no CarpetLib::check_bboxes = no CarpetLib::interleave_communications = yes CarpetLib::combine_sends = yes Carpet::time_refinement_factors = "[1,1,1,2,4,8,16,32,64,128,256]" Carpet::init_3_timelevels = "no" Carpet::init_each_timelevel = "no" Carpet::init_fill_timelevels = "yes" Carpet::enable_all_storage = no Carpet::regrid_during_recovery = no CarpetRegrid2::regrid_every = 32 CarpetRegrid2::snap_to_coarse="yes" CarpetRegrid2::num_centres = 1 CarpetRegrid2::num_levels_1 = 7 CarpetRegrid2::position_x_1 = 0 CarpetRegrid2::position_y_1 = 0 CarpetRegrid2::position_z_1 = 0 CarpetRegrid2::radius_1[ 1] = 90 CarpetRegrid2::radius_1[ 2] = 45 CarpetRegrid2::radius_1[ 3] = 20 CarpetRegrid2::radius_1[ 4] = 8 CarpetRegrid2::radius_1[ 5] = 4 CarpetRegrid2::radius_1[ 6] = 2 # MODEL initbase::initial_data_setup_method = init_some_levels ActiveThorns = "IDAnalyticBH" ADMBase::initial_data="schwarzschild" ADMBase::initial_lapse="psi4_psi2" ADMBase::initial_shift="zero" IDAnalyticBH::mass = 1. IDAnalyticBH::a_Kerr = 0. admbase::metric_type = "Physical" #--- numerics #------------------------------------------------------------------------------ # Matter: #------------------------------------------------------------------------------ ActiveThorns = "Grhydro EOS_Omni Constants" #ActiveThorns = "Refluxing" grhydro::riemann_solver = "Marquina" grhydro::grhydro_eos_type = "general" grhydro::grhydro_eos_table="Ideal_Fluid" grhydro::recon_method = "ppm" grhydro::grhydro_stencil = 3 grhydro::bound = "flat" HydroBase::Prolongation_Type = "WENO" Grhydro::initial_Gamma=1.66666666666666 Grhydro::rho_abs_min=1.0e-13 Grhydro::initial_rho_abs_min=1.0e-13 Grhydro::grhydro_atmo_tolerance=0.0001 eos_omni::poly_gamma = 1.66666666666666 eos_omni::poly_gamma_ini = 1.66666666666666 eos_omni::poly_k = 0.01 EOS_Omni::gl_gamma = 1.66666666666666 EOS_Omni::gl_k = 0.01 grhydro::Grhydro_MaxNumSandRVars = 16 TmunuBase::stress_energy_storage = "yes" TmunuBase::stress_energy_at_RHS = "yes" TmunuBase::timelevels = 1 TmunuBase::prolongation_type = "none" HydroBase::timelevels = 3 HydroBase::evolution_method = "grhydro" SpaceMask::use_mask = "yes"

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Nans in Tmunu in development version of ET (mercurial carpet)
by Yosef Zlochower 07 Mar '11

07 Mar '11

Hi, I have a parameter file that seems to work well for the released version of ET. The parfile has matter evolution on top of a vacuum GR evolution. In the development version the eTXX gfs contain nans at it=1 when I use the following parameters TmunuBase::timelevels = 3 TmunuBase::prolongation_type = SET TO DEFAULT VALUE but have finite values for these option TmunuBase::timelevels = 1 TmunuBase::prolongation_type = "none" -- Dr. Yosef Zlochower Center for Computational Relativity and Gravitation Assistant Professor School of Mathematical Sciences Rochester Institute of Technology 85 Lomb Memorial Drive Rochester, NY 14623 Office:74-2067 Phone: +1 585-475-6103 yosef(a)astro.rit.edu CONFIDENTIALITY NOTE: The information transmitted, including attachments, is intended only for the person(s) or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and destroy any copies of this information.

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Meetinq minutes
by Roland Haas 07 Mar '11

07 Mar '11

Present were: Tanja, Frank, Roland, Ian, Eloisa, Bruno, Peter ET paper: * no further progress on text * TOV parameter file for test cases has been submitted and is being tested * Kerr/pertrubed BH test ** Bruno,Eloisa,Peter,Ian are working on it ** use puncture initial data with spin to have physical perturbation (see turduckening paper, arXiv:0809.3533) upcoming Einstein Toolkit release (end of May): * want to use OpenMP in testsuites * provide tarball for all the sources files ready to be compiled * create list of changes file in repository * versions used: ** Carpet/git, Carpet/hg will become development version after release ** simfactory/perl * finish transition to EOS_Omni (testsuites, documentation, transition guides, ...) * address testsuite accuracy issues (tolerance per variable issues, dependencies of results on number of processors) ** re-read old discussions concerning this 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 Spring workshop
by Christian Reisswig 07 Mar '11

07 Mar '11

Dear Einstein Toolkit users, the Einstein Toolkit Spring workshop https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Spring_2011 will be held from Tue, 04/26/11 - Fri, 04/29/11 at the Cahill Center for Astronomy and Astrophysics at Caltech. Registration can be done by replying to this email. For further information, please refer to the website above. cheers, Christian -- ----------------------------------------------------------------- Christian Reisswig Cahill Center for Astronomy and Astrophysics California Institute of Technology -----------------------------------------------------------------

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ET Meeting Reminder
by Frank Loeffler 06 Mar '11

06 Mar '11

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/info/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Some points of tomorrows discussion will be: 1) ET paper status 2) Last week we agreed to have a short Einstein Toolkit workshop at CalTech from noon April 26th to noon April 29th. That being said, the core of the meeting will happen until April 28th, with the last day 'reserved' for loosely working together, otherwise known as hacking away. Information about the workhop will be posted to the wiki: https://docs.einsteintoolkit.org/et-docs/index.php?title=ET_Workshop_Spring… The two primary topics of the workshop will be the remaining work on a) MHD b) EOS_Omni 3) First plans / goals for next release end of May. Frank Löffler

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