Users December 2013

users@lists.einsteintoolkit.org

12 participants
20 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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CarpetReduce: Formerly working par file now yields 'Simulation domain volume and reduction weight sum differ'
by Scott Hawley 23 Jan '14

23 Jan '14

Hi, I'm pretty sure I haven't changed a par file which "used to work." Now I'm getting the 'Simulation domain volume and reduction weight sum differ' error. I've read a few previous posts about this... http://lists.einsteintoolkit.org/pipermail/users/2011-September/001457.html http://lists.einsteintoolkit.org/pipermail/users/2012-September/002540.html http://lists.einsteintoolkit.org/pipermail/trac/2011-October/002465.html ...but haven't understood how they apply to my case. I'm not using CarpetMask, and haven't changed anything about the boundary points or grid structure. Can anyone offer a suggestion? Thanks. Output log and par file follow. -Scott % /opt/local/bin/openmpirun -np 1 ./exe/cactus_bruiser -roe --logdir=log /Users/shawley/runs/cactus/bruiser/bruiser_test.par IN DIRECTORY: /Users/shawley/Cactus -------------------------------------------------------------------------------- 10 1 0101 ************************ 01 1010 10 The Cactus Code V4.0 1010 1101 011 www.cactuscode.org 1001 100101 ************************ 00010101 100011 (c) Copyright The Authors 0100 GNU Licensed. No Warranty 0101 -------------------------------------------------------------------------------- Cactus version: 4.1.1 Compile date: Dec 20 2013 (12:34:14) Run date: Dec 20 2013 (13:02:27-0600) Run host: (pid=99492) WARNING level 1 in thorn CarpetReduce processor 0 host Working directory: /Users/shawley/Cactus (line 137 of /Users/shawley/.mojaveconfig/Cactus/bruiser/build/CarpetReduce/mask_test.c): Executable: ./exe/cactus_bruiser -> Simulation domain volume and reduction weight sum differ Parameter file: /Users/shawley/runs/cactus/bruiser/bruiser_test.par -------------------------------------------------------------------------------- % cat bruiser_test.par | grep -v '^#' Cactus::cctk_run_title = "BruiserSetBG, FMR BBH" Cactus::cctk_full_warnings = yes Cactus::cctk_itlast = 0 ActiveThorns = "AEILocalInterp Boundary CartGrid3D CoordBase SymBase Slab Carpet CarpetLib CarpetInterp CarpetReduce CarpetSlab CarpetRegrid IOUtil SphericalSurface NaNChecker ADMBase ADMCoupling ADMMacros CoordGauge SpaceMask StaticConformal BruiserSetBG BruiserConstraints AHFinderDirect ADMAnalysis ADMConstraints LoopControl InitBase CarpetIOBasic CarpetIOScalar CarpetIOASCII TimerReport TmunuBase GenericFD" ActiveThorns = "CarpetIOHDF5 CarpetIOASCII" SphericalSurface::nsurfaces = 3 SphericalSurface::maxntheta = 39 SphericalSurface::maxnphi = 76 SphericalSurface::ntheta [0] = 39 SphericalSurface::nphi [0] = 76 SphericalSurface::nghoststheta[0] = 2 SphericalSurface::nghostsphi [0] = 2 SphericalSurface::ntheta [1] = 39 SphericalSurface::nphi [1] = 76 SphericalSurface::nghoststheta[1] = 2 SphericalSurface::nghostsphi [1] = 2 SphericalSurface::ntheta [2] = 39 SphericalSurface::nphi [2] = 76 SphericalSurface::nghoststheta[2] = 2 SphericalSurface::nghostsphi [2] = 2 IO::out_dir = $parfile Carpet::domain_from_coordbase = yes driver::ghost_size = 4 InitBase::initial_data_setup_method="init_all_levels" Carpet::prolongation_order_time = 0 Carpet::prolongation_order_space = 1 Carpet::convergence_level = 0 ADMMacros::spatial_order = 4 ADMBase::initial_data = "BruiserSetBG, Kerr-Schild" ADMBase::lapse_timelevels = 2 ADMBase::shift_timelevels = 2 ADMConstraints::constraints_timelevels = 2 ADMBase::metric_timelevels = 2 CoordBase::domainsize = minmax CoordBase::spacing = numcells CoordBase::xmin = -36.0 CoordBase::ymin = -36.0 CoordBase::zmin = -36.0 CoordBase::xmax = 36.0 CoordBase::ymax = 36.0 CoordBase::zmax = 36.0 CoordBase::ncells_x = 12 CoordBase::ncells_y = 12 CoordBase::ncells_z = 12 CartGrid3D::type = coordbase CartGrid3D::avoid_origin = no NaNChecker::check_every = 524288 NaNChecker::action_if_found = terminate Carpet::max_refinement_levels = 7 CarpetRegrid::refinement_levels = 7 CarpetRegrid::refined_regions = "manual-coordinate-list" CarpetRegrid::smart_outer_boundaries = yes CarpetRegrid::coordinates = "[ [([-36,-36,-36]:[36,36,36]:[3,3,3])], [([-36,-36,-36]:[36,36,36]:[1.5,1.5,1.5])], [([-19.5,-19.5,-19.5]:[19.5,19.5,19.5]:[0.75,0.75,0.75])], [([-12,-9,-9]:[12,9,9]:[0.375,0.375,0.375])], [([-8.25,-4.125,-4.125]:[-1.875,4.125,4.125]:[0.1875,0.1875,0.1875]),([1.875,-4.125,-4.125]:[8.25,4.125,4.125]:[0.1875,0.1875,0.1875])], [([-6.375,-1.6875,-1.6875]:[-3.75,1.6875,1.6875]:[0.09375,0.09375,0.09375]), ([3.75,-1.6875,-1.6875]:[6.375,1.6875,1.6875]:[0.09375,0.09375,0.09375])] ]" Carpet::verbose = "no" Carpet::veryverbose = "no" BruiserSetBG::bh1_m = 1.0 BruiserSetBG::bh1_a = 0.5 BruiserSetBG::bh1_theta = 0.0 BruiserSetBG::bh1_phi = 1.57 BruiserSetBG::bh1_x = -5.00 BruiserSetBG::bh1_y = 0.0 BruiserSetBG::bh1_z = 0.0 BruiserSetBG::bh1_vx = 1.0e-33 BruiserSetBG::bh1_vy = 0.0 BruiserSetBG::bh1_vz = 0.0 BruiserSetBG::bh2_m = 1.0 BruiserSetBG::bh2_a = 0.5 BruiserSetBG::bh2_theta = 0.0 BruiserSetBG::bh2_phi = 0.0 BruiserSetBG::bh2_x = 5.00 BruiserSetBG::bh2_y = 0.0 BruiserSetBG::bh2_z = 0.0 BruiserSetBG::bh2_vx = 1.0e-33 BruiserSetBG::bh2_vy = 0.0 BruiserSetBG::bh2_vz = 0.0 BruiserSetBG::r_mask = 0.9 BruiserConstraints::skip_solver = "no" BruiserConstraints::use_fma = "no" BruiserConstraints::nlevels = 7 BruiserConstraints::nvcycle = 1 BruiserConstraints::preswp = 3 BruiserConstraints::bruiser_verbosity = 5 BruiserConstraints::sor_factor = 1.4 BruiserConstraints::cgtol = 1.0e-8 SpaceMask::use_mask = yes AHFinderDirect::find_every = 1 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::N_horizons = 2 AHFinderDirect::origin_x [1] = -5.0 AHFinderDirect::initial_guess__coord_sphere__x_center [1] = -5.0 AHFinderDirect::initial_guess__coord_sphere__radius [1] = 2.0 AHFinderDirect::which_surface_to_store_info [1] = 0 AHFinderDirect::origin_x [2] = 5.0 AHFinderDirect::initial_guess__coord_sphere__x_center [2] = 5.0 AHFinderDirect::initial_guess__coord_sphere__radius [2] = 2.0 AHFinderDirect::which_surface_to_store_info [2] = 1 AHFinderDirect::set_mask_for_individual_horizon [2] = no TimerReport::output_all_timers = "yes" IOBasic::outInfo_every = 1 IOBasic::outInfo_reductions = "minimum maximum" IOBasic::outInfo_vars = " ADMBase::alp " IOScalar::outScalar_every = 1 IOScalar::outScalar_vars = " grid::coordinates ADMBase::metric ADMBase::curv " IOASCII::out2D_every = 1 IOASCII::out2D_vars = " BruiserConstraints::phi " IOHDF5::out_criterion = time IOHDF5::out_dt = 1.0 IOHDF5::out_vars = " ADMBase::metric ADMBase::curv BruiserSetBG::bruiser_mask BruiserConstraints::phi " BruiserConstraints::output_method = "IOHDF5"

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Backports
by Ian Hinder 20 Dec '13

20 Dec '13

Hi, There was some discussion in https://trac.einsteintoolkit.org/ticket/1504 about how to mark Einstein Toolkit tickets as requiring a backport to the current release. We already introduced a method for this in the past; if you put the keyword "backport" in the keywords field, the tickets requiring backports can be queried using a standard TRAC query, e.g. https://trac.einsteintoolkit.org/query?status=accepted&status=assigned&stat… In the above query, I have included closed tickets, as there are no current open tickets with the backport keyword. I have added a link on the ET TRAC homepage which shows the number of open tickets with the backport keyword, and provides a link to the query. I think this should be sufficient. -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Mojave|Simfactory|Fortran(thorn): F90 compiler rejecting "_##" in var names
by Scott Hawley 20 Dec '13

20 Dec '13

I'm getting an error I've never seen before. The GNU Fortran compiler (gfortran-mp-4.8) is tripping over the use of "_##" in variable names, which are being generated via the build process. I'm familiar with underscores being an extension, however I've never seen pound signs before in variable names and I can't find any statements online as to these characters being allowed. Presumably this is an extension that I need to enable -- any suggestions? I've already got -std=gnu enabled.* Eclipse > Mojave > Build... /usr/bin/python simfactory/lib/sim.py build --mdbkey=make -j 8 --verbose bruiser --thornlist /Users/shawley/ThornLists/ThornListBruiser --optionlist /Users/shawley/options.bruiser.mac IN DIRECTORY: /Users/shawley/Cactus ...snip... COMPILING /Users/shawley/Cactus/arrangements/CactusBase/Fortran/src/paramcheck.F90 Warning: Nonexistent include directory "/Users/shawley/Cactus/arrangements/CactusBase/Fortran/src/include" Warning: Nonexistent include directory "/Users/shawley/Cactus/arrangements/CactusBase/Fortran/src/include" /Users/shawley/.mojaveconfig/Cactus/bruiser/build/Fortran/paramcheck.f90:6.34: integer, parameter :: cctki_use_##cctk_dim = kind(cctk_dim) 1 Error: PARAMETER at (1) is missing an initializer Two more questions: 1. What is the simfactory analog of "SILENT=no"? I see "--verbose" is already enabled, yet I'd like to see exactly what command (& flags) is being used to invoke the Fortran compiler. 2. Can the warning re. no "include" directory be safely ignored? Thanks, Scott * GNU Fortran manual, page 41: "...By default, '-std=gnu' allows the compiler to accept both types of extensions..."

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Fwd: Cactus Error
by Steven R. Brandt 16 Dec '13

16 Dec '13

I'm getting this error from Cactus at runtime when running on Ubuntu. Any idea what it means? Cheers, Steve -------- Original Message -------- Subject: Cactus Error Date: Mon, 16 Dec 2013 15:03:19 -0600 From: Adam Oler <msu-aoler(a)student.mcneese.edu> To: Steven Brandt <sbrandt(a)cct.lsu.edu> cactus_Cfg1: /home/theoler/workspace/CaFunWave/Cactus/arrangements/Carpet/CarpetLib/src/mem.cc:83: mem<T>::mem(size_t, size_t, T*, size_t) [with T = double, size_t = long unsigned int]: Assertion `memsize >= vectorlength * nelems * sizeof (T)' failed. Rank 0 with PID 18862 received signal 6 Writing backtrace to 200x2/backtrace.0.txt Aborted (core dumped)

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Meeting Minutes
by Roland Haas 16 Dec '13

16 Dec '13

Present: Frank, Roland, Peter, Varadarajan Parthasarathy, Ian, Barry, Philipp svn to git transition: * three hosting options considered: ** GitHub ** BitBucket ** self-hosted using gitlab * arguments for GitHub/BitBucket (both seem about equal as far as offered features go): ** larger hosting infrastructure, hopefully with high reliability, ssl certificate management ** larger user based, familiarity of users with hosting service ** both offer APIs for scripted access (Ian and Barry have experience with BitBucket and GitHub) ** create EinsteinToolkit "Team" to manage large number of repositories (done) * arguments for self-hosting ** full control ** easier to automate repository operations ** easier to integrate ticketing system on a per-toolkit basis ** branding of URL with "our" name * Ian will send around the access information for his test repositories (done) * Frank had send out URL for self-hosted checkout of GRHydro: git clone https://git.einsteintoolkit.org/git/GRHydro External libraries size issues: * all want to reduce link time * executable size, CactusJar size reduction welcomed by all * Ian would like to reduce overall repository size for machines with tight quotas on $HOME * will implement the following scheme using Boost as a testing ground: ** ExternalLibraries no longer contain source tarball ** if at build time they detect that they need to compile from source, they will download the tarball (if not already there) into a Cactus-tree wide cache directory ** these source tarballs will not be part of Formaline tarball, however the actual ExtenalLibraries thorn (ie patches, configures.sh, an thus the exact URL used to download the tarball) source is part of the Formaline tarball. This ensures that the code can be recompiled in the future using only information from the Formaline tarball Retiring thorns: * will remove LegoExcision since it has been deprecated and announced to be removed in the past * clarify wiki to clearly specify that the deprecation notice should state that "the thorn will be removed in one of the future releases without further notice" Next call: We will not have a phone call next week (Dec 23rd, not on Dec 30th). The next ET phone call will be Jan 6th 2014 at the usual time. Yours, Roland

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 14 Dec '13

14 Dec '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#. We didn't have time last week to finish all of the discussions that we started, so we will continue to discuss our plans of how and when to retire thorns. I also suggest to remove all testsuites using Exact that have counter-parts from EinsteinExact. In addition, any other question or comment is of course welcome. Current status of the development version: all tests except those in ADM (deprecated) and one Carpet testsuite pass. Frank

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 13 Dec '13

13 Dec '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#. Some topics this call will likely be: * subversion to git transition: ** high level: why? What do we want to achieve? ** low level: how do we do it? (hosting at ET servers or conventional provider) -> can be tested here: git clone https://git.einsteintoolkit.org/git/GRHydro (an old version of GRHydro, likely to be combined with GRHydro_InitData in the final convertion) gitweb (or similar) isn't installed yet, but would be. * sources in ExternalLibraries: ** what to we want to achieve? (Reduce disk and/or executable size? Link time? Download time?) Frank

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Teleconference.
by Varadarajan Parthasarathy 11 Dec '13

11 Dec '13

I am Varadarajan Parthasarathy, doing my PhD at CAMK, Warsaw. I am interested in contributing to Einstein Toolkit and got to know that there is a teleconference every Monday. I would like to know if I can participate in it vis Skype or is there a preferred method to register for this. In case if the group is on skype, could you inform me with the corresponding name so that I can add it. Regards, Varadarajan

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CPP flags
by Yosef Zlochower 10 Dec '13

10 Dec '13

Hi, Every now and then I rediscover a bug that I make when I use one of the simfactory option files as a starting point for our local cluster. Since our local cluster is similar to Lonestar, I start from one of the Lonestar configuration Howerver, the option " CPP_OPENMP_FLAGS = -openmp " Leads to failed compiles because cpp -openmp BLAH causes the output of cpp to go to a file called penmp rather than stdout. I just wonder if other people were bitten by this. On Noether, this caused the compile of GSL to fail (btw, only GSL, the rest of ET compiled fine). -- Dr. Yosef Zlochower Center for Computational Relativity and Gravitation Associate 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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Users December 2013