Users August 2019

users@lists.einsteintoolkit.org

8 participants
15 discussions

Einstein Toolkit Meeting Reminder
by Steven R. Brandt 31 Oct '19

31 Oct '19

Hi Please consider joining the weekly Einstein Toolkit phone call at 9:30 am US central time on Mondays. 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 --Steve

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Agenda for Monday's Meeting
by Steven R. Brandt 30 Oct '19

30 Oct '19

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

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New Einstein Toolkit Release (Chien-Shiung Wu)
by Steven R. Brandt 30 Oct '19

30 Oct '19

=== Release Announcement === We are pleased to announce the sixteenth release (code name "Tesla") of the Einstein Toolkit, an open, community developed software infrastructure for relativistic astrophysics. The highlights of this release are Five new thorns have been added: * GiRaFFE * GiRaFFEfood * ShiftedKerrSchild * GiRaFFE_to_HydroBase * ID_converter_GiRaFFE In addition, bug fixes accumulated since the previous release in Feb 2018 have been included. The Einstein Toolkit is a collection of software components and tools for simulating and analyzing general relativistic astrophysical systems that builds on numerous software efforts in the numerical relativity community including CactusEinstein, the Carpet AMR infrastructure and the relativistic magneto-hydrodynamics code GRHydro. For parts of the toolkit, the Cactus Framework is used as the underlying computational infrastructure providing large-scale parallelization, general computational components, and a model for collaborative, portable code development. The toolkit includes modules to build complete codes for simulating black hole spacetimes as well as systems governed by relativistic magneto-hydrodynamics. The Einstein Toolkit uses a distributed software model and its different modules are developed, distributed, and supported either by the core team of Einstein Toolkit Maintainers, or by individual groups. Where modules are provided by external groups, the Einstein Toolkit Maintainers provide quality control for modules for inclusion in the toolkit and help coordinate support. The Einstein Toolkit Maintainers currently involve postdocs and faculty from six different institutions, and host weekly meetings that are open for anyone to join in. Guiding principles for the design and implementation of the toolkit include: open, community-driven software development; well thought out and stable interfaces; separation of physics software from computational science infrastructure; provision of complete working production code; training and education for a new generation of researchers. For more information about using or contributing to the Einstein Toolkit, or to join the Einstein Toolkit Consortium, please visit our web pages at http://einsteintoolkit.org. The Einstein Toolkit is primarily supported by NSF 1550551/1550461/1550436/1550514 (Einstein Toolkit Community Integration and Data Exploration). The Einstein Toolkit contains about 200 regression test cases. On a large portion of the tested machines, almost all of these tests pass, using both MPI and OpenMP parallelization. The changes between this and the previous release include: == Larger changes since last release == * Support has been added for GCC8. * Built-in OpenMPI tarball has been upgraded to 1.10.7 Note, we still recommend using the system MPI that is installed natively on your system. * And many bug fixes. Notably, a significant correctness problem for NewRad was addressed which caused many simulations with more than two ranks to fail https://trac.einsteintoolkit.org/ticket/2182 == New thorns or tools == * GiRaFFE (~1,600 lines of code): Solves the GRFFE equations in the formalism of Paschalidis and Shapiro [2] using the same reconstruction (PPM) and staggered vector potential methods as IllinoisGRMHD. * GiRaFFEfood (~1,300 lines of code): Code validation initial data and basic diagnostics. Contains Five 1D tests in flat spacetime (fast wave, Alfvén wave, degenerate Alfvén wave, "three-wave", FFE breakdown), One 3D test in flat spacetime (aligned rotator), and Three 3D tests in curved spacetimes ("Exact Wald" solution, "Magnetospheric Wald" solution, and split monopole). * ShiftedKerrSchild (~230 lines of code): Sets up all 3+1 quantities for a Kerr-Schild spacetime with an arbitrary radial shift, to mitigate effects of extreme spacetime curvature near r_{KS}=0. See Appendix of code release paper for full discussion. * GiRaFFE_to_HydroBase and ID_converter_GiRaFFE (~230 lines of code): Acts as a translation layer to convert 3-velocities in HydroBase's Valencia formalism to/from the 3-velocity found in the induction equation (vi = ui/u0; native to GiRaFFE). == Upcoming changes for the next releases == == New thorns planned for the next relases == * Seed_Magnetic_Fields-modified Extended Seed_Magnetic_Fields thorn for binary neutron stars. Supercedes Seed_Magnetic_Fields thorn. * Meudon_Bin_NS-modified Modifications to Meudon BNS initial data thorn to disable the overwriting of initial lapse/shift, which acts to significantly reduce coordinate eccentricity. Supercedes Meudon_Bin_NS thorn. * VolumeIntegrals_GRMHD Nice GRMHD volume integration thorn, currently depends on IllinoisGRMHD and Carpet. Performs volume integrals on arbitrary "Swiss-cheese"-like topologies, and even interoperates with Carpet to track NS centers of mass. * VolumeIntegrals_vacuum Nice GRMHD volume integration thorn, currently depends on ML_BSSN. There is a bit of code duplication and duplicated functionality between VI_GRMHD and VI_vacuum, to ensure that VI_vacuum can be used without enabling a GRMHD code. There is probably a better way of doing this, but I haven't had the time to think deeply about this. * particle_tracerET Solves the ODE \partial_t xi = vi for typically thousands of tracer particles, using an RK4 integration atop the current timestepping. E.g., one RK4 substep in the particle integration might occur every 16 RK4 substeps in the GRMHD evolution. These tracer particle positions are quite useful for visualizing magnetic field lines in a consistent way from frame-to-frame in a movie (recall that in the GRMHD approximation, the magnetic field lines stay attached the fluid elements they thread Flux Freezing?). Note that the velocity must be consistent with the velocity appearing in the GRMHD induction equation. This thorn reads in the HydroBase vel[] vector gridfunction, which assumes the Valencia formalism, and converts it into the induction equation velocity. * smallbPoynET Computes bi, b2, and three spatial components of Poynting flux. It also computes (-1-u0), which is useful for tracking unbound matter. * LeanBSSNMoL and NPScalars: LeanBSSNMoL evolves Einstein's Equations with the BSSN formulation. NPScalars computes the Newman-Penrose scalars. For the conformal factor it uses the "W" version, i.e. W=\gamma^{-1/6}, and it employs the usual "1+log" and "Gamma-driver" gauge conditions. Also available, in the "new_gauge" branch, is the shift condition of Figueras et al for their evolutions of higher dimensional BHs, see: https://arxiv.org/abs/1702.01755 https://arxiv.org/abs/1512.04532 * Proca arrangement: This repository (https://bitbucket.org/canuda/proca/src) provides the tools to evolve the Einstein-Proca system as first described in https://arxiv.org/abs/1505.00797 == How to upgrade from Tesla (ET_2018_02) == To upgrade from the previous release, use GetComponents with the new thornlist to check out the new version. See the Download page (http://einsteintoolkit.org/download/) on the Einstein Toolkit website for download instructions. == Machine notes == Supported (tested) machines include: * Default Debian, Ubuntu, Fedora, CentOS, Mint, OpenSUSE and MacOS (Homebrew and MacPorts) installations * Bluewaters * Comet * Cori * Draco * Edison * Golub * Hydra * Marconi * Minerva * Queenbee 2 * Stampede 2 * SuperMIC * Wheeler * TACC machines: defs.local.ini needs to have sourcebasedir = $WORK and basedir = $SCRATCH/simulations configured for this machine. You need to determine $WORK and $SCRATCH by logging in to the machine. * A new configuration for KNL nodes is being worked on, but not yet included in the release (but compilation works and tests mostly pass). All repositories participating in this release carry a branch ET_2018_02 marking this release. These release branches will be updated if severe errors are found. The "Chien-Shiung Wu" Release Team on behalf of the Einstein Toolkit Consortium (2018-09-17) * Steven R. Brandt * Samuel D. Cupp * Peter Diener * Roland Haas * Roberto De Pietri Sep, 2018

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Error running nsns_test.par with file resu.d
by Atul Kedia 15 Sep '19

15 Sep '19

Hello, I am trying to do a test run with nsns_test.par from the default ETK package from directory /Cactus/repos/wvuthorns_diagnostics/NSNS_parameter_files/ and getting the following error: ERROR from host epycfe.crc.nd.edu process 1 while executing schedule bin HydroBase_Initial, routine Meudon_Bin_NS::Meudon_Bin_NS_initialise in thorn Meudon_Bin_NS, file /afs/ crc.nd.edu/user/i/isuh/astroph/Cactus/08132019/Cactus/configs/sim/build/Meu… : -> File "resu.d" does not exist. ABORTING cactus_sim: /afs/ crc.nd.edu/user/i/isuh/astroph/Cactus/08132019/Cactus/configs/sim/build/Car…: int Carpet::Abort(const cGH*, int): Assertion `0' failed. I obtained the file "resu.d" from http://astro.phys.wvu.edu/zetienne/resu.d but don't know where I should put the file. I think this is a Lorene data file (based on http://dspace-unipr.cineca.it/bitstream/1889/3328/1/Thesis_Maione.pdf). Does anyone know where to place it? Thank you, Atul Kedia, Physics Graduate student University of Notre Dame

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errors while compiling Einstein toolkit
by Mattia 11 Sep '19

11 Sep '19

After the compilation I get the following list of errors: CST error 1: -> Missing thorn ExternalLibraries/BLAS CST error 2: -> Missing thorn ExternalLibraries/FFTW3 CST error 3: -> Missing thorn ExternalLibraries/GSL CST error 4: -> Missing thorn ExternalLibraries/HDF5 CST error 5: -> Missing thorn ExternalLibraries/hwloc CST error 6: -> Missing thorn ExternalLibraries/LAPACK CST error 7: -> Missing thorn ExternalLibraries/libjpeg CST error 8: -> Missing thorn ExternalLibraries/LORENE CST error 9: -> Missing thorn ExternalLibraries/MPI CST error 10: -> Missing thorn ExternalLibraries/OpenSSL CST error 11: -> Missing thorn ExternalLibraries/PAPI CST error 12: -> Missing thorn ExternalLibraries/pthreads CST error 13: -> Missing thorn ExternalLibraries/zlib CST error 14: -> Thorn 'CT_MultiLevel' requires the capability 'MPI'. Please add a thorn that provides 'MPI' to your ThornList or remove 'CT_MultiLevel' from it ! CST error 15: -> Thorn 'Carpet' requires the capability 'MPI'. Please add a thorn that provides 'MPI' to your ThornList or remove 'Carpet' from it ! CST error 16: -> Thorn 'CarpetIOHDF5' requires the capability 'HDF5'. Please add a thorn that provides 'HDF5' to your ThornList or remove 'CarpetIOHDF5' from it ! CST error 17: -> Thorn 'CarpetInterp' requires the capability 'MPI'. Please add a thorn that provides 'MPI' to your ThornList or remove 'CarpetInterp' from it ! CST error 18: -> Thorn 'CarpetLib' requires the capability 'MPI'. Please add a thorn that provides 'MPI' to your ThornList or remove 'CarpetLib' from it ! CST error 19: -> Thorn 'CarpetReduce' requires the capability 'MPI'. Please add a thorn that provides 'MPI' to your ThornList or remove 'CarpetReduce' from it ! CST error 20: -> Thorn 'EOS_Omni' requires the capability 'HDF5'. Please add a thorn that provides 'HDF5' to your ThornList or remove 'EOS_Omni' from it ! CST error 21: -> Thorn 'GiRaFFEfood' requires the capability 'GSL'. Please add a thorn that provides 'GSL' to your ThornList or remove 'GiRaFFEfood' from it ! CST error 22: -> Thorn 'Hydro_RNSID' requires the capability 'HDF5'. Please add a thorn that provides 'HDF5' to your ThornList or remove 'Hydro_RNSID' from it ! CST error 23: -> Thorn 'IOHDF5' requires the capability 'HDF5'. Please add a thorn that provides 'HDF5' to your ThornList or remove 'IOHDF5' from it ! CST error 24: -> Thorn 'IOHDF5Util' requires the capability 'HDF5'. Please add a thorn that provides 'HDF5' to your ThornList or remove 'IOHDF5Util' from it ! CST error 25: -> Thorn 'IOJpeg' requires the capability 'libjpeg'. Please add a thorn that provides 'libjpeg' to your ThornList or remove 'IOJpeg' from it ! CST error 26: -> Thorn 'Interpolate2' requires the capability 'LAPACK'. Please add a thorn that provides 'LAPACK' to your ThornList or remove 'Interpolate2' from it ! CST error 27: -> Thorn 'LlamaWaveToy' requires the capability 'LAPACK'. Please add a thorn that provides 'LAPACK' to your ThornList or remove 'LlamaWaveToy' from it ! CST error 28: -> Thorn 'Meudon_Bin_BH' requires the capability 'LORENE'. Please add a thorn that provides 'LORENE' to your ThornList or remove 'Meudon_Bin_BH' from it ! CST error 29: -> Thorn 'Meudon_Bin_NS' requires the capability 'LORENE'. Please add a thorn that provides 'LORENE' to your ThornList or remove 'Meudon_Bin_NS' from it ! CST error 30: -> Thorn 'Meudon_Mag_NS' requires the capability 'LORENE'. Please add a thorn that provides 'LORENE' to your ThornList or remove 'Meudon_Mag_NS' from it ! CST error 31: -> Thorn 'NullNews' requires the capability 'MPI'. Please add a thorn that provides 'MPI' to your ThornList or remove 'NullNews' from it ! CST error 32: -> Thorn 'QuasiLocalMeasures' requires the capability 'LAPACK'. Please add a thorn that provides 'LAPACK' to your ThornList or remove 'QuasiLocalMeasures' from it ! CST error 33: -> Thorn 'SphericalHarmonicDecomp' requires the capability 'HDF5'. Please add a thorn that provides 'HDF5' to your ThornList or remove 'SphericalHarmonicDecomp' from it ! CST error 34: -> Thorn 'SphericalHarmonicDecomp' requires the capability 'GSL'. Please add a thorn that provides 'GSL' to your ThornList or remove 'SphericalHarmonicDecomp' from it ! CST error 35: -> Thorn 'SphericalHarmonicRecon' requires the capability 'HDF5'. Please add a thorn that provides 'HDF5' to your ThornList or remove 'SphericalHarmonicRecon' from it ! CST error 36: -> Thorn 'SphericalHarmonicRecon' requires the capability 'FFTW3'. Please add a thorn that provides 'FFTW3' to your ThornList or remove 'SphericalHarmonicRecon' from it ! CST error 37: -> Thorn 'SphericalHarmonicRecon' requires the capability 'MPI'. Please add a thorn that provides 'MPI' to your ThornList or remove 'SphericalHarmonicRecon' from it ! CST error 38: -> Thorn 'SphericalHarmonicReconGen' requires the capability 'HDF5'. Please add a thorn that provides 'HDF5' to your ThornList or remove 'SphericalHarmonicReconGen' from it ! CST error 39: -> Thorn 'SystemTopology' requires the capability 'hwloc'. Please add a thorn that provides 'hwloc' to your ThornList or remove 'SystemTopology' from it ! CST error 40: -> Thorn 'SystemTopology' requires the capability 'MPI'. Please add a thorn that provides 'MPI' to your ThornList or remove 'SystemTopology' from it ! CST error 41: -> Thorn 'TGRtensor' requires the capability 'LAPACK'. Please add a thorn that provides 'LAPACK' to your ThornList or remove 'TGRtensor' from it ! CST error 42: -> Thorn 'TwoPunctures' requires the capability 'GSL'. Please add a thorn that provides 'GSL' to your ThornList or remove 'TwoPunctures' from it ! CST error 43: -> Thorn 'TwoPunctures_KerrProca' requires the capability 'GSL'. Please add a thorn that provides 'GSL' to your ThornList or remove 'TwoPunctures_KerrProca' from it !

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meeting minutes for 2019-08-29
by Haas, Roland 29 Aug '19

29 Aug '19

Present: Chris, Frank, Helvi, Maria, Roland, Toni, Zach ET meeting at KCL: * will have zoom set up for remote participation: https://zoom.us/j/355206842 * program is available at: https://sites.google.com/view/eetm2019/home Upcoming ET release: * planned for October * pan to add Peter Diener's self-force code, will be separate checkout but same git-tags * find out which tickets are critical for release * Steve is working on list of developers for Zenodo based DOI for the release ET website: * LSU is tightening its accessibility rules for website design * the set of accessibility rules would make it very difficult if these rules applies to our websites There will not be a call next week due to the ET meeting at KCL. 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://pgp.mit.edu .

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CactusTutorial
by Tomas Andrade 28 Aug '19

28 Aug '19

Hi, I am running the CactusTutorial online. In the section 'Prerequisites', we are told to install a few packages (xcode, gcc, git, etc). To try to do so, I opened a terminal within Jupyter, and typed sudo xcodebuild -license I got the error message: /bin/sh: 1: sudo: not found So, I can't download any of the prerequisites. I am able to continue and download Cactus with 'GetComponents' and run 'simfactory', but the build of 'einsteintoolkit' fails due to lack of the C compiler. Any advice? thank you! Tomas -- Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir informació confidencial o protegida legalment i s’adreça exclusivament a la persona o entitat destinatària. Si no consteu com a destinatari final o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant el missatge com els fitxers adjunts que hi pugui haver. Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener. This email message and any attachments it carries may contain confidential or legally protected material and are intended solely for the individual or organization to whom they are addressed. If you are not the intended recipient of this message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any part of it. If you have received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account.

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QK Frame
by Carlos Lousto 28 Aug '19

28 Aug '19

Hi, We have been working with my student Nicole to define a global (not merely asymptotic for extraction) quasi-kinnnersley tetrad starting from a frame (psi1=0=psi3) and we were wondering if anyone in the collaboration have implemented it (or tried to) since we are finding difficulties when evaluated close or in between the black holes. Thanks, Carlos Lousto https://ccrg.rit.edu/user/carlos.lousto >

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Error when compiling Einstein Toolkit
by Mattia 26 Aug '19

26 Aug '19

When compiling on my laptop which runs Ubuntu 16.04 I get the following errors: make[1]: *** [/home/mattia/Cactus/configs/sim/config-data/make.thornlist] Errore 1 Makefile:256: set di istruzioni per l'obiettivo "sim" non riuscito make: *** [sim] Errore 2 the second line says something like: th set of instruction for the objective "sim" has not succeded What does it mean?

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Meeting minutes for 2019-08-22
by Steven R. Brandt 22 Aug '19

22 Aug '19

Present: Frank Loeffler, Steve, Peter, Bill, Zach, Helvi, ... (I forgot to write this down during the meeting, please let me know if I missed you) Does HARM have an advantage over Cactus for neutron star evolutions? - It can excise the center of the grid and possibly the z-axis - Cactus lacks spherical coords, however Spherical GRMHD should help, also Spherical BSSN Code (Zach added all optimizations) - Zach is working on magnetized BNS merger, letting Harm do the long term evolution using a static spacetime Developing a handoff code. A new driver thorn based on AMReX is being developed: AMReX https://amrex-codes.github.io/amrex/ ETK meeting in London 2-6 of September Schedule will be up soon Zenodo DOI. List of names is complete. Still filling in people Plan is to sort anyone on the list who participates in the release to the top. Release - Peter's code in the ET - Separate checkout from the ET, but with the same tag. - Steve is reviewing Peter's code, help would be welcome - Zach wants the Fishbone Moncrief thorn to be included. Generates NRPy but NRPy is not required. Zach noticed that his recent NRPy code is 20% slower with the Intel compiler.

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Users August 2019