Users September 2016

users@lists.einsteintoolkit.org

17 participants
23 discussions

Re: [Users] [ET Trac] [Einstein Toolkit] #1326: running loopcontrol on strange number of threads fails
by Erik Schnetter 11 Apr '19

11 Apr '19

Do you have a backtrace? -erik On Sunday, March 22, 2015, Einstein Toolkit < trac-noreply(a)einsteintoolkit.org> wrote: > #1326: running loopcontrol on strange number of threads fails > ------------------------------------+--------------------------------------- > Reporter: rhaas | Owner: > Type: defect | Status: new > Priority: minor | Milestone: > Component: EinsteinToolkit thorn | Version: > Resolution: | Keywords: LoopControl > ------------------------------------+--------------------------------------- > > Comment (by rhaas): > > This still happens even with current (Sun Mar 22 18:46:21 CET 2015) trunk, > though failure looks a bit different now: > {{{ > actus_sim: > /data/rhaas/postdoc/gr/ET_trunk/configs/sim/build/LoopControl/loopcontrol.cc:312: > T {anonymous}::divexact(T, T) [with T = int]: Assertion `i % j == 0' > failed > }}} > > -- > Ticket URL: <https://trac.einsteintoolkit.org/ticket/1326#comment:1> > 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.perimeterinstitute.ca/personal/eschnetter/

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CarpetIOHDF5 to S5 converter for yt
by Roland Haas 06 Oct '16

06 Oct '16

Hello Jonah, Einstein Toolkit users, I think you were working on a plugin to read S5 files into yt, right? Do you also have a converter tool to convert CarpetIOHDF5 3d output files (vertex centered, mesh refined) to S5 files? If only cell centering is supported this is also fine as or this project a slight inaccuracy does not matter. I would be working with Nathan Goldbaum locally to read them into yt so once I have them in that format I will hopefully be home free. 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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Changing I/O parameters between simulations restarts
by dumsani 06 Oct '16

06 Oct '16

Hi, When running long simulations with checkpointing, it might sometimes be useful to change certain parameters, especially I/O (e.g. the frequency of outputting a certain variable). Is this possible in Cactus/Simfactory? I notice that upon recovery (in the next re-start) Simfactory reads the parameters from a checkpoint file, not from any of the parfiles dumped within the job directory. Any suggestions/responses will be highly appreciated. Thank you, Dumsani

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Merging CarpertIOHDF5 output from several checkpoints
by dumsani 01 Oct '16

01 Oct '16

Hi, I have simulation data from various Simfactory checkpoints written out by CarpetIOHDF5. I'd like to collect these data (for one variable, say) into a single file. I was wondering if the tools hdf5_merge and/or hdf5_recombine tools are meant for that. Or are there other ways to in Cactus to do this? Thank you, Dumsani

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Simulation of GW150914 binary black hole merger
by Barry Wardell 30 Sep '16

30 Sep '16

Dear Einstein Toolkit users, We have prepared a new example for the Einstein Toolkit gallery consisting of a simulation of the spacetime of the gravitational wave event GW150914 detected by LIGO in September 2015. The example can be found at https://einsteintoolkit.org/about/gallery/gw150914 The gallery page consists of a short description, some details of the physics parameters and computational requirements, as well as the parameter file and thornlist. We provide a tutorial for obtaining and compiling the code and running the simulation, which should work on any of the machines supported by SimFactory (http://simfactory.org). We also provide a tutorial for visualising the spacetime using the VisIt visualisation software. Also available is a ~600 MB archive containing a subset of the simulation output, including waveforms and horizon quantities, as well as two time slices of 3D data for visualisation. Lastly, we provide a set of Mathematica notebooks demonstrating how the simulation data can be processed an analysed using the SimulationTools (http://simulationtools.org) software package. The simulation utilises entirely open and public codes including the Einstein Toolkit and the Llama multiblock infrastructure (http://llamacode.org). We ask that if you make use of the parameter file or the example data, then please cite the GW150914 Einstein Toolkit example and data [1], the Einstein Toolkit [2], the Llama multi-block infrastructure [3], the Carpet mesh-refinement driver [4], the apparent horizon finder AHFinderDirect [5], the TwoPunctures initial data code [6], QuasiLocalMeasures [7], Cactus [8], and the McLachlan spacetime evolution code [9]. Please let us know if you have any problems; we will be happy to help! Barry Wardell, Ian Hinder and Eloisa Bentivegna -- [1] Barry Wardell, Ian Hinder and Eloisa Bentivegna. Simulation of GW150914 binary black hole merger using the Einstein Toolkit (doi:10.5281/zenodo.155394) [2] Frank Löffler, Joshua Faber, Eloisa Bentivegna, Tanja Bode, Peter Diener, Roland Haas, Ian Hinder, Bruno C. Mundim, Christian D. Ott, Erik Schnetter, Gabrielle Allen, Manuela Campanelli, and Pablo Laguna. The Einstein Toolkit: A Community Computational Infrastructure for Relativistic Astrophysics. Classical and Quantum Gravity, 29(11):115001, 2012. (doi:10.1088/0264-9381/29/11/115001) [3] Denis Pollney, Christian Reisswig, Erik Schnetter, Nils Dorband, Peter Diener. High accuracy binary black hole simulations with an extended wave zone. Phys.Rev. D83 (2011) 044045. (doi:10.1103/PhysRevD.83.044045) [4] Erik Schnetter, Scott H. Hawley, and Ian Hawke. Evolutions in 3-D numerical relativity using fixed mesh refinement. Class. Quantum Grav., 21:1465–1488, 2004. (doi:10.1088/0264-9381/21/6/014) [5] Jonathan Thornburg. A Fast Apparent-Horizon Finder for 3-Dimensional Cartesian Grids in Numerical Relativity. Class. Quantum Grav., 21:743–766, 2004. (doi:10.1088/0264-9381/21/2/026) [6] Marcus Ansorg, Bernd Brügmann, and Wolfgang Tichy. A single-domain spectral method for black hole puncture data. Phys. Rev. D, 70:064011, 2004. (doi:10.1103/PhysRevD.70.064011) [7] Olaf Dreyer, Badri Krishnan, Deirdre Shoemaker, and Erik Schnetter. Introduction to isolated horizons in numerical relativity. Phys. Rev. D, 67:024018, 2003. (doi:10.1103/PhysRevD.67.024018) [8] Tom Goodale, Gabrielle Allen, Gerd Lanfermann, Joan Massó, Thomas Radke, Edward Seidel, and John Shalf. The Cactus framework and toolkit: Design and applications. In Vector and Parallel Processing – VECPAR'2002, 5th International Conference, Lecture Notes in Computer Science, Berlin, 2003. Springer. [9] J. David Brown, Peter Diener, Olivier Sarbach, Erik Schnetter, and Manuel Tiglio. Turduckening black holes: an analytical and computational study. Phys. Rev. D, 79:044023, 2009. (doi:10.1103/PhysRevD.79.044023)

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meeting minutes for 2016-09-26
by Roland Haas 30 Sep '16

30 Sep '16

Present: Frank, Matt, Roberto, Roland, Zach, Ian, Erik, Steve, Peter, Vassili Jenkins: * Ian and Barry are working on setting up the git super repository, hoping to get things up and running in a day or so Piraha: * Roland asks for higher level documentation, for example excerpts from the piraha paper Gallery: * consistency checks are done Hangouts: * Frank contacted google and it seems as if accounts for larger numbers of participants are institution accounts and are hard to get * Frank is investigating alternative VoIP setups, Roland mentions to use screenleap for slide presentations during talks (http://www.screenleap.com/) * LSU has a webex account that could be used, this is problematic for Linux users that have to call in via phone Hackathon topics: * include citiations in code. We had a discussion on how we want to include this, in the end we decided against it as there was not enough interest. * overlapping computation and communication using FunHPC. Erik has a proof of concept and it would be a starting point. https://bitbucket.org/eschnett/funhpc.cxx . We will try for this. * time will be decided on a doodle poll Docker container for the ET: * Ian has a container on dockerhub which can be found by searching for einsteintoolkit https://hub.docker.com/r/ianhinder/jenkins-einsteintoolkit/ 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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question about ML_BSSN::fixAdvectionTerms
by Slinker, Kyle Patrick 29 Sep '16

29 Sep '16

Hello, I'm wondering if anybody can tell me about the ML_BSSN::fixAdvectionTerms parameter (which I think was new in Somerville). I have been trying to reproduce some old results and discovered this morning that having this parameter set to "off" is what was causing the discrepancy. What does it do? The description "Modify driver and advection terms to work better?" is vague enough I don't know what to make of it. From McLachlan_BSSN.m it looks like it's switching how the advection terms in the 1+log and Gamma-driver conditions are handled. What changes is it making to these equations? And what is the purpose of them? If setting the parameter to "on" reproduces old results (and if it lives up to its name and fixes things), should "on" be the default behavior? Thanks. Kyle Slinker

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Einstein Toolkit Meeting Reminder
by Roland Haas 25 Sep '16

25 Sep '16

Hello, Please consider joining the weekly Einstein Toolkit phone call at 9:30 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/ We use a Google hangout, with the URL: https://hangouts.google.com/call/5xt7voshalqmdcztr4zhfeox2ia Please suggest additional topics that you would like to add to the agenda. Roland Haas -- 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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EHfinder
by dlshcbmuipmam＠gmail.com 25 Sep '16

25 Sep '16

Hi, My aim is to find simulate the event horizon of binary blackhole. However, the documentation of EHfinder is hard to understand, and there is no existing parameter file on internet or inside the toolkit which use the EHfinder for my reference. (Well, there is a test par file inside ET, using exact Kerr metric, but it is not very useful) Can anyone introduce how to input the metric data into EHfinder? (I am not even sure should I do the EHfinder analysis with the simulation, or after the simulation then input the data in some ways) It is even better if you can provide an example par file using EHfinder. Thank you.

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thorns providing citations
by Frank Loeffler 23 Sep '16

23 Sep '16

Hi, This is a proposal about how thorns can provide citations of resources (papers, ...), and how Cactus could use those to output a list of 'used resources'. I would like to make this the topic for the October-hack-a-day, if I find one or two more interested people. It shouldn't take more than that day to get something working. Before that, however, we should discuss what this should actually look like. The rest of this email is details about the proposal. If you are not interested, you can stop reading here. If you are, please let us know what you think after you've read it. While I said 'resources', I mean citations, usually to papers, but really it could be anything. There is also the question of how to cite something, and in the following I am assuming bibtex entries, as that is what most likely most people would find useful. First of all, thorns would need to have a way to provide citations. Thorns already provide all kinds of stuff, and most of that is 'announced to Cactus' in configuration.ccl, so let's use that, and not create yet another .ccl file: PROVIDES CITATION name AS "xyz" PROVIDES CITATION name IN bibtex filename, relative to thorn dir REQUIRES CITATION name This gives each citation a name, and would use that in a key-value table as key, where the value is a bibtex-entry, verbatim and (in this proposal) unparsed by Cactus. The name should ideally be the same as the key in the bibtex entry, but it doesn't need to be. We could decide to enforce equality, but then would have to parse the entry / bib file. This mechanism would only provide a way to define citations, and use them if you can be sure another thorn already provides it (REQUIRES). The next question would be how to tell Cactus that a certain citation should be included in the output, and what that output should look like. We already have two "classes" of citations in the ET: "requested" and "optional". "requested" citations should be cited whenever that piece of code was used, while "optional" are, well, optional. Thus, we should have a way to provide those. Also, whether a citation should be included might depend on parameters (we do have a few examples of those), and not just thorn activation. Thus, I believe the best way to include this is schedule.ccl: CITATION name CITATION OPTIONAL name These could be stand-alone, top-level statements, or be inside if-blocks, similar to, e.g., STORAGE statements. These statements only use the name of the citation as defined above - not the actual citation string itself. Once a citation is marked as 'being used', it will not be 'unmarked' within that run. Using this information, Cactus will then provide output regarding which citations are used, by which thorn, and of which type (requested, optional). This output is updated (overwritten) each time something is added (but waits until the regular thorn-activation sequence is completed). The output should, at least, consist of: - one bibtex file containing all known entries - two lists of keys, in machine readable format: requested/optional - machine readable information about which thorn requested what how Of course, depending on our wishes, part of this can and should be configurable via parameters. Frank Loeffler

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