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Einstein Toolkit Meeting Reminder
by Frank Loeffler 10 Oct '16

10 Oct '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 Frank Loeffler

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Uninitialised variables
by Ian Hinder 09 Oct '16

09 Oct '16

Hi, If I add a thorn to a simulation part-way though, its Cactus variables won't be present in the checkpoint file on the first recovery. The code which detects this is in Carpet/CarpetIOHDF5/src/Input.cc and the warning is: CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING, "variable '%s' timelevel %d has not been read", fullname, tl); In this case, there is no final error message and abort, unlike in the case of partially-read gridfunctions. Is this a deliberate decision, because for partially-read gridfunctions the results are definitely wrong, whereas not reading variables at all might be OK? In my particular case, the variables are scalar integers. What value would the variables have in this case? Does Carpet initialise variables to 0? I seem to see 0, but haven't checked carefully. -- Ian Hinder http://members.aei.mpg.de/ianhin

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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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Re: [Users] Merging CarpertIOHDF5 output from several checkpoints
by dumsani 04 Oct '16

04 Oct '16

Hi Roland, Yeah, I got this version of CarpetHDF5 from your Bitbucket public repo. I've made it past the error now by creating a symbolic link under the VisIt installation directory which points to the system's libdl.so. The installation has worked out successfully. Now I will move on to trying that solution about the HDF5 data from various restarts. Thanks a lot for your kind assistance. Regards, Dumsani On 04/10/2016 23:13, Roland Haas wrote: > Hello Dumsani, > >> To begin with, I am trying the option where I must compile the >> updated CarpetHDF5 reader plugin into my VisIt installation. I traced >> that version down to this site >> https://bitbucket.org/rhaas80/carpethdf5/overview (thanks to the >> communication thread). At the moment, I need to resolve a few issues >> in the build (it fails due to a missing library): > You are free to use that one. It is not quite the official ET version > of the reader though, rather my own extended version. The official one > is in here: > > https://svn.cactuscode.org/VizTools/CarpetHDF5/trunk/ > > (found onhttp://cactuscode.org/documentation/visualization/VisIt/ > which one gets to after following about 4 links from the ET site, this > is a bit roundabout). > > The instructions are the same though. > > I have to admit I have never seen that error message. libdl.so lives > in /lib/x86_64-linux-gnu/ on my linux system. It should only appear as > "-ldl" in CMakeFiles/?CarpetHDF5Database.dir/link.txt . > > Yours, > Roland > >

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Re: [Users] Merging CarpertIOHDF5 output from several checkpoints
by dumsani 04 Oct '16

04 Oct '16

Hi Roland, I use VisIt too for the HDF5 output and sure, it does pick up the files from all processes (var.file_*.h5) to open them as as a single (virtual) database. Your second point does answer my question anyway. Thanks. I'll have to figure out some work-around, e.g. processing the output from each individual checkpoint directory. Regards, Dumsani On 30/09/2016 22:54, Roland Haas wrote: > Hello Dumsani, > >> Now, for purposes of visualizing the data, for instance, one would be >> interested in collecting all these data chunks into a single file. >> The question is how to bundle these into a single file. I wanted to >> know if any of the available Carpet tools can help with this. > This depends on the visualization software you would like to use. VisIt > will automatically use all rho files if you open the rho.file_0.h5 file > so you typically do not have to do anything. It will however not > combine files from the different output-???? directories. I do not know > of any way to have VisIt read them all and present them as a single > database. > > If you want to combine really combine the files, you can use the > hdf5_slicer command that is part of CarpetIOHDF5 and that you can find > in exe/sim/hdf5_slicer (it can be used to combine files if you give it > the out3d-cube option). For your files, if you want a single file (keep > in mind Ian's comment it will just copy the datasets, no actual merging > of the datasets happens) you can use: > > hdf5_slicer --out3d-cube output-????/<parfile>/{rho,eps}.file_*.h5 > rho.h5 > > Yours, > Roland > >

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meeting minutes for 2016-10-03
by rhaas＠illinois.edu 03 Oct '16

03 Oct '16

Present: Roland, Frank, Steve, Ian, Eloisa, Erik, Roberto, Vassili, Zach Failing Jenkins tests: * currently failing https://build-test.barrywardell.net/job/EinsteinToolkit/lastCompletedBuild/… * WENO test -> Roland will take care of it, NaNChecker -> Roland, Frank: will write C code to produce NaNs * ML_BSSN constraint failures: push change to ML_BSSN_Helper -> push fix to ML_BSSN_Helper. Roland gets SEGFAULTs when applying this patch in ml-gw1d-small tests (in CarpetLib's copy_from routine CarpetLib/gdata.cc:188) * perl @INC will drop "." in 5.26. Which will break compiles. Steve points out that one can adjust PERL5PATH env variable to fix this without a code change. A code change will still be applied for future versions. ET website: * gallery could use some language polish * try and make gallery examples use only ET thornlists * aim for this in the next release Include Llama in ET: * Erik tasked with starting the process of investigating whether it can be included * needs to meet the guidelines for the ET * needs documentation and basic examples, Vassili will talk with Erik about this at MW24 Update LORENE: * have second thorn LORENE2 for new version * try and make choice between the two of them a run-time choice * Roland suggests to patch LORENE1 in ET to fix handling of piecewise polytropes since the fix was included in LORENE after the file format update. Roland will provide the patch (from the original authors). * want to keep backwards compatible, list both in ThornList, eventually give preference to LORENE2 if only one can be compiled at the same time * Roberto mentions that the code to regenerate the BNS data files is included in LORENE and can be used to regenerate the public data files in the new format 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 03 Oct '16

03 Oct '16

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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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