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Grid structure inconsistency & errors in surface mask locations
by Seven Eight 16 Apr '21

16 Apr '21

Hi, I was wondering if anybody could help me spot the problem(s) in (possibly) my parameter file? I am trying to run a BBH simulation with mass ratio = 3. The parameter b=3 and the punctures were set at +3 and -1 on the x axis (as I understand the setup requires, so that the center of mass is at 0). I set up the CarpetGrid refinement domains accordingly. The simulation runs for about 8000 steps and ends with an error concerning the grid, which I put here (error log and parameter file attached): https://gist.github.com/konrad-topolski/1f292fbb234232e68dd76e4fc784e481 The differences between this parameter file and the one originally provided with Einstein Toolkit was that I had removed any reflectionsymmetry180 and I commented out the Carpet Mask variables concerning the surfaces, i.e I simulated without: CarpetMask::excluded_surface [0] = 0 CarpetMask::excluded_surface_factor[0] = 1.0 CarpetMask::excluded_surface [1] = 1 CarpetMask::excluded_surface_factor[1] = 1.0 CarpetMask::excluded_surface [2] = 2 CarpetMask::excluded_surface_factor[2] = 1.0 I did so because there was some weird behaviour with Surface mask location - it correctly localized the puncture 0 (at +3), but couldn't locate the puncture 1 (at -1) - it said it was at [e^273, ..., ...] etc. Hence the question, how to set up the puncture tracker, AHFinderDirect and CarpetMask correctly? I also set up the target masses instead of the bare ones. I am currently playing around with some options, but in case I don't get anywhere, I would much appreciate any help. Best regards Konrad Topolski

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Meeting Minutes 2021-04-15
by Gabella, William E 15 Apr '21

15 Apr '21

Present: Roland H, Bill G, Ken S, Peter D, Karim S, Steve B, Atul K, Indrani B, Erik S, Zach E, Maria H, Miguel G Chair: Roland H, Minutes: Bill G * SPEC benchmark contribution [https://bitbucket.org/einsteintoolkit/tickets/issues/2470 task] [RH, SB] Steve, no new news. * ET 2021 summer workshop [https://docs.google.com/spreadsheets/d/1zNnN5kTh_X0_Le_UDCFbTlavOcjwLNh6pxR… date selection] Roland, another virtual only ETK meeting this summer hosted by NCSA. Trying to avoid other large meetings. Fill out the spreadsheet in the mailing list and linked on the above for conflicts. A full week, 5 days and 1/2 day for the school in the morning likely. Schedule: Votes 8 of 13 are yes for August 16-20. And July 12 to 16, 4 yes's and 2 no. July 26-30, 7 yes and 1 no. August 16-20 and July 26-30 seem more preferred. Check with LIGO meetings and make an announcement within the week. Roland, collecting ideas for lecture topics. You as a user or other people that would like to hear about ETK and basics like Num Rel by Helvi, and hydrohynamics and magneto-hydrodynamics. Steve will give intro tutorial. Yosef on writing a more advanced ETK thorn. Still in brainstorming phase so please send emails. Erik, would like Wave Extraction and a bit of theory behind it, generic how to analyze the data that come out of the ETK, and how to read them into Python or Mathematica and what you can do with it. Roland, Also thinking about KuiBit, or Ian Hinder's tools, and Wolfgang's PostCactus. How to use and to program in them. Roland, Presentations, getting input from numerical astrophysics groups, AMRex, Charm++, etc. Athena version with full GR in it. Erik, consider GR 1D by Connor, black hole formation with hydro but cannot handle black hole itself. Roland, idea is to have the competition give a presentations. Atul, last years meeting there was desire for Lorene tutorial / introduction. Maria agrees. Lorene with ETK and not the independent one. Roland, read data or construct data? RIT on constructing and reading is the thorn. Maria, would like how to integrate with tabulated EOS, and using it. Construction of initial data with various EOS in the ETK, in all the various forms for the EOS. Roland will contact Josh Faber (RIT) to ask about the construction of EOS, and to ask if they would show us how to use the generated data in the toolkit. Will also have Lightning talks, 7 + 2 minutes. * release planning [ZE] ** release [http://einsteintoolkit.org/testsuite_results/index.php testsuite status] [https://docs.einsteintoolkit.org/et-docs/Release_Details Release Details] Zach, one month before Gallery examples need to be tested--- Feature Freeze May 15th. Steve, not tested BBH example recently, but running testsuites, QBC, Deep Bayou, and generic linuxes... about 15 hydro tests do not pass QBC and DB---assertion error in con2prim, maybe not unusual, see on other systems (discussed last week too). These are all Intel compiler and not GCC. Discussion of QB which mostly passes, QBC with failures, and Deep Bayou with failures between Steve and Roland. Looks like the Intel 19 compiler might be in common with the failures. Gallery examples after the feature freeze definitely. Testers should test the example earlier if you have not run it recently. There are tickets for each of the examples. "Testing each example" tickets will be put in the details; see link above and "Gallery Example volunteers" section. * [http://blackholesathome.net/ BlackHoles@Home] & the Toolkit [ZE] Zach, giving the APS talk on Sunday and in preparation the BlackHoles@Home website is updated, and code validation has been added. Runs binary BH on a desktop computer, and presents the gallery example from the ETK. Details there on what he did. Perfect agreement for l=2, but less so for l=4 because of high frequency gauge mode bouncing off of refinement levels. BH@Home does not use the symmetry about the z=0 plane. Can have resolution in different directions independently. Would like to link to the ETK in library form, interpolation to small cartesian grid patch over to the toolkit as a library to get isolated and apparent horizons from ETK. Has a proof of principle with Roland in Bitbucket using ETK as a library. So ETK will be in BH@Home to do this code verification and comparison. Steve, BH@Home the users running them do not know what sims they are running? Zach, trying to be very transparent with the users, no visualization yet. Goal is 1M of time in an hour on a desktop. Have two servers with good 10GB fiber lines for receiving the data and large storage 70 TB---with 20k users in mind. Postdoc on client-server interface working. Linux and Mac versions are good, but Windows is a bit more difficult. Looking to launch in August of 2021. Checkpointing and resuming from checkpointing for now. Setting up jobs from the server and passing them out to clients and resuming when a desktop disappears off the net. [https://www.einsteintoolkit.org/tools/unanswered.php unanswered question on mailing list] None [https://bitbucket.org/einsteintoolkit/tickets/issues?status=open&status=new… open tickets sorted by update time] Compiling on MacOS resolved or partially so in private emails. [https://bitbucket.org/einsteintoolkit/tickets/issues?status=new&status=open… tickets ready for review] * AOB Erik, do we follow up on those who try ETK? Do we know why they leave? Can we help more? Maybe a questionnaire after a few days---the "onboarding process." Maybe two questionnaires, one when they register and another a few days after the start using it. Is there an Outreach section in someone's grant for resources? Roland, we currently do not follow-up. Record of emails and hash of emails in the login...which we could figure out. Steve, have been getting many membership and tutorial requests in the last days. Anyone teaching or running tutorials using ETK? No one knows of any. -- ============================== William Gabella Research Assistant Professor Department of Physics and Astronomy Nashville, TN USA (o) 615-343-2713

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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 14 Apr '21

14 Apr '21

Hello, Please consider joining the weekly Einstein Toolkit phone call at 9:00 am US central time on Thursdays. 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 --The Maintainers

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Need help building Einstein Toolkit: clang: error: unsupported option '-fopenmp'
by Murray Wolinsky 13 Apr '21

13 Apr '21

Hi All, Thanks so much for making the Einstein Toolkit software available! I'm using the CactusTutorial.ipynb that I got from your site. I'm trying to build ET on my 2015 Macbook Pro running OS 10.15.7. I'm stuck at the cell (after) *Building the Einstein Toolkit* . I modified that cell to get past issues with zlib . The cell now looks like: %%bash export ZLIB_DIR=/usr/local/opt/zlib/lib export LDFLAGS="-L/usr/local/opt/zlib/lib" export CPPFLAGS="-I/usr/local/opt/zlib/include" export PKG_CONFIG_PATH="/usr/local/opt/zlib/lib/pkgconfig" ./simfactory/bin/sim build -j2 --thornlist ../einsteintoolkit.th Running that cell eventually stops with the errors COMPILING CactusBase/CoordBase/src/Domain.c COMPILING configs/sim/bindings/build/ADMCoupling/cctk_ThornBindings.c clang: error: unsupported option '-fopenmp' make[3]: *** [Domain.c.o] Error 1 make[2]: *** [make.checked] Error 2 make[1]: *** [/Users/murray/Cactus/configs/sim/lib/libthorn_CoordBase.a] Error 2 make[1]: *** Waiting for unfinished jobs.... clang: error: unsupported option '-fopenmp' make[3]: *** [cctk_ThornBindings.c.o] Error 1 make[2]: *** [cctk_Bindings/make.checked] Error 2 make[1]: *** [/Users/murray/Cactus/configs/sim/lib/libthorn_ADMCoupling.a] Error 2 make: *** [sim] Error 2 Can you help? I'm confused by the error message coming from clang, since the ET seems to use gcc, but my attempt to force gcc, by including the exports below, made no difference: export CC=gcc-10 export CXX=gcc-10 I really appreciate any help you are able to provide! Thank you. Murray (Wolinsky) ______________________________________________________ Additional (likely irrelevant) notes: I used brew to install the prerequisites. It seemed to have gone more-or-less ok. Brew did issue a somewhat concerning message regarding hdf5: ==> Pouring hdf5-1.12.0_1.catalina.bottle.1.tar.gz Warning: hdf5 dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. But it didn't provide any guidance into fixing the potential problem. Itried brew reinstall hdf5 and brew no longer complains. I also had some issues with the subversion installation. But I don't think they're responsible for my current problem. Also, when I did the step *Configuring SimFactory for your machine*, I got the output: Here we will define some necessary Simulation Factory defaults. Determining local machine name: mw-3.local --------------------SUMMARY--------------------: [default] user = murray email = murray allocation = NO_ALLOCATION ------------------END SUMMARY------------------: Contents successfully written to /Users/murray/Cactus/repos/simfactory2/etc/defs.local.ini which looks OK, but the NO_ALLOCATION message seems like it might be of concern?

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3D Carpet component with one grid point along the z direction
by Gabriele Bozzola 13 Apr '21

13 Apr '21

Hello, one of my evolutions produced the attached file. What is interesting about this file is that refinement level 10 has a component that has shape (1, 53, 105). So, we have only one point along the z direction. I am not entirely sure how this came to be, but the problem is that the HDF5 attribute 'delta' reports a cell width of 0 along the z direction: In [12]: with h5py.File("alp.xyz.file_0.h5") as f: ...: print(f['ADMBASE::alp it=55296 tl=0 rl=10 c=0'].shape) (1, 53, 105) In [13]: with h5py.File("alp.xyz.file_0.h5") as f: ...: print(f['ADMBASE::alp it=55296 tl=0 rl=10 c=0'].attrs['delta']) [0.072 0.072 0. ] I would have expected the value of 0.072, even if the cell has only one grid point. Is this a bug? Thanks, Gabriele

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(virtual) ET school at UIUC 2021
by Roland Haas 13 Apr '21

13 Apr '21

Hello all, this year is UIUC's turn to organize a school and workshop for the ET. Given that COVID mandated safety measures still in place on campus and them not being lifted before fall semester (end of August) any such meeting will have to be virtual again. My plan would be to have a 1 week long school but each school day being only 3-4 hours long (say 8am US Central time to 1pm with a 35 minute break around 10am) which should allow students in the EU to join as well (8am Central being 3pm Central EU and 1pm being 8pm). The first order of business will be to find a week that is free of known competing meetings. As a first cut, please mark days that you know of a competing meeting in this document: https://docs.google.com/spreadsheets/d/1zNnN5kTh_X0_Le_UDCFbTlavOcjwLNh6pxR… Please all add conflicts that you are aware on by the time of the ET call this week (Thursday) so that a date can be decided on at that point. Please also forward suggestions for possible lecture topics and tutorials and interesting developments in and outside of the the ET you would like to hear about to me or any of the other maintainers. 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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Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 12 Apr '21

12 Apr '21

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

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Stopped making output
by Hee Il Kim 09 Apr '21

09 Apr '21

Hi, Though it might not be an issue of ET. Have you ever seen ET runs stopped making every output (even the stdout), even though the processes are running? I have seen this issue on new and old NVMe storages with various versions of OpenMPI. It happened in more than a day of runs. Oh, not all the processes are running. One process is in Dl state, so the every output stopped. Do you have any hints on this issue? There's no specific limits set for the files. The other write/read tasks on the disks are ok. Thanks for your help in advance. Hee Il

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Meeting Minutes 2021-04-08
by Steven Brandt 08 Apr '21

08 Apr '21

Present: Roland, Steve, Peter, Bill, Ken Sible, Indrani Banerjee, Miguel, Atul, Erik, Zach, Maria Chair: Peter Notes: Steve New machines added: deepbayou (db.hpc.lsu.edu) qb3 (qbc.loni.org) SPEC - GPL2 Release update POWER will be added Please verify your favorite machines in simfactory LORAINE vs LORAINE2 is an ongoing discussion. Which will be the default? Roland is putting together patches Roland started running testsuites and has uploaded the latest batch of results Maybe the hydro tests aren't the best? Please add tests to the testsuite. File names are machine__mpi_threads.txt. Results should be checked in to https://bitbucket.org/einsteintoolkit/testsuite_results Mailing list: User who can't login to the tutorial server was helped. Tickets: Peter looked at ticket 963 this week. Peter found that it affected performance dramatically. Test it out on the new McLachlan rewrite branch. The rewrite seems to not have the constraint damping terms. He suggests keeping the ticket open and considering putting these things into current master. Roland says he will put POWER into the master thornlist. It's just a single file. We have a cactus utilities repository that often refers to CVS, etc. Roland is cleaning up. Ticket 2516, different results for different number of cores. Peter says we should not forget about this one. Ken update on LaTex parser. BSSN tutorial notebook is finished. https://mybinder.org/v2/gh/zachetienne/nrpytutorial/HEAD?filepath=Tutorial-… https://www.youtube.com/watch?v=A9IWYpQe6Fo Parser was extracted from the root nrpy directory and will made availale through pip tomorrow. This should make it easier to use. Next week: Chair: Roland Minute Taker: Bill Two weeks: Chair: Bill Minute Taker: Atul

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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 07 Apr '21

07 Apr '21

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