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Agenda for Thursday's Meeting
by reminders＠einsteintoolkit.org 20 Jun '22

20 Jun '22

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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Re: [Users] Combine multiple h5 files
by Hamilton, Maria 17 Jun '22

17 Jun '22

Thank you so much for the help! _______________________ Maria C. Babiuc Hamilton, Ph.D. Professor, Department of Physics College of Science, Marshall University, 1 John Marshall Drive, Huntington, WV, 25755 Room S 257, Phone: (304)696-2754 ________________________________ From: Roland Haas Sent: Wednesday, June 15, 2022 4:29 PM To: Chris Stevens Cc: Hamilton, Maria; users(a)einsteintoolkit.org Subject: Re: Combine multiple h5 files Hello all, Chris' answer is absolutely correct. The utilities are built by default by Simfactory and by doing `make sim-utils` using a non-simfactory build. hdf5_merge is the tool to use to combine multiple HDF5 files, eg different variables or multiple segments of the same simulation. It won't merge output files from multiple processes into a single file (so foo.xyz.file_0.h5 and foo.xyz.file_1.h5 cannot be merged but foo.xyz.file_0.h5 and bar.xyz.file_0.h5 can be merged). If you need merge files foo.xyz.file_0.h5 and foo.xyz.file_1.h5 into foo.xyz.h5 then you can use the hdf5_slicer utility and its --out3d-cube option (hdf5_slicer --help gives some examples). Yours, Roland > KIa ora Maria, > > For me, there are hdf scripts located in Cactus/exe/<Build name>, > such as hdf5_merge, which should do what you are after. These > potentially may only be there for certain build options but someone > more knowledgeable than me can probably expand on that. > > Cheers, > > Chris > > [cid:8795d7d8-3669-4adf-905d-788d81a3ba8c] > > > [cid:3a28163e-f206-41a5-8619-e8b15edd91b0] > > > > Dr Chris Stevens > > Lecturer in Applied Mathematics > > Rm 602, Jack Erskine building > > School of Mathematics and Statistics > > T: +64 3 369 0396 (Internal 90396) > > University of Canterbury | Te Whare Wānanga o Waitaha > > Private Bag 4800, Christchurch 8140, New Zealand > > https://urldefense.com/v3/__http://www.chrisdoesmaths.com__;!!DZ3fjg!7WZG6j… > <https://urldefense.com/v3/__http://www.chrisdoesmaths.com/__;!!DZ3fjg!7WZG6… > > > > > Director > SCRI Ltd > https://urldefense.com/v3/__http://www.scri.co.nz__;!!DZ3fjg!7WZG6jdWvLk-xY… > <https://urldefense.com/v3/__http://www.scri.co.nz/__;!!DZ3fjg!7WZG6jdWvLk-x… > > > > ________________________________ > From: users-bounces(a)einsteintoolkit.org > <users-bounces(a)einsteintoolkit.org> on behalf of Hamilton, Maria > <babiuc(a)marshall.edu> Sent: 16 June 2022 08:02 To: Roland Haas > <rhaas(a)illinois.edu> Cc: users(a)einsteintoolkit.org > <users(a)einsteintoolkit.org> Subject: [Users] Combine multiple h5 files > > You don't often get email from babiuc(a)marshall.edu. Learn why this is > important<https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__… > > Hi, > > I have a quick question: my output has a series of ....xyz.file_...h5 > and I would like to look at them. Do I have to combine them? If yes, > is there a way to combine them in one single file? > > Maria > > _______________________ > Maria C. Babiuc Hamilton, Ph.D. > Professor, Department of Physics > College of Science, Marshall University, > 1 John Marshall Drive, Huntington, WV, 25755 > Room S 257, Phone: (304)696-2754 > -- 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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Combine multiple h5 files
by Hamilton, Maria 15 Jun '22

15 Jun '22

Hi, I have a quick question: my output has a series of ....xyz.file_...h5 and I would like to look at them. Do I have to combine them? If yes, is there a way to combine them in one single file? Maria _______________________ Maria C. Babiuc Hamilton, Ph.D. Professor, Department of Physics College of Science, Marshall University, 1 John Marshall Drive, Huntington, WV, 25755 Room S 257, Phone: (304)696-2754

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FUKAv2 Release
by Samuel Tootle 09 Jun '22

09 Jun '22

Dear ETK community members, The following is a notification of the release of the second version of the Frankfurt/Kadath (FUKA) initial data (ID) codes. FUKA is a collection of publicly available initial data codes to provide access to highly asymmetric, spinning compact object binaries such as binary black holes, binary neutron stars, and black hole-neutron star binaries. FUKA was originally released June, 2021 (https://hyperspace.uni-frankfurt.de/2021/06/25/fuka-frankfurt-uni-kadath-in…), however, development has continued in order to enable the reliable generation of initial data for extremal configurations (i.e., highly asymmetric binaries with different near extremal spins) while providing an intuitive interface to the user and minimizing the workflow to obtain such ID. To this end, FUKAv2 is a complete rewrite of the solver codes to enable each binary solver to utilize super-imposed isolated compact object solutions to generate the initial setup. This provides a stable setup for each binary solver to obtain a converged solution with only minimal effort on the frontend by the user. Additionally, the solvers are now capable of automating the regridding procedure to obtain the desired final resolution while minimizing computation costs. Finally, the key features available within the original FUKAv1 codes have also been integrated into v2 allowing one to easily obtain eccentricity reduced initial data either by using the built-in 3.5th order post-Newtonian estimates or by providing eccentricity reduction parameters manually (e.g., those obtained from iterative eccentricity reduction). Overall, when comparing to the original v1 codes FUKAv2 is more than 5x more efficient when solving the ID for asymmetric spinning binaries with a vastly more robust framework to maximize convergence. Even more so, the effort on the user has been significantly reduced by removing the need to manually create setups, solve, then regrind. The latest version of FUKA along with the thorns enabling the import of FUKA ID into the Einstein Toolkit are available at: https://bitbucket.org/fukaws/ As a final note, I will discuss some of these details during my lightning talk at the ETK Workshop next week which is currently scheduled for Tuesday, 11:50am PST. Warm regards, Samuel Tootle PhD Candidate Goethe Universität Frankfurt

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question about ML_CCZ4 parameters
by Bruno Giacomazzo 09 Jun '22

09 Jun '22

Together with a student of mine we are trying to use the CCZ4 formulation implemented in McLachlan. We saw that most parameters are the same as in BSSN, but there are damping factors that need to be selected. In Alic et al 2013 (https://link.aps.org/doi/10.1103/PhysRevD.88.064049) they mention 3 damping factors (k1, k2, and k3), but in the param.ccl of McLachlan/ML_CCZ4 only k1 and k2 are mentioned (assuming they are the same). Is it because k3 is hardcoded to the value suggested in Alic et al 2013? Or does McLachlan/ML_CCZ4 use a different set of evolution equations (in which case, is there a reference)? We were able to find some example parameter files (for example the ones from the Parma group https://einstein.pr.infn.it/gravity/Research/BNS2015.html) and we found that they used indeed k1 and k2 from Alic et al 2013: ML_CCZ4::dampk1 = 0.05 ML_CCZ4::dampk2 = 0 We also saw that they added ML_CCZ4::ML_Theta to the Dissipation vars and set ML_CCZ4::apply_dissipation = "never". The other parameters look the same as when using BSSN. Since I never used ML_CCZ4 I want to be sure that I'm setting the parameters correctly and the damping factors seem to be the most delicate point. Thanks, Bruno -- Prof. Bruno Giacomazzo Department of Physics University of Milano-Bicocca Piazza della Scienza 3 20126 Milano Italy email: bruno.giacomazzo(a)unimib.it phone: (+39) 02 6448 2321 web: http://www.brunogiacomazzo.org ---------------------------------------------------------------------- There are only 10 types of people in the world: Those who understand binary, and those who don't ----------------------------------------------------------------------

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Meeting minutes for 2022-06-09
by Bing-Jyun Tsao 09 Jun '22

09 Jun '22

Present: Beyhan, Roland, Steven, Miguel, Peter, Yosef, Leo, Johnny Chair: Beyhan Minutes: Johnny - ET release <https://www.einsteintoolkit.org/about/releases/ET_2022_05_announcement.html> (detail <https://docs.einsteintoolkit.org/et-docs/Release_Details>): - need to update TOV star case [Peter] - GRHydro issue: works in other clusters but not at RIT [Roland]. Might be a compiler issue or inappropriate memory access with using stack or heap. [Yosef]. - Roland: Still collecting bug report - Add CI run to self force code [Peter] - Issue with Whisky [Beyhan] - ET summer school <https://einsteintoolkit.github.io/et2022uidaho/> at Idaho: - zoom meetings are arranged and will be sent out to participants today or tomorrow [Leo] - Separate meeting (Thursday morning) for discussion on numerical relativity, even for people who didn’t register - ground transportation arranged [Leo] - Hackathon: Jessica will be the main contact, but she will be taking a day off on Wednesday [Leo]. Please add hackathon topics that can be worked out in a day with guidance [Roland], topics link <https://bitbucket.org/einsteintoolkit/tickets/issues?status=new&status=open…> from Roland's previous email. - Questions in the mailing lists: No unanswered questions. - Tickets (bitbucket <https://bitbucket.org/einsteintoolkit/tickets/issues?status=new&status=open> ) - Updates on Riemann release needs to be reviewed [Roland] - Release: thorn guide needs to be updated [Roland] - Other: - Roland: student for summer has started, initializing Einstein Toolkit. - new time for weekly meeting No meeting next week due to ET summer school. Next call: Chair and Minutes: Roland and Steven (TBD)

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Failing tests on Expanse
by Gabriele Bozzola 09 Jun '22

09 Jun '22

Hello, Some network configurations were recently changed on SDSC's Expanse and I wanted to update the Simfactory entry to add an env variable (as recommended by XSEDE's help desk). I did so and ran the tests and found numerous failures. According to an expanse_2_64.log file I have on my computer, these tests did not fail in the past. The tests fail only for 2 MPI processes. An example of a test that fails is rnsA2, and this is the the tail of the log file: INFO (Carpet): MPI is enabled INFO (Carpet): Carpet is running on 2 processes WARNING level 0 from host exp-4-26.expanse.sdsc.edu process 0 in thorn Carpet, file /home/sbozzolo/Cactus/arrangements/Carpet/Carpet/src/SetupGH.cc:148: -> The environment variable CACTUS_NUM_PROCS is set to 1, but there are 2 MPI processes. This may indicate a severe problem with the MPI startup mechanism. Rank 0 with PID 1194507 received signal 6 cactus_sim: /home/sbozzolo/Cactus/arrangements/Carpet/Carpet/src/helpers.cc:275: int Carpet::Abort(const cGH*, int): Assertion `0' failed. Writing backtrace to rnsA2/backtrace.0.txt Rank 1 with PID 1194508 received signal 6 Writing backtrace to rnsA2/backtrace.1.txt srun: error: exp-4-26: tasks 0-1: Aborted (core dumped) IBRUN: launch command: srun -n 2 --ntasks-per-node 2 /expanse/lustre/projects/uic383/sbozzolo/ettests_2proc/SIMFACTORY/exe/cactus_sim -L 3 /expanse/lustre/projects/uic383/sbozzolo/ettests_2proc/output-0000/arrangements/EinsteinInitialData/Hydro_RNSID/test/rnsA2.par IBRUN: MPI job exited with code: 134 Other tests behave similarly, e.g. Vaidya2: INFO (Carpet): MPI is enabled INFO (Carpet): Carpet is running on 2 processes WARNING level 0 from host exp-4-26.expanse.sdsc.edu process 0 in thorn Carpet, file /home/sbozzolo/Cactus/arrangements/Carpet/Carpet/src/SetupGH.cc:148: -> The environment variable CACTUS_NUM_PROCS is set to 1, but there are 2 MPI processes. This may indicate a severe problem with the MPI startup mechanism. Rank 0 with PID 1183519 received signal 6 Writing backtrace to Vaidya2/backtrace.0.txt cactus_sim: /home/sbozzolo/Cactus/arrangements/Carpet/Carpet/src/helpers.cc:275: int Carpet::Abort(const cGH*, int): Assertion `0' failed. Rank 1 with PID 1183520 received signal 6 Writing backtrace to Vaidya2/backtrace.1.txt srun: error: exp-4-26: tasks 0-1: Aborted (core dumped) IBRUN: launch command: srun -n 2 --ntasks-per-node 2 /expanse/lustre/projects/uic383/sbozzolo/ettests_2proc/SIMFACTORY/exe/cactus_sim -L 3 /expanse/lustre/projects/uic383/sbozzolo/ettests_2proc/output-0000/arrangements/EinsteinExact/EinsteinExact_Test/test/Vaidya2.par IBRUN: MPI job exited with code: 134 Given that I see in the testsuite_results repo the same failing tests (as run by Roland), I can exclude that the new env variable that I added is the reason for the failures. Any idea of what is going on? Thanks, Gabriele

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Community Discussion on NR Waveform Accuracy & Data Format
by Zach Etienne 09 Jun '22

09 Jun '22

Dear Einstein Toolkit enthusiasts, During the 2022 North American Einstein Toolkit Summer School, we will be hosting a special community-wide discussion on numerical relativity gravitational wave accuracy in the context of upcoming gravitational-wave observatories, and the associated data format. For the purposes of the discussion, *no registration is required* -- just join the Zoom link below. Event details: Title: Discussion on NR gravitational wave accuracy & data format, in the context of upcoming gravitational-wave observatories Discussion leader: Deirdre Shoemaker Date/Time: Thursday, June 16 at 8:25AM Pacific Time; 10:25AM Central Time; 11:25AM Eastern Time; 4:25PM WEST/BST; visit https://tinyurl.com/3a355b4e for more conversions. Duration: 1 hour, 25 minutes Zoom link: https://uidaho.zoom.us/j/89655618250 *Please be sure to update your Zoom client to the latest version in advance, to minimize chances of connection problems.* Hope to see you there for this very important conversation! Sincerely, -The NA ET Summer School 2022 SoC Gabrielle Allen Steven Brandt Zachariah Etienne Roland Haas Christiana Pantelidou Leonardo Werneck Helvi Witek

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ET hackathon on Wed June 15th (during the 2022 NA ET summer school at UIdaho)
by Roland Haas 08 Jun '22

08 Jun '22

Hello all, For the hackathon on Wednesday June 15th (for remote participants and those that are opting out of the field trip to LIGO) some suggested projects would be needed. Easiest is to mark or create tickets on: https://trac.einsteintoolkit.org by adding the word "hackathon" in one of the comments so that a search https://bitbucket.org/einsteintoolkit/tickets/issues?status=new&status=open… can find them. Ideally with some sort of longer description of what a possible fix / extension would entail. The hackahton is in 3 weeks, though some advance warning about project will be good so that participants can see what projects are available. Participants would mark a project as claimed by adding a "Claimed by <ME> for 2022-06-15 hackathon" as a comment. 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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Fwd: [nr-community-call] Applications for the NR community summer school 2022 close Thu Jun 9
by Helvi Witek 07 Jun '22

07 Jun '22

Dear (aspiring) numerical relativists, Applications for the NR community summer school 2022 close on Thursday, Jun 9, so please apply by then for full consideration. The original announcement is attached below. Please also register if you want to stream the lectures virtually: * https://icerm.brown.edu/events/re-22-f20w1 <https://urldefense.com/v3/__https://icerm.brown.edu/events/re-22-f20w1__;!!…> Graduate students: Please note that ICERM requires a letter of support from your advisor for in-person participation. If you have not sent one yet, please do so by Jun 9 as well. Please feel free to circulate this information within the NR community. Best, The organizing committee, Nils Vu, Thomas Helfer, Elias Most, Helvi Witek, Scott Field, and Leo Stein --------------------------------------------- Dr. Helvi Witek Assistant Professor Department of Physics University of Illinois at Urbana-Champaign 247 Loomis Lab 1110 W Green St Urbana, IL 61801 --------------------------------------------- -------- Forwarded Message -------- Subject: [nr-community-call] Applications for the NR community summer school 2022 close Thu Jun 9 Date: Tue, 7 Jun 2022 06:08:29 -0500 From: Nils Vu <nils.vu(a)black-holes.org> To: nr-community-call(a)black-holes.org <nr-community-call(a)black-holes.org> Dear (aspiring) numerical relativists, Applications for the NR community summer school 2022 close on Thursday, Jun 9, so please apply by then for full consideration. The original announcement is attached below. Please also register if you want to stream the lectures virtually: * https://icerm.brown.edu/events/re-22-f20w1 <https://urldefense.com/v3/__https://icerm.brown.edu/events/re-22-f20w1__;!!…> Graduate students: Please note that ICERM requires a letter of support from your advisor for in-person participation. If you have not sent one yet, please do so by Jun 9 as well. Please feel free to circulate this information within the NR community. Best, The organizing committee, Nils Vu, Thomas Helfer, Elias Most, Helvi Witek, Scott Field, and Leo Stein — Original announcement from May 3, 2022: > Dear (aspiring) numerical relativists, > > Applications are now open for the first NR community summer school, > Aug 8–12, 2022, at ICERM, Brown University, US. > > This one-week summer school brings together early career researchers > (graduate students and postdocs) interested in learning the > state-of-the-art in numerical relativity, from the basics to advanced > topics. Our preliminary program is: > > * Intro & advanced NR (Helvi Witek & Katy Clough) > * Relativistic hydrodynamics (Elias Most) > * Gravitational waves (Deirdre Shoemaker) > * High-performance computing (Eloisa Bentivegna) > * Hackathon > * Evening talks, side program, NR community codes hands-on sessions > > > No prior exposure to numerical relativity is required, though basic > familiarity with computational physics and general relativity would be > desirable. > > The school is planned as an in-person event with streaming options > available for the lecture program. ICERM will be able to offer limited > funding for some participants. > > Applications are open now on this web page: > > * https://icerm.brown.edu/events/re-22-f20w1 > <https://urldefense.com/v3/__https://icerm.brown.edu/events/re-22-f20w1__;!!…> > > > Even if you are planning to participate online, please register and > indicate so in your application. We particularly encourage > applications from participants from diverse backgrounds and > underrepresented communities. > > With warm regards, > The organizing committee, > Nils Vu, Thomas Helfer, Elias Most, Helvi Witek, Scott Field, and Leo > Stein -- You received this message because you are subscribed to the Google Groups "NR community call" group. To unsubscribe from this group and stop receiving emails from it, send an email to nr-community-call+unsubscribe(a)black-holes.org. -- You received this message because you are subscribed to the Google Groups "NR community call" group. To unsubscribe from this group and stop receiving emails from it, send an email to nr-community-call+unsubscribe(a)black-holes.org.

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