Users April 2023

users@lists.einsteintoolkit.org

8 participants
10 discussions

Thorn setup taking too much time in cluster
by Shamim Haque 1910511 06 Jun '23

06 Jun '23

Hello, I am trying to run BNSM using IllinoisGRMHD on HPC Kanad at IISER Bhopal. While I have tested the parfile to be running fine on debug queue (1 node) and high memory queue (3 nodes), I am unable to run the simulation in a queue with 9 nodes (144 cores). The output file suggests that the setup of listed thorns is not complete within 24 hours, which is the max walltime for this queue. Is there a way to sort out this issue? I have attached the parfile and outfile for reference. Regards Shamim Haque Senior Research Fellow (SRF) Department of Physics IISER Bhopal ᐧ

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meeting minutes for 2023-04-27
by Roland Haas 27 Apr '23

27 Apr '23

Present: Roland, Peter, Leo, Steve, Zach, Sam, Yosef ET release: * Elliptica Reader will be postponed to next release ** needs a library of ID ** comparison between ET and published result * FUKA: on track * partialTracer_ET: on track * release managers will start drafting release announcement * release date is: 2023-05-24 Testsuite status: * newly failing test in GRHydro_InitData/magtov_poloidal ** Peter debugged and found that issue is with Fortran if condition. Fortran does not short-circuit logic or guarantee order of evaluation. Peter will file pull request. Unanswered question: * http://lists.einsteintoolkit.org/pipermail/users/2023-April/008906.html Cactus hangs on startup. Steve had been in contact with Shamin Haque about this. Problem still persists even in most recent try. Steve will respond. Tickets on mailing list: * https://bitbucket.org/einsteintoolkit/tickets/issues/2719 issue in GetComponents when dealing with symbolic links. Workaround exists. Currently affects KadathThorn * https://bitbucket.org/einsteintoolkit/tickets/issues/2623 compile failure when paths contain ":". Had some discussion of updating or replacing autoconf in Cactus with something else. Tickets ready for review: * in code freeze state, only important bug fixes SPECv8 review * waiting to hear back from SPEC organizers * contribution still on track to be included CarpetX: * Zach asked about any horizon finder for CarpetX based runs ** Roland says that currently no working version exists ** AHFinderDirect may be portable using Sam's and Roland's work to interface CarpetX's interpolator interface with Cactus' interpolator interface. Native CarpetX may already include support for derivatives. ** Sam worked on interpolator but also no longer quite recalls the current state next chair: Peter next minute taker: Steve 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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Meeting minutes for 2023-04-20
by Leonardo Rosa Werneck 27 Apr '23

27 Apr '23

Hi all, Apologies for the long delay. Here are the minutes from last week’s call. Chair : Johnny Minutes : Leo Present : Peter, Alireza, Johnny, Roland, Zach, Leo, Yosef -> Next ET Release * Feature freeze coming up April 26, 2023 * Elliptica reader - Alireza is taking a look at the latest comments made to the ticket. Trajectories differences are due to issues in the parameter file, which are being fixed. - Will there be initial data files available? Yes. The solver will be made open source soon. Roland says a reasonable number of files is a requirement if the code is not open source. * Fuka reader - There is a compilation issue related to the fact that GetComponents does not download the code's submodules. Samuel should take a look at it as soon as possible. * particle_tracerET - All tests passing. * TwoPunctures_BBHSF - Leo and will contact Cheng-Hsin regarding additional tests that may have been requested. * kuibit - Gabriele was able to restore compatibility with Python 3.7. * CarpetX pre-release - Steve will be the coordinator. * The next release will be named Schwarzschild. * The preliminary release data will be May 24, 2023. * Peter will run the TOV gallery example. Johnny will run the Scalar Wave gallery example. * SPEC: Roland reports we are still on track for the inclusion. -> Unanswered questions on the mailing list * The mailing list server was updated last week and should be back online. -> Open tickets * Building PAPI on Linux broke after a recent attempt to fix compilation issues on macOS. Roland already has a pull request that fixes the issue, but it needs to be reviewed. * NRPyPN may be movied from arrangements/EinsteinInitialData to utils/InitialData, since it is not a thorn. Zach is the assignee and will review it. * Zach suggested the default values of grid resolution for TwoPunctures are too low and should be adjusted. Roland says: changing parameters' default values is tricky, and thus not recommended. That being said, we could update the values in readily available parameter files that use TwoPunctures. * KadathThorn assume git repository and use non-POSIX functionality. *Had to leave* ------ Leonardo R. Werneck, Ph.D. Postdoctoral researcher Office EP 314 | Department of Physics | University of Idaho 875 Perimeter Dr. MS 0903 Moscow, ID 83844-0903, USA leonardo(a)uidaho.edu <mailto:leonardo@uidaho.edu> https://leowerneck.github.io <https://leowerneck.github.io/>

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Problem with Llamawavetoy
by Enzo Iubini 24 Apr '23

24 Apr '23

Good morning. My name is Enzo Iubini and I'm a master's student from Chile currently working on binary black holes. I want to use the Einstein Toolkit to create simulations, and I currently know how to create thorns (thanks to the tutorial) and run parfiles. At the moment I'm trying to run the Llamawavetoy parfile for the multipatch wave equation, which is found in this link: https://einsteintoolkit.org/gallery/multipatch/index.html. The problem is, this simulation returns several HDF5 files, for which I have some questions. 1. For example, the u.0.xz.h5 returns several files, one of which is 'LLAMAWAVETOY::u it=0 tl=0 m=0 rl=0' . My question is: What do 'it', 'tl' and 'rl' represent? I have several other files with different 'it' 's , I thought it meant "iteration" but each one of them has size (183,29) and I'm really confused as to how to interpret them. 2. Once I have my data, how do I plot them? I tried to understand all the data inside these folders, but I can't make sense of them. Tried to plot each one of these files based on what I thought they meant, but all I get is different 1-d wave plots and I can't make a 2d or 3d plot of them. 3. Also tried to use VisIt. Should I save these files and later upload them on VisIt? I'm trying to understand the data first so I can plot it later, but I'm having trouble understanding all of it overall. I'm sorry if this is a lot of questions, I hope you can help me understand so I can manage to work further. Thanks a lot for your time! Best regards, Enzo.

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mailing list server maintenance this week
by Roland Haas 12 Apr '23

12 Apr '23

Hello all, The ET mailing list server which hosts this list and others related to the ET will be down for maintenance today. It should be back in service by end of the week. 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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Meeting minutes for 2023-04-06
by Bing-Jyun Tsao 06 Apr '23

06 Apr '23

Participants: Leo, Johnny, Roland, Peter, Keith, Zach, Samuel, Steve - ET_2023_05 - Elliptica reader (and solver timeline) Ticket #2619 <https://bitbucket.org/einsteintoolkit/tickets/issues/2619/include-ellipitca…> -- gave (final) final deadline for tests: 4/12; thorns are already in manifest to stay on track, but may be removed depending on final status - [LW] Extend deadline by 1 week, generate thorn again with Kranc/NRPy by Friday - test will require same random generator of particles on different machines - Need testers for gallery examples: BNS: Roland, BBH: Steve - [SB] SuperMike-III (LSU) add to list of machines that works, Deep-Bayou tested - Name for the release: [SB] suggest “Schwarzschild” - [RH] Now changing current CI to add Elliptica - CarpetX <https://docs.einsteintoolkit.org/et-docs/CarpetX_Transition> code review -- Erik is champion for CarpetX; Steve would be the coordinator (keep track of who reviewed what) for the review - ET uptime monitor, original uptime free service shutting down, set up in github: [1] <https://einsteintoolkit.github.io/uptime/> [RH] - mailing list: - [2] <http://lists.einsteintoolkit.org/pipermail/users/2023-April/008903.html> “Thorn setup taking too much time in cluster”, Steve suggested that the simulation wasn’t purged, but will need to go over parameter file to find why this happens - open tickets - [LW] close two tickets #2300 <https://bitbucket.org/einsteintoolkit/tickets/issues/2300/update-add-piecew…> #2690 <https://bitbucket.org/einsteintoolkit/tickets/issues/2690/include-new-illin…> (include piecewise polytrope and tabulated EOS), IllinoisGRMHD will not be touched for next release, will just add implementation to GRAIL instead, [ZE] new thorn GRAIL_ET - [RH] [ZE] manage old thorns that people use, especially now CarpetX will be included [SB] instead of download the whole toolkit, record which thorns users download and warn that old thorns are no longer maintained [RH] popularity contest <https://bitbucket.org/einsteintoolkit/tickets/issues/2065/add-a-debian-styl…> - [SB] suggestion: give a name to Cactus in ETK, “CactusET” - #1775 <https://bitbucket.org/einsteintoolkit/tickets/issues/1775/add-boost-to-et> [RH] several thorns use Boost, huge to compile and require many dependencies [SB] only generate headers for boost and not compile the entire package, link to an external thorn - No meeting next week for APS, next meeting in two weeks (04/20): - Chair: Johnny, minute: Steve

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Einstein Toolkit Meeting Reminder
by reminders＠einsteintoolkit.org 05 Apr '23

05 Apr '23

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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Agenda for Thursday's Meeting
by reminders＠einsteintoolkit.org 03 Apr '23

03 Apr '23

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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number of thesis using the Einstein Toolkit codes
by Roland Haas 03 Apr '23

03 Apr '23

Hello all, for a report to the NSF I am trying to obtain an idea of who many student thesis were using (were enabled by) the Einstein Toolkit. So if you are a student or are working with a student and have used the Einstein Toolkit as part of your thesis work in between 2022-07-01 and 2023-06-30 it would be great if you could let me know. You do not have to have defended in this period, just having used the toolkit. 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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Re: [Users] An error occurred in make Lorene/Codes/Bin_star
by Leonardo Rosa Werneck 01 Apr '23

01 Apr '23

Dear Jimmy, Have the Lorene libraries been compiled (i.e., running make at Lorene’s home directory) before going in Lorene/Codes/Bin_star and running make? Could you please share the contents of your local_settings? Best, Leo ------ Leonardo R. Werneck, Ph.D. Postdoctoral researcher Office EP 314 | Department of Physics | University of Idaho 875 Perimeter Dr. MS 0903 Moscow, ID 83844-0903, USA leonardo(a)uidaho.edu <mailto:leonardo@uidaho.edu> https://leowerneck.github.io <https://leowerneck.github.io/> > On Mar 24, 2023, at 10:00 AM, users-request(a)einsteintoolkit.org wrote: > > An error occurred in make Lorene/Codes/Bin_star

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Users April 2023