Users March 2023

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14 participants
27 discussions

Einstein Toolkit Meeting Reminder
by reminders＠einsteintoolkit.org 22 Mar '23

22 Mar '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. ** DAYLIGHT SAVING TIME WARNING ** Please note that the US / EU has already / not yet transitioned to / from daylight saving time. The phone call will be at 15:00 Central EU time. https://docs.einsteintoolkit.org/et-docs/Main_Page#Weekly_Users_Call --The Maintainers

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BNSM/TOV simulation error
by Spandan Sarma 19306 22 Mar '23

22 Mar '23

Hello, I was trying to run the BNSM simulation from the ET gallery on the institute cluster KANAD at IISER Bhopal in the short queue (max nodes: 16; walltime: 24 hrs) of our queuing system, but the following error came up: The grid structure is inconsistent. It is impossible to continue. WARNING level 0 from host n16 process 0 in thorn CarpetLib, file /home2/shamims/ET_short1/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2105: -> The grid structure is inconsistent. It is impossible to continue. cactus_sim: /home2/shamims/ET_short1/Cactus/arrangements/Carpet/Carpet/src/helpers.cc:275: int Carpet::Abort(const cGH*, int): Assertion `0' failed. Rank 0 with PID 4473 received signal 6 Writing backtrace to nsnstohmns1/backtrace.0.txt WARNING level 0 from host n63 process 128 in thorn CarpetLib, file /home2/shamims/ET_short1/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2105: -> The grid structure is inconsistent. It is impossible to continue. cactus_sim: /home2/shamims/ET_short1/Cactus/arrangements/Carpet/Carpet/src/helpers.cc:275: int Carpet::Abort(const cGH*, int): Assertion `0' failed. Rank 128 with PID 1350 received signal 6 Writing backtrace to nsnstohmns1/backtrace.128.txt WARNING level 0 from host n63 process 141 in thorn CarpetLib, file /home2/shamims/ET_short1/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2105: -> The grid structure is inconsistent. It is impossible to continue. cactus_sim: /home2/shamims/ET_short1/Cactus/arrangements/Carpet/Carpet/src/helpers.cc:275: int Carpet::Abort(const cGH*, int): Assertion `0' failed. After this issue, I tried performing the simulation using the same parameter file in the debug queue (max:1 node), and it worked fine. But upon trying out the TOV simulation example in the debug queue, the same error came: [1mWARNING level 0 from host n85 process 0 in thorn CarpetLib, file /home2/shamims/ET_debug/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2105: -> [0m The grid structure is inconsistent. It is impossible to continue. WARNING level 0 from host n85 process 0 in thorn CarpetLib, file /home2/shamims/ET_debug/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2105: -> The grid structure is inconsistent. It is impossible to continue. cactus_sim: /home2/shamims/ET_debug/Cactus/arrangements/Carpet/Carpet/src/helpers.cc:275: int Carpet::Abort(const cGH*, int): Assertion `0' failed. I am unable to understand what the issue is. I have attached parameter files, the runscript, and the output files for both the simulations (TOV and BNSM) for reference. Thanks in advance for the help. Regards, -- Spandan Sarma BS-MS' 19 Department of Physics (4th Year), IISER Bhopal

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Meeting minutes for 2023-03-16
by Leonardo Rosa Werneck 21 Mar '23

21 Mar '23

Hi all, Here are the minutes of today’s meeting: Chair: Steve Minute taker: Leo Present: Steve, Leo, Sam, Cheng-Hsin, Zach, Roland, Peter, Yosef * ET_release - Elliptica reader: Alireza said testing should be completed in the next two weeks. Beyhan expressed some concern about the fact that there are lots of files for the Elliptica library, but Steve and Roland assured this is fine as long as the library is reviewed properly. One important thing to keep in mind is that if the library provide any globals outside of a namespace, the names of these globals must be prefixed with the libraries' name. - Fuka reader: Review finished a while back and should be good to go. - CarpetX pre-release: Review is progressing slowly. - particle_tracerET: Review completed last week and should be merged into master today. - Baikal reads/writes: Code modifications were very minor and should be merged into master today. - TwoPunctures_BBHSF: Review is complete and pull request is being created. - NPScalars_SF: Review hasn't started yet, but Peter will perform the "do no harm" review asap. Pull request should be created soon. - kuibit: The new version of the code requires Python 3.8+. Steve hoped that kuibit would support Python 3.7, since that's what installed in some of the LSU clusters. That being said, both Steve and Peter have successfully installed kuibit with Python 3.7 by using Gabriele's suggestion: $ pip install --upgrade 'kuibit<=1.4.0' - Overall comments on the release: everything is progressing timely. We will begin discussing the release name soon (maybe next week). * ET school: Scientific committee information will be released today; registration will open soon and a modest fee will be charged to cover basic expenses; hotel near the RIT closed, but there will be free shuttles to/from the hotels. * CI tests: NRPyEllipticET test is broken (Leo will look into it). * List of clusters and testers have been added to the release details web page (https://docs.einsteintoolkit.org/et-docs/Release_Details). Next chair: Peter Next minute taker: ChatGPT/Zach ------ 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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Agenda for Thursday's Meeting
by reminders＠einsteintoolkit.org 20 Mar '23

20 Mar '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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spam on ET ticketing system
by Roland Haas 17 Mar '23

17 Mar '23

Hello all, The ET ticket system has been hit by lots of spam (~40 of them) in the last 2 hours (and it continues). For now I have restricted ticket creation to users with a bitbucket account. That is one must now hold a valid bitbucket account to create a ticket (but does not have to be a member of 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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Setting up ETK on an AMD Rome cluster
by Vaishak Prasad 16 Mar '23

16 Mar '23

Dear All, Greetings from India. I am trying to get the ETK working on an AMD Rome powered supercomputer at ICTS, India. I am working with gcc (11.1.0, 12.2.0) and openmpi. The compilation is successful but every one of the tests and runs fails due to seg faults at the vectorization stage. On recompiling the toolkit without vectorization, the tests run (except for one test of ML_BSSN which fails due to a relative error ~ 1e-14). I am attaching the backtrace (from the gallery BBH run), make log (with vectorization) and the optionlist herewith. Requesting help! With regards -- Vaishak Prasad

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Einstein Toolkit Meeting Reminder
by reminders＠einsteintoolkit.org 15 Mar '23

15 Mar '23

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Agenda for Thursday's Meeting
by reminders＠einsteintoolkit.org 13 Mar '23

13 Mar '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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Agenda for Thursday's Meeting
by reminders＠einsteintoolkit.org 13 Mar '23

13 Mar '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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Re: [Users] [Maintainers] New Tutorial Account Requested
by Steven R. Brandt 09 Mar '23

09 Mar '23

Dear Enzo, CactusTutorial.ipynb shows you how to run simulations. For example, to run interactively, it shows that you do this: ./simfactory/bin/sim create-run helloworld \ --parfile arrangements/CactusExamples/HelloWorld/par/HelloWorld.par So create a simulation name, e.g. multipatch, and pass your parfile. --Steve On 3/9/2023 3:50 PM, Enzo Iubini wrote: > Hello Steve, I'm sorry to bother but I forgot one thing. > > I was told that I could learn about Einstein Toolkit by running some > done simulations and shifting parameters to see how the code works. > I tried working with this Multipatch wave equation : > https://einsteintoolkit.org/gallery/multipatch/index.html > > But I do not know how to run it. I see I have a parameter file, but > don't I need the ccl files as well? (the schedule, init, boundary) How > do I work with these? > > This would help me so much, I hope you can help me out. > > Best regards, > Enzo > > El jue, 9 mar 2023 a las 18:38, Enzo Iubini (<egic.enzo(a)gmail.com>) > escribió: > > Hello Steve, thanks for your thoughtful answer. > > Just for clarification, I just meant it was a black box for me as > I'm still trying to understand the basics. :D > > So I ran all the cells once more and they didn't show anything > different. If I could ask for a favour, could you run all the > cells and then send me that jupyter notebook? I know the > simulation will not run correctly on my computer but I could see > which warnings (or lack thereof) arise when you run the code and > maybe figure out if something is wrong with my computer, or > anything similar. > > I would appreciate it very much, I've got to learn the Einstein > Toolkit and I have no one here in Chile to help me, but I'll try > my best this year! > > Thank you again, I'll wait for your answer. > > Best regards, > Enzo > > > > El mié, 8 mar 2023 a las 17:59, Steven R. Brandt > (<sbrandt(a)cct.lsu.edu>) escribió: > > > On 3/8/2023 2:13 PM, Enzo Iubini wrote: >> Thank you Steve! >> >> My problem is: the simulation gifs of the Wave Equation and >> Heat Equation notebooks on the tutorial folder are not >> showing correctly. > > So I just clicked through the heat equation notebook. The cell > that ends with: > > ## play animation > from IPython.display import HTML > HTML(anim.to_html5_video()) #playback option 1 > #HTML(anim.to_jshtml()) #playback option 2 > > Played an animation for me. Initially, there is a spike at the > center of the grid, and it evolves to become flat. (It also > printed a deprecation warning about the "close_event" > function, whatever that is). > > Did you click through to this cell or did you stop at the one > before? Because the one before it just displays a still image. > > The WaveEquation also worked for me by just clicking through > the cells in order. > >> >> I'm trying to understand how Cactus works, so I ran every >> cell in the notebook while looking at the Terminal and seeing >> how each file is created and its contents. >> The problem comes when I finally run the simulations, which >> take a while. > This happens in seconds for me. >> So after the running is complete, there's this section called >> "Extract data from hdf5 files". >> The files exist, as I have previously checked, but the time >> steps array is actually a [0,0] array in the heat equation, >> and a very random array in the wave equation. >> In both cases, when plotting the simulations, the solution >> does not change from the initial condition. > Did you modify the cells from the original tutorial? Because > this all just worked for me. >> >> I tried to open the data files to see if I could understand >> what was going on but I'm unable to open these kind of files, >> and Cactus being a black box leaves me helpless to see where >> the mistake is coming from. > > So I disagree that Cactus is a black box since it is open > source and the purpose of these tutorials is to show how it > works... but it's a very big non-black box which can be > overwhelming. > > I think your problem is the hdf5 files, not Cactus. Hdf5 is a > file format that Cactus uses. You can open them with commands > like h5ls, or Python's h5py library (which the notebook > provides some examples of usage). > >> >> I want to work on the problems at the end of these notebooks, >> but not correctly seeing the solution makes me think there's >> something wrong since the beggining, and I have not changed >> anything else from the initial notebook. > > So I'm not 100% sure what's going on, but I suspect you've > either not clicked far enough or you have modified the > notebook. Please check and let me know. > > --Steve > >> >> Has this happened to anyone before? >> >> I'm sorry for the long email, I'm very new to this software >> and there's so much to learn! :-) >> Thank you in advance. >> >> - Enzo >> >> El mié, 8 mar 2023 a las 14:02, Steven R. Brandt >> (<sbrandt(a)cct.lsu.edu>) escribió: >> >> You've come to the right place. What's the problem? >> >> --Steve >> >> On 3/7/2023 7:41 PM, Enzo Iubini wrote: >>> Hello! >>> Thank you for approving my tutorial account. >>> >>> I have a small question. I'm having a bit of trouble >>> with some tutorial notebooks, in particular the Heat >>> Equation and Wave Equation notebooks, where the >>> simulations are not running properly. The question is, >>> who can I contact to get support with this? I would not >>> want to bug you if this is not your job, but I'm a >>> little lost and got nobody to ask for help. >>> >>> Thank you in advance. >>> Greetings! >>> >>> Enzo Iubini >>> >>> El lun, 5 dic 2022 a las 13:12, Steven R. Brandt >>> (<sbrandt(a)cct.lsu.edu>) escribió: >>> >>> Approved. :) >>> >>> --Steve >>> >>> On 12/5/2022 9:53 AM, >>> RegistrationBot(a)einsteintoolkit.org wrote: >>> > Einstein Toolkit maintainers: >>> > >>> > New Tutorial Request: >>> > Name: http://orcid.org/0000-0001-9327-0832 >>> > Email: egic.enzo(a)gmail.com >>> > Organization: ORCID >>> > Why: Hello! >>> > My name is Enzo Iubini and I'm doing my Master's >>> degree in Applied Mathematics. I study at >>> Universidad de Chile, and my work is about binary >>> black holes. My proffessor has recommended me to try >>> Einstein toolkit, but I'm having trouble >>> understanding how to work around it, therefore I'd >>> really like to have a tutorial account. >>> > I do not have a homepage. >>> > >>> > Thanks in advance! >>> > >>> > >>> > The above user has requested a tutorial account. >>> > >>> > Thanks, >>> > Einstein Toolkit Registration Bot >>> > >>> > _______________________________________________ >>> > Maintainers mailing list >>> > Maintainers(a)einsteintoolkit.org >>> > >>> http://lists.einsteintoolkit.org/mailman/listinfo/maintainers >>>

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