Users June 2022

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19 participants
25 discussions

abstract deadline for EU ET meeting in Dublin tomorrow
by Roland Haas 30 Jun '22

30 Jun '22

Hello all, The abstract submission deadline for the EU ET Meeting in Dublin is July 1st, 2022 (tomorrow). https://sites.google.com/view/eetm2022/registration Deadline for registration: July 15, 2022. Deadline for registration with abstract submission: July 1, 2022. 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 2022-06-30
by Miguel Gracia 30 Jun '22

30 Jun '22

Present: Keith, Roland H., Steven B., Miguel G., Yosef Z., Shanshan R., Leo W., Zach E.. Chair: Yosef Z. Minutes: Miguel G. Next ET Release: * Canuda scalar and complex fields ticket<https://bitbucket.org/einsteintoolkit/tickets/issues/2485/include-complex-a…> Roland will contact the authors. A reviewer will be needed. Anybody from UTAustin? * FLRW solver ticket<https://bitbucket.org/einsteintoolkit/tickets/issues/2549/inlcude-flrwsolve…> .Helvi was a reviewer, Roland can help. The solver somehow needs python, uncertain if those dependancies can change. * SelfForce-1D ticket<https://bitbucket.org/einsteintoolkit/tickets/issues/2602/include-regge-whe…> SelfForce will be reviewed by Peter. * NRPyElliptic (no ticket yet, talk<https://einsteintoolkit.github.io/et2022uidaho/lectures/10-Lecture3/index.h…>) Zach is creating a ticket for it. The Thorn is ready. The documentation remains unfinished. Leo is working on it. * FUKA v2 (maybe, see announcement<http://lists.einsteintoolkit.org/pipermail/users/2022-June/008586.html>) Just the reader would no that hard but FUKA has Kadath and other library dependencies . Authors should be contacted. * ID readers for SGRID<https://einsteintoolkit.github.io/et2022uidaho/lectures/09-Talk2/index.html> and Elliptica<https://einsteintoolkit.github.io/et2022uidaho/lectures/20-Talk4/index.html>. Including more initial data solvers in the toolkit is a good idea. Will require commitment from the authors. ET summer school<https://einsteintoolkit.github.io/et2022uidaho> at Idaho recap [ZE] General positive feedback, excellent GPU based tutorials. Talks on initial data solvers were exciting, Most of initial solvers are going to be open source. ~ 35 participants in person and ~100 virtual. The recordings will be available in the ET Youtube channel but not soon. The videos are not edited, looking for volunteers to help with basic cropping video editing. Roland the first volunteer. Finalizing budget numbers. The reimbursements are being process. Going to take some time. * Missing updates for gallery examples [RH] * BBH<https://www.einsteintoolkit.org/gallery/bbh/index.html> Steve ran it partially. Will try to finish it soon * TOV<https://www.einsteintoolkit.org/gallery/ns/index.html> Peter was in charge of this one. * BNS<https://www.einsteintoolkit.org/gallery/bns/index.html> Yosef: intel 19 is not working. works fine with gcc. He will update once they found what is causing the problem. • Next ET school hosted by RIT or LSU? TBD * Unanswered question on mailing list: No question Open tickets #2615 Roland is answering to the ticket. #2604 Sanshan: Problems compiling the toolkit in MacOs Monterrey, could be a machine naming issue. Adding -fopenmp -lgfortran in LDFLAGS, on an intel based Mac in the optionlist might fix it. #963 Zach will update the reference for clarification. # 2613 Can be closed, Steve approved. #2612 Steve agreed Roland’s fix. # 2611 Roland will work on it and close it. Next calls: Chair: Steve Minutes: Roland end of the call *

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Einstein Toolkit Meeting Reminder
by reminders＠einsteintoolkit.org 29 Jun '22

29 Jun '22

Hello, Please consider joining the weekly Einstein Toolkit phone call at 8:30 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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Fwd: European Einstein Toolkit Meeting in Dublin, 29 August - 2 September 2022
by Helvi Witek 29 Jun '22

29 Jun '22

Dear all, The next European Einstein Toolkit Meeting will take place from 29 August – 2 September 2022 at University College Dublin, Ireland. There will be some time for contributed talks, where you can present your research. This is a reminder that the *deadline for abstract* submission will be *this Friday, 1 July 2022* here https://sites.google.com/view/eetm2022. Best wishes Helvi (on behalf of the scientific organizing committee: Christiana Pantelidou Bruno Giacomazzo Helvi Witek Miguel Zilhao) --------------------------------------------- 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: European Einstein Toolkit Meeting in Dublin, 29 August - 2 September 2022 Date: Fri, 1 Apr 2022 10:57:18 -0500 From: Helvi Witek <hwitek(a)illinois.edu> To: wav-wg(a)lisamission.org Dear all, The next European Einstein Toolkit Meeting will take place from 29 August – 2 September 2022 at University College Dublin, Ireland. The Einstein Toolkit is a community-driven Open Source software platform of core computational tools to advance and support research in relativistic astrophysics and gravitational physics, including Numerical Relativity, studies of Neutron stars and Magnetohydrodynamics. The first two days of the meeting will include lectures and tutorials geared towards new users of the toolkit. The following three days will focus on the status and future development of the toolkit, including scientific talks as well as dedicated discussion sessions. For more information and to register, please use this link: https://sites.google.com/view/eetm2022 There is no registration fee. Everyone is welcome. Participants from underrepresented and traditionally disadvantaged backgrounds are particularly encouraged to register. You are welcome to send questions or informal inquiries to european.einstein.toolkit2022[AT]gmail.com We look forward to welcoming you to Dublin. Best regards, The local organising committee. -- --------------------------------------------- Dr. Helvi Witek Assistant Professor Department of Physics University of Illinois at Urbana-Champaign 247 Loomis Lab 1110 W Green St Urbana, IL 61801 ---------------------------------------------

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Agenda for Thursday's Meeting
by reminders＠einsteintoolkit.org 27 Jun '22

27 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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Extracting the last iteration from 3D CarpetIOHDF5 output files
by Lorenzo Ennoggi 27 Jun '22

27 Jun '22

Hello, I have a set of 3D output files from CarpetIOHDF5 (rho.xyz_file<n>.h5), each containing many iterations, and I want to create a set of new CarpetIOHDF5 files containing the data related to the last iteration. I have tried something, but I couldn't get anything to work, so I am asking for help here. For each file rho.xyz_file<n>.h5, I used the hdf5_extract utility to create a new file containing the dataset related to the last iteration ("HYDROBASE::rho it=1067600 tl=0 rl=0 c=<n>") and the group "Parameters and Global Attributes". However, when I try to open the set of new files with VisIt I get the following error: VisIt could not read from the file > "/home/lorenzo/CBD_prod_WZ9_400_140_280_output-0014/Output/rho.xyz_it1067600_tl0_rl0_c* > database". The generated error message was: There was an error opening > /home/lorenzo/CBD_prod_WZ9_400_140_280_output-0014/Output/rho.xyz_it1067600_tl0_rl0_c* > database. It may be an invalid file. VisIt tried using the following file > format readers to open the file: CarpetHDF5 The following error(s) may be helpful in identifying the problem: > *Tried to access an invalid index 1 (Maximum = 0).* I thought that maybe some metadata in the new files are telling VisIt that there are multiple iterations available, which is not true; I'm not completely sure this is really the issue, though. In the new files, the attributes "GH$iteration" and "carpet_global_time" from the group "Parameters and Global Attributes" are still respectively set to the first iteration (992800) and the first time (148920) available in the original files, while I am extracting the last iteration (1067600, time 160140). Also, in the new files, the dataset "Grid Structure v5" (a string) still contains "grid_times:[[[148920,148919.85000000001,148919.69999999998]]]", which also looks wrong. Therefore, I used h5py to generate new files in which I fixed "GH$iteration", "carpet_global_time" and "Grid Structure v5", but I still get the same error from VisIt. I have also thought about re-running the simulation that produced the original files from the last checkpoint and just dump the last iteration, but that simulation was run some time ago and the code I am using has evolved quite a bit in the meantime, to the point that some parameters are not even defined anymore. Is there any other attribute/dataset I should edit in order to fix the new files? Are there smarter ways to extract an iteration from a set of 3D CarpetHDF5 output files? Please let me know if you need additional information from my end. Thank you very much, Lorenzo Ennoggi

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meeting minutes for 2022-06-23
by Roland Haas 23 Jun '22

23 Jun '22

Present: Roland, Keith, Steve, Johnny, Miguel future candidates for inclusion in ET * Canuda scalar and complex fields * FLRW solver * SelfForce1D * NRPyElliptic solver and reader * FUKA v2 * ID reader for SGRID, Elliptica ET summer school * no recap of Idaho meeting (no organizers present) * videos will be available soon, Roland guesses sometime next week * should send email when available * should make sure they are in ET Youtube channel https://www.youtube.com/channel/UC8IObWZ7_wEbWnbIKVIQRYQ * ET ET meeting in Dublin coming up https://sites.google.com/view/eetm2022 Unanswered questions: * no unanswered questions No new tickets Tickets for review * Steve will take a look at https://bitbucket.org/einsteintoolkit/tickets/issues/2613 updates-to-tutorial-notebook-for-riemann 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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Einstein Toolkit Meeting Reminder
by reminders＠einsteintoolkit.org 22 Jun '22

22 Jun '22

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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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Users June 2022