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Plotting all refinement levels using Kuibit
by José Ferreira 09 Oct '24

09 Oct '24

Dear toolkit community, I’m struggling to find a way to plot a 1D quantity in Kuibit without merging the different meshes originated from the mesh refinement. As a workaround, I have made a Python script that reads the file of a grid function and plots every point along the axis and its corresponding value. I can share this script if somebody is interested, but it is not very good as it breaks once you use checkpoints and has hardcoded paths. However, it gets the job done, as you can see in an example plot below, where it is hopefully obvious that there is an increase in the number of points as z approaches 0. Obviously, a solution that uses Kuibit would be much better. However, I cannot come up with such a solution and so I’m writing this e-mail. From the documentation, the object that represents the simulation data (including the mesh refinement levels), is the |HierarchicalGridData|, and I know how to go from a grid function to this object. For instance, to get the |HierarchicalGridData| that represents the real part of a scalar field along the x-axis at t=0, we do |sd = SimDir("<output>") gf = sd.gf phi1=gf.x["phi1"].get_time(0) | All I have to do now is plot this somehow. As it turns out, this is impossible, because according to the documentation We cannot plot directly this object, because it is a complicated object. To plot it, we have to merge the refinement levels to a single |UniformGridData|. We can do this with |refinement_levels_merged()|. But, all of the information regarding the mesh refinement levels is here, so it should be possible to extract this information and plot it, right? Looking at the methods and variables in |HierarchicalGridData| I came up with nothing. Does anybody have a solution to this? Thank you in advance, Best Regards, José Ferreira

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Installation error
by Stefanos Tsiopelas 08 Oct '24

08 Oct '24

Dear all, I am trying to install Einstein Toolkit on MacOS Ventura and at the last stage of the compilation I encounter this error: ld: library not found for -l/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/lib/libz.tbd collect2: error: ld returned 1 exit status However, when checking the location, the file is indeed there. To install the packages, I use homebrew. Attached is the config-info file. Kindest regards, Stefanos Tsiopelas Uniwersytet Wrocławski [cid:400ea55e-bee6-4608-92c4-b898fee1d63d]<https://uni.wroc.pl/>[cid:2f62d8e6-9fcf-4898-b3b2-7a02479b1a15]<https://uwr.edu.pl/inicjatywa-doskonalosci-uczelnia-badawcza>[cid:be632b3f-23e3-4ea2-9058-9dbfeadf0cd4] Wiadomość ta oraz wszelkie załączone do niej pliki są poufne i mogą być prawnie chronione. Jeżeli nie jest Pani/Pan zamierzonym adresatem niniejszej wiadomości, nie może Pani/Pan jej ujawniać, kopiować, dystrybuować ani też w żaden inny sposób udostępniać lub wykorzystywać. O błędnym zaadresowaniu wiadomości proszę niezwłocznie poinformować nadawcę i usunąć wiadomość.

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Agenda for Thursday's Meeting
by rhaas＠illinois.edu 07 Oct '24

07 Oct '24

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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Postdoctoral Research Position in Numerical Relativity and Strong Field Gravity at Urbana Champaign
by Helvi Witek 03 Oct '24

03 Oct '24

Dear all, we are inviting applications for a postdoctoral research position at the University of Illinois Urbana Champaign. The focus of the position will be numerical relativity and strong field gravity. The successful candidate will work with Dr. R. Haas and Prof. H. Witek. Applicants should submit their application material (1) a curriculum vitae, including a list of publications (2) a research statement (limited to 3 pages, 1 inch margin, 11-12pt) containing a summary of previous and current research, and future plans (3) contact information for three referees who will be asked to write letters of recommendation by 1 December 2024 here: *https://my.physics.illinois.edu/join/#id1900 <https://my.physics.illinois.edu/join/#id1900> * Please find the detailed announcement below. Best wishes Helvi -- Announcement: The Illinois Relativity Group at the Department of Physics and the National Center for Supercomputing Applications (NCSA) at the University of Illinois Urbana-Champaign invites applications for a postdoctoral research associate position with a focus on numerical relativity in strong field gravity, neutrino radiation transport and numerical methods in astrophysics. The successful candidate will have a strong background in scientific software development using parallelization frameworks similar to MPI or related expertise. Expertise in GPU programming will be beneficial. The appointment is to commence in Fall 2025 and last for a two-year term with a potential extension to a third year. The postdoctoral associate is intended to partially work on developing a hybrid Monte-Carlo (particle) M1-Moment (fluid-like) neutrino transport scheme based on the Einstein Toolkit / CarpetX simulation framework as part of the E=mc2 project. This is a multi-institution collaborative project with collaborators at LSU, RIT, UIdaho, UTAustin, and UWYO to develop numerical infrastructure and methods. E=mc2 targets simulations of binary neutron star mergers including all relevant microphysics to obtain astrophysically relevant predictions of properties of the merger process and the subsequent evolution of the merger remnant. The successful candidate will join Dr. Roland Haas, Prof. Helvi Witek, and their team (including postdoc Dr. Deborah Ferguson, six graduate students and undergraduate students). The successful candidate will become a member of the Illinois Relativity Group (which includes Prof. Stu Shapiro, Prof. Nico Yunes, Asst. Prof. Hector O. Silva, Research Professor Antonios Tsokaros and Research Professor Elena Koptieva). They will also become a member of the Illinois Center for Advanced Studies of the Universe (ICASU). While expected to be based in the the Department of Physics, the postdoctoral research associate will be able to interact and collaborate with researchers at NCSA, which currently hosts the largest GPU enabled supercomputer in the ACCESS-CI program and has active collaborations with researchers in parallelization frameworks (MPI, Charm++), machine learning, as well as numerical methods in the department of computer science and school of engineering. Interested candidates must have completed a Ph.D. in Physics, Astrophysics or a related field before the start date. They must submit their application package online here: https://my.physics.illinois.edu/join/#id1900 (Haas/Witek) Applicants are requested to submit (1) a curriculum vitae, including a list of publications (2) a research statement (limited to 3 pages, 1 inch margin, 11-12pt) containing a summary of previous and current research, and future plans (3) contact information for three referees who will be asked to write letters of recommendation The deadline for applications and all letters of recommendation is December 1, 2024, for full consideration. The anticipated starting date of the position is August 15, 2025, though other starting times may be negotiated. Please contact Roland Haas (rhaas(a)illinois.edu) and Helvi Witek (hwitek(a)illinois.edu) if you have any questions about the position itself, or Deanna Frye (ddebord(a)illinois.edu) if you have any questions about the application form. Candidates from underrepresented groups in STEM are particularly encouraged to apply. The University of Illinois System is an equal opportunity employer, including but not limited to disability and/or veteran status, and complies with all applicable state and federal employment mandates. Please visit Required Employment Notices and Posters (https://www.hr.uillinois.edu/cms/one.aspx?portalId=4292&pageId=5705) to view our non-discrimination statement and find additional information about required background checks, sexual harassment/misconduct disclosures, and employment eligibility review through E-Verify (https://e-verify.uscis.gov/web/media/resourcesContents/E-Verify_Participati…). Applicants with disabilities are encouraged to apply and may request a reasonable accommodation under the Americans with Disabilities Act (2008) to complete the application and/or interview process. --------------------------------------------- Dr. Helvi Witek Associate Professor Department of Physics University of Illinois at Urbana-Champaign 247 Loomis Lab 1110 W Green St Urbana, IL 61801 ---------------------------------------------

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Meeting minutes for 2024-10-03
by Lucas Timotheo Sanches 03 Oct '24

03 Oct '24

Present: Lucas (minutes), Maxwell Rizzo, Roland Hass, Johnny Tsao, Zachariah Etienne, Samuel Cupp, Peter Diener, Steven Brandt # Etienne(chair)Timeline: Steve says he will look at the Z4C thorn to see if it has test cases. Roland says that gcc14 requires that we rehaul our autoconf process. He proposes his updated autoconf for inclusion but warns that further testing is needed because autoconf is sensitive. Steve suggested that we put it into master and see what it breaks. Roland will see a PR for that. # Questions in the mailing list Schedule options in uninitialized refinement levels: Roland says he will respond to it. # Tickets 2824: Will be closed by the inclusion of the listings package. Some other related tickets will also be closed by this. 2821: Zach asks what is the update policy on external libraries. Roland says there is no official cadency, we update them when something breaks or someone needs something newer. In AMReX and some other CarpetX dependencies, Erik is updating them more frequently and manually at every release. 2820: Steve asks that they include test cases that work with those changes. Roland will comment on that on the PR. Reviewer is needed. 2818: Roland couldn't trace the error. He suggests we compile each file selectively and see where the error comes up.

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Einstein Toolkit Meeting Reminder
by rhaas＠illinois.edu 02 Oct '24

02 Oct '24

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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Error with CarpetIOHDF5 Checkpoint Iteration
by Wei Sun 02 Oct '24

02 Oct '24

Hello, I encountered an error with CarpetIOHDF5 when reaching the checkpoint iteration, which stops my job if I use too many nodes for parallel processing. I am wondering if this issue is related to the HDF5 library I used during building and if there is a way to resolve it. I utilized the bundled HDF5 from the toolkit itself. The warnings I received are as follows: *WARNING Level 1* from host d24cepyc083.crc.nd.edu, process 0, while executing schedule bin CCTK_CHECKPOINT, routine CarpetIOHDF5::CarpetIOHDF5_EvolutionCheckpoint in thorn CarpetIOHDF5, file /Cactus/configs/sim/build/CarpetIOHDF5/Output.cc:442: "Values for DISTRIB=CONSTANT grid variable 'TERMINATIONTRIGGER::watchminutes' (time level 0) differ between processors 0 and 95; only the array from processor 0 will be stored." *WARNING Level 1* from host d24cepyc083.crc.nd.edu, process 0, while executing schedule bin CCTK_CHECKPOINT, routine CarpetIOHDF5::CarpetIOHDF5_EvolutionCheckpoint in thorn CarpetIOHDF5, file /Cactus/configs/sim/build/CarpetIOHDF5/Output.cc:442: "Values for DISTRIB=CONSTANT grid variable 'QUASILOCALMEASURES::qlm_z_p_p[2]' (time level 0) differ between processors 0 and 2; only the array from processor 0 will be stored." Best regards, Wei

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Agenda for Thursday's Meeting
by rhaas＠illinois.edu 30 Sep '24

30 Sep '24

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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meeting minutes for 2024-09-26
by Roland Haas 26 Sep '24

26 Sep '24

Present: Roland, Bill, Lucas, Maxwell, Sam, Steve, Zach ET release ========== new thorns: * TOVola - Maxwell will review, will contact Zach, Roland will add instructions, https://bitbucket.org/einsteintoolkit/tickets/issues/2823 * Z4c: Steve will review, need test cases, https://bitbucket.org/einsteintoolkit/tickets/issues/2748/inclusion-of-z4c-… * Roland will add proposed thorns to master Mailing list ============ * Roland provided updated on transition, some accounts are being disabled due to bad email addresses / too many bounces * could be due to transition of mailing list server and changes in email relay server used NRPy+ ===== Zach has been reworking the way NRPy+ can be used, making it possible to use. Called NRPy-inline, can contain NRPy+ code in C++ code in between MRPYSTART/NRPYEND tags which nrpy+ can then expand. Useful to eg handle tensorial expressions. Steve brought up possible ways of nicely interacting this with a make based build system. Zach has been exploring Currently only available in NRPy+ git repository, using pip install from there, documentation is very sparse right now https://github.com/nrpy/nrpy Open questions ============== * Roland will respond to comment on Jordan Nicoules question, https://lists.einsteintoolkit.org/pipermail/users/2024-September/009463.html * NR community calls are looking for speakers, https://lists.einsteintoolkit.org/pipermail/users/2024-September/009459.html Open tickets ============ * https://bitbucket.org/einsteintoolkit/tickets/issues/2824/carpetx-documenta… Lucas checked that lstlisting is present in default LaTeX install on Ubuntu, Roland will test on macOS * https://bitbucket.org/einsteintoolkit/tickets/issues/2814/tensortypealias-s… Steve suggest to include this in the next ET release. Roland would prefer if things were only included in the ET once tested and documented 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 rhaas＠illinois.edu 25 Sep '24

25 Sep '24

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