Users February 2020

users@lists.einsteintoolkit.org

23 participants
29 discussions

Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 24 Feb '20

24 Feb '20

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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Boundary issues solving wave equations with MoL
by Severin Frank 22 Feb '20

22 Feb '20

Dear all, I'm trying to solve a wave equation that describes radial oscillations of a TOV star, depending on radius r and t in Llama multipatch coordinates (Thornburg04). The equation has a structure of Ẍ=AX′+BX″+CX\ddot{X} = A X' + B X'' + C X I rewrote it as set of coupled equations to evolve it with the MoL thorn: X˙=Π H˙=Π′\dot{H} = \Pi' Π˙=AH+BH′+CX\dot{\Pi} = AH + B H' +C X or as noted in my code as it is attached: Pidot = A*H + B*drH + C*Xi Hdot = drPi Xidot = Pi For MoL registered as evolved variables are Xi with rhs Xidot, Pi with rhs Pidot and H with rhs Hdot. The spatial derivatives drH and drPi are also calculated during the schedule of MoL_CalcRHS in my thorn. Boundary conditions are applied for r>R and an interval near the TOV radius r=R. if (grid_r(i,j,k) >= (TOV_surface - rprec) .AND. grid_r(i,j,k) <= (TOV_surface + rprec) )then H(i,j,k) = 0 drPi(i,j,k) = 0 else if ( grid_r(i,j,k) > (TOV_surface + rprec) ) then Xi(i,j,k) = 0 Pi(i,j,k) = 0 H(i,j,k) = 0 end if if (grid_r(i,j,k) > (TOV_surface + rprec) )then Xidot(i,j,k) = 0 Hdot(i,j,k) = 0 Pidot(i,j,k) = 0 else if (grid_r(i,j,k) >= (TOV_surface - rprec) .AND. grid_r(i,j,k) <= (TOV_surface + rprec) )then Hdot(i,j,k) = 0 Pidot(i,j,k) = B(i,j,k)*drH(i,j,k) + C(i,j,k)*Xi(i,j,k) end if Problems occur close to the surface of the star. My evolved variables start do diverge close to the surface after a few iterations. Looking at the data it seems that the divergence is founded by the values of H. I tried following things to encircle the issues: * If I put Pidot = B*drH + C*Xi the values seem to be ok, whereas for Pidot = A*H the divergence appears. The A-factor only amplifies this behavior. If I put Pidot = H it behaves the same, but much slower. * If I use drXi instead of H (as it is commented out), it does not make any difference. * If I enlarge the size of the interval (e.g. TOV_surface + 5*rprec) the same divergence appears, but shifted towards grid points next to the interval. Also the divergence appears a few iterations later. * If I change the drXi or H values close to the surface manually (e.g. using a backsided differentiation, or put specific values by hand) it also shifts the divergence (like above). So far I don't know how to remedy this issue, but maybe I'm overlooking something obvious. Does anyone have an idea on what I could try? Thanks a lot! Best regards and merry Christmas, Severin Frank

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Hyperbolic encounters using example parameter files
by Øyvind Christiansen 21 Feb '20

21 Feb '20

Hi, I'm trying to change at first the bbh.par file from the arxiv-1111.3344 folder in Cactus and later the GW150914 example at the gallery at the einsteintoolkit website, to simulate hyperbolic encounters at large impact parameters where there's overlap of validity with the post-Newtonian approximation. I'm naively changing the TwoPunctures parameters to aim momentum a bit off of each other and start out at a larger distance. Changing the distance I also change the origin_x and initial_guess__coord_sphere__x_cent, and initial_x parameters in AHFinderDirect and PunctureTracker. I also adjust dtfac because of using larger momenta. My questions: Are there any other parameters I should be changing as well to accommodate this scenario? How accurate and physical results will bbh.par yield? Is GW150914 gallery necessary? If so, should I expect reasonable results using it, when working with it black-box like this? Are there any subtleties to changing the masses? For example regarding the initial_guess__coord_sphere__radius in AHFinder? I couldn't find too much documentation on TwoPunctures. I'm assuming the units are G=c=Ms=1. Thank you for any help and/or direction! Øyvind Christiansen Master student, Oslo

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Meeting Minutes for 2020-02-20
by Bill Gabella 20 Feb '20

20 Feb '20

Present: Steve B, Bill G, Roland H, Peter D, Alois Peter Schaffarczyk, Liu Haoyang, Zach E., Maria B-H, Vassili Chair: Steve Minutes: Bill * Next release is in April 2020. * Update on potential codes to be included for next release ** Baikal ETK code from Zach Zach has not had time to make the change where at run time you can choose different kernels, 8th order or less, and whether you want to add the Tmunu in. Six kernels to ask, needs time to pull that together. It does work and they use it. Helvi is reviewing it. ** Upgrade to Illinois GRMHD Extends the capabilities to use piece-wise polytrope and hybrid EOS, agrees with old version. Ready for review. No changes planned; documented in Jupyter notebooks. Should pass all the code / unit tests in ETK. Would like to extend to piece-wise polytrope initial data for single TOV star. Roland was original reviewer and the new version feature update is the piece-wise polytrope and the hybrid EOS---you run the Jupyter notebooks and they generate the GRMHD thorn. ** Zach also has a TOV code which he might want to contribute Nrpy TOV Thorn (Nrpy TOV ID) could come into play. Leo Vernick (lead author, back in Brazil) has a C code version. Run Numpy, and Nrpy puts it on the grid, even deals with star surface, avoids it and avoids Gibbs phenomenon. Has a student optimizing the C code generation from Nrpy, and doing an extra pass at the post CSE output. Not able to speed up the C code generation, but have sped up the Nrpy code a lot. Needs a reviewer. ** Steve would like Presync in ** Peter says that he will have updates to the self-force code Previously thought there was a problem with code, not behaving like previous version, but now believes it does. Will be minor updates / capabilities to reduce the window function to zero size, a distribution function source, that should be read by the next release. Nothing major after that fix. * Workshop at LSU and registration page has been tested. Dates August 3-7, 2020. Has some money to support travel for students. Website at https://www.cct.lsu.edu/Einsteintoolkitworkshop . Steve looking for people to present and give tutorials. Zach has a student with interesting Nrpy Wave Toy that might be available. * Steve wants to switch to Python3 for Simfactory (Python 2 no longer officially supported). hwloc fails to build on Master for generic config. Need to have locality setup correctly for Python3 to work, otherwise trying to interpret Unicode in PIP downloads fails with clear error message. * For above additions to the ETK, create a ticket to add your code to Master branch by March so that it can get tested. Steve thinks there is a ticket for the Python3 conversion. [from bottom of agenda] unanswered questions on mailing list https://www.einsteintoolkit.org/tools/unanswered.php open tickets sorted by update time https://bitbucket.org/einsteintoolkit/tickets/issues?status=open&status=new… tickets ready for review https://bitbucket.org/einsteintoolkit/tickets/issues?status=new&status=open… -- ===================================== William Gabella Research Assistant Professor Department of Physics and Astronomy Vanderbilt University Nashville, TN USA b.gabella(a)vanderbilt.edu (o) 615-343-2713users

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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 19 Feb '20

19 Feb '20

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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Workshop announcement "New Frontiers in Strong Gravity" July 2020 in Benasque
by Helvi Witek 18 Feb '20

18 Feb '20

** *Dear colleagues,* * We would like to announce a two-week workshop “New frontiers in strong gravity” taking place in Benasque, Spain, from Jul 05–18 2020. The workshop’s web page is at http://benasque.org/2020relativity/. Please see the announcement below. Limited travel funds are available, with priority given to PhD students. We would appreciate it if you could forward the announcement to interested researchers in our field. Best wishes, Helvi (on behalf of the organizers D. Blas, P. Figueras, E. Lim, L. Stein, H. Witek, S. Nissanke) New frontiers in strong gravity The highly nonlinear, strong-field regime of gravity holds the key to address long-standing puzzles in modern physics. These range from deeply theoretical questions concerning a consistent theory of quantum gravity and resulting modifications to general relativity, over the stability properties of black holes in traditional general relativity, to new insight into nuclear matter under extreme conditions in the context of neutron star and multimessenger astronomy. In this two-week workshop (Jul 05–18, 2020) we will bring together leading experts as well as junior scientists and PhD students in these diverse research areas, to encourage communication and training across the fields and foster new research collaborations. Invited speakers include: • Samaya Nissanke • Tessa Baker • Roberto Emparan • Katy Clough • Enrico Barausse • Deirdre Shoemaker • Will East • Aaron Zimmerman • Thomas Sotiriou • Mihalis Dafermos • Maria Okounkova • David Mateos • Anne Davis • Rachel Rosen • Niels Warburton • Laura Bernard • Harald Pfeiffer The number of participants is limited. We ask students to upload a short CV (maximal 2 pages). Limited travel support will be available, with priority given to students. To apply for travel support please include some text justifying your request for support on the registration page. Registration will close on May 25. Registration and more information is at the workshop’s web page, http://benasque.org/2020relativity/. * -- --------------------------------------------- Dr. Helvi Witek Assistant Professor Department of Physics University of Illinois at Urbana-Champaign 247a Loomis Lab 1110 W Green St Urbana, IL 61801 ---------------------------------------------

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Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 17 Feb '20

17 Feb '20

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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NSNSTOHMNS(Gallery example) Plotting issues
by Atul Kedia 17 Feb '20

17 Feb '20

Dear all, I am trying to plot and make movie for the NSNSTOHMNS Gallery example using the support scripts provided. On using the VisIt support scripts as given in the example, I do get some figures named [rho_000000000.png, ... , rho_000000231.png], but they are all usually black screens or look like tv white noise. Details of the simulation: I ran it on a cluster with 8 cores. My run data for mp_Psi4_l2_m2_r300.00.asc and rho.xy.h5 and the sample Results given in the gallery example are of the same order of magnitude(although not identical). So I doubt any problems on the data generation end. I am using VisIt version 3.0.2 and FFMPEG version 4.2.1, and am loading python/3.7.3. I get these when I run the command visit -cli -nowin -s rho.movie.py - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ... ... VisIt: Message - Rendering window 1... VisIt: Error - The compute engine running on crcfe01.crc.nd.edu has exited abnorm ally. VisIt: Error - Scalable Render Request Failed (VisItException) viewer: Obtained null data reader for rendered image for engine crcfe01.crc.nd.ed u. Running: engine_ser3.0.2 -idle-timeout 480 -host 127.0.0.1 -port 5600 VisIt: Message - Rendering window 1... VisIt: Message - Saving window 1... VisIt: Message - Saved rho_000000000.png ... ... s/nsnstohmns_in_saeng/output-0000/nsnstohmns/rho.xy.h5". VisIt: Message - Closed the compute engine on host crcfe01.crc.nd.edu. ffmpeg version 4.2.1 Copyright (c) 2000-2019 the FFmpeg developers built with gcc 4.8.5 (GCC) 20150623 (Red Hat 4.8.5-39) configuration: --prefix=/afs/crc.nd.edu/group/mathews/tools/ffmpeg/4.2.1 --disable-x86asm libavutil 56. 31.100 / 56. 31.100 libavcodec 58. 54.100 / 58. 54.100 libavformat 58. 29.100 / 58. 29.100 libavdevice 58. 8.100 / 58. 8.100 libavfilter 7. 57.100 / 7. 57.100 libswscale 5. 5.100 / 5. 5.100 libswresample 3. 5.100 / 3. 5.100 Unrecognized option 'crf'. Error splitting the argument list: Option not found ffmpeg version 4.2.1 Copyright (c) 2000-2019 the FFmpeg developers built with gcc 4.8.5 (GCC) 20150623 (Red Hat 4.8.5-39) configuration: --prefix=/afs/crc.nd.edu/group/mathews/tools/ffmpeg/4.2.1 --disable-x86asm libavutil 56. 31.100 / 56. 31.100 libavcodec 58. 54.100 / 58. 54.100 libavformat 58. 29.100 / 58. 29.100 libavdevice 58. 8.100 / 58. 8.100 libavfilter 7. 57.100 / 7. 57.100 libswscale 5. 5.100 / 5. 5.100 libswresample 3. 5.100 / 3. 5.100 Input #0, image2, from 'rho_%09d.png': Duration: 00:00:09.28, start: 0.000000, bitrate: N/A Stream #0:0: Video: png, rgb24(pc), 640x640, 25 fps, 25 tbr, 25 tbn, 25 tbc Unknown encoder 'theora' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any help would be greatly appreciated. Thank you, best regards, Atul Kedia Physics Graduate student University of Notre Dame.

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arXiv-1111.3344 collapse example errors
by Justin Verde 17 Feb '20

17 Feb '20

Hi everyone, I'm a new user to the toolkit and have been trying to run the TOV collapse example from arXiv-1111.3344 on my home system with 4 cores. I keep getting the following errors before the job crashes: =============================================== Error: Thorn CartesianCoordinates not found Error: Thorn corecollapsecontrol not found Error: Thorn TriggerTerminationManual not found Activation failed - 3 errors in activation sequence WARNING level 0 from host euler process 0 in thorn Cactus, file /home/verde029/ETK/Cactus/configs/sim/build/Cactus/main/SetParams.c:93: -> CCTKi_SetParameter: Error at line 66 in parameter file /home/verde029/simulations/collapse_crash_test/output-0000/tov_collapse_vc_l3.par while activating thorns -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. ============================================ I can't find anything on these thorns through the thorn documentation guide. Have the thorns or par file been updated, or is there a quick workaround to update the file? I appreciate any help! -- Kindest Regards, Justin Verde

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Re: [Users] Fwd: Re: meeting minutes for 2020-02-06
by Steven R. Brandt 13 Feb '20

13 Feb '20

What command did you use to build? Did you use simfactory? Did you install all the prerequisites? I.e. what do you see when you type "which gfortran" or "which mpirun"? --Steve On 2/13/2020 2:46 PM, Bilal Hameed wrote: > > Dear Sir, > > I am using ET_RELEASE = ET_2019_10 in Ubuntu 18.04. Sir I am > trying to run module weylscale4. This module needs a thorn named > "Iosurfacer". I have this thorn's folder in cactus/repos/pughio but > this thorn is not included in thornlist So when I try to include it > for my example it gives following error, > > CST error in /home/bilal/Cactus/lib/sbin/CST (at 376) > -> Missing thorn cactuspughio/IsoSurfacer > > ------------------------------------------------------ > > /home/bilal/Cactus/lib/make/make.configuration:214: recipe for target > '/home/bilal/Cactus/configs/weyl/config-data/make.thornlist' failed > make[1]: *** > [/home/bilal/Cactus/configs/weyl/config-data/make.thornlist] Error 1 > Makefile:256: recipe for target 'weyl' failed > make: *** [weyl] Error 2 > > On 13/2/20 12:39 AM, Steven R. Brandt wrote: >> >> Hi Bilal, I assume by "ADM" you mean "EinsteinBase::ADMBase?" >> >> Can you tell us (1) what operating system you're on, (2) what version >> of the einstein toolkit you're using? (3) show us the exact error >> message? (4) show us what command you are using to compile? >> >> Thanks. >> >> --Steve >> >> >> >> -------- Forwarded Message -------- >> Subject: Re: [Users] meeting minutes for 2020-02-06 >> Date: Wed, 12 Feb 2020 23:35:06 +0500 >> From: bilal hameed awan <bilalhameedawan962(a)gmail.com> >> To: Steven R. Brandt <sbrandt(a)cct.lsu.edu> >> >> >> >> Dear Brandt Sir, >> Sir I am trying to run module weylscal4. I >> get an error missing thorn "ADM", issue is I can't find any thorn >> ..../ADM in thornlist. >> Please help me. >> >> Regards >> Bilal Hameed. >> >> On Tue, Feb 11, 2020, 9:29 PM Steven R. Brandt <sbrandt(a)cct.lsu.edu >> <mailto:sbrandt@cct.lsu.edu>> wrote: >> >> OK, I have this imported from SVN: >> https://github.com/EinsteinToolkit/cactuscode >> >> Some of you already have commit rights on it. I'm happy to have more. >> >> We apparently have a docker image in >> https://github.com/stevenrbrandt/et-websites already... and >> apparently I made it, though I don't remember doing so. Maybe I'm >> older than I think. >> >> What I need is someone to help with the content. >> >> --Steve >> >> On 2/11/2020 10:04 AM, Steven R. Brandt wrote: >>> >>> >>> On 2/11/2020 8:21 AM, Ian Hinder wrote: >>>> >>>> >>>>> On 10 Feb 2020, at 16:37, Steven R. Brandt >>>>> <sbrandt(a)cct.lsu.edu <mailto:sbrandt@cct.lsu.edu>> wrote: >>>>> >>>>> So the question is, what do we do about the website? We don't >>>>> have the time, person-power, or budget to maintain it. At >>>>> present, the website is full of things that are horribly out >>>>> of date and likely does more harm than good for anyone reading it. >>>>> >>>> Hi Steve, >>>> >>>> For time, person power and budget, how would this change if it >>>> were moved to be under the ET website? >>> >>> I don't have a dollar or hour figure, but the svn repo is >>> maintained by CCT, which sits on a server which has to be >>> upgraded from time to time and there are svn client server >>> version issues, etc. Similar issues apply to the webserver. The >>> machine has to be upgraded from time to time, which includes >>> going and getting new docs, etc. If we put a webserver on github >>> and served cactuscode.org <http://cactuscode.org> out of a >>> docker image like we do for the ET, that would simplify upgrades >>> and refreshing. It would also help us to document what the >>> website does and make it possible to host it elsewhere if that >>> ever becomes necessary or desirable. >>> >>> My belief is that if we want to keep a cactuscode.org >>> <http://cactuscode.org> website, we should all help in updating >>> it and making it worthwhile. >>> >>>> >>>> Is the issue related to keeping the content up-to-date, or >>>> infrastructure issues like maintaining a separate webserver etc? >>> Mostly, it's keeping the content relevant, but the website >>> updated and running is a bit of a hassle too. >>>> >>>> Deleting content which is out of date would help. >>> Right, but there's a lot of content and I don't have the time to >>> go through it all--I don't think anyone does. I think we need to >>> ask what the minimum thing is that we want. What are the >>> critical set of pages? >>>>> >>>>> We could make a website that's just a few well-chosen pages >>>>> with a similar template to the ETK. >>>>> >>>> Reducing the amount of administrative duplication is certainly >>>> desirable. >>> >>> It's more than desirable IMHO, it's necessary. Also, in recent >>> months we've been working to decentralize administration and >>> make sure that more than one person knows how to keep various >>> things running. This is another opportunity to continue that trend. >>> >>> --Steve >>> >>>> >>>> -- >>>> Ian**Hinder >>>> Research Software Engineer >>>> University of Manchester, UK >>>> >> _______________________________________________ >> Users mailing list >> Users(a)einsteintoolkit.org <mailto:Users@einsteintoolkit.org> >> http://lists.einsteintoolkit.org/mailman/listinfo/users >>

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