Users April 2020

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14 participants
24 discussions

Re: [Users] GRHydro::check_GRHydro_C2P_failed error
by Beyhan Karakaş 19 Apr '20

19 Apr '20

Dear Roberto, With respect to the question, I wanted to state that the issue with the GRHydro thorn which gave "retval" was overcomed by increasing resolution to dx=0.375 as you have suggested. But simulation stopped with NANs again at 1300 simulation time. Just as in the previous simulation, AHFinderDirect has searched for horizon after finding it for the first time at 825 but could not find again. I do not know how this problem could be solved. Output and error file are attached. Best regards, Beyhan. On Fri, Apr 17, 2020 at 6:45 PM Beyhan Karakaş <beyhannkarakas(a)gmail.com> wrote: > Dear Roberto, > > After increasing resolution to dx=0.375 there has not been any error in > the merger and afterwards so far (around 1077 simulation time) > But AHFinderDirect has been searching for horizon after finding it at 825. > Output file is attached. Doesn't it have to find the same horizon and how > it is changing during the evolution? > > I am looking forward to hearing from you. > > Best regards, > > Beyhan. > > On Tue, Apr 14, 2020 at 9:10 PM Beyhan Karakaş <beyhannkarakas(a)gmail.com> > wrote: > >> Dear Roberto, >> >> Thank you very much for your consideration and reply. When I change the >> resolution to dx=0.375 it requires 16 gb of ram and simulation becomes 9 >> times slower and it would take 2.5 days to reach the 1000 simulation time. >> I will try to do this and , if possible, inform you about the result. >> >> Best regards, >> >> Beyhan. >> >> >> On Tue, Apr 14, 2020 at 8:32 PM Roberto De Pietri < >> roberto.depietri(a)unipr.it> wrote: >> >>> Dear Beyjann >>> >>> From the output, it seems that the two stars just merged and then a >>> prompt collapse to Black Hole. An Apparent Horizon was found. >>> >>> INFO (AHFinderDirect): proc 0: searching for horizon 1/1 >>> INFO (AHFinderDirect): AH 1/1: r=2.18345 at (-0.000000,0.000000,0.000000) >>> INFO (AHFinderDirect): AH 1/1: area=376.8755139 m_irreducible=2.738192857 >>> 5952 558.000 | 129.2759814 | 0.0003459 | 0.0000439 | >>> 8.9127188 | 8.4903683 | 151.5039356 | 301.5059049 >>> >>> Dear Beyhan; >>> >>> Quite likely just resolution. >>> >>> But at the next iteration, AH finder was not able to find it again, and >>> indeed the interior of the black hole was >>> not excised and conservative to primitive failed close to the >>> singularity. >>> >>> Resolution of dx=0.75 it is not enough for simulation, and leas dx=0.375 >>> is needed for having running simulation >>> when black hole form and at least 0.25 to have some useful data. >>> >>> Roberto >>> >>> On 14 Apr 2020, at 17:22, Beyhan Karakaş <beyhannkarakas(a)gmail.com> >>> wrote: >>> >>> Dear to whom it may concern, >>> >>> I am using Mayer release on Fedora 31. I have made some changes in the >>> parameter file that was created by De Pietri, Feo, Maione and Loeffler in >>> 2016 (which could be downloaded from >>> http://www.fis.unipr.it/numrel/Research/BNS2016.html >>> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.fis.un…>). >>> Some of the Parma Groups' thorns were used in the parameter file added to >>> the end of the mail. >>> >>> Initial data for equal mass (M_1,2=1.7 M_sun) binary neutron stars was >>> generated on LORENE using SLy EOS. Table of it was attached. Initial data >>> could be downloaded from https://bitbucket.org/beyhank/bns >>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbitbucket…> >>> . >>> >>> GRHydro thorn starts to give retval after 504 simulation time and stops >>> the simulation at 756 with NANs (BH formed at 558). I suppose the error >>> persists either "EinsteinEvolve/GRHydro" or "PRThorns/GRHydro" is used. >>> >>> I do not know whether this error is resulted from low resolution or >>> something else. Same setting does not seem to give any error for the >>> configuration M_1,2=1.2 M_sun. >>> >>> Output, error and parameter files are attached. >>> >>> Best regards, >>> >>> Beyhan. >>> >>> >>> --------------------------------------------------------------------------------- >>> # The Parma Thorns >>> !TARGET = $ARR >>> !TYPE = git >>> !URL = https://bitbucket.org/GravityPR/prthorns.git >>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbitbucket…> >>> !REPO_PATH= $2 >>> !CHECKOUT = >>> PRThorns/TempPool >>> PRThorns/Meudon_Bin_NS >>> PRThorns/Hydro_RNSID >>> PRThorns/GRHydro >>> PRThorns/GRHydro_Analysis >>> PRThorns/GRHydro_InitData >>> <tnisan12.par><tnisan12.err><tnisan12.out><eos_sly4_pp.d> >>> _______________________________________________ >>> Users mailing list >>> Users(a)einsteintoolkit.org >>> >>> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.eins… >>> >>> >>>

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Meeting Minutes for Apr. 16, 2020
by Hamilton, Maria 16 Apr '20

16 Apr '20

Present: Erik Schnetter, Maria Hamilton, Zach Etienne, Peter Diener, Roland Haas, William Gabella, Steven Brandt, Miguel Zilhao, Zhichao Zhao, Beyhan, Chrisopher Evans, Liu Haoyang Chair: Peter Minutes: Maria Peter opens the meeting with the agenda. * Future of ET: the new grant is awarded - https://www.nsf.gov/awardsearch/showAward?AWD_ID=2004879&HistoricalAwards=f… - Roland intends to have a wiki open to users - It will consist on 3 parts: Carpetx, NRPy and Canuta * Eric gives a presentation of AMReX (https://amrex-codes.github.io/amrex/index.html), the software the new driver Carpetx is based on (https://bitbucket.org/eschnett/cactusamrex ). * Zach had some questions on the indexing in AMRex, which is different from Carpet indexing, and Eric offered to give a Workshop on it. AMRex output is ineffective, and he is also working at a different file output (https://wci.llnl.gov/simulation/computer-codes/silo). * Zach gives a review of NRPy, which can be separated in 3 categories: - Register grid functions and parameters - Baikal - integration ET and NRPy - GPU kernels * Miguel gave a brief description of Canuta, that models Gravity augmented with other fields * Roland requires an update update on potential codes to be included in next release - BaikalETK: Zach, Helvi will have it reviewed in short time) - PreSync: Steve refers to documentation * Timeline of upcoming release freeze: May 7 * Roland does not have new updates for testsuites results, but the test system has changed, and some tests need to be redone. * Lastly, Peter discusses with Miguel about an unanswered question on the mailing list regarding summation by parts. * Erik raises the question about a standard Benchmark and offers to run one. * The meeting adjourns. _______________________ 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

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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 15 Apr '20

15 Apr '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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GRHydro::check_GRHydro_C2P_failed error
by Beyhan Karakaş 14 Apr '20

14 Apr '20

Dear to whom it may concern, I am using Mayer release on Fedora 31. I have made some changes in the parameter file that was created by De Pietri, Feo, Maione and Loeffler in 2016 (which could be downloaded from http://www.fis.unipr.it/numrel/Research/BNS2016.html). Some of the Parma Groups' thorns were used in the parameter file added to the end of the mail. Initial data for equal mass (M_1,2=1.7 M_sun) binary neutron stars was generated on LORENE using SLy EOS. Table of it was attached. Initial data could be downloaded from https://bitbucket.org/beyhank/bns . GRHydro thorn starts to give retval after 504 simulation time and stops the simulation at 756 with NANs (BH formed at 558). I suppose the error persists either "EinsteinEvolve/GRHydro" or "PRThorns/GRHydro" is used. I do not know whether this error is resulted from low resolution or something else. Same setting does not seem to give any error for the configuration M_1,2=1.2 M_sun. Output, error and parameter files are attached. Best regards, Beyhan. --------------------------------------------------------------------------------- # The Parma Thorns !TARGET = $ARR !TYPE = git !URL = https://bitbucket.org/GravityPR/prthorns.git !REPO_PATH= $2 !CHECKOUT = PRThorns/TempPool PRThorns/Meudon_Bin_NS PRThorns/Hydro_RNSID PRThorns/GRHydro PRThorns/GRHydro_Analysis PRThorns/GRHydro_InitData

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Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 13 Apr '20

13 Apr '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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Meeting Minutes for 2020-04-09
by Helvi Witek 09 Apr '20

09 Apr '20

Meeting minutes for 2019-06-06 Present: Beyhan, Bill Gabella, Christopher Evans, Liu Haoyang, Maria Hamilton, Peter Diener, Roland Haas, Steven Brandt, Helvi Witek * Welcome to new participants in the call! * Questions regarding setup of GRHydro (Beyhan) ** recommendation to share parameter- and log-files via mailing list to enable trouble-shooting * Chairs / Minute takers for following meetings ** 16 April: Peter / Maria ** 23 April: Steve / Bill ** 30 April: Helvi / Steve * Update on codes to be included in upcoming release ** BaikalETK (contributed by Zach Etienne; under review by Helvi Witek) *** under review ** PreSync (contributed by Steve Brandt; under review by Roland Haas) *** review ongoing *** test thorn identified bugs; fix under way * Timeline of upcoming release ** Can be found on https://docs.einsteintoolkit.org/et-docs/Release_Details#Schedule_for_ET_20… ** planned release on 31 May 2020 ** expect only minor bug-fixes. ** Gallery Examples:. *** volunteers found for most examples. *** multipatch gallery example: Beyhan volunteered. Thank you! * no unanswered questions on mailing list -- --------------------------------------------- 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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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 08 Apr '20

08 Apr '20

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Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 06 Apr '20

06 Apr '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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optimal nodes, mpi tasks, and cpus per mpi task?
by Bill Gabella 03 Apr '20

03 Apr '20

Okay just a little advice from the community, running a qc0 BBH merger example on our HPC at Vanderbilt and trying to tune my parameters. WE use Slurm / SBATCH and the ones I am working with are: o amount of memory per node o number of nodes o numpy of MPI tasks o if more than one cpu per task helps One example was 4 GB per node, 4 nodes, 4 MPI tasks, and 2 CPUs per task. Was a little slower than 1 CPU per task---perhaps memory. I have learned from you all that ETK is a memory hog more than a CPU hog, ur, to say lots of memory helps vs lots of cores. Any examples you have of simple, vanilla BBH would be good. My SBATCH script includes #SBATCH --mem 4000 # amount of memory per node #SBATCH --nodes=4 # Like -24, number of nodes on which to run #SBATCH -n 4 # Total number of mpi tasks requested, def 1 task/1 cpu #SBATCH -c 2 # Number of cpus per mpi task #SBATCH -t 1:00:00 # Run time (d-hh:mm:ss) and was told to use srun and not mpirun -np XXXX, myparFile="qc0-mclachlan.par" myCactusExe="/labs/einstein/20191028/Cactus/exe/cactus_sim" ##echo "mpirun -np 4 $myCactusExe $myparFile" ##mpirun -np 4 $myCactusExe $myparFile echo "srun $myCactusExe $myparFile" srun $myCactusExe $myparFile Eventually I want to get Simfactory running and see several HPC's that use Slurm in the machine database directory. Still I think I need to understand these parameters to tune the scripts Simfactory uses. thanks, bill e.g. -- ===================================== William Gabella Research Assistant Professor Department of Physics and Astronomy Vanderbilt University Nashville, TN USA b.gabella(a)vanderbilt.edu (o) 615-343-2713

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Fwd: error message on the static jupyter notebook
by Bill Gabella 02 Apr '20

02 Apr '20

Maybe this should go to the users list? I am spam'ing it to Users and Maintainers, sorry:) bill e.g. -------- Forwarded Message -------- Subject: error message on the static jupyter notebook Date: Thu, 2 Apr 2020 15:23:50 -0500 From: Bill Gabella <b.gabella(a)vanderbilt.edu> Organization: Vanderbilt University To: maintainers(a)einsteintoolkit.org When I go to the static Jupyter notebook under Downloads: Tutorial New users I see an error message. The link is https://nbviewer.jupyter.org/github/nds-org/jupyter-et/blob/master/CactusTu… and the error is a "Host Error" via Cloudflare...sometimes that is for illegal downloads:) See attached graphic. bill e.g. -- ===================================== William Gabella Research Assistant Professor Department of Physics and Astronomy Vanderbilt University Nashville, TN USA b.gabella(a)vanderbilt.edu (o) 615-343-2713

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Users April 2020