Users September 2022

users@lists.einsteintoolkit.org

15 participants
19 discussions

Regarding configuration of workstation
by Indrani Banerjee 13 Oct '22

13 Oct '22

Hello everyone, I am planning to buy a workstation from my project. Can anyone suggest what should be its minimal configuration so that I can install Einstein Toolkit in it and use it to generate numerical waveforms? Thanks in advance. With best regards, Indrani ********************************************** Indrani Banerjee Assistant Professor Department of Physics & Astronomy, National Institute of Technology, Rourkela Odisha-769008, India email: banerjeein(a)nitrkl.ac.in, indrani.physics1(a)gmail.com **********************************************

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Postdoc position in computational astrophysics
by Agnieszka Janiuk 29 Sep '22

29 Sep '22

Dear colleagues, I am looking for a postdoc candidates working in the area of computational astrophysics. The main focus of our research is gamma ray bursts engines. We study both collapsing massive stars and binary neutron star mergers. The position will be for 2 years. The starting date is negotiable, and funding is available immediately. The announcement is available here on my Institute website: https://www.cft.edu.pl/job-post?x=EiWaTt7eTXbjydfXfk62ICbSKmq1|e4f0131c22f9… Deadline for applications is 28 October 2022. Please forward this email to anybody who you think might be interested! Contact address for further questions: agnes @ cft.edu.pl regards Agnieszka Janiuk -- -- prof. dr hab. Agnieszka Janiuk | tel. +48 22 116 20 06 Center for Theoretical Physics | fax. +48 22 843 13 69 Polish Academy of Sciences | www: https://www.cft.edu.pl/pages/agnieszka-janiuk Al. Lotnikow 32/46 | 02-668 Warsaw, Poland |

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meeting minutes for 2022-09-29
by Roland Haas 29 Sep '22

29 Sep '22

Present: Roland, Steve, Peter, Beyhan, Johnny, Keith, Leo, Sam, Yosef ET testing: * testing has begun * keep test "life" for 1month rather than 1week * would want some volunteers to run on some clusters ** Peter will run at Stockholm * name for next release: Kovalevskaya (https://en.wikipedia.org/wiki/Sofya_Kovalevskaya) * open questions: ** Roland to respond to http://lists.einsteintoolkit.org/pipermail/users/2022-August/008667.html suggest to write a basic SLURM Cactus batch * open tickets: ** Peter will run tests runs on https://bitbucket.org/einsteintoolkit/tickets/issues/963/improve-mclachlan-… ** urgently need reviewer for https://bitbucket.org/einsteintoolkit/tickets/issues/2647/incorrect-weno-co… ** Leo has fix for https://bitbucket.org/einsteintoolkit/tickets/issues/2642/toolkit-fails-to-… and will apply it and close the ticket chair next week: Peter note taker: Johnny 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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Einstein Toolkit Meeting Reminder
by reminders＠einsteintoolkit.org 28 Sep '22

28 Sep '22

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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Agenda for Thursday's Meeting
by reminders＠einsteintoolkit.org 26 Sep '22

26 Sep '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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Computing Apparent Horizons
by Mario Imbrogno 24 Sep '22

24 Sep '22

Dear Einstein-Toolkit community, my name is Mario Imbrogno and I am a Ph.D. student at the University of Calabria (UniCal, Cosenza, Italy) under the supervision of prof. Sergio Servidio. Our research group had developed a spectral code to solve the Einstein equations via a pseudo-spectral technique [Meringolo C, Servidio S, and Veltri P "A spectral method algorithm for numerical simulations of gravitational fields." Classical and Quantum Gravity 38.7 (2021): 075027], and I am studying different cases of merging two and more black holes, in vacuum conditions. Now I have to compute the apparent horizons (AHs) just for our initial conditions, and I have read that the Einstein Toolkit implements the AHFinderDirect, a code that can detect the AHs. My questions are: is there a way to compute such AHs by, just uploading our 3D cartesian BSSN fields and using the AHFinderDirect code? Who is(are) the user(s) that mainly use(s) such code? Who can I ask? Where can I find a detailed guide in which I can learn how to upload my data using the AHFinderDirect code? If someone will help us, there is no problem for us to include as a co-author of our paper. Best regards, Mario Imbrogno

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Issue with black hole binary evolution employing IGM
by Federico Cattorini 23 Sep '22

23 Sep '22

Hello Erik, Thanks for your reply. I followed your suggestions and found two strings that may be indicative of what's going on. In the standard outputs 'CCTK_Proc14.out' and 'CCTK_Proc15.out' the last lines read INFO (IllinoisGRMHD): Font fix failed! INFO (IllinoisGRMHD): i,j,k = 67 63 16, stats.failure_checker = 0 x,y,z = 3.392857e+00 8.892857e+00 2.392857e+00 , index=111739 st_i = -1.002115e+08 2.298583e+08 -1.221746e+08, rhostar = 1.573103e+02, Bi = -1.064528e+03 1.120144e+03 2.972675e+03, gij = 6.643816e+00 5.521615e-01 4.380688e-01 7.244355e+00 -1.685406e-03 6.830374e+00, Psi6 = 1.803534e+01 I assume this means that there are issues in the con2prim of IGM. That INFO is printed by harm_primitives_lowlevel.C: // Use the new Font fix subroutine > int font_fix_applied=0; > if(check!=0) { > font_fix_applied=1; > CCTK_REAL u_xl=1e100, u_yl=1e100, u_zl=1e100; // Set to insane > values to ensure they are overwritten. > if (gamma_equals2==1) { > check = > font_fix_gamma_equals2(u_xl,u_yl,u_zl,CONSERVS,PRIMS,METRIC_PHYS,METRIC_LAP_PSI4,eos); > } else { > check = > font_fix_general_gamma(u_xl,u_yl,u_zl,CONSERVS,PRIMS,METRIC_PHYS,METRIC_LAP_PSI4,eos); > } > //Translate to HARM primitive now: > prim[UTCON1] = METRIC_PHYS[GUPXX]*u_xl + METRIC_PHYS[GUPXY]*u_yl + > METRIC_PHYS[GUPXZ]*u_zl; > prim[UTCON2] = METRIC_PHYS[GUPXY]*u_xl + METRIC_PHYS[GUPYY]*u_yl + > METRIC_PHYS[GUPYZ]*u_zl; > prim[UTCON3] = METRIC_PHYS[GUPXZ]*u_xl + METRIC_PHYS[GUPYZ]*u_yl + > METRIC_PHYS[GUPZZ]*u_zl; > if (check==1) { > CCTK_VInfo(CCTK_THORNSTRING,"Font fix failed!"); > CCTK_VInfo(CCTK_THORNSTRING,"i,j,k = %d %d %d, > stats.failure_checker = %d x,y,z = %e %e %e , index=%d st_i = %e %e %e, > rhostar = %e, Bi = %e %e %e, gij = %e %e %e %e %e %e, Psi6 = > %e",i,j,k,stats.failure_checker,X[index],Y[index],Z[index],index,mhd_st_x_orig,mhd_st_y_orig,mhd_st_z_orig,rho_star_orig,PRIMS[BX_CENTER],PRIMS[BY_CENTER],PRIMS[BZ_CENTER],METRIC_PHYS[GXX],METRIC_PHYS[GXY],METRIC_PHYS[GXZ],METRIC_PHYS[GYY],METRIC_PHYS[GYZ],METRIC_PHYS[GZZ],METRIC_LAP_PSI4[PSI6]); > exit(1); // Let's exit instead of printing potentially GBs of log > files. Uncomment if you really want to deal with a mess. > } > } > stats.failure_checker+=font_fix_applied*10000; > stats.font_fixed=font_fix_applied; > Can I do anything that may help pinpoint the cause of this error? Thanks in advance, Federico Il giorno gio 15 set 2022 alle ore 15:30 Erik Schnetter <schnetter(a)gmail.com> ha scritto: > Federico > > Thanks for including the output, that is helpful. > > There are parameters "Carpet::verbose" and "Carpet::veryverbose". You > can set them to "yes" and recover from a checkpoint. This gives more > information about what the code is doing, and thus where it crashes. > > The output you attached is only from the first MPI process. Other > processes' output might contain a clue. You can add the command line > option "-roe" to Cactus when you run the simulation. This will collect > output from all processes. > > -erik > > On Thu, Sep 15, 2022 at 9:20 AM Federico Cattorini > <f.cattorini(a)campus.unimib.it> wrote: > > > > Hello everyone, > > > > I am experiencing some issue in a number of GRMHD simulations of black > hole binaries employing IllinoisGRMHD. > > > > As an example, I will write about an unequal-mass BHB configuration > (with q = 2) that I'm running. > > > > After approximately ten orbits, the run stops with no error codes or any > other message that could help me identify the issue. The last lines of the > standard output are > > > > INFO (IllinoisGRMHD): ***** Iter. # 353949, Lev: 9, Integrating to time: > 3.160260e+03 ***** > > INFO (IllinoisGRMHD): C2P: Lev: 9 NumPts= 569160 | Fixes: Font= 393 VL= > 179 rho*= 2 | Failures: 0 InHoriz= 0 / 0 | Error: 7.124e-02, ErrDenom: > 4.838e+13 | 4.51 iters/gridpt > > INFO (IllinoisGRMHD): ***** Iter. # 353949, Lev: 9, Integrating to time: > 3.160269e+03 ***** > > Simfactory Done at date: gio 04 ago 2022 11:43:01 CEST > > > > > > > > I tried restarting my simulation from the latest checkpoint, but the > same sudden stop occurred at the same timestep. > > > > At first, I thought about some problem with IGM. The last INFO is > printed by IllinoisGRMHD_driver_evaluate_MHD_rhs.C, so I put some prints in > it to identify the spot where the error occurs. > > Unfortunately, I drew a blank, since the stop seems to occur just after > the end of IllinoisGRMHD_driver_evaluate_MHD_rhs: > > > > INFO (IllinoisGRMHD): ***** line 52: entering > IllinoisGRMHD_driver_evaluate_MHD_rhs ***** > > INFO (IllinoisGRMHD): ***** Iter. # 353949, Lev: 10, Integrating to > time: 3.160251e+03 ***** > > INFO (IllinoisGRMHD): ***** line 100: > IllinoisGRMHD_driver_evaluate_MHD_rhs ***** > > INFO (IllinoisGRMHD): ***** line 204: just before > reconstruct_set_of_prims_PPM ***** > > INFO (IllinoisGRMHD): ***** DEBUG END of > IllinoisGRMHD_driver_evaluate_MHD_rhs ***** > > Simfactory Done at date: gio 04 ago 2022 19:44:55 CEST > > > > > > I tried to restart the simulation and run it on pure MPI. It ran for a > few more iterations, then stopped as well: > > > > INFO (IllinoisGRMHD): ***** line 52: entering > IllinoisGRMHD_driver_evaluate_MHD_rhs ***** > > INFO (IllinoisGRMHD): ***** Iter. # 353565, Lev: 10, Integrating to > time: 3.156831e+03 ***** > > INFO (IllinoisGRMHD): ***** line 100: > IllinoisGRMHD_driver_evaluate_MHD_rhs ***** > > INFO (IllinoisGRMHD): ***** line 204: just before > reconstruct_set_of_prims_PPM ***** > > INFO (IllinoisGRMHD): ***** DEBUG END of > IllinoisGRMHD_driver_evaluate_MHD_rhs ***** > > Simfactory Done at date: ven 05 ago 2022 19:00:13 CEST > > > > > > The simulation setup is as follows: > > > > Allocated: > > Nodes: 10 > > Cores per node: 48 > > SLURM setting > > SLURM_NNODES : 10 > > SLURM_NPROCS : 20 > > SLURM_NTASKS : 20 > > SLURM_CPUS_ON_NODE : 48 > > SLURM_CPUS_PER_TASK : 24 > > SLURM_TASKS_PER_NODE: 2(x10) > > Running: > > MPI processes: 20 > > OpenMP threads per process: 24 > > MPI processes per node: 2.0 > > OpenMP threads per core: 1.0 > > OpenMP threads per node: 48 > > > > > > while the pure-MPI setup is > > > > Allocated: > > Nodes: 10 > > Cores per node: 48 > > SLURM setting > > SLURM_NNODES : 10 > > SLURM_NPROCS : 480 > > SLURM_NTASKS : 480 > > SLURM_CPUS_ON_NODE : 48 > > SLURM_CPUS_PER_TASK : 1 > > SLURM_TASKS_PER_NODE: 48(x10) > > Running: > > MPI processes: 480 > > OpenMP threads per process: 1 > > MPI processes per node: 48.0 > > OpenMP threads per core: 1.0 > > OpenMP threads per node: 48 > > > > > > I am using The Lorentz version of ET. > > > > I've had this issue for two binary BH simulations, both unequal-mass > with q = 2. My colleague Giacomo Fedrigo experienced the same problem > running an equal-mass simulation. > > > > I attach the q = 2 (s_UUmis_Q2) parameter file and the ET config-info > file. Also, I attach the st. error and output of my q = 2 run and of > Giacomo's run (b1_UUmis_a12b_pol3_r56_gauss_9). The st. outputs were cut > for readability reasons. > > > > Can someone please help me with this? > > > > Thanks in advance, > > > > Federico > > _______________________________________________ > > Users mailing list > > Users(a)einsteintoolkit.org > > http://lists.einsteintoolkit.org/mailman/listinfo/users > > > > -- > Erik Schnetter <schnetter(a)gmail.com> > http://www.perimeterinstitute.ca/personal/eschnetter/ >

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Meeting Minutes 2022-09-22
by Bruno Giacomazzo 22 Sep '22

22 Sep '22

Present: Leo Werneck (chair), Bruno Giacomazzo (minute taker), Steven Brandt, Beyhan, Peter Diener, Gabriele Bozzola, Keith, Roland Haas, Samuel Cupp, Zachariah Etienne *1) vote on modules suggested for inclusion for the next release* *1a) Canuda scalar and complex fields* -- proposed by Miguel Zilhao Zach asks if it was reviewed since he didn't hear anything recently. Roland said that the review finished. No one opposed the inclusion. *1b) FLRW solver* -- proposed by Hayley Macpherson No one opposed the inclusion. *1c) SelfForce-1D* -- proposed by Samuel Cupp Peter mentioned that there are new functionalities that have been added. Roland asked if there are new examples, but Peter said no. Steve asked for examples with movies. No one opposed the inclusion. *1d) NRPyEllipticET* -- proposed by Leo Werneck, Thiago Assumpcao, Zach Etienne Roland mentioned that there are no test cases included with it. No one opposed the inclusion with the condition that at least a test case is added. Leo mentioned that some documentation of WVUThorns does not show correctly online and Roland said that html latex is stricter than pdflatex when checking latex syntax. *2) ET release* Roland said that is coming up in November, all thorns compile, and all tests pass. Test results are available on http://einsteintoolkit.org/testsuite_results/index.php Steve reminded people that the subversion servers are going to be switched off. There seems to be only one still used and maybe it is time to move to another versioning system any repository still on svn. Gabriele said that kuibit will soon require python 3. Zach mentioned that NRPy will continue to support python 2 since python 2 is still used on many HPC systems. Steve suggested checking which is the default version of python available in the clusters we use. *4) unanswered question on mailing list* Regarding configuration of workstation (Indrani Banerjee): no volunteer found to answer this question yet. Not clear whether it would be possible to compute waveforms on a workstation. *5) open tickets sorted by update time* The following tickets were discussed: #2644: NaNs in ADMBASE metric components with RNSID -> no volunteer found #2642: Toolkit Fails to Compile on Sawtooth (Idaho National Lab) -> it seems that C++ 14 standard is needed and this should solve the issue. #2643: Adding read/write declarations to Meudon ID thorns -> it is a pull request (please have a look) #2641: ML_BSSN macro usage bypasses personalized read/write macros *6) tickets ready for review* #2630: WaveMoL example computes energy from unsynchronized grid variables #181: AEILocalInterp should not off-centre the interpolation stencil by default #2364: avoid opening and closing HDF5 files multiple times during output #963: Improve McLachlan accuracy No comment on any of these tickets. *7) Other comments* Zach said that the update to Baikal will be a regular update (as suggested by Roland) and he will open a pull request. Next Chair: Steve Next Minute Tacker: Roland

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Einstein Toolkit Meeting Reminder
by reminders＠einsteintoolkit.org 21 Sep '22

21 Sep '22

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Agenda for Thursday's Meeting
by reminders＠einsteintoolkit.org 19 Sep '22

19 Sep '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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