Users July 2020

users@lists.einsteintoolkit.org

13 participants
24 discussions

Accessing the summer school tutorial server
by Alessandro Ciarfella 31 Jul '20

31 Jul '20

Hi, Don't know if this is the right place where to post this question but I'll try. I tried to access the tutorial for the upcoming summerschool at https://etk.cct.lsu.edu <https://etk.cct.lsu.edu/>. However, when I try to click on CILogon I am redirected to a page where I have to sign in my Github account. However, having been registered to the tutorial through my university account ac4870(a)rit.edu <mailto:ac4870@rit.edu> when I try to login through my Github account I get this error message. 403: Forbidden. Alessandro is not authorized. New gmail accounts are not currently being accepted. Please use your university account or Github. How can I solve this issue? Can this be related to the fact that I had previously created a github account to access the Tutorial For New Users on the Einstein relativistic toolkit website? Thanks, Alessandro Ciarfella

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Re: [Users] ET building issues
by Mario Gutierrez Abed (PGR) 31 Jul '20

31 Jul '20

Thanks again Roland, It does seem that your suspicion is correct; it appears that I do have both gcc-10 and gfortran-10 installed, and the Macports selection is being overridden. See the attached text files you requested. Best, Mario -------------------------------------------- Mario L Gutierrez Abed M.L.Gutierrez-Abed2(a)newcastle.ac.uk School of Mathematics, Statistics & Physics Newcastle University On 7/31/20, 12:04, "Roland Haas" <rhaas(a)illinois.edu> wrote: Hello Mario, hmm. Odd. The error message looks like the one gfortran-10 produces. Can you please attach, as a text file, the content of the file configs/sim/config-info as well as the file configs/sim/OptionList ? There is some automatism in simfactory's setup-silent and it will *first* probe for gcc-10 and gcc-mp-10 and only of that does not exist will it use "gcc" (ie the macports select setting is effectively ignored). Can you also please check if you have gfortran-10 installed at all (the executable is called gfortran-mp-10)? If possible, it would be best to keep the conversation on the mailing list by using "reply-all" (I try to set reply-to but sometimes I miss it). Yours, Roland > Thanks Roland, > > I'm actually not using gcc10 or gfortran10; my current versions are gcc 9.3.0 and gfortran 4.8.5 (see attached screenshot). I did make sure to run the command lines: > > sudo port select mpi openmpi-gcc9-fortran > sudo port select gcc mp-gcc9 > > as indicated on the tutorial notebook. > > Best, > Mario > > -------------------------------------------- > Mario L Gutierrez Abed > M.L.Gutierrez-Abed2(a)newcastle.ac.uk > School of Mathematics, Statistics & Physics > Newcastle University > > > > > On 7/31/20, 11:18, "Roland Haas" <rhaas(a)illinois.edu> wrote: > > Hello Mario, > > are you compiling using gcc-10 and gfortran-10 by any chance? > > Then please see here for a workaround: > > https://bitbucket.org/einsteintoolkit/tickets/issues/2403/compile-failure-w… > > https://bitbucket.org/einsteintoolkit/tickets/issues/2406/cactus-fails-to-l… > > basically by adding -fcommon and -fallow-argument-mismatch to the > compiler flags. > > The tutorial notebook > > https://github.com/nds-org/jupyter-et/blob/master/CactusTutorial.ipynb > > also contains information on the workaround. > > A proper fix is ready to be deployed to the released code but we were > holding off until after the workshop to not accidentally introduce more > (unknown) issues on top of the one for which we have a workaround. > > Yours, > Roland > > > Hi, > > > > I’m setting up the ET for the first time in preparation for the upcoming workshop tutorials, and I’ve ran into some “mismatch” issues (see attached screenshot) upon executing the following command line: > > > > ./simfactory/bin/sim build -j2 --thornlist ../einsteintoolkit_08_2020.th > > > > The error messages give no indication whatsoever as to how to fix them, so I’m at a loss here. Any help would be much appreciated. > > > > Best, > > Mario > > > > -------------------------------------------- > > Mario L Gutierrez Abed > > M.L.Gutierrez-Abed2(a)newcastle.ac.uk > > School of Mathematics, Statistics & Physics > > Newcastle University > > > > [A screenshot of a cell phone Description automatically generated] > > > > > -- > 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 . > -- 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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ET building issues
by Mario Gutierrez Abed (PGR) 31 Jul '20

31 Jul '20

Hi, I’m setting up the ET for the first time in preparation for the upcoming workshop tutorials, and I’ve ran into some “mismatch” issues (see attached screenshot) upon executing the following command line: ./simfactory/bin/sim build -j2 --thornlist ../einsteintoolkit_08_2020.th The error messages give no indication whatsoever as to how to fix them, so I’m at a loss here. Any help would be much appreciated. Best, Mario -------------------------------------------- Mario L Gutierrez Abed M.L.Gutierrez-Abed2(a)newcastle.ac.uk School of Mathematics, Statistics & Physics Newcastle University [A screenshot of a cell phone Description automatically generated]

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Meeting Minutes 2020-07-30
by Steven R. Brandt 30 Jul '20

30 Jul '20

Present: Roland, Steve, Zach, Peter, Maria, Miguel Garcia, Atul Kedia, Bilal Hameed, Yosef Workshop: - Looking for Panel ideas - Talk about Gravitational wave extraction and post-processing - Panel idea: Near Future Problems for Numerical Relativity Gallery Testing - Sean had to move last week, did not have time - Atul and Peter started updated the website (index.html) + Will add details on how to generate plots + Peter wanted to add another plot Gcc 10 struggle - Made new release branch, run test suites - Ready for the next point release - Release will happen after the workshop No unanswered questions Usual open tickets

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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 29 Jul '20

29 Jul '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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Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 27 Jul '20

27 Jul '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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problems about binary neutron star simulations
by HUI Hon Ka 24 Jul '20

24 Jul '20

Dear all, I encountered some problem while carrying out some binary neutron star simulations and would like to know if anyone can help me out. I followed the BNS example on the site (nsnstohmns) but adopted the "Hybrid" eos for the BNS Meudon initial data generated with certain tabular nuclear models. #####-----#####-----#####-----#####-----#####-----#####-----#####-----#####-----##### Problem 1: I understand that I need to assign the following parameters accordingly, Meudon_Bin_NS::eos_table = "Hybrid" EOS_Omni::hybrid_gamma_th EOS_Omni::n_pieces EOS_Omni::hybrid_k0 EOS_Omni::hybrid_gamma[] EOS_Omni::hybrid_rho[] but I am not sure whether it is correct to also set GRHydro::GRHydro_eos_table = "Hybrid" ? or should I set GRHydro::GRHydro_eos_table = "Ideal_Fluid" ? In the BNS example nsnstohmns, despite using a polytropic BNS model, the parameter file shows GRHydro::GRHydro_eos_type = "General" instead of "Polytype" GRHydro::GRHydro_eos_table = "Ideal_Fluid" instead of "2D_Polytrope" What is the particular reason for this setting ?? #####-----#####-----#####-----#####-----#####-----#####-----#####-----#####-----##### Problem 2: Here is one of the error I encountered. WARNING level 1 from host emc4 process 0 in thorn CarpetLib, file /home/hkhui/Cactus/configs/sim/build/CarpetLib/dh.cc:161: -> /home/hkhui/Cactus/configs/sim/build/CarpetLib/dh.cc:837: [ml=0 rl=7 c=0] The following grid structure consistency check failed: Refinement prolongation: All points must have been received needrecv.empty() WARNING level 1 from host emc4 process 0 in thorn CarpetLib, file /home/hkhui/Cactus/configs/sim/build/CarpetLib/dh.cc:161: -> /home/hkhui/Cactus/configs/sim/build/CarpetLib/dh.cc:983: [ml=0 rl=7 c=0] The following grid structure consistency check failed: Synchronisation and boundary prolongation: All points must have been received needrecv.empty() It seems this error is associated with the following settings in the parfile CoordBase::xmin = 0.00 CoordBase::ymin = -396.00 CoordBase::zmin = 0.00 CoordBase::xmax = +396.00 CoordBase::ymax = +396.00 CoordBase::zmax = +396.00 CoordBase::dx = 9.00 CoordBase::dy = 9.00 CoordBase::dz = 9.00 CarpetRegrid2::num_levels_1 = 7 CarpetRegrid2::position_x_1 = 15.1875 CarpetRegrid2::radius_1[1] =240.0 CarpetRegrid2::radius_1[2] =120.0 CarpetRegrid2::radius_1[3] = 60.0 CarpetRegrid2::radius_1[4] = 28.125 # nsnstohmns 26.125 CarpetRegrid2::radius_1[5] = 19.875 # nsnstohmns 17.875 CarpetRegrid2::radius_1[6] = 11.0 # nsnstohmns 13 The initial size of the stars of my model: Coordinate separation between the two stellar centers : 45 km Coordinate equatorial radius (phi=0) a1 = 10.16960419148 km Coordinate equatorial radius (phi=pi/2) a2 = 9.872118702179 km Coordinate equatorial radius (phi=pi): 10.19931065979 km Coordinate polar radius a3 = 9.925176860927 km I used the nsnstohmns parfile while changing the eos part and the resolution only, for the set of par above, I set [5] and [6] so that they together cover the separation (19.875+11 M > 45km) and I set [4] so that this refinement region of the 1st star cover some region of the 2nd star. I would like to know if there is any rule for setting the AMR region (the radius par above), I varied these radius parameters and end up with either error about the grid structure (see above err message) or the c2p conversion error, but never been able to carry out simulation to merger. If the problem is not about the AMR region radius setting, what could be the problem? #####-----#####-----#####-----#####-----#####-----#####-----#####-----#####-----##### Problem 3: I have carried the BNS simulation with stars of slightly larger R initially with my nuclear eos, and adopted exactly the same parfile setting as nsnstohmns with Time::dtfac = 0.35, it happens that the NSTracker thorn loses track of the stars. The rho_max position suddenly moved so fast that I suspect the result is wrong. And the position of the star is not updated anymore after certain time step. What could cause such false result?? ----------------------------------------------------------------------------------------------------------------------- Iteration Time | *me_per_hour | GRHYDRO::dens | *ROBASE::rho | *::w_lorentz | *STRAINTS::H | *axrss_mb | | sum maximum | maximum | maximum | maximum | maximum ----------------------------------------------------------------------------------------------------------------------- INFO (NSTracker): Found star at (15.1875,0.28125,0) 200 4.922 | 113.9376773 | 0.0001258 0.0027456 | 0.0011040 | 1.3729137 | 0.0031954 | 989 INFO (NSTracker): Found star at (15.1875,0.5625,0) 400 9.844 | 114.5209435 | 0.0001258 0.0026962 | 0.0011407 | 1.5612539 | 0.0050456 | 991 INFO (NSTracker): Found star at (15.1875,0.84375,0) 600 14.766 | 114.7115204 | 0.0001259 0.0014155 | 0.0006785 | 1.6008531 | 0.0038587 | 993 INFO (NSTracker): Found star at (15.1875,1.125,0) 620 15.258 | 114.1468585 | 0.0001259 0.0011319 | 0.0005486 | 1.6009425 | 0.0036545 | 1084 INFO (NSTracker): Found star at (14.9062,1.6875,0) 660 16.242 | 113.7788398 | 0.0001259 0.0007284 | 0.0003032 | 1.6088940 | 0.0033746 | 1084 INFO (NSTracker): Found star at (14.9062,1.96875,0) 668 16.439 | 113.6618707 | 0.0001259 0.0006774 | 0.0002687 | 1.6088572 | 0.0033143 | 1084 INFO (NSTracker): Found star at (14.625,1.96875,0) 672 16.537 | 113.4731182 | 0.0001259 0.0006559 | 0.0002538 | 1.6088969 | 0.0032825 | 1084 INFO (NSTracker): Found star at (14.625,2.25,0) 676 16.636 | 112.2718493 | 0.0001259 0.0006351 | 0.0002415 | 1.6090522 | 0.0032501 | 993 INFO (NSTracker): Found star at (14.625,2.53125,0) 684 16.833 | 112.1253398 | 0.0001259 0.0005958 | 0.0002184 | 1.6093073 | 0.0031844 | 993 INFO (NSTracker): Found star at (14.625,2.8125,0) 688 16.931 | 111.9626309 | 0.0001259 0.0005780 | 0.0002090 | 1.6111194 | 0.0031493 | 993 ... INFO (NSTracker): New star location not set (0.5625,-0.28125,0) because too far from old (13.7812,7.875,0). 884 21.755 | 99.6235324 | 0.0001259 0.0002227 | 0.0000792 | 1.9277784 | 0.0066220 | 1183 INFO (NSTracker): New star location not set (0.84375,0.28125,0) because too far from old (13.7812,7.875,0). 1004 24.708 | 99.9757198 | 0.0001259 0.0001761 | 0.0001082 | 2.0183873 | 0.0088739 | 1183 INFO (NSTracker): New star location not set (1.125,-0.5625,0) because too far from old (13.7812,7.875,0). 1008 24.806 | 100.0596083 | 0.0001259 0.0001782 | 0.0001092 | 2.0194414 | 0.0089929 | 1183 ... INFO (NSTracker): New star location not set (3.9375,-21.375,0) because too far from old (13.7812,7.875,0). 2244 55.223 | 99.3936843 | 0.0001258 0.0000634 | 0.0000347 | 2.5307425 | 0.0051844 | 1189 ... INFO (NSTracker): New star location not set (11.25,-45,33.75) because too far from old (13.7812,7.875,0). 4028 99.127 | 98.5126340 | 0.0001270 0.0000141 | 0.0000075 | 3.0658306 | 0.0034565 | 1190 #####-----#####-----#####-----#####-----#####-----#####-----#####-----#####-----##### Any help will be greatly appreciated.. Yours, Hon-ka -- Open WebMail Project (http://openwebmail.org)

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Meeting Minutes 2020-07-23
by Gracia Linares, Miguel 23 Jul '20

23 Jul '20

Present: Peter D., Roland H., Federico C., Miguel G., Zach E., Steve B., Beyhan, Alois S., Maria H., Bilal Chair: Zach E. Minutes: Miguel G. * Online ET workshop<https://www.cct.lsu.edu/Einsteintoolkitworkshop>, August 3-7 2020 [SB]. * Schedule (https://docs.google.com/spreadsheets/d/11waMmS73k6mxBxQVIC6eZH4hFjLsxVpH_tg…) Steve: Trying to get the agenda together, does not have anything on Friday but a discussion panel could fit. Zach: suggested future directions in numerical relativity (code development like gpu support) as topic. Steve: needs titles and abstracts (Peter D. will send it today) Steve is setting up the new workshop tutorial server, similar to the ETK tutorial. Steve needs volunteers to try the new server (people interested should provide him their email address). Steve: Speakers should send him a list of their technical needs (python packages, thorns, etc.) and all the extra material needed for their tutorials (jupyter notebooks, etc.). Roland: asked if there’s a Workshop tutorial repo… Steve said No but he can do it, he’s still making changes and running tests, eventually will require some cleaning. Steve: Students thinks students should run the workshop tutorial in advance. Steve: Recording the session would be great. Steve: 30 people signed up already. He will send a second announcement to the mailing list soon. * Gallery testing: tasks<https://bitbucket.org/einsteintoolkit/tickets/issues?kind=task&milestone=ET…> [RH] * BNS: In progress, needs to be uploaded, some differences post-merger. Roland: No movie for BNS, hopefully the person in charge will have it soon. * BBH: Peter Schaffarczyk (Kiel), Atul Kedia (Notre Dame) In progress. Peter: editing webpage where they have collected all the material, should be finished soon. * gcc-10 / gfortran-10 [RH] About backporting process: Roland: asked Zach if there any pending backporting for WVUThorns , Boundary fix should go to Master or not? Zach will make a decision and try to make time to patch in a reasonable time frame. * Open tickets No new open tickets. Zach’s student while reading documentation found that the web browser (safari and Chrome) were not rendering the latex equations correctly. The issue could cause missing math symbols . The problem is the Latex to HTML conversion process, done automatically by Jenkins server… Two possible solutions 1) go back to old version, 2) update Jenkins server. Federico C. could help. * Extra questions: Bilal Asked: “Can I solve Einstein's constraints by conformal method using the ETK?” Zach: Elliptic solvers in the toolkit like CT_MultiLevel thorn could be useful. Beyhan——Rotation profile in BNS remnants? Roland: PostCactus wiki page (https://docs.einsteintoolkit.org/et-docs/Analysis_and_post-processing) could be helpful. * Next minute taker and call chair: 07/30/2020: Chair: Roland H. Minute taker: Steven B. * No call on the Workshop week. Call ended. ——————————————— Miguel Gracia, Postdoctoral Researcher, Center for Relativistic Astrophysics, Boggs Bldg. 1-35, Georgia Institute of Technology, 770 State Street, Atlanta, GA, 30313, USA.

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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 22 Jul '20

22 Jul '20

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

20 Jul '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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