Users June 2020

users@lists.einsteintoolkit.org

12 participants
23 discussions

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

29 Jun '20

Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers

1 0

CST error
by Bilal Hameed 29 Jun '20

29 Jun '20

I am trying to install new version of ET in jupyter notebook. I followed the instructions but get CST errors as in the screenshot.

2 4

meeting minutes for 2020-06-25
by Roland Haas 25 Jun '20

25 Jun '20

Present: Roland, Federico, Steve, Peter S., Miguel, Yosef, Maria, Zach emails rejected by mailing lists * affects also University accounts that are outsourced GMail * 4 known cases that contacted people personally, most likely many more * Steve and Roland will look into this gallery testing * BNS: runs were done, need to be uploaded * BBH: Atul and Peter S. working on plots ** Peter S. asked about files with horizon meshes, in VTK files ** Peter S. asked about detail of horizons and which ones exist. 1&2 are intiial apparent horizons, 3 is the one that forms around the 2 and co-exists for a while gcc-10 / gfortran-10 * needs reviewers urgently * https://bitbucket.org/einsteintoolkit/tickets/issues/2431/review-changes-re… test.cactuscode.org conversion to gh-pages * not much progress yet * Ian converted thornguide list pages * issues: https://github.com/EinsteinToolkit/cactuscode.org/issues?q=is:open+is:issue… Online ET workshops * August 3-7th as was originally planned for the on-site workshop * https://www.cct.lsu.edu/Einsteintoolkitworkshop * calling for volunteers * please suggest suggestions to Steve * Yosef has notes and screencast for wave equation, would be ok to give short tutorial * Roland can give a tutorial on how to use the reduction interface in running code * Zach will give a NRPy+ tutorial * will have talks as well slow Baikal compilation * Zach split's source code following Erik's advise to move inlined FD calculations to function calls * this reduced compile time by a factor of ~400 * code generation time is ~2 times faster * run speed unaffected There will not be an ET call on July 2nd. The next call will be July 9th 2020. 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 .

1 0

Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 24 Jun '20

24 Jun '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

1 0

Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 22 Jun '20

22 Jun '20

Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers

1 0

Fwd: Using finite temperature EOS with GRHydro in BNS simulation
by rhaas＠illinois.edu 21 Jun '20

21 Jun '20

> ---------- Forwarded message --------- From: Beyhan Karakaş <beyhannkarakas(a)gmail.com> Date: Sat, Jun 20, 2020 at 7:34 PM Subject: Using finite temperature EOS with GRHydro in BNS simulation To: Einstein Toolkit Users <users(a)einsteintoolkit.org> Dear to whom it may concern, I am using Turing release on Fedora 31. I have been trying to perform a binary neutron star merger simulation via finite temperature equation of state (might be misleading) with GRHydro. As far as I can see, this question was replied by Roland previously in http://lists.einsteintoolkit.org/pipermail/users/2019-February/006756.html. Parameters were added as has been suggested but If Meudon_BNS_ID does not refer to source code of Meudon_Bin_NS then I could not find where Meudon_BNS_ID or Meudon_Bin_NS ID is located in Cactus, if it does I will try to work on it. In this setting, is it enough to use IOUtil parameter -filereader_ID_vars = "all" - to allow initial temperature, entropy and electron fraction to be read from the file? I have tried to use APR eos with SFH0 eos table from stellarcollapse.org ( https://stellarcollapse.org/~evanoc/Hempel_SFHoEOS_rho222_temp180_ye60_vers… ) and got "EOS errori n prim2con_hot" in this setting and do not know how this might be overcomed. Besides that, I suppose WhiskyTHC allows nuclear eos table to be used with Lorene initial data by providing this table in pizza format and uses some conversion of units but do not know what will be needed for Einstein Toolkit. Parameter, error and output files are attached. Best regards, Beyhan. -- 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 .

3 3

Re: [Users] [ET Trac] #2414: include con2prim framework by Siegel, Moesta et al. into ET
by Vasileios Paschalidis 18 Jun '20

18 Jun '20

Hi Roland and Zach, Just saying that my students Pedro Espino and Gabriele worked on this. We already have a working code that is interfaced with ILGRMHD, but the interface is generic enough and should be straightforward to include it in other codes as well. It is a summer project for us. There are some final outstanding issues that we need to iron out, and as soon as we are happy with it, our goal is to work with you and share the code with the ET. Cheers, Vasilis On Thu, Jun 18, 2020, 9:04 AM Roland Haas <trac-noreply(a)einsteintoolkit.org> wrote: > #2414: include con2prim framework by Siegel, Moesta et al. into ET > Reporter: Roland Haas > Status: new > Milestone: > Version: > Type: proposal > Priority: major > Component: EinsteinToolkit thorn > > Comment (by Roland Haas): > > Relevant bits from today’s ET call minutes ( > http://lists.einsteintoolkit.org/pipermail/users/2020-June/007479.html): > > Other groups are ading these methods, like Gabriele Bozzola to > IllinoisGRMHD, and Wolfgang Kastaun is also working on these methods. > Wolfgang's method has > a proof of solution to roots...if it has a solution. ZE, often with AMR > the conservatives can be ill-valued. His code has a lot of dependencies, > Boost, Ninja, etc. > > ZE, the ideal interface for any GRMHD code is not a con2prim solver that > does everything at all points, but one where you call it and it does it at > one point. > Convenient if you can do it in one OpenMP loop, so the point-by-point is > better. Suppose it fails to find a root, if it fails fall-back to another > method. Make the interface a point-wise method. RH agrees. But > point-wise is maybe the > other extreme, you may want that it takes a 1D array of data and then > flags individual SIMD-parallelization a Newton-Raphson method. ZE, in some > cases it is > faster to us a quartic solver in some cases. > > RH, if this is a summer project for other groups with an end time, suggest > waiting until the end of summer to see what their results are. > > ‌ > > -- > Ticket URL: > https://bitbucket.org/einsteintoolkit/tickets/issues/2414/include-con2prim-… > _______________________________________________ > Trac mailing list > Trac(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/trac >

1 0

Meeting Minutes 2020-06-18
by Bill Gabella 18 Jun '20

18 Jun '20

Present: Steve B, Bill G, Roland H, Peter D, Peter S, Atul K, Mario GA, Federico C, Miguel G, Antoni RB, Yosef Z, Liu H, Zach E, Maria H Chair: Steve Minutes: Bill * gcc 10 issues [RH] RH, good news collected bits and pieces for compiling on gcc 10 and gfortran 10 and working on his workstation, patch to flesh, patch to cactus test repos, to event horizon finder, patches to GRHydro and XXX due to inconsistent types, more wrong than before but at least consistent, so the compiler is happy, LAPACK to newest version, patch to HDF5 that we check out, compiles and running the testsuite on many machines. We can backport these changes. This is the most trouble with a new compiler release. Have had compilers change on us, like gcc 4 to 5 where inline syntax changed. These seems to be the worst compiler upgrade we have had. ** 2403, https://bitbucket.org/einsteintoolkit/tickets/issues/2403 ** also affects CCTK_Reduce subroutines which is already incorrect F77 since they are variadic functions which FORTRAN never supported. Real world examples where this fails are known and were reported in 2004, http://cactuscode.org/pipermail/users/2004-September/001224.html by Roberto de Pietri. ** also affects EOS_Omnik, GRHydro [RH] * reviewers for proposed inclusions [RH] ** ReadInterpolate https://github.com/rhaas80/ReadInterpolate.git thorn ticket 2416 https://bitbucket.org/einsteintoolkit/tickets/issues/2416 no reviewer Takes 3d output from cactus and interpolates onto a different cactus grid. Uses AI Local Interp and not much internals of Cactus. Is a testsuite but no good documentation. Yosef is interested in this thorn and could review. Steve B wants to come up with Obscure Cactus Knowledge question for the meetings. Educational and spreads the knowledge base, should encourage humorous answers from us illiterati. ** POWER https://git.ncsa.illinois.edu/elihu/Gravitational_Waveform_Extractor ticket 2413 https://bitbucket.org/einsteintoolkit/tickets/issues/2413 Zach is reviewer waveform extractor (or its post-summer versions) [RH] ** con2prim methods https://arxiv.org/abs/1712.07538 ticket 2414 https://bitbucket.org/einsteintoolkit/tickets/issues/2414 Maria is reviewer [RH] Other groups are aiding these methods, like Federico Cipoletta to GRHydro, and Wolfgang XX is also working on these methods. Wolfgang's method has a proof of solution to roots...if it has a solution. ZE, often with AMR the conservatives can be ill-valued. His code has a lot of dependencies, Boost, Ninja, etc. ZE, the ideal interface for any GRMHD code is not a con2prim solver that does everything at all points, but one where you call it and it does it at one point. Convenient if you can do it in one OpenMP loop, so the point-by-point is better. Suppose it fails to find a root, if it fails fall-back to another method. Make the interface a point-wise method. RH agrees. But point-wise is maybe the other extreme, you may want that it takes a 1D array of data and then flags individual SIMD-parallelization a Newton-Raphson method. ZE, in some cases it is faster to us a quartic solver in some cases. RH, if this is a summer project for other groups with an end time, suggest waiting until the end of summer to see what their results are. ** NRPyPN https://nbviewer.jupyter.org/github/zachetienne/nrpytutorial/blob/master/NR… ticket 2417 https://bitbucket.org/einsteintoolkit/tickets/issues/2417 no reviewer Steve says he might review this, and Peter D says he can help. ZE, has made a couple of modifications. And Antoni RB has shared their Mathematica notebook with Zach and testing NRPyPN and has not found any errors. Techniques in the two efforts is different, particularly the radial component to inject in two punctures. Useful with permission, to copy the method from the Antoni et al. notebook. ARB, will look at NRPyPN next week and compare with our expression. There is some freedom in some coefficients, but in the end Zach's method will work better in some parts of parameter space, and will compare. * gallery testing: tasks https://bitbucket.org/einsteintoolkit/tickets/issues?kind=task&milestone=ET… [RH] ** BNS: Shawn Rsofsky (UIUC). In progress, needs to be uploaded, some differences post-merger. Shawn has done the simulation and plots but has not uploaded the data. RH re-ran it and does get the same waveforms, so the plots will not change. **BBH: Peter Schaffarczyk (KEIL), Atul Kedia (Notre Dame) in progress Peter S, took more time than expected. Configure a new machine in Berlin. Is over with same time, and working on the graphics and figures. Gnuplot graphics are finished. Made afigure of the horizons and looks a little different than the main page and discussing that. Atul, Figures for Curvature Scalars is taking some time, and Ian Hinder is advising. Focus mainly on the graphics. * test.cactuscode.org issues https://github.com/EinsteinToolkit/cactuscode.org/issues?q=is:open+is:issue… [SB] Nine critical issues at the above link. SB advocates for not have the Link to Live Wavetoy Example, https://github.com/EinsteinToolkit/cactuscode.org/issues/17 . General agreement. RH, fine to remove Live example, may on the other hand take the 1D scalar wave equation into a Jupyter notebook and run on the tutorial server. JPEG thorn should still work. Have a cell that opens the Jpeg file. SB says had trouble compiling it. SB, it would be nice to grow our collection of notebooks for tutorials in general. * Online ET Workshop https://www.cct.lsu.edu/Einsteintoolkitworkshop [SB] SB, not having an in-person event in August, very minimally we should have a training for new users. Live instructors. Good to have some talks too, work being done with the toolkit, state of AMRex at that time. Looking for help and suggestions. ZE, would student talks be good? Have a student working on ETK. SB, that would be great. Like to see NRPy tutorials. ZE, have a collection of tutorials about constructing thorns. SB, think about things you would like to present. Putting together an agenda. For online event maybe 3 hours a day is the limit. * Next chair(s) and minute taker(s) 6-25 Chair Peter S.; Minute taker Roland 7-02 Chair Roland; Minute taker Steve * Other issues? MH asks about con2prim. RH, Univ. of Arizona talking with Zach about Illinois GRMHD code modifications. Will wait for results at end of summer. MH your (SB) Christmas Tree? SB, too lazy to take it down (and put back up?)---so keep it unplugged until Christmas time. ZE, Quick update, recent update bug fix to Baikal on very special numbers of API process there was an interface with the boundary thorn that caused an exit and that is fixed. Also other issue that with gcc 9+ Bailkal takes a long time to compile. So refactored the code and properly doc-tested and had one successful expt with scalar wave with calculation not done inline but by function call and do not see a performance hit. Hopefully next week can report that it is compiling fine/faster on gcc 9+ . * unanswered questions on mailing list https://www.einsteintoolkit.org/tools/unanswered.php No unanswered email found. * open tickets sorted by update time https://bitbucket.org/einsteintoolkit/tickets/issues?status=open&status=new… Tkt 2418 https://bitbucket.org/einsteintoolkit/tickets/issues/2418/have-declare_cctk… not entirely clear what you want the macro to do, discuss offline. RH, intended as a discussion item, could add extra checks to Cactus. * tickets ready for review https://bitbucket.org/einsteintoolkit/tickets/issues?status=new&status=open… --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

1 0

Re: [Users] Einstein toolkit installation issues
by Roland Haas 18 Jun '20

18 Jun '20

Hello Camilo, you are affected by gfortran-10 and gcc-10 reporting errors for code that compiled by gfortran-9 and gcc-9. You can either try and uninstall gcc-10 and gfortran-10 or, most likely easier, edit the file simfactory/mdb/optionlists/generic-mp-10.cfg and change all gfortran-10, gcc-10, g++-10 to gfortran-9, gcc-9, g++-9 then reconfigure once more using the modified option list: simfactory/bin/sim build --reconfig --optionlist simfactory/mdb/optionlists/generic-mp-10.cfg There are also options you can add to F90FLAGS, CFLAGS, CXXFLAGS and LDFLAGS to have gfortran-10 and gcc-10 revert to the old behaviour. Please see these ET tickets for details: https://bitbucket.org/einsteintoolkit/tickets/issues/2403/compile-failure-w… https://bitbucket.org/einsteintoolkit/tickets/issues/2406/cactus-fails-to-l… The fixes developed in there and in a couple of other tickets (since the options are not a solution for the general case since they are compiler version specific) will be backported to the release branch as soon as they are fully tested and reviewed. Yours, Roland > Dear Roland, > > I removed the file campos(a)MacBook.ini, then I run echo >..., and ru > n ./simfactory..., and it started to compile. It seems it finished with no problems (picture 12.06.24). When I tried to build the toolkit using the j2 option, it produced an error (picure 12.07.05) related to the Xcode, so I typed the command suggested by the error but at the end of the process it produced an error (pic 12.09.36) > > I started the whole process again, updating the Xcode, refreshing all the prerequisites but I got the same error. I'm not sure if it's connected with the previous error with campos@MacBook. It does not look like though. > > Thank you! > > Best, > Camilo > > ----- Message from Roland Haas <rhaas(a)illinois.edu> --------- > Date: Tue, 16 Jun 2020 16:53:01 -0500 > From: Roland Haas <rhaas(a)illinois.edu> > Reply-To: rhaas(a)illinois.edu > Subject: Re: [Users] Einstein toolkit installation issues > To: Camilo Posada <camilo.posada(a)physics.slu.cz> > > > Hello Camilo, > > > >> Dear Roland, > >> > >> I run the commands you mentioned but I keep getting the following erro > r: > >> > >> > >> Error: specified value campos@MacBook for key nickname does not > >> match converted pattern ^[a-zA-Z0-9_+-\.]+$ > >> > >> I keep seeing the same file: campos(a)MacBook.ini, in the > >> mdb/machines directory, so I believe the problem is there. What do > >> you think? > > > > Well maybe. Depends on whether the file keeps reappearing if you delete > > it, then run > > > > echo >$HOME/.hostname "compos_MacBook" > > > > then run ./simfactory/bin/sim setup-silent again. > > > > The presence of the file alone is not the issue, only if it is actually > > used. > > > > Certainly it cannot hurt to remove it to verify it is not being > > recreated. What has me more confused is that running these two commands > : > > > > echo >$HOME/.hostname "compos_MacBook" > > > > ./simfactory/bin/sim setup-silent > > > > there should have been a file > > simfactory/mdb/machines/compos_MacBook.ini (ie with an underscore). > > > > Yours, > > Roland > > > > -- > > My email is as private as my paper mail. I therefore support > encryptingand signing email messages. Get my PGP key from > http://pgp.mit.edu . > > ----- End message from Roland Haas <rhaas(a)illinois.edu> ----- > Camilo Posada, Ph.D. > Institute of Physics > Silesian University in Opava > Bezručovo nám. 13, CZ-74601 Opava -- 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 .

2 1

Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 17 Jun '20

17 Jun '20

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

Users June 2020