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Roundoff errors
by Steven R. Brandt 16 Nov '17

16 Nov '17

Given the recent discussion of roundoff errors and failing tests, I thought I'd share this article I came across on HPCWire. https://www.hpcwire.com/2017/11/13/tensors-come-age-ai-revolution-will-help… --Steve

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Re: [Users] Error in thorn Vectors
by Eloisa Bentivegna 14 Nov '17

14 Nov '17

On 10/11/17 22:34, Hamilton, Maria wrote: > Hello Eloisa, > > This is strange. I did do a fresh checkout and tried to compile it with the > osx-homebrew.cfg but I am getting this error: > > checking for M_PI... no > configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to CPPFLAGS. > > I added the flag to CPPFLAGS, I even added a new flag FDBITSFLAGS="-D_XOPEN_SOURCE=500 which I found on the internet, but the same error persisted. > > I am running Cactus on a Mac Laptop, OSX High Sierra and recommended brewed packages including gcc 7.2.0 > > Please let me know how to fix it. Dear Maria, if you're following a tutorial (say, the one at https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users), please open a ticket to report which set of instructions do not work on your system. For instance, are you using Simfactory? Where exactly did you modify CPPFLAGS? Best, Eloisa

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Joining users email list
by Cupp, Samuel 09 Nov '17

09 Nov '17

Hello, This is Samuel Cupp from LSU. I would like to be added to the users email list. I was told to just email the list to get that to happen. This is the email address I would like added. Thanks in advance! Samuel Cupp

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Re: [Users] About the thorn Einstein exact
by Ian Hinder 09 Nov '17

09 Nov '17

On 5 Nov 2017, at 09:28, Nisa Amir <nisaamir(a)math.qau.edu.pk> wrote: > Actually, when in the einsteinexact thorn there is a mathematica package named EinsteinExact. The documentation said that if you want to add some new space time add the space time in that mathematica package. I want to add non kerr which is in polar coordinates to that package, so that it generates a new thorn but I dont know how to do that. > Kindly guide me. Hi, Yes, you can add a new spacetime to the Metrics package (in Cactus/arrangements/EinsteinExact/m/Metrics/metrics). See the examples in there. For example, Schwarzschild.m: (* ::Package:: *) { "Name" -> "Schwarzschild", "Description" -> "Schwarzschild spacetime", "Dimensions" -> 4, "Coordinates" -> {t, r, \[Theta], \[Phi]}, "Parameters" -> {M}, "Metric" -> {{-1 + 2 M / r, 0, 0, 0}, {0, 1/(1 - 2 M / r), 0, 0}, {0, 0, r^2, 0}, {0, 0, 0, r^2 Sin[\[Theta]]^2}}, "SignDet" -> -1 } The EinsteinExact package then uses this information to generate an exact solution thorn, which can be used for initial data in a numerical relativity evolution. However, it only supports metrics which are explicitly given in Cartesian coordinates, so for example, the Schwarzschild example won't work with it (the Metrics package is generic, and is used also in other contexts, outside EinsteinExact). There is a check in arrangements/EinsteinExact/m/EinsteinExact.m that the metric is in Cartesian coordinates. I suspect that the only reason for this check is that it wouldn't know what Cactus gridfunctions to use for anything else. Since you want to do the evolution in polar coordinates, I assume that you are going to have some mapping between x, y and z, and r, th and ph? I must admit I have never tried to do something like this. There are people on this list who have done evolutions in polar coordinates; maybe one of them could give some advice about whether what you are trying to do is feasible? Maybe you could give more details about what you are trying to do? PS: *please* include users(a)einsteintoolkit.org in the CC when you reply. If you reply just to me, then nobody else benefits from the discussion, and nobody else has the opportunity to help you. -- Ian Hinder http://members.aei.mpg.de/ianhin

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Re: [Users] Error in thorn Vectors
by Eloisa Bentivegna 07 Nov '17

07 Nov '17

On 06/11/17 20:09, Hamilton, Maria wrote: > Hello Eloisa, > > From my memory I'd say I am using the development version. > Is there a way to check this out? Hi! Since the ET is hosted in a collection of repositories, the direct way would be to check which branch of each you're on. Alternatively, you can simply start with a fresh checkout (of, say, the last release) and see if you encounter the same problem. I am posting this to the list in case someone else has a better solution. In any case, please include this information when you open the ticket. > I tried to open ticket at: https://trac.einsteintoolkit.org, but I got this message: > Submission rejected as potential spam I am not sure why this happens. Did you post as anonymous, or included your (institutional) address email in the Reporter field? Eloisa

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meeting minutes for 2017-11-06
by Roland Haas 07 Nov '17

07 Nov '17

Present: Bill, Steve, Roland, Eloisa, Miguel, Chris, Eloisa, Ian, Sam, Qian Tutorial: * needs some work to enable plotting when using console * Bill will test it * expect to get feedback from new users * would like to have it up before supercomputing (next week) ET Jenkins server: * had hardware failure at NCSA, slow to tells users that system is back * should now be back * 6 failing tests ** prolongation one is new, need input from Erik, want trac ticket ** SphericalHarmonicReconGen: could be bug in the reader or in PITTNull code. PITTNull is sensitive to optimization since it includes the full Einstein field equations. Check if using -O3 instead of -Ofast would help. ** have generic.cfg and generic-opt.cfg, get rid of debian.cfg, ubuntu.cfg etc. Working groups: * have sent email to individual (co-)leads for projects to write project description and add to wiki * Steve & Sam have new thornlist to test which thorns work * Eloisa & Helvi have draft of cosmology working group draft. Will have wider review next week. ET call next week: * decide based on agenda by Sunday next week * Eloisa will host if needed Steve will add her to stevenrbrandt.org organization * Steve will send regular reminders Software carpentry style tutorials * interest by persons at NCSA to have software carpentry type tutorials for a scientific code, suggested to use ET tutorials as a starting point * would provide existing tutorials to the person together with some help on how to use them Standing items: * mailing list: Eloisa will contact Maria about what release she is running 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 .

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Error in thorn Vectors
by Hamilton, Maria 06 Nov '17

06 Nov '17

After the last Cactus update, I got this error: Checking status of thorn Vectors COMPILING arrangements/CactusUtils/Vectors/src/vectors.cc In file included from /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors.h:18:0, from /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors.cc:1: /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors-4-SSE.h: In function 'CCTK_REAL4 k4sum(CCTK_REAL4_VEC)': /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors-4-SSE.h:709:29: error: '_mm_hadd_ps' was not declared in this scope CCTK_REAL4_VEC const x2 = _mm_hadd_ps(x1, x1); ^~~~~~~~~~~ /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors-4-SSE.h:709:29: note: suggested alternative: '_mm_add_ps' CCTK_REAL4_VEC const x2 = _mm_hadd_ps(x1, x1); ^~~~~~~~~~~ _mm_add_ps In file included from /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors.h:30:0, from /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors.cc:1: /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors-8-SSE2.h: In function 'CCTK_REAL8 k8sum(CCTK_REAL8_VEC)': /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors-8-SSE2.h:753:29: error: '_mm_hadd_pd' was not declared in this scope CCTK_REAL8_VEC const x2 = _mm_hadd_pd(x1, x1); ^~~~~~~~~~~ /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors-8-SSE2.h:753:29: note: suggested alternative: '_mm_add_pd' CCTK_REAL8_VEC const x2 = _mm_hadd_pd(x1, x1); ^~~~~~~~~~~ _mm_add_pd make[4]: *** [vectors.cc.o] Error 1 make[3]: *** [make.checked] Error 2 make[2]: *** [/Users/babiuc/Cactus/configs/ET/lib/libthorn_Vectors.a] Error 2 make[1]: *** [ET] Error 2 make: *** [ET-rebuild] Error 2? Please advise. thank you, Maria ?

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Cactus Tutorial
by Steven R. Brandt 04 Nov '17

04 Nov '17

The attached file is the html rendering of a Jupyter notebook version of Cactus tutorials advocated by Ian and Roland. It is my proposal to use this going forward. To run this tutorial, you can either go to the NDS machine (which I propose should be the default tutorial machine from now on): https://www.einsteintoolkit.nationaldataservice.org/#/ Alternatively, you may run it in docker. docker run --name myjupyter -d -p 8888:8888 ndslabs/jupyter-et If you don't like Jupyter, you can open a console on the NDS machine, or you can get a command line interface by doing this docker run -it ndslabs/jupyter-et bash Which is a machine that already has the requisite cactus packages installed. You can then use the attached html to enter instructions one by one. Please send comments, flames, etc. Thanks. --Steve

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Cannot access x,y,z,r when inheriting grid in c
by Chris Stevens 03 Nov '17

03 Nov '17

Hi all, this hopefully is a dumb question, but I cannot for the life of me get access to the x,y,z,r coordinates defined in CartGrid3D. Suppose I have a thorn X that wants to access these coordinates from test.cc, then the thorn should inherit: grid, the .cc should #include "cctk_Arguments.h" and the line that accesses, say x[0], should be called after DECLARE_CCTK_ARGUMENTS. Unfortunately doing this results in an error: [maths02:86267] *** Process received signal *** [maths02:86267] Signal: Segmentation fault (11) [maths02:86267] Signal code: Address not mapped (1) [maths02:86267] Failing at address: (nil) Which is analogous to the error message you get by defining a grid variable in interface.ccl without the accompanying STORAGE: in schedule.ccl, i.e. the memory is not allocated. I am using Llama as my coordinate system, but I know this basically is a wrapper for CartGrid3D and these coordinates are still set. I see the printout from CartGrid3D. I try to access these coordinates at, for example, CCTK_INITIAL, when the grid structure is already setup. I have also tried later time bins such as CCTK_POSTSTEP. Example files that access these coordinates are: CTGBase::debug.cc ADMDerivatives::calc_derivs.cc Coordinates::cylinderinbox.cc However I am not having any luck reverse-engineering these. Any ideas would be appreciated. Chris -- Dr Chris Stevens Department of Mathematics Rhodes University Room 5 Ph: +27 46 603 8932 Web: www.chrisdoesmaths.com <http://www.chrisdoesmaths.com>

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Re: [Users] Carpet options to switch off mesh refinement
by dumsani 02 Nov '17

02 Nov '17

On 02/11/2017 10:46, Ian Hinder wrote: > On 2 Nov 2017, at 01:41, dumsani <g14n8326(a)campus.ru.ac.za> wrote: > >> I think I have figured it out eventually. Thanks, Ian. > Good to hear! Would it be useful to summarise the cause of the problem to the mailing list, in case it helps others? > The following 3 options were enough, as you suggested. Carpet::max_refinement_levels = 1 Carpet::refinement_factor = 1 CarpetRegrid2::num_centres = 0 After setting these properly, it turned out the crash wasn't due to Carpet. It was now due to inappropriate memory allocation by the scheduler in my initial data code. Thanks

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