Trac May 2018

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62 discussions

[Einstein Toolkit] #2055: Move gallery examples to EinsteinExamples repository
by Einstein Toolkit 28 Aug '18

28 Aug '18

#2055: Move gallery examples to EinsteinExamples repository -------------------------------------+-------------------------------------- Reporter: hinder | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit website | Version: development version Keywords: | -------------------------------------+-------------------------------------- The [http://einsteintoolkit.org/gallery.html Einstein Toolkit Gallery examples] parameter files could be moved from the [https://bitbucket.org/einsteintoolkit/www/src/master/gallery/?at=master www] repository to the [https://bitbucket.org/einsteintoolkit/einsteinexamples/src/master/par/?at=m… EinsteinExamples] repository and arrangement. This would mean: * They are checked out when someone downloads the ET, avoiding a separate web browser or curl download * They will have branches like the rest of the ET, so they can be associated with a given release if necessary Note that this will separate them from the other related material on the website, such as thornlists, images, etc, but I think it is worth it to make it easier for new users. Eventually, we hope that all the gallery examples will use the standard ET thornlist anyway. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/2055> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #2042: new thorns for hydro analysis
by Einstein Toolkit 28 Aug '18

28 Aug '18

#2042: new thorns for hydro analysis -------------------------+-------------------------------------------------- Reporter: knarf | Owner: Type: enhancement | Status: new Priority: optional | Milestone: Component: Other | Version: development version Keywords: | -------------------------+-------------------------------------------------- The LSU and Parma groups developed, and used for publications, a set of two thorns for analysis of hydro quantities, in particular for mode analysis. We would like to have those included in the Einstein Toolkit. We are aware that a few things are still missing for that (documentation, test suites), but before we go that extra step and create all of that, we want to be sure the following is seen as 'ok': The main thorn (GRHydro_Analysis, _not_ to be specific to GRHydro, it only inherits hydrobase - could and should probably be renames) does reductions of quire a few quantities. In practice, the memory required for this turned out to be a problem on some machines. These reductions are done at ANALYSIS, which means even telling Cactus to allocate/deallocate not once, globally, but instead doing that every time step does not help. Thus, there is a second thorn, a utility thorn called 'TempPool'. It's task is nothing else than to provide an array of grid functions that are always allocated, but which can be used by other thorns for, reductions - and, and this is the interesting part - can be re-used by other thorns, for other reductions after that; within the same time step in ANALYSIS. This is how TempPool is used by GRHydro_Analysis. TempPool is not tied to GRHydro_Analysis. Any other thorn can also request storage there, but there currently isn't another thorn. It just seemed to good idea to split this functionality. The book keeping already now makes sure that the number of allocated grid functions is only as large the maximum of any thorn using it. The relevant code can be found here: https://bitbucket.org/GravityPR/prthorns/src I'd like another developer to have a look and give input. Once/If this is deemed ok to be included, we will add the necessary documentation and test suites and make a proper proposal for inclusion. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/2042> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #2119: The binary neutron star gallery example gives different results with the release candiate.
by Einstein Toolkit 22 Aug '18

22 Aug '18

#2119: The binary neutron star gallery example gives different results with the release candiate. ---------------------+------------------------------------------------------ Reporter: diener | Owner: Type: defect | Status: new Priority: blocker | Milestone: ET_2018_02 Component: Other | Version: development version Keywords: | ---------------------+------------------------------------------------------ The late part of the waveform plot looks very different in the release candidate than on the gallery page. For l=2, m=2 mode of psi_4 extracted at R=300 (that seems to be the correct data file as otherwise the scale on the y-axis don't match) the merger seem to happen slightly later and the waveform after merger is completely different. The gallery page plot: [[Image(/home/diener/tmp/mp_Psi4_l2_m2_r300.00.png)]] The new plot: [[Image(/home/diener/tmp/mp_Psi4_l2_m2_r300.00_new.png)]] -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/2119> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #2131: Boundary thorn
by Einstein Toolkit 22 Aug '18

22 Aug '18

#2131: Boundary thorn -------------------------------------------------------+-------------------- Reporter: miguel.zilhao.nogueira@… | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: Boundary | -------------------------------------------------------+-------------------- i was trying to do a (unigrid) run with "scalar" boundary conditions on some variables but with uneven boundary width, ie width of 2 grid points on the x and y axis and 0 on the z axis. in the documentation of the Boundary thorn it states that one should create a table passing this information in an array called "BOUNDARY_WIDTH": "The table handle identifies a table which holds extra arguments for the particular boundary condition that is requested. For example, if a negative value is passed for the boundary width, then the boundary condition will look in this table for a 2d-element integer array, which holds the width of each face of the boundary (for a d dimensional grid variable). (The first element of the array holds the width of the ‘-x’ face, the second the ‘+x’ face, the third the ‘-y’ face, etc.)" so i've accordingly created the following table {{{ call Util_TableCreateFromString(param_table_handle, "BOUNDARY_WIDTH = { 2 2 2 2 0 0 }") {{{ and then registered the variables with {{{ ierr = Boundary_SelectGroupForBC(cctkGH, CCTK_ALL_FACES, -one, & param_table_handle, "ScalarBase::phi", "scalar") }}} however, i was getting errors like the following: {{{ Boundary/src/Check.c:130: BndSanityCheckWidths: Assertion `dim < (int)sizeof(dims)' failed. }}} inspecting that file, this is only triggered if {{{(boundary_widths[i] > 100 || boundary_widths[i] < 0)}}} which meant that my BOUNDARY_WIDTH array was likely not being parsed correctly. digging a little bit deeper, i've found the following in ScalarBoundary.c:138 (and analogous for the other files under CactusBase/Boundary/src): {{{ /* Determine boundary width on all faces */ /* allocate memory for buffer */ gdim = CCTK_GroupDimI(gi); if (gdim > max_gdim) { width_alldirs = (CCTK_INT *)realloc(width_alldirs, 2 * gdim * sizeof(CCTK_INT)); max_gdim = gdim; } /* fill it with values, either from table or the boundary_width parameter */ if (widths[i] < 0) { err = Util_TableGetIntArray(tables[i], gdim, width_alldirs, "BOUNDARY_WIDTH"); }}} it seems to me that this last line should be instead {{{ err = Util_TableGetIntArray(tables[i], 2 * gdim, width_alldirs, "BOUNDARY_WIDTH"); }}} for consistency with the rest of the file and with the documentation, right? indeed, with this change the errors disappeared. i've attached a simple patch that applies this on this file, but i guess an equivalent change would be needed also for the rest of the Boundary files... if this patch is correct, could this be ported to the current release? and if it's not correct, is there anything i'm missing, in order to register the boundary conditions? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/2131> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #2008: NaNs when running static tov on >40 cores
by Einstein Toolkit 22 Aug '18

22 Aug '18

#2008: NaNs when running static tov on >40 cores -----------------------------------+---------------------------------------- Reporter: allgwy001@… | Owner: Type: defect | Status: new Priority: unset | Milestone: Component: Other | Version: ET_2016_05 Keywords: | -----------------------------------+---------------------------------------- I've been trying to run the static tov example parameter file on an HPC cluster using >40 cores, but this results in NaNs in the data. I can't remember whether the issue first appears at 40 or 41 cores (and won't be able to check this for the next few days), but using 41+ cores definitely gives me NaNs. I remember testing with 39 cores and several other lower values (down to 4), but these runs all seemed fine. So far, I've been able to run larger simulations (e.g. BBHs) on more than 40 cores (same cluster) without any apparent issues. I'll attach the static tov parameter file I used (I think I changed one or two outdated parameters), as well as the PBS script and error/output files from a static tov run on 44 cores. The static tov runs were intended for speed test purposes. The results of the speed tests I've run so far (on fewer than 40 cores) seem quite strange to me, so I'm going to attach a text file with walltimes and CPU times for these runs, too. Any comments would be appreciated! -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/2008> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1263: Multipole does not handle variable names correctly
by Einstein Toolkit 13 Aug '18

13 Aug '18

#1263: Multipole does not handle variable names correctly -----------------------------------+---------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: Multipole | -----------------------------------+---------------------------------------- When you specify variables for Multipole to decompose, you have the option of giving it a "name" for the variable to be used in the output filename. This is useful if you are decomposing Psi4r, with imaginary part Psi4i, and want the file to just be named "Psi4". If you don't specify a name, it is supposed to use the original variable name. However, at the moment, this last part seems to be broken. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1263> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1201: Incorrect dtshift in Exact with shift_add_{x, y, z} parameters
by Einstein Toolkit 09 Aug '18

09 Aug '18

#1201: Incorrect dtshift in Exact with shift_add_{x,y,z} parameters -----------------------------------+---------------------------------------- Reporter: barry.wardell | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- The Exact thorn has shift_add_{x,y,z} parameters for adding a constant to the shift. Considering these as a coordinate transformation using a vector v^i = [shift_add_x, shift_add_y, shift_add_z], such a transformation should affect both the shift and its time derivative. This is because the time derivative in the new coordinates differs from the time derivative in the old coordinates by a term v^j d(beta^i)/dx^j. This is correctly implemented as a 4D coordinate transformation in the EinsteinExact thorns and I have verified that the difference relative to the Exact thorn is given by this missing term. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1201> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1097: Describe Tmunu in GRHydro
by Einstein Toolkit 09 Aug '18

09 Aug '18

#1097: Describe Tmunu in GRHydro -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- Describe in GRHydro's documentation how Tmunu is defined -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1097> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #2158: Without MPI installed, Cactus doesn't build
by Einstein Toolkit 09 Aug '18

09 Aug '18

#2158: Without MPI installed, Cactus doesn't build ---------------------------------+-------------------- Reporter: Steven R. Brandt | Type: defect Status: new | Priority: unset Milestone: | Component: Other Version: development version | Keywords: ---------------------------------+-------------------- I attempted to test our automatic building of Cactus on a system without MPI installed. In principle, thorn MPI should build and the system should work. Instead, I get this: {{{ MPI: Building... Making all in config Making all in contrib Making all in opal Making all in include Making all in asm CC asm.lo ln -s "../../opal/asm/generated/atomic-amd64-linux.s" atomic-asm.S CPPAS atomic-asm.lo CCLD libasm.la ../../libtool: line 6000: cd: NO_BUILD/lib: No such file or directory libtool: link: cannot determine absolute directory name of `NO_BUILD/lib' Makefile:1584: recipe for target 'libasm.la' failed make[6]: *** [libasm.la] Error 1 Makefile:2153: recipe for target 'all-recursive' failed make[5]: *** [all-recursive] Error 1 Makefile:1702: recipe for target 'all-recursive' failed make[4]: *** [all-recursive] Error 1 Died at /home/etuser/Cactus/arrangements/ExternalLibraries/MPI/src/build.pl line 74. /home/etuser/Cactus/arrangements/ExternalLibraries/MPI/src/make.code.deps:9: recipe for target '/home/etuser/Cactus/configs/sim/scratch/done/MPI' failed make[3]: *** [/home/etuser/Cactus/configs/sim/scratch/done/MPI] Error 17 /home/etuser/Cactus/lib/make/make.thornlib:112: recipe for target 'make.checked' failed make[2]: *** [make.checked] Error 2 /home/etuser/Cactus/lib/make/make.configuration:181: recipe for target '/home/etuser/Cactus/configs/sim/lib/libthorn_MPI.a' failed make[1]: *** [/home/etuser/Cactus/configs/sim/lib/libthorn_MPI.a] Error 2 Makefile:256: recipe for target 'sim' failed make: *** [sim] Error 2 The command '/bin/sh -c ./simfactory/bin/sim build -j8 --thornlist ../einsteintoolkit.th' returned a non-zero code: 1 }}} The test system is made from docker {{{ FROM ubuntu RUN apt-get update RUN apt-get install -y python3 RUN apt-get install -y libfftw3-dev libssl-dev libhdf5-dev subversion gcc curl libjpeg-turbo?-dev git make pkg-config g++ libpapi-dev patch libgsl- dev libhwloc-dev python liblapack-dev numactl gfortran RUN adduser etuser USER etuser WORKDIR /home/etuser ENV USER etuser RUN curl -kLO https://raw.githubusercontent.com/gridaphobe/CRL/master/GetComponents RUN chmod a+x GetComponents RUN ./GetComponents --parallel https://bitbucket.org/einsteintoolkit/manifest/raw/master/einsteintoolkit.th RUN echo testme > .hostname WORKDIR /home/etuser/Cactus RUN ./simfactory/bin/sim setup-silent RUN ./simfactory/bin/sim build -j8 --thornlist ../einsteintoolkit.th }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/2158> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #660: Make MHD multipatch-aware
by Einstein Toolkit 09 Aug '18

09 Aug '18

#660: Make MHD multipatch-aware -----------------------------------+---------------------------------------- Reporter: tbode | Owner: tbode Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: | -----------------------------------+---------------------------------------- At least the Con2PrimM routines need to be multipatch-aware. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/660> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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