Users February 2015

users@lists.einsteintoolkit.org

8 participants
13 discussions

Einstein Toolkit Meeting Reminder
by Frank Loeffler 14 May '15

14 May '15

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. My agenda contains: - Fall workshop - PLEASE let us know if you come [1]! - Hotel booking - Release planning - release date: Mon Oct 24 2011 - freeze date: Mon Sep 26 - the day of the call! - branch name: ET_2011_10 - List of release-concerning bugs [2] - ET paper: proposed "freeze" by Oct 3rd (Mon after this call) As always: feel free to add to this list. Frank Loeffler [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Fall_2011#Fall_Einstei… [2] https://trac.einsteintoolkit.org/query?status=!closed&milestone=ET_2011_11&…

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 27 Feb '15

27 Feb '15

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Meeting Minutes for 2015-02-23
by Roland Haas 23 Feb '15

23 Feb '15

Present: Roland, Ian, Peter, Steve, Yosef, Philipp, TwoPunctures: * fix is accepted. impact is unclear, should only affect convergence speed * Yosef suspects that this affects the direction that the solver takes since it only affects the preconditioner McLachlan rewrite branch: * latest news: Erik wanted to run benchmarks, Ian will also try but is very busy, same for Peter MHD constrained transport: * Philipp, and the Caltech group have started discussion of constrained transport algorithms but have not reached a decision what to do * current best practice is to add some resistivity to the computation of the electric field, this is consistent with constrained transport. The numerical coefficient is 1e-3 -- 1e-4 . Currently this is under heavy development and not even in Zelmani yet. TOVSolver tying to GRHydro: * Roland will go ahead and remove the linkage Hydro in Kranc: * Ian Hawke (Southampton) is interested in doing a full timestep evolution scheme (some predictor/corrector) in Kranc Yours, Roland

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 20 Feb '15

20 Feb '15

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Configurations for PRACE machines
by Ian Hinder 17 Feb '15

17 Feb '15

Hi all, We are interested in running on some European PRACE machines that we have not used before. Does anyone have SimFactory (or other) Cactus configurations for Curie, Hornet or Mare Nostrum? We would like to get these working with the ET, and then commit their definitions to SimFactory. -- Ian Hinder http://members.aei.mpg.de/ianhin

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No Einstein Toolkit Meeting
by Frank Loeffler 13 Feb '15

13 Feb '15

Hi, There will not be an Einstein Toolkit meeting coming Monday. The next meeting will be in about one week on Monday, February 23th, at the usual time. Frank Löffler

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Another roadblock: error: 'CCTK_COMPLEX32' undeclared
by Islam, Tanzima 11 Feb '15

11 Feb '15

Hi All, I reconfigured my environment with the following: -------------------------------------------------------- gmake cabopenmp F90=mpif90 F77=mpif77 TAR=/bin/tar PATCH=/usr/bin/patch MPI_DIR=/usr/local/tools/mvapich-gnu MPI_INC_DIRS=/usr/local/tools/mvapich-gnu/include MPI_LIB_DIRS=/usr/local/tools/mvapich-gnu/lib MPI_LIBS="mpich psm_infinipath" DISABLE_REAL16=yes This step fails with the following error messages: COMPILING arrangements/CactusTest/TestAllTypes/src/initial.c /Apps/Cactus-all/Cactus/configs/cabopenmp/build/TestAllTypes/initial.c: In function 'TestAllTypes_C': /Apps/Cactus-all/Cactus/configs/cabopenmp/build/TestAllTypes/initial.c:11: error: 'CCTK_COMPLEX32' undeclared (first use in this function) /Apps/Cactus-all/Cactus/configs/cabopenmp/build/TestAllTypes/initial.c:11: error: (Each undeclared identifier is reported only once Apps/Cactus-all/Cactus/configs/cabopenmp/build/TestAllTypes/initial.c:11: error: for each function it appears in.) /Apps/Cactus-all/Cactus/configs/cabopenmp/build/TestAllTypes/initial.c:11: error: expected expression before 'restrict' /Apps/Cactus-all/Cactus/configs/cabopenmp/build/TestAllTypes/initial.c:11: error: 'CCTK_REAL16' undeclared (first use in this function) /Apps/Cactus-all/Cactus/configs/cabopenmp/build/TestAllTypes/initial.c:11: error: expected expression before 'restrict' /Apps/Cactus-all/Cactus/configs/cabopenmp/build/TestAllTypes/initial.c:23: error: 'vreal16' undeclared (first use in this function) /Apps/Cactus-all/Cactus/configs/cabopenmp/build/TestAllTypes/initial.c:28: error: 'vcomplex32' undeclared (first use in this function) /Apps/Cactus-all/Cactus/configs/cabopenmp/build/TestAllTypes/initial.c:28: warning: implicit declaration of function 'CCTK_Cmplx32' gmake[3]: *** [initial.c.o] Error 1 gmake[2]: *** [make.checked] Error 2 gmake[1]: *** [/Apps/Cactus-all/Cactus/configs/cabopenmp/lib/libthorn_TestAllTypes.a] Error 2 gmake: *** [cabopenmp] Error 2 -------------------------------------------------------- I googled and found that I am supposed to use the "DISABLE_REAL16=yes" flag, which I did. I am not sure what else to do. Any suggestion?? Thanks! --Tanzima

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Update on compilation: Problem in linking with "pthread_atfork"
by Islam, Tanzima 10 Feb '15

10 Feb '15

Hi All, Slight update: Instead of using sim, I used gmake <config> name to build the executable. Seems like this time I configured my compilers correctly, so that everything built without a problem. However, the last task of linking everything to build the executable failed: because it could not link to libpthread, I am assuming. I could not find the file where linking step is included. Could I specify -lpthread manually there? ----------------------------------------------------------------------------------------------------------- Creating cactus_cab in /p/lscratche/islam3/Apps/Cactus/exe from ExternalLibraries/BLAS CactusBase/Boundary CactusBase/CartGrid3D CactusNumerical/Cartoon2D CactusBase/CoordBase CactusDoc/CoreDoc CactusExamples/DemoInterp CactusNumerical/Dissipation CactusElliptic/EllBase CactusElliptic/EllSOR ExternalLibraries/F5 ExternalLibraries/FFTW3 CactusExamples/FleshInfo CactusUtils/Formaline CactusBase/Fortran ExternalLibraries/GSL ExternalLibraries/HDF5 CactusConnect/HTTPD CactusConnect/HTTPDExtra CactusExamples/HelloWorld CactusWave/IDScalarWave CactusWave/IDScalarWaveC CactusWave/IDScalarWaveCXX CactusWave/IDScalarWaveElliptic CactusExamples/IDWaveMoL CactusBase/IOASCII CactusBase/IOBasic CactusPUGHIO/IOHDF5 CactusPUGHIO/IOHDF5Util CactusIO/IOJpeg CactusBase/IOUtil CactusBase/InitBase CactusNumerical/InterpToArray ExternalLibraries/LAPACK CactusNumerical/LocalInterp CactusNumerical/LocalReduce ExternalLibraries/MPI CactusNumerical/MoL CactusUtils/NaNChecker CactusUtils/Nice CactusUtils/NoMPI CactusNumerical/Noise CactusNumerical/Norms ExternalLibraries/OpenSSL CactusPUGH/PUGH CactusPUGH/PUGHInterp CactusPUGH/PUGHReduce CactusPUGH/PUGHSlab CactusNumerical/Periodic CactusNumerical/ReflectionSymmetry CactusNumerical/RotatingSymmetry180 CactusNumerical/RotatingSymmetry90 CactusExamples/SampleBoundary CactusExamples/SampleIO CactusNumerical/Slab CactusNumerical/SlabTest CactusConnect/Socket CactusNumerical/SpaceMask CactusNumerical/SphericalSurface CactusBase/SymBase TAT/TATelliptic CactusUtils/TerminationTrigger CactusTest/TestArrays CactusTest/TestComplex CactusTest/TestCoordinates CactusTest/TestFortranCrayPointers CactusTest/TestFortranDependencies1 CactusTest/TestFortranDependencies2 CactusTest/TestFpointerNULL CactusTest/TestFreeF90 CactusTest/TestGlobalReduce CactusTest/TestInclude1 CactusTest/TestInclude2 CactusTest/TestLocalReduce CactusTest/TestLoop CactusTest/TestPar CactusTest/TestReduce CactusTest/TestSchedule CactusTest/TestStrings CactusTest/TestTable CactusTest/TestTimers CactusTest/TestTypes CactusBase/Time CactusExamples/TimerInfo CactusUtils/TimerReport CactusWave/WaveBinarySource CactusExamples/WaveMoL CactusExamples/WaveToy1DF77 CactusExamples/WaveToy2DF77 CactusWave/WaveToyC CactusWave/WaveToyCXX CactusWave/WaveToyExtra CactusWave/WaveToyF77 CactusWave/WaveToyF90 CactusWave/WaveToyFreeF90 ExternalLibraries/curl ExternalLibraries/flickcurl ExternalLibraries/git ExternalLibraries/hwloc ExternalLibraries/libjpeg ExternalLibraries/libpng ExternalLibraries/libxml2 ExternalLibraries/lua ExternalLibraries/zlib userApps/Cactus/configs/cab/scratch/external/MPI/lib/libmpi.a(ompi_mpi_init.o): In function `ompi_warn_fork': ompi_mpi_init.c:(.text+0xf4a): undefined reference to `pthread_atfork' collect2: ld returned 1 exit status gmake[1]: *** [/p/lscratche/islam3/Apps/Cactus/exe/cactus_cab] Error 1 gmake: *** [cab] Error 2 ----------------------------------------------------------------------------------------------------------- Thanks! --Tanzima

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Trouble compiling ADMMass_Parameters.c when building libthorn_CactusBindings.a
by Islam, Tanzima 09 Feb '15

09 Feb '15

Hi all, I have been trying to build Cactus on a Linux machine with Intel hardware and I am following instructions listed here: https://docs.einsteintoolkit.org/et-docs/Tutorial_for_New_Users#Compile_Exe… Unfortunately, I have been stuck and cannot make sense of the following error messages: ---------------------------------------------------------------- Checking status of thorn Cactus Checking status of thorn CactusBindings COMPILING configs/sim/bindings/Parameters/ADMMass_Parameters.c user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:22: error: expected specifier-qualifier-list before 'CCTK_REAL8' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c: In function 'CCTKi_BindingsCreateADMMassParameters': user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:59: error: 'struct <anonymous>' has no member named 'ADMMass_Debug' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:71: error: 'struct <anonymous>' has no member named 'ADMMass_Excise_Horizons' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:83: error: 'struct <anonymous>' has no member named 'ADMMass_distance_from_grid_boundary' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:96: error: 'struct <anonymous>' has no member named 'ADMMass_number' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:109: error: 'struct <anonymous>' has no member named 'ADMMass_surface_distance' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:122: error: 'struct <anonymous>' has no member named 'ADMMass_use_all_volume_as_volume_radius' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:134: error: 'struct <anonymous>' has no member named 'ADMMass_use_surface_distance_as_volume_radius' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:146: error: 'struct <anonymous>' has no member named 'ADMMass_volume_radius' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:159: error: 'struct <anonymous>' has no member named 'ADMMass_x_max' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:172: error: 'struct <anonymous>' has no member named 'ADMMass_x_min' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:185: error: 'struct <anonymous>' has no member named 'ADMMass_x_pos' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:198: error: 'struct <anonymous>' has no member named 'ADMMass_y_max' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:211: error: 'struct <anonymous>' has no member named 'ADMMass_y_min' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:224: error: 'struct <anonymous>' has no member named 'ADMMass_y_pos' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:237: error: 'struct <anonymous>' has no member named 'ADMMass_z_max' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:250: error: 'struct <anonymous>' has no member named 'ADMMass_z_min' user/Apps/Cactus_2015/Cactus/configs/sim/build/CactusBindings/Parameters/ADMMass_Parameters.c:263: error: 'struct <anonymous>' has no member named 'ADMMass_z_pos' make[3]: *** [ADMMass_Parameters.c.o] Error 1 make[2]: *** [Parameters/make.checked] Error 2 make[2]: *** Waiting for unfinished jobs.... make[1]: *** [user/Apps/Cactus_2015/Cactus/configs/sim/lib/libthorn_CactusBindings.a] Error 2 make[1]: *** Waiting for unfinished jobs.... make: *** [sim] Error 2 Error while executing command "/bin/bash -c '{ :; } && { cd user/Apps/Cactus_2015/Cactus && make -j2 sim 2>&1; }'": Command returned exit status 2 ---------------------------------------------------------------- I clearly see that the file: configs/sim/bindings/Parameters/ADMMass_Parameters.c does define a structure with those fields. Could any of you please help in this regard? Thank you! --Tanzima

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Meeting Minutes for 2015-02-09
by Roland Haas 09 Feb '15

09 Feb '15

Present: Roland, Ian, Frank, Matt, Peter, Erik, Steve Changing user guide: * agree to change * point to recommedantion for Fortran modules McLachlan rewrite branch: * no progress to report Reading Carpet data into yt: * current state is as of Enzo/yt workshop * needs to parse/obtain metadata from Carpet files * two projects existed: by Frank/Steve integrated into yt, by Sherwood Richers which was more stand alone * interest by multiple groups to do volume renderings * Frank to try and find he current code and put it into some sort of public repository No call next week due to Mardi Gras. Yours, Roland

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Users February 2015