Trac October 2012

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[Einstein Toolkit] #631: Documentation fails to build
by Einstein Toolkit 25 Oct '12

25 Oct '12

#631: Documentation fails to build ---------------------+------------------------------------------------------ Reporter: hinder | Owner: Type: defect | Status: new Priority: blocker | Milestone: Component: Cactus | Version: Keywords: | ---------------------+------------------------------------------------------ With the current ET, I cannot build the documentation: [ianhin@login-damiana EinsteinToolkit]$ make AllDoc Creating user documentation UsersGuide.pdf Running pdflatex.... ! Argument of \CA@getsvndate has an extra }. ! Paragraph ended before \CA@getsvndate was complete. ! Argument of \CA@getsvndate has an extra }. ! Paragraph ended before \CA@getsvndate was complete. ! Paragraph ended before \@parse@version was complete. ! Missing number, treated as zero. ! Missing = inserted for \ifnum. ! Missing number, treated as zero. ! LaTeX Error: Missing \begin{document}. ! Undefined control sequence. Problem in . See doc/UsersGuide/LATEX_MESSAGES. make: *** [UsersGuide] Error 1 I am attaching LATEX_MESSAGES. I have tried this both on damiana and on my laptop. I consider this a blocker issue which could delay the release. We must have working documentation. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/631> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1143: Optimise calls to CCTK_VarDataPtr
by Einstein Toolkit 25 Oct '12

25 Oct '12

#1143: Optimise calls to CCTK_VarDataPtr -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- Cactus calls CCTK_VarDataPtr each time DECLARE_CCTK_ARGUMENTS is executed for each grid function. This routine performs string looks and is thus unreasonably expensive. The attached patch remembers variable indices in static variables. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1143> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1123: GRHydro update
by Einstein Toolkit 25 Oct '12

25 Oct '12

#1123: GRHydro update -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: GRHydro | -----------------------------------+---------------------------------------- attached please find a set of patches for GRHydro. Unless objections are raised I will apply them near the end of the week, -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1123> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1146: close and garbage collect all objects when closing files
by Einstein Toolkit 24 Oct '12

24 Oct '12

#1146: close and garbage collect all objects when closing files -------------------+-------------------------------------------------------- Reporter: rhaas | Type: enhancement Status: new | Priority: minor Milestone: | Component: Other Version: | Keywords: -------------------+-------------------------------------------------------- this tries to make sure no memory leaks exist. Does not (yet) check that there are no dangling references. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1146> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1110: Make Trigger part of the ET
by Einstein Toolkit 24 Oct '12

24 Oct '12

#1110: Make Trigger part of the ET -----------------------------------+---------------------------------------- Reporter: knarf | Owner: Type: enhancement | Status: new Priority: minor | Milestone: ET_2012_11 Component: EinsteinToolkit thorn | Version: development version Keywords: | -----------------------------------+---------------------------------------- It would be good to make AEIThorns::Trigger part of the ET -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1110> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1137: MoL parameter for skipping MoL_PostStep on initial data
by Einstein Toolkit 24 Oct '12

24 Oct '12

#1137: MoL parameter for skipping MoL_PostStep on initial data -------------------------+-------------------------------------------------- Reporter: bentivegna | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: MoL | -------------------------+-------------------------------------------------- The following patch introduces a parameter for controlling whether MoL overwrites the boundaries of initial data (via genuine boundary conditions, or syncs and prolongation). Some exact solutions provide pointwise values for all the grid points, and thus don't need any sort of boundary treatment. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1137> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1142: checkpoint_ID overwrites checkpoint files after each recovery
by Einstein Toolkit 24 Oct '12

24 Oct '12

#1142: checkpoint_ID overwrites checkpoint files after each recovery ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: eschnett Type: defect | Status: new Priority: critical | Milestone: Component: Carpet | Version: Keywords: | ----------------------+----------------------------------------------------- Apparently, the parameter checkpoint_ID overwrites checkpoint files after each recovery, i.e. overwrites the checkpoint file from one which just recovered, potentially damaging this checkpoint file irreversibly e.g. if variables changed in post_recover_variables. Simfactory's default parameter settings and examples should be changed back to separating restarts from each other, so that this kind of problem is avoided. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1142> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1124: 'make tags' doesn't properly handle symlinks
by Einstein Toolkit 24 Oct '12

24 Oct '12

#1124: 'make tags' doesn't properly handle symlinks -------------------------------------------+-------------------------------- Reporter: Matt Kinsey <kins@…> | Type: defect Status: new | Priority: minor Milestone: Cactus_4.1.0 | Component: Cactus Version: Cactus_4.0.0 | Keywords: -------------------------------------------+-------------------------------- When generating ctags for the cactus tree, 'make tags' currently ignores all symlinks. This results in a large number of thorns in my cactus tree not getting tagged because GetComponents put them in CACTUS_ROOT/repos and linked to them. I'm not sure if this is intended but I have a feeling it isn't... This fixes the problem, but I've only tested it on my checkout: {{{ matt@krang:~/maya/Cactus$ diff Makefile.backup Makefile 312c312 < find src arrangements $ \ --- > find -L src arrangements \( \ 317c317 < # find src arrangements \( -name '*.[cChF]' -o -name '*.F77' -o -name '*.cc'$ \ --- > # find -L src arrangements $ -name '*.[cChF]' -o -name '*.F77' -o -name '*.cc'$ \ 327c327 < find src arrangements \( \ --- > find -L src arrangements \( \ }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1124> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1144: allow ${parfile} in parameter files to allow ${parfile}/subdir
by Einstein Toolkit 24 Oct '12

24 Oct '12

#1144: allow ${parfile} in parameter files to allow ${parfile}/subdir -------------------------+-------------------------------------------------- Reporter: knarf | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: | -------------------------+-------------------------------------------------- -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1144> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1125: LORENE hard codes OpenMP options into compile options
by Einstein Toolkit 24 Oct '12

24 Oct '12

#1125: LORENE hard codes OpenMP options into compile options -------------------+-------------------------------------------------------- Reporter: rhaas | Type: defect Status: new | Priority: major Milestone: | Component: EinsteinToolkit thorn Version: | Keywords: LORENE -------------------+-------------------------------------------------------- Currently LOERENE's configuration.sh contains {{{ CXXFLAGS = ${CXXFLAGS} ${CPPFLAGS} ${CPP_OPENMP_FLAGS} }}} which always uses OpenMP independent of the option list's OPENMP=yes/no setting. The attached patch duplicates (unfortunately there seems to be no way to access this variables from within a per-thorn configuration script) the logic used in Cactus' configure to set OPENMP_MODE based on OPENMP. Without it compilation of a Cactus fails at link if OpenMP is not selected: {{{ g++ -o "/home/lovelace/trunk/Cactus/exe/cactus_sim" -DMPICH_IGNORE_CXX_SEEK -DKRANC_VECTORS -g3 -march=native -std=gnu++0x -rdynamic -O2 "/home/lovelace/trunk/Cactus/configs/sim/datestamp.o" -L/home/lovelace/trunk/Cactus/configs/sim/lib -lthorn_Cactus -lthorn_CactusBindings -lthorn_CarpetEvolutionMask -lthorn_IOHDF5 -lthorn_IOHDF5Util -lthorn_CarpetIOScalar -lthorn_ML_WaveToy -lthorn_Meudon_Mag_NS -lthorn_HTTPDExtra -lthorn_HTTPD -lthorn_RotatingSymmetry90 -lthorn_NoExcision -lthorn_Hydro_InitExcision -lthorn_ML_BSSN_Helper -lthorn_GaugeWave -lthorn_NullPsiInt -lthorn_hwloc -lthorn_PUGHInterp -lthorn_Cartoon2D -lthorn_SetMask_SphericalSurface -lthorn_EHFinder -lthorn_EOS_IdealFluid -lthorn_ModifiedSchwarzschildBL -lthorn_Multipole -lthorn_CarpetTracker -lthorn_SphericalHarmonicRecon -lthorn_QuasiLocalMeasures -lthorn_TGRtensor -lthorn_Exact -lthorn_Periodic -lthorn_IOJpeg -lthorn_CarpetRegrid -lthorn_TestGlobalReduce -lthorn_CarpetInterp2 -lthorn_Vaidya2 -lthorn_GRHydro_InitData -lthorn_TestLoop -lthorn_LegoExcision -lthorn_ADMMass -lthorn_ADM -lthorn_CarpetSlab -lthorn_NoMPI -lthorn_PunctureTracker -lthorn_CarpetRegrid2 -lthorn_IDScalarWaveElliptic -lthorn_IDScalarWaveCXX -lthorn_IDScalarWaveC -lthorn_IDScalarWave -lthorn_ML_ADMQuantities -lthorn_ML_BSSN -lthorn_WaveToyExtra -lthorn_CarpetMask -lthorn_ML_CCZ4_Helper -lthorn_ML_CCZ4 -lthorn_AHFinderDirect -lthorn_Meudon_Bin_BH -lthorn_ADMConstraints -lthorn_ML_ADMConstraints -lthorn_PUGHSlab -lthorn_TestFortranDependencies1 -lthorn_TwoPunctures -lthorn_CalcK -lthorn_IOBasic -lthorn_NullExact -lthorn_NullConstr -lthorn_NullNews -lthorn_CarpetInterp -lthorn_IDBrillData -lthorn_Extract -lthorn_WaveBinarySource -lthorn_WaveToyFreeF90 -lthorn_WaveToyF90 -lthorn_WaveToyF77 -lthorn_WaveToyCXX -lthorn_WaveToyC -lthorn_IDAxiOddBrillBH -lthorn_CarpetIOBasic -lthorn_CarpetIOASCII -lthorn_Minkowski -lthorn_SlabTest -lthorn_Dissipation -lthorn_SphericalSurface -lthorn_EOS_Hybrid -lthorn_EOS_Polytrope -lthorn_DistortedBHIVP -lthorn_Meudon_Bin_NS -lthorn_LORENE -lthorn_LAPACK -lthorn_IDAxiBrillBH -lthorn_EllSOR -lthorn_NewRad -lthorn_IOASCII -lthorn_NullSHRExtract -lthorn_NullEvolve -lthorn_NullInterp -lthorn_NullDecomp -lthorn_NullGrid -lthorn_AHFinder -lthorn_RotatingDBHIVP -lthorn_SphericalHarmonicDecomp -lthorn_WeylScal4 -lthorn_IDConstraintViolate -lthorn_TOVSolver -lthorn_GRHydro -lthorn_TmunuBase -lthorn_SpaceMask -lthorn_EOS_Omni -lthorn_IDAnalyticBH -lthorn_ShiftedGaugeWave -lthorn_CarpetIOHDF5 -lthorn_HDF5 -lthorn_NaNChecker -lthorn_PUGHReduce -lthorn_PUGH -lthorn_CarpetReduce -lthorn_Carpet -lthorn_CarpetLib -lthorn_ADMAnalysis -lthorn_zlib -lthorn_libjpeg -lthorn_Time -lthorn_TestTypes -lthorn_TestTimers -lthorn_TestTable -lthorn_TestStrings -lthorn_TestSchedule -lthorn_TestReduce -lthorn_TestPar -lthorn_TestMath -lthorn_TestLocalReduce -lthorn_TestInclude2 -lthorn_TestInclude1 -lthorn_TestFreeF90 -lthorn_TestFpointerNULL -lthorn_TestFortranDependencies2 -lthorn_TestCoordinates -lthorn_TestComplex -lthorn_TestArrays -lthorn_TerminationTrigger -lthorn_TATelliptic -lthorn_SystemStatistics -lthorn_SymBase -lthorn_SummationByParts -lthorn_Socket -lthorn_ReflectionSymmetry -lthorn_OpenSSL -lthorn_NullVars -lthorn_Norms -lthorn_Nice -lthorn_MoL -lthorn_ML_WaveToy_Test -lthorn_ML_CCZ4_Test -lthorn_ML_BSSN_Test -lthorn_LocalReduce -lthorn_LocalInterp -lthorn_InterpToArray -lthorn_Fortran -lthorn_FFTW3 -lthorn_EllBase -lthorn_EinsteinExact_Test -lthorn_EOS_Base -lthorn_CoordGauge -lthorn_Constants -lthorn_BLAS -lthorn_AEILocalInterp -lthorn_ADMMacros -lthorn_ADMCoupling -lthorn_Formaline -lthorn_RotatingSymmetry180 -lthorn_Slab -lthorn_Hydro_Analysis -lthorn_HydroBase -lthorn_InitBase -lthorn_KerrSchild -lthorn_LoopControl -lthorn_Vectors -lthorn_GSL -lthorn_GenericFD -lthorn_IDLinearWaves -lthorn_IDFileADM -lthorn_IOUtil -lthorn_StaticConformal -lthorn_ADMBase -lthorn_Boundary -lthorn_TimerReport -lthorn_MPI -lthorn_Noise -lthorn_CartGrid3D -lthorn_CoordBase -lthorn_Cactus -lthorn_CactusBindings -lthorn_Formaline- cactus-source -L/home/lovelace/trunk/Cactus/configs/sim/scratch/external/hwloc/lib -L/home/lovelace/trunk/Cactus/configs/sim/scratch/external/LORENE/Lib -L/home/lovelace/trunk/Cactus/configs/sim/scratch/external/LAPACK -L/home/lovelace/trunk/Cactus/configs/sim/scratch/external/HDF5/lib -L/home/lovelace/trunk/Cactus/configs/sim/scratch/external/zlib/lib -L/home/lovelace/trunk/Cactus/configs/sim/scratch/external/libjpeg/lib -L/home/lovelace/trunk/Cactus/configs/sim/scratch/external/FFTW3/lib -L/home/lovelace/trunk/Cactus/configs/sim/scratch/external/BLAS -L/home/lovelace/trunk/Cactus/configs/sim/scratch/external/GSL/lib -L/usr/lib -Wl,-rpath,/home/lovelace/trunk/Cactus/configs/sim/scratch/external/hwloc/lib -Wl,-rpath,/home/lovelace/trunk/Cactus/configs/sim/scratch/external/LORENE/Lib -Wl,-rpath,/home/lovelace/trunk/Cactus/configs/sim/scratch/external/LAPACK -Wl,-rpath,/home/lovelace/trunk/Cactus/configs/sim/scratch/external/HDF5/lib -Wl,-rpath,/home/lovelace/trunk/Cactus/configs/sim/scratch/external/zlib/lib -Wl,-rpath,/home/lovelace/trunk/Cactus/configs/sim/scratch/external/libjpeg/lib -Wl,-rpath,/home/lovelace/trunk/Cactus/configs/sim/scratch/external/FFTW3/lib -Wl,-rpath,/home/lovelace/trunk/Cactus/configs/sim/scratch/external/BLAS -Wl,-rpath,/home/lovelace/trunk/Cactus/configs/sim/scratch/external/GSL/lib -Wl,-rpath,/usr/lib -lpthread -lhwloc -llorene_export -llorene -llorenef77 -llapack -lhdf5_hl_cpp -lhdf5_cpp -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz -lm -lz -ljpeg -lfftw3 -lblas -lgsl -lgslcblas -lm -lmpich -lfmpich -lcrypt -ldl -lgfortran /home/lovelace/trunk/Cactus/configs/sim/scratch/external/LORENE/Lib/liblorene_export.a(bin_ns_aux.o): In function `Bin_NS': /home/lovelace/trunk/Cactus/configs/sim/scratch/build/LORENE/Lorene/Export/C++/Source/bin_ns_aux.C:333: undefined reference to `GOMP_parallel_start' /home/lovelace/trunk/Cactus/configs/sim/scratch/build/LORENE/Lorene/Export/C++/Source/bin_ns_aux.C:333: undefined reference to `GOMP_parallel_end' /home/lovelace/trunk/Cactus/configs/sim/scratch/external/LORENE/Lib/liblorene_export.a(bin_ns_aux.o): In function `Bin_NS::Bin_NS(int, double const*, double const*, double const*, char const*) [clone ._omp_fn.0]': /home/lovelace/trunk/Cactus/configs/sim/scratch/build/LORENE/Lorene/Export/C++/Source/bin_ns_aux.C:334: undefined reference to `omp_get_num_threads' /home/lovelace/trunk/Cactus/configs/sim/scratch/build/LORENE/Lorene/Export/C++/Source/bin_ns_aux.C:334: undefined reference to `omp_get_thread_num' /usr/lib/libmpich.so: undefined reference to `MPL_trid' /usr/lib/libmpich.so: undefined reference to `MPL_trvalid' /usr/lib/libmpich.so: undefined reference to `MPL_env2int' /usr/lib/libmpich.so: undefined reference to `MPL_trrealloc' /usr/lib/libmpich.so: undefined reference to `MPL_trspace' /usr/lib/libmpich.so: undefined reference to `MPL_trDebugLevel' /usr/lib/libmpich.so: undefined reference to `MPL_TrSetMaxMem' /usr/lib/libmpich.so: undefined reference to `MPL_trlevel' /usr/lib/libmpich.so: undefined reference to `MPL_trmalloc' /usr/lib/libmpich.so: undefined reference to `MPL_putenv' /usr/lib/libmpich.so: undefined reference to `MPL_env2bool' /usr/lib/libmpich.so: undefined reference to `MPL_env2range' /usr/lib/libmpich.so: undefined reference to `MPL_trcalloc' /usr/lib/libmpich.so: undefined reference to `MPL_trfree' /usr/lib/libmpich.so: undefined reference to `MPL_env2str' /usr/lib/libmpich.so: undefined reference to `MPL_trstrdup' /usr/lib/libmpich.so: undefined reference to `MPL_trdump' /usr/lib/libmpich.so: undefined reference to `MPL_trinit' collect2: ld returned 1 exit status make[1]: *** [/home/lovelace/trunk/Cactus/exe/cactus_sim] Error 1 make[1]: Leaving directory `/home/lovelace/trunk/Cactus' make: *** [sim] Error 2 }}} The MPL errors are due to a missing link library for libmpl in the Ubuntu.cfg file (separate ticket). Also note that both the old and the patched version actually use "CPP_OPENMP_FLAGS" not "CXX_OPENMP_FLAGS" in the CXX options. This looks like an error to me. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1125> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac October 2012