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The annotated tag, ET_2013_11_v0 has been created at 742f55da2047ca7cf03ffe91afdca2ed8d0c1e2e (tag) tagging 390fe95c7756d5102226ccb48eadbcee62e1a52d (commit) replaces carpet-6-init tagged by Frank Löffler on Fri Dec 27 22:58:48 2013 -0600

- Log ----------------------------------------------------------------- create tag ET_2013_11_v0

Anton Khirnov (2): CarpetIOHDF5: remove a superfluous H5Pclose call. CarpetIOHDF5: avoid variable shadowing.

Christian Reisswig (3): Introduce parameter "additional_overlap_zones" to control the amount of additional (user-requested) overlap zones. CarpetInterp: New ENO2 interpolator. Merge branch 'master' of carpetcode.org:carpet

David Radice (1): CarpetIOHDF5: Sliced HDF5 output index file not stored correctly

Erik Schnetter (312): CarpetLib: Allow assigning a region to itself CarpetLib: Allow (again) merging regions that contain process trees Carpet: Disable storage for point_classification CarpetLib: Implement bboxset::contains(vect) CarpetLib: Store level_boxes in dh structure CarpetLib: Do not interpolate from buffer zones, if requested CarpetIOASCII: Pass vectors by reference CarpetIOASCII: White space change CarpetIOASCII: Implement using grid::coordinates to output coordinates Carpet: Remove outdated backtrace function declarations CarpetLib: Clean up backtrace generation Carpet: Correct errors with adaptive time stepping LoopControl: Change printstats default to "no" Remove Carpet's mechanisms to deal with how to call isnan CarpetIOF5: Correct calls to Carpet::Timer Carpet: Correct #ifdefs in CarpetSimpleMPIDatatypeLength Carpet: Requirements: Add aliased function to invalidate variables Carpet: Re-indent timer macros CarpetLib: Remove restrict qualifier from pointer cast Carpet: Correct errors in adaptive step size handling Carpet: Requirements: Warn about unnecessary syncs Carpet: Requirements: Add precondition to clause_t::active_on_timelevel CarpetRegrid2: Perform domain decomposition only when a refinement level changes CarpetRegrid2: Correct snapping to coarse grid for cell centering Carpet, CarpetRegrid2: When comparing refined regions treat non-existing levels as empty Carpet: Execute CPINITIAL only after initial data setup, not after recovering Carpet, CarpetLib: Move #define _GNU_SOURCE to correct file CarpetLib: Update cycle.h from upstream CarpetIOF5: Free HDF5 data when closing files Carpet: Add test cases checking cctk_time during initial data setup Carpet: Set NPROCS for kasner test cases Carpet: Correct comment CarpetRegrid2: Use "isfinite" instead of "not isnan" Carpet: Correct switch statement in CarpetMPIDatatype CarpetLib: Use correct MPI reduction operator for product reductions CarpetLib: Add self-checks to MPI reduction operators CarpetReduce: Avoid duplicate local variables CarpetReduce: Use self-defined MPI operators for complex numbers CarpetReduce: Do not access NULL pointer CarpetMask: Add missing OpenMP reduction clause CarpetLib: Define dh members tallying the size of refinement boundaries LoopControl: Add missing copyprivate CarpetIONirvana: Require MPI Allow padding in transport operators CarpetLib: Re-enable OpenMP collapse clauses CarpetLib: Set up all timers on all processes all the time CarpetLib: Make th::time_interpolation_during_regridding public CarpetIOF5: Various improvements Carpet: Simplify code Carpet: Turn time level / prolongation operator warning into an info message CarpetLib: Support padding in enovol prolongation operator Carpet: Re-apply init_fill_timelevels after postregridinitial CarpetLib: Use "process" instead of "processor" in comments and output CarpetLib: Add default case to switch statement CarpetLib: Correct process number in bbox output Carpet: Initialise TimerNode fields in correct order Carpet: Avoid unused and uninitialised variables Carpet: Check return value of dup() CarpetRegrid2: Correct output of refinement level during AMR CarpetRegrid2: More verbose info output during regridding CarpetLib: Check HRSCC_GLL_ELEMENT_HH instead of HRSCC_HH CarpetLib, CycleClock: Move cycle counting clock into its own thorn Carpet: Use dup2 instead of dup do control destination file descriptor CarpetLib: Ensure allocated memory is aligned for vectorisation CycleClock: Reduce wait time for determining cycle tick CycleClock: Determine elapsed time via integer arithmetic CycleClock: Optimise x86-64 PGI implementation CycleClock: Support Blue Gene/Q CycleClock: Abort compile if architecture is not supported CycleClock: Undo debugging change Carpet: Remove backup files CarpetReduce: Remove empty file Carpet: Initialise all timing variables CarpetReduce: Support array padding (cctk_ash) CarpetReduce: Clean up code defining reduction weight masks CycleClock: Handle Cray compiler CarpetLib: Rewrite array padding LoopControl: Rewrite LoopControl: Circumvent Cray compiler bug LoopControl: Run tests only with 2 processes CarpetLib: Remove unused variables CarpetIOBasic: Simplify code and avoid compiler warnings CarpetIOHDF5: Remove unused variables, initialise other variable to avoid compiler warnings CarpetIOHDF5: Make variable unsigned to avoid compiler warning CarpetLib: Explicitly convert values to signed CarpetLib: Use C++ wrapper madd instead of mul and add CarpetLib: Disable DGFE operators if building without DGFE to avoid compiler warnings CarpetIOBasic: Simplify code and avoid compiler warnings (again) Carpet: Correct load-balancing algorithm to really prefer splitting in the z direction LoopControl: Store loop bounds in the provided variables LoopControl: Correct indexing error with vectorisation CarpetIOASCII: Update test results after domain decomposition change Carpet: Return cctk_ash instead of cctk_lsh in CCTK_ArrayGroupSizeB Carpet: Use cctk_ash where necessary in poisoning and checksumming CarpetLib: Rename argument to vect::index from lsh to ash LoopControl: Add assert statements to loop macros to catch indexing errors LoopControl: Update Fortran macros to follow cctk_Loop API TestLoopControl: New thorn TestLoopControl: Use module loopcontrol LoopControl: Correct Fortran macros; provide Fortran wrappers LoopControl: More self-checking TestLoopControl: Correct errors in testing ghost zones LoopControl: Rename macro arguments to help avoid name clashes CarpetLib, LoopControl: Correct required/optional capabilities CarpetLib: Implement and correct head, tail, init, last in the vect class CarpetRegrid2: Correct min_fraction LoopControl: Correct Fortran OpenMP definitions LoopControl: Add debug assert statements when array padding is enabled LoopControl: Avoid compiler warnings CarpetRegrid2: Output all verbose messages with veryverbose as well CarpetRegrid2: Correct another error in handling min_fraction LoopControl: Reduce number of arguments passed to selftest routine LoopControl: Remove restrict qualifiers from shared data structures CarpetLib: Change default to interpolate_from_buffer_zones=no Carpet: Beautify screen output CarpetLib: Do not memoize OpenMP thread id LoopControl: Remove trivial vector lengths for j and k direction LoopControl: Simplify STL data type usage LoopControl: Improve OpenMP parallelisation CarpetProlongateTest: Correct default parameter values for interpolator test LoopControl: Output statistics to a file instead of stdout LoopControl: Share cache lines for SMT threads LoopControl: Correct parallelisation errors (mark variables volatile) CarpetReduce: Improve code layout Revert "CarpetLib: Change default to interpolate_from_buffer_zones=no" CarpetLib: Store level-wide set of buffer zones CarpetLib: Correct implementation of "don't interpolate from buffer zones" CarpetLib: Set interpolate_from_buffer_zones to "no" by default Carpet: New aliased function GetRegriddingEpochs CarpetIOASCII: Use CCTK_BUILTIN_UNREACHABLE CarpetIntegrateTest: Use ReflectionSymmetry for bitant mode Replace Cactus complex number type with C/C++ complex numbers CarpetProlongateTest: Increase test case tolerances for higher order prolongation CarpetIntegrateTest: Modernize test parameter file Carpet: Add CactusTimer functions to get all clock values of a timer Carpet: Output timer tree at shutdown CycleClock: Add parameter to disable registering a Cactus clock LoopControl: Output statistics into per-process files, not into a single file Carpet: Output all clocks in the timer tree Carpet: Use C++ style cast to avoid compiler warning Carpet: Correct output of load balancing statistics CarpetReduce: Don't require a valid cctkGH unless really needed CarpetReduce: New parameter min_max_time_interpolation LoopControl: Simplify #if sequence LoopControl: Improve OpenMP parallelisation of get_num_fine_threads CarpetIO*: Output complex numbers as pair of real numbers Requirements: New thorn Replace abs() by fabs() Requirements: Use vector instead of set to store ignored variables Requirements: White space cleanup Carpet: Call Requirements before, not after the respective actions Requirements: Beautify code Requirements: Remove dependency on defs.hh Requirements: Remove duplication from info messages Requirements: Add todo-note to invalidate non-written regions in partial projections Requirements: Break lines to make code more readable Requirements: Minor code re-shuffling and cleanup Carpet, Requirements: Pass timelevel_offset Requirements: Some source code cleanup Requirements: Add Frank's html generator script Requirements: Rename parameter print_changes to output_changes Requirements: Simplify logic to detect changes in gridpoint_t Requirements: Warn about Requirements.hh being publicly visible Requirements: Re-order if statement (no change in meaning) Requirements: Modify iteration arguments in Requirements.hh Carpet: Do not restrict variables marked as "don't restrict" Requirements: Remove some duplicate code Requirements: Correct handling of timelevels in BeforeRoutine and AfterRoutine Carpet: Don't call Requirements when only asking about allocated storage Requirements: Don't use identifiers starting with an underscore Requirements: Unify order of #include statements Requirements: Change location output format Requirements: Output iteration number in warnings and error messages Requirements: Change location output order; output map before timelevel Requirements: Use location_t to output warnings and errors CarpetLib: Remove unused/unfinished bboxtree class Carpet: Exit restriction early if no groups should be restricted Carpet: Small performance improvement in SyncGroupsByDir Carpet: Take tapering into account during postrestrict Requirements: Whitespace change CarpetLib: Vectors is currently required, not optional CarpetReduce: Offset reduction weights when periodic boundaries are used CarpetLib: Correct alignment mechanism when allocating memory CarpetIOF5: Correct calculating the I/O processor numbers CarpetIOF5: Do not output irrelevant "Writing simulation metadata" messages CarpetInterp2: Convert some loop bounds to int CarpetIOASCII: Indentation change CarpetLib: Add some comments explaining implementation CarpetLib: Add constructors to create a vector from a low-dimensional vector and a scalar CarpetLib: Rename vect::zip to vect::vzip CarpetLib: Change meaning of vect::count to count true (non-zero) elements CarpetLib: Only check cache line size if it is used CarpetLib: More verbose error output if sanity check fails CarpetLib: Don't explicitly #include cctk_Config.h CarpetLib: Don't define static_assert CarpetLib: Correct isnorma() for complex numbers CarpetLib: Add routines for integer division that always round down CarpetLib: Disable unused refluxing face descriptions CarpetLib: Add missing #include files to cacheinfo.cc CarpetLib: Correct some type declarations for 4d grid structures CarpetLib: Remove now outdated definitions of idiv and imod CarpetLib: Provide idiv and imod implementations for vect<CCTK_REAL,...> CarpetIO*: New parameter CarpetIO*::out_group_separator CarpetLib: Provide rint, round, trunc, and lrint for vectors CarpetLib: Correct vect::count CarpetLib: Use C++ standard methods to compare containers CarpetLib: Use imod instead of % operator in bbox class CarpetLib: Remove superfluous check that all indices are non-negative CarpetLib: New function bbox::is_poison to check for poison CarpetLib: Replace more uses of operator% by calls to imod CarpetLib: New function bbox::anti_contracted_for CarpetLib: New class bboxset2 LoopControl: Implement automatic performance improvements TestBBoxSet2: New thorn Requirements: Re-order #include statements Requirements: Enforce 80 character line length limit Requirements: Check return value of CCTK_TraverseString CarpetIOF5: Implement lower-dimensional output (i.e. 1d lines, 2d slices) Carpet: Use fabs() instead of abs() Carpet: Provide global instead of process-local timer output Carpet: Disable automatic synchronisation after restriction Carpet: Remove unused, broken code Carpet: Output list of compute nodes only in verbose mode CarpetLib: Disable bboxset2 by default Requirements: Do not mark current timelevel as invalid after time level cycling CarpetLib: Provide manual look-alikes for certain C++11 features CarpetLib: Instantiate some templates that are necessary on some systems CarpetLib: Don't use run-together right angle brackets in templates CarpetLib: Whitespace change CarpetLib: Re-implement part of bboxset2 for pre-C++11 compilers CarpetLib: Add optional dependency on Boost CarpetLib: Update GetCacheInfo1 API LoopControl: Update GetCacheInfo1 API CarpetIOF5: Use CCTK_BUILTIN_UNREACHABLE instead of __builtin_unreachable CarpetLib: Use CCTK_BUILTIN_UNREACHABLE instead of __builtin_unreachable CarpetReduce: Use CCTK_ERROR CarpetReduce: Add test case for reduction weights on periodic domains LoopControl: Do not output statistics by default LoopControl: Turn hard-coded parameters into Cactus parameters LoopControl: Use random() instead of rand() LoopControl: Sort statistics output LoopControl: Describe unoptimized time with respect to actual time, not vice versa LoopControl: Improve error output handling LoopControl: Correct logic that chooses tile sizes LoopControl: Correct example parameter file descriptions LoopControl: Add example parameter file for dynamic optimizations CarpetLib: New parameter use_loopcontrol_in_operators CarpetLib: Use OpenMP collapse clause in Fortran transport operators LoopControl: Declare some variables as potentially unused CarpetLib: Calculate stepped buffer zones only in debug mode CarpetLib: Do not use LoopControl for restriction operators when parallelizing via gdata.cc LoopControl: Use C++ constructure to initialize lc_descr_t LoopControl: Whitespace change LoopControl: Add OpenMP barrier after loop ends LoopControl: Correct check whether vectorization is enabled Carpet: Support group tag "map0group" Carpet: Correct "map-0-group" implementation Carpet: Do not use dynamic_cast CarpetLib: Store registered gh, dh, th, gf, data etc. via sets, not via lists CarpetLib: Add comment in gdata class CarpetLib: Remove some outdated, commented-out code Carpet: Add aliased function Driver_TotalMemoryUsed CarpetLib: Use posix_memalign to allocate aligned memory CycleClock: Automatically start clock when it is created CarpetRegrid2: Always set do_recompose when adaptive_refiment is true Carpet: Store amount of allocated memory in grid scalars Carpet: Turn timer calls into no-ops when timer hierarchy does not exist Carpet: Release all memory when shutting down CarpetLib: Free ggf data structures in ggf, not in gf<T> CarpetLib: Ensure that gh/dh/th destructors are called in the right order CarpetLib: Ensure oldstorage is empty in ggf destructor Carpet: Remove aliased function Driver_TotalMemoryUsed LoopControl: Correct indentation in statistics screen output LoopControl: Output LoopControl's memory usage CarpetLib: Do not reallocate communication buffers; instead, keep them around Timers: Move all timer-related code into a new thorn Timers Timers: Add parameters to disable all timers CarpetLib: Some harmless code cleanup CarpetLib: Small code simplification CarpetLib: Use CCTK_Error LoopControl: Make explore_eagerly_before_iteration and settle_after_iteration work LoopControl: Turn fine thread communicators into global (static) variables LoopControl: Introduce memory pool for lc_params and lc_setup LoopControl: Optimize strlen LoopControl: Output final statistics also if periodic statistics were requested Carpet: Output timers before they are destructed at Shutdown CarpetLib: Correct type error for nbytes in memory allocation CarpetLib: Use malloc (again) instead of posix_memalign LoopControl: Avoid non-standard C++ feature LoopControl: Update Fortran macros CarpetLib: Optimize memory allocation when message_count_multiplier>1 CarpetLib: Correct memory allocation error in communication buffers LoopControl: Initialize num_smt_threads explicitly during loop startup LoopControl: Explicitly check for consistent loop arguments from the caller LoopControl: Add debug output to help track down assertion failure LoopControl: Initialize fine thread communicators ahead of time LoopControl: Disable debug checks CarpetInterp2: Explicitly convert values to CCTK_REAL CarpetRegrid2: Correct wording of error message Carpet: Introduce parameter max_time_levels Carpet: Modernize error reporting Carpet: Comment out unused routine Carpet: Initialise number of timelevels at the right time CarpetLib: Add sanity check for number of time levels Carpet: Make dependency on CycleClock optional CycleClock: Do not abort when no good clock is available CarpetLib: Define elapsed() when CycleClock provides no timer CarpetInterp2: Make code compile when CARPETINTERP2_CHECK is not set CarpetInter2: Avoid const warnings CarpetLib: Remove commented-out code CarpetLib: Remove unnecessary parentheses LoopControl: Avoid nans in statistics output

Frank Löffler (16): CarpetIOHDF5: cast string constant to char array to get rid of compiler warning CarpetIOHDF5: comment unused variable (commented because code using it is also commented CarpetRegrid2: Allow pseudo-2D domains CarpetRegrid2: Testsuite for trivial domains in z direction Merge branch 'master' of carpetcode.org:carpet output more verbose info (variable index and nr of timelevels make gridpoint_t a class make bool members of gridpoint_t class private, provide accessors and use them Merge branch 'master' of carpetcode.org:carpet Let set_ accessors return whether something was changed Make set_* functions be void again, add location_t struct (unused so far) use parameter to enable output if state of variable changes Requirements: pass iteration down and print in debug output; also print when something changes (readable string) swap upper/lower case for location output Requirements: fix a couple of bugs in the debug output CycleClock: define CycleClock_Setup() without HAVE_TICK_COUNTER

Ian Hinder (21): Support more than one hierarchy of timers Add a timer tree for measuring time spent in each Carpet mode Requirements: Add comments Requirements: Move clause class into separate files Requirements: Move clauses class and some utility functions to separate files Requirements: Move all_clauses class to a separate file Requirements: Move location class to a separate file Revert part of "Requirements: Beautify code" Requirements: Move gridpoint class to a separate file Requirements: Move all_state class to separate files Requirements: Move flag variables into gridpoint class Requirements: Pass all_clauses as a reference argument rather than using a global variable Requirements: Remove unneeded #includes Rename new max_time_levels parameter as max_timelevels to be consistent with other uses of "timelevels" in parameter names in Carpet CarpetInterp2: Add timers for fasterp interpolation CarpetInterp2: Add parameter "interp_barrier" to add a barrier before interpolating CarpetInterp2: Add a barrier after interpolating Timers: Output all clocks in XML timer tree files CarpetInterp2: Time only interpolation using Interpolate timer, and enable more timers for tracing Carpet: Add a barrier between prolongation and sync controlled by sync_barriers parameter Carpet: Remove accidentally-committed extra arguments to Timer constructor

Peter Diener (3): Fix in order to compile with IBM compilers. Merge branch 'master' of carpetgit@carpetcode.org:carpet Reduce time spent in cycling timelevels if there is only one timelevel.

Roland Haas (42): Carpet: fix mg level count typo during intialization CarpetIOASCII: do not output coordinate column labels for grid arrays in CarpetIOHDF5: output index files for sliced output if requested CarpetIOHDF5: close all HDF5 objects when output file is closed CarpetIOHDF5: fix check for missing datasets when called in FileReader mode CarpetLib: add volume averaged cc eno operator CarpetLib: support padding in non-OpenMP transport operator CarpetLib: clear boundary slice offsets in dh::regrid() CarpetProlongateTest: restrict tests to 2 processes, reduce regions, CarpetEvolutionMask: compute a mask indicating where buffers are CarpetEvolutionMask: limit buffer_mask test to one process CarpetIOHDF5: remove index files along with checkpoint files Requirements: add missing include file LoopControl: disable smt by default CarpetProlongateTest: add tests for higher order restriction CarpetIOHDF5: delay browsing of input files CarpetIOHDF5: support IO->alias option in reader CarpetIOHDF5: use simple_extents rather than storage size on disk CarpetIOHDF5: fix reading of new-style grid structures CarpetIOHDF5: remove two compiler warnings CarpetIOHDF5: check whether map exists before accessing it CarpetProlongateTest: update test data CarpetIOHDF5: correct output method name in INFO message Carpet: correct wording of error message about number of time levels CarpetLib: add some code for electric fence like functionality Carpet: use electric fence provided by CarpetLib CarpetEFenceTest: test electric fence in CarpetLib Carpet: add new group tag no_split_directions Carpet: fix no_split_directions implementation CarpetSlab: pass size of allocated chunk to memory object CarpetTest: make compile again CarpetTest: recreate test data in new CarpetIOASCII format CarpetTest: add no_split_in_directions tag Carpet: remove duplicate myproc variable in SetupGH CarpetLib: make electric_fence parameter restricted Carpet: skip CheckFence routine if electric_fence is off CarpetLib: use map instead of set for dh::gfs LoopControl: provide omp_get_max_threads fallback CarpetLib: code layout changes when using map for allgfs Revert "CarpetLib: make electric_fence parameter restricted" CarpetLib: introduce accessor in gdata to query electric_fence Carpet: use gdata::fence_is_energized to query electric_fence

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