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path: root/Carpet/CarpetIOHDF5/src
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* CarpetIOHDF5: zero cctk_nghostzones attribute unless ghost zones are writtenRoland Haas2012-09-11
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* Remove all #warning statementsErik Schnetter2012-09-11
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* CarpetIOHDF5: use version 1.6 of the HDF5 API within hdf5_recombinerknarf2012-09-11
| | | | | | | There are still systems with only version 1.6 installed, or broken installs of version 1.8 (Debian system packages at least up to squeeze). These systems benefit from a compiling hdf5_recombiner, while version 1.8 is not really required to be used here.
* CarpetIOHDF5: Simplify makefileErik Schnetter2012-09-11
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* CarpetIOHDF5: More internal error checkingErik Schnetter2012-09-11
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* CarpetLib: Change API to obtain pointer to grid function dataErik Schnetter2012-09-11
| | | | | | | | Change the API to obtain a pointer to grid function data: - Use a function "typed_data_pointer" instead of overloading the () operator (because this looks nicer) - Don't use a virtual function (because this isn't needed) - Update all uses
* CarpetIOHDF5: hdf5toascii_slicer take patch.iorigin into account when ↵Roland Haas2012-09-11
| | | | | | | | | | | computing coordinates of points this is the same issue (just seems from the other side of the output) as in "CarpetIOHDF5: Correct iorigin attribute for 2D output", namely that iorigin is stored in multiples of the stride for the given refinement level --- Carpet/CarpetIOHDF5/src/util/hdf5toascii_slicer.cc | 6 +++--- 1 files changed, 3 insertions(+), 3 deletions(-)
* hdf5_slicer: close input files as soon as possible to conserve memory and ↵Roland Haas2012-09-11
| | | | | | | | file descriptors --- Carpet/CarpetIOHDF5/src/util/hdf5_slicer.cc | 13 +++++-------- 1 files changed, 5 insertions(+), 8 deletions(-)
* CarpetIOHDF5: let the hdf5_slicer write out a cctk_nghostzones attribute whichroland haas2012-09-11
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* mergeknarf2012-09-11
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| * CarpetIOHDF5: Update to new gdata::copy_from APIErik Schnetter2012-09-11
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| * CarpetIOHDF5: Introduce API to checkpoint only a subset of groupsErik Schnetter2011-12-14
| | | | | | | | | | | | | | Introduce a new API to checkpoint only a subset of group, via an aliased function IO_SetCheckpointGroups. This can be used for simulation spawning, i.e. off-loading certain calculations (e.g. analysis) outside of the main simulation.
| * CarpetIOHDF5: plug memory leak introduced in one_file_per_group_optionRoland Haas2011-12-14
| | | | | | | | | | IOUtil_DefaultIORequest returns a fresh copy of the default IO request, rather than just a pointer to it. It has to be freeed afterwards.
| * CarpetIOHDF5: Add missing -D option to make utilities buildErik Schnetter2011-12-14
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| * CarpetIOHDF5: additional check ensuring that a default request is used if theRoland Haas2011-12-14
| | | | | | | | | | | | | | | | | | | | | | | | | | current request does not exist for one_file_per_group output this is re #410: --8<-- by Erik Schnetter --8<-- The corresponding code in CarpetIOHDF5.cc, which outputs data that are not slices, uses the same algorithm. However, it contains an additional check ensuring that a default request is used if the corresponding request does not exist. Look for calls to IOUtil_DefaultIORequest to find this code. I believe that an equivalent logic would correct this problem in OutputSlice.cc. --8<-- by Erik Schnetter --8<--
* | CarpetIOHDF5: Use CXX flags for CXX compilerknarf2012-09-11
|/ | | | | | | | Currently CarpetIOHDF5 uses the c compiler options with the c++ compiler to build the utilities. This can lead to warnings about flags not supported by c++ (only by c). This patch let's it use the c++ compiler options instead.
* CarpetIOHDF5: print more information for ID and termination checkpointknarf2011-12-14
| | | | | | CarpetIOHDF5 already prints the iteration and time for periodic checkpoints. This patch adds this to both of initial data checkpoints (also after restart) and termination checkpoints.
* CarpetIOHDF5: fix parameters to GetAllActive to pass metalevel instead ofRoland Haas2011-12-14
| | | | | | map number this hopefully fixes ticket #446
* CarpetIOHDF5: Remove unnecessary function declarationErik Schnetter2011-12-14
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* CarpetIOHDF5: New parameter skip_recover_variablesErik Schnetter2011-12-14
| | | | | Introduce a new parameter skip_recover_variables that skips recovery on a set of variables.
* Adapt Carpet to hierarchical timersIan Hinder2011-12-14
| | | | | | | | Specifically, remove any hierarchy information that has been added to the name of timers, as well as any code for creating timers dynamically, as these are now unnecessary. Additionally, time some previously-untimed parts of the code and make timer names in some places more consistent.
* CarpetIOHDF5: Typo in commentErik Schnetter2011-12-14
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* CarpetIOHDF5: avoid accessing non existend refinement levels for grid arraysroland haas2011-12-14
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* CarperIOHDF5: Correct stride in recoveryErik Schnetter2011-12-14
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* CarpetIOHDF5: Correct stride for grid arraysErik Schnetter2011-12-14
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* CarpetIOHDF5: Use hg::baseextent instead of Carpet::maxspacereflevelfactErik Schnetter2011-12-14
| | | | | | Use hg::baseextent instead of Carpet::maxspacereflevelfact to determine the stride of a refinement level, because this works independent of the stride on the finest level.
* * encapsulate read of potentially not present attributecott2011-12-14
| | | | | in an H5E_BEGIN_TRY H5E_END_TRY environment. This prevents hate crimes.
* CarpetIOHDF5: Store cell centering offset with grid function attributesErik Schnetter2011-12-14
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* CarpetIOHDF5: make sliced 3D output depend on out3D_XXXRoland Haas2011-12-14
| | | | rather than always ocuring together with the old-style 3D output.
* CarpetIOHDF5: Checkpoint and recover delta times (time step sizes)Erik Schnetter2011-12-14
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* CarpetIOHDF5: Check that MPI datatypes are defined before using themErik Schnetter2011-12-14
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* CarpetIOHDF5: Remove grid hierarchy consistency tests that don't apply hereErik Schnetter2011-12-14
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* CarpetIOHDF5: fix way hyperslab is computedRoland Haas2011-12-14
| | | | | to compute the hyperslab one needs to base its location on the extent of the data in memory not in the extent that we want to output.
* CarpetIOHDF5: make sure metadata matches old codeRoland Haas2011-12-14
| | | | | * add some attributes to metadata to match what the old code wrote * only tag object names with components of there are more than one
* CarpetIOHDF5: add option to not output the buffer zonesRoland Haas2011-12-14
| | | | | | | This is implemented by re-computing the allactive bboxset that dh::regrid computes and outputting only the part of each component that intersects allactive. This changes the number of components since the intersection might be non-rectangular-box.
* CarpetIOHDF5: add support for output on multiple processorsRoland Haas2011-12-14
| | | | | add code to honor IO::ioproc_every to output data unchunked (for 3d output only)
* CarpetIOHDF5: turn on 3d output in OutputSlice.ccRoland Haas2011-12-14
| | | | | | | | Register new-style output code as an IO method with IOUtil for 3d output. The new code is not quite as capable as the old code, since it does not include Ian Hinder's indexing facility and so far outputs all data on the root processor. It does support the new-style output_symmetry_points etc. options however.
* CarpetIOHDF5: Set times correctly after recoveringErik Schnetter2011-12-14
| | | | | | Recovery happens level-by-level in Cactus. When recovering the refinement level times and the global time, set them correctly according to the current refinement level.
* CarpetIOHDF5: Correct iorigin attributeErik Schnetter2011-12-14
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* CarpetIOHDF5: Index file supportIan Hinder2011-12-14
| | | | | | | | | | | | | Scanning the attributes of a large CarpetIOHDF5 output file, as is necessary in the visitCarpetHDF5 plugin, can be very time consuming. This commit adds support for writing an "index" HDF5 file at the same time as the data file, conditional on a parameter "CarpetIOHDF5::output_index". The index file is the same as the data file except it contains null datasets, and hence is very small. The attributes can be read from this index file instead of the data file, greatly increasing performance. The datasets will have size 1 in the index file, so an additional attribute (h5space) is added to the dataset to specify the correct dataset dimensions.
* CarpetIOHDF5: Correct error in outputting distributed grid arraysErik Schnetter2011-12-14
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* CarpetIOHDF5: Comment out unused local variableErik Schnetter2011-12-14
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* CarpetIOHDF5: Update to new dh classesErik Schnetter2011-12-14
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* CarpetIOHDF5: Remove explicit bboxset normalizationsErik Schnetter2011-12-14
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* CarpetIOHDF5: Initialise times on all time levels while recoveringErik Schnetter2011-12-14
| | | | | Initialise the times of all time levels of grid arrays while recovering.
* CarpetIOHDF5: Improve handling termination checkpointsErik Schnetter2011-12-14
| | | | | When checkpoints of initial data are disabled, but termination checkpoints are enabled, then do checkpoint the initial data.
* CarpetIOHDF5: Add comments and indent one lineErik Schnetter2011-12-14
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* Re-organise time level handlingErik Schnetter2011-12-14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Store the current Cactus time (and not a fake Carpet time) in the th "time hiearchy". This removes the now redundant "leveltimes" data structure in Carpet. Add past time levels to th, so that it can store the time for past time levels instead of assuming the time step size is constant. This allows changing the time step size during evolution. Share the time hierarchy between all maps, instead of having one time hierarchy per map. Simplify the time level cycling and time stepping code used during evolution. Improve structure of the code that loops over time levels for certain schedule bins. Introduce a new Carpet variable "timelevel", similar to "reflevel". This also makes it possible to avoid time interpolation for the past time levels during regridding. The past time levels of the fine grid then remain aligned (in time) with the past time levels of the coarse grid. This is controlled by a new parameter "time_interpolation_during_regridding", which defaults to "yes" for backwards compatibility. Simplify the three time level initialisation. Instead of initialising all three time levels by taking altogether three time steps (forwards and backwards), initialise only one past time level by taking one time step backwards. The remaining time level is initialised during the first time step of the evolution, which begins by cycling time levels, which drops the non-initialised last time level anyway. Update Carpet and the mode handling correspondingly. Update the CarpetIOHDF5 checkpoint format correspondingly. Update CarpetInterp, CarpetReduce, and CarpetRegrid2 correspondingly. Update CarpetJacobi and CarpetMG correspondingly.
* CarpetIOHDF5: Correct more attribute namesErik Schnetter2011-12-14
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* CarpetIOHDF5: Correct attribute nameErik Schnetter2011-12-14
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