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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: Store cell centering offset with grid function attributesErik Schnetter2011-12-14
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* CarpetIOHDF5: Checkpoint and recover delta times (time step sizes)Erik Schnetter2011-12-14
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* 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: 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.
* 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: Allow different numbers of ghost zones on different levelsErik Schnetter2011-12-14
| | | | | | | Allow different numbers of ghost zones and different spatial prolongation orders on different refinement levels. This causes incompatible changes to the checkpoint file format.
* Import CarpetErik Schnetter2011-12-14
| | | | Ignore-this: 309b4dd613f4af2b84aa5d6743fdb6b3
* CarpetIOHDF5: Change order in which scheduled functions are declaredErik Schnetter2008-09-05
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* Schedule the initialisation of checkpointing interval counterThomas Radke2008-09-02
| | | | | | | | variables also in the POST_RECOVER_VARIABLES bin so that the last checkpoint iteration counter starts counting from the recovered iteration number. (see also discussion thread starting at http://lists.carpetcode.org/archives/developers/2008-August/002309.html)
* CarpetIOHDF5: Use CCTK_REAL instead of long long for timing measurementsErik Schnetter2008-01-30
| | | | darcs-hash:20080130222154-dae7b-113029d4e40be633fca3253f5e2d47f656ae41ac.gz
* CarpetIOHDF5: Produce fewer warnings with HDF5 1.8 librariesErik Schnetter2008-01-30
| | | | darcs-hash:20080130222322-dae7b-223b30e93a6f7860c1234ed181453c77b1ee056e.gz
* CarpetIOHDF5: Make macro "HDF5_ERROR" safeErik Schnetter2008-01-11
| | | | | | | Enclose the macro "HDF5_ERROR" in a do { ... } while (0) pair to make it safe to use with a trailing semicolon. darcs-hash:20080111111512-dae7b-b65c7b375ee6ac882b59414db2810f06fcc3d799.gz
* Temporary hack to fix hdf5-1.8.0-beta5 compatibility issuescott2007-11-30
| | | | darcs-hash:20071130052144-fff0f-57258dcf6536be5b2d8a14f2a5ef5be56d6f038f.gz
* CarpetIOHDF5: Record time spent in I/OErik Schnetter2007-10-03
| | | | darcs-hash:20071003194857-dae7b-d8bb68e9c4ee52559fea874b3f80a57eebf9650f.gz
* CarpetIOHDF5: evaluate IO::recover_and_remove parameterThomas Radke2006-06-07
| | | | | | | If IO::recover_and_remove is set, the recovery file will also be removed after IO::checkpoint_keep successful checkpoints have been written. darcs-hash:20060607102431-776a0-92edd93f6dc004ab824b237fbd03ee732f7a3841.gz
* CarpetIOHDF5: Correct handling of "use_grid_structure_from_checkpoint"Erik Schnetter2006-05-08
| | | | | | | Correct errors in the handling of the parameter "use_grid_structure_from_checkpoint". darcs-hash:20060508193609-dae7b-c5cf907171eb31e8298669cf4bd4aa03f2c79429.gz
* CarpetIOHDF5: Add parameter "use_grid_structure_from_checkpoint"Erik Schnetter2006-04-13
| | | | | | | | | | | Add a parameter "use_grid_structure_from_checkpoint" that reads the grid structure from the checkpoint file, and sets up the Carpet grid hierarchy accordingly. The Carpet grid hierarchy is written unconditionally to all checkpoint files. darcs-hash:20060413202124-dae7b-f97e6aac2267ebc5f5e3867cbf78ca52bbd33016.gz
* CarpetIOHDF5: fix declaration of scheduled routineThomas Radke2006-02-09
| | | | | | | | | | | | The scheduled routine CarpetIOHDF5_CloseFiles() was declared to return an int and take no arguments. Instead it must be declared to take a 'const cGH* const' argument. It should also return void. See http://www.cactuscode.org/old/pipermail/developers/2006-February/001656.html. This patch also fixes a couple of g++ warning about signed-unsigned integer comparisons. darcs-hash:20060209165534-776a0-24101ebd8c09cea0a9af04acc48f8e2aa2961e34.gz
* CarpetIOHDF5: bugfix for writing checkpointsThomas Radke2006-02-06
| | | | | | | | Accumulate any low-level errors returned by HDF5 library calls and check them after writing a checkpoint. Do not remove an existing checkpoint if there were any low-level errors in generating the previous one. darcs-hash:20060206183846-776a0-549e715d7a3fceafe70678aaf1329052dce724bb.gz
* CarpetIOHDF5: Change #include "hdf5.h" to <hdf5.h>Erik Schnetter2005-11-19
| | | | darcs-hash:20051119212924-dae7b-3447198d7a1d4090ffc6cff4cde12ccf037c5e8f.gz
* CarpetIOHDF5: fixed a problem with IOHDF5::use_reflevels_from_checkpoint = ↵Thomas Radke2005-09-06
| | | | | | | | | | | "yes" during recovery When IOHDF5::use_reflevels_from_checkpoint is set, the parameter CarpetLib::refinement_levels is steered to take the number of levels found in the checkpoint. This steering used to happen during parameter recovery where it didn't have any effect if the parameter had been set in the parfile already. Now it's done in a separate routine scheduled at STARTUP. darcs-hash:20050906140808-776a0-bae608c103b161ac67690da2a8803bdff84cf2f4.gz
* CarpetIOHDF5: bugfix for outputting the same variable into multiple filesThomas Radke2005-08-23
| | | | | | | | | | Before a variable is output it is checked whether it has been output already during the current iteration (eg. due to triggers). This check was only variable-based and therefore caused problems when the same variable was to be output to multiple files (using different alias names). Now the check has been extended to also take the output filenames into account. darcs-hash:20050823135345-776a0-1555987b4aee34bb646e67f491375dbcc44dddad.gz
* CarpetIOHDF5: implement parallel I/OThomas Radke2005-06-24
| | | | | | | | | | | | | | Like CactusPUGHIO/IOHDF5, CarpetIOHDF5 now also provides parallel I/O for data and checkpointing/recovery. The I/O mode is set via IOUtils' parameters IO::out_mode and IO::out_unchunked, with parallel output to chunked files (one per processor) being the default. The recovery and filereader interface can read any type of CarpetIOHDF5 data files transparently - regardless of how it was created (serial/parallel, or on a different number of processors). See the updated thorn documentation for details. darcs-hash:20050624123924-776a0-5639aee9677f0362fc94c80c534b47fd1b07ae74.gz
* CarpetIOHDF5: added logic to keep specific checkpoints aroundThomas Radke2005-06-10
| | | | | | | | The parameter IO::checkpoint_keep is steerable at any time now (after you've updated CactusBase/IOUtil/param.ccl) so that you can keep specific checkpoints around. Please see the thorn documentation of CactusBase/IOUtil for details. darcs-hash:20050610091144-776a0-b5e90353851eb1d7871f16b05d1b47748599d27a.gz
* CarpetIOHDF5: implement parallel recoveryThomas Radke2005-05-27
| | | | | | | All processors open the checkpoint file and recover their portions from it in parallel. No MPI communication is needed anymore. darcs-hash:20050527124239-776a0-25d4fa77b50ea22fb2b25c87e399d95090c7eaf2.gz
* CarpetIOHDF5: bugfix for checkpoint/recoveryThomas Radke2005-04-12
| | | | | | | | | | | | | | | | | | | | | | | CarpetIOHDF5 used to output unchunked data only, ie. all ghostzones and boundary zones were cut off from the bboxes to be output. This caused problems after recovery: uninitialized ghostzones led to wrong results. The obvious solution, calling CCTK_SyncGroup() for all groups after recovery, was also problematic because that (1) synchronised only the current timelevel and (2) boundary prolongation was done in a scheduling order different to the regular order used during checkpointing. The solution implemented now by this patch is to write checkpoint files always in chunked mode (which includes all ghostzones and boundary zones). This also makes synchronisation of all groups after recovery unnecessary. Regular HDF5 output files can also be written in chunked mode but the default (still) is unchunked. A new boolean parameter IOHDF5::out_unchunked (with default value "yes") was introduced to toggle this option. Note that this parameter has the same meaning as IO::out_unchunked but an opposite default value. This is the only reason why IOHDF5::out_unchunked was introduced. darcs-hash:20050412161430-776a0-d5efd21ecdbe41ad9a804014b816acad0cd71b2c.gz
* CarpetIOHDF5: Use CCTK_REAL instead of double for meta dataErik Schnetter2005-04-11
| | | | | | | | Use the type CCTK_REAL instead of double for storing meta data in the HDF5 files. This is necessary if CCTK_REAL has more precision than double. darcs-hash:20050411170627-891bb-374e4c2581155d825f9a1925b1d4319051bc36d6.gz
* CarpetIOHDF5: write a "carpet_version" integer attribute to tag data output ↵Thomas Radke2005-02-14
| | | | | | and checkpoint files darcs-hash:20050214163413-776a0-77171dd6e4746b5d889bfcbe515c0d6f59c6ba10.gz
* global: Remove $Header$ keywords from Carpet arrangementErik Schnetter2005-01-01
| | | | darcs-hash:20050101162121-891bb-ac9d070faecc19f91b4b57389d3507bfc6c6e5ee.gz
* CarpetIOHDF5: allow individual output frequencies in option strings, give ↵tradke2004-12-01
| | | | | | some better info output for IO::verbose = "full" darcs-hash:20041201113424-3fd61-188206cd3e0ad315a9219fbc1b123af8ab5bff62.gz
* CarpetIOHDF5: some code cleanuptradke2004-11-30
darcs-hash:20041130150933-3fd61-b07a8e91c055082ff3ddebccf11a07d368c7b47c.gz
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