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* Introduce a tree data structure to speed up domain decompositionErik Schnetter2008-06-20
| | | | | | | | | Introduce a tree data structure "fulltree", which decomposes a single, rectangular region into a tree of non-overlapping, rectangular sub-regions. Move the processor decomposition from the regridding thorns into Carpet. Create such trees during processor decomposition. Store these trees with the grid hierarchy.
* CarpetIOHDF5: Correct recovery error when Carpet::regrid_in_level_mode=noErik Schnetter2008-06-17
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* Merge branch 'master' of carpetgit@carpetcode.dyndns.org:carpetErik Schnetter2008-06-15
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| * Fixed "origin" and "delta" output attributes to workChristian Reisswig2008-06-11
| | | | | | | | for generalized grids.
* | CarpetIOHDF5: Correct error in determining checkpointing intervalErik Schnetter2008-06-02
|/ | | | Correct error in determining checkpointing interval after restarting.
* don't evaluate the IO::out_single_precision parameter when outputting ↵Thomas Radke2008-05-26
| | | | integer-type grid variables
* CarpetIOHDF5: Take regrid_in_level_mode into account when recoveringErik Schnetter2008-05-21
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* CarpetIOHDF5: Implement checkpoint_every_walltime_hoursErik Schnetter2008-05-12
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* also include HDF5 in the active thorns listThomas Radke2008-03-18
| | | | This isn't necessary but very convenient to generate complete thornlists with the MakeThornList script.
* update example parfiles so that they work again with the newest Carpet versionThomas Radke2008-03-18
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* add missing file info header lines in CarpetIOHDF5 testsuite filesThomas Radke2008-03-17
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* fixed output files so that they reflect WaveToy's new timelevel ↵Thomas Radke (AEI)2008-03-17
| | | | initialisation scheme (ie. explicite initialisation of all three timelevels, resulting in slightly different output data)
* recreated checkpoint file because the grid structure parameter format has ↵Thomas Radke (AEI)2008-03-17
| | | | changed
* - also activate thorn InitBase and set Carpet::init_each_timelevel = "yes"Thomas Radke (AEI)2008-03-17
| | | | - don't output sum norms (not suitable for testsuites)
* CarpetIOHDF5: Adapt to API change in Carpet::MakeMultigridBoxesErik Schnetter2008-02-20
| | | | darcs-hash:20080220003219-dae7b-0505c565d4989163b001ee53b1ff6577211649f1.gz
* CarpetIOHDF5: Change some CCTK_REAL to double to make HDF5 native typesErik Schnetter2008-02-19
| | | | | | | Change some CCTK_REAL variables to double, because they are read by HDF5 routines as "native double". darcs-hash:20080219052326-dae7b-0bca03938f51c0ed598e671f5278659e6e051827.gz
* CarpetIOHDF5: Make code saferErik Schnetter2008-02-19
| | | | | | Change sprintf to snprintf. Add assert statements. darcs-hash:20080219052249-dae7b-abbdbb9df6c099cdd62ebaac135b654062659619.gz
* CarpetIOHDF5: Re-organise HDF5 attribute writingErik Schnetter2008-02-19
| | | | | | | Add functions which write a single HDF5 attribute. Call these functions to write the attributes. darcs-hash:20080219052032-dae7b-dbb3e2ee3aad27cce26735639b9065c86cc9cef3.gz
* CarpetIOHDF5: Add the new Formaline ids to the output filesErik Schnetter2008-02-03
| | | | | | | Write attributes containing the configuration, source tree, and run ids into the output files. darcs-hash:20080203190955-dae7b-e22cbe007b26040e7131b1f93307382dc0cc5882.gz
* Checkpointing: Fix creative permutation of arguments in call to WriteMetaDatacott2008-02-03
| | | | | | | Fix creative change of argument order to a call to WriteMetaData which resulted in nioprocs=-1. This should fix checkpoint/recovery. darcs-hash:20080203024904-fff0f-5d3514b62c80cd2920ac45a98758fff8c00135c1.gz
* Bugfix to MapIsCartesian-Attributereisswig2008-01-31
| | | | | | | Without this bugfix, whenever there is an aliased function "Multipatch_MapIsCartesian" function, the corresponding write call of this attribute fails because the attribute's scalar dataspace was already closed. darcs-hash:20080131151816-79e7e-3678879958c776fc1240e8b93f054732c64b62c5.gz
* 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: Use new-style communication routinesErik Schnetter2008-01-30
| | | | darcs-hash:20080130221846-dae7b-08cd77d33269fc3ec8d20db87731b2b2097d5d38.gz
* CarpetIOHDF5: Add attribute specifying whether coordinate system is CartesianErik Schnetter2008-01-28
| | | | | | | | Add an HDF5 attribute "MapisCartesian" specifying whether the coordinate system is Cartesian. This attribute is added if there is a thorn providing this information. darcs-hash:20080128155820-dae7b-759cc1608ba8a7c9d34203b114ceb3836db0f64d.gz
* CarpetIOHDF5: choose HDF5 1.6 API when compiling utilities with HDF5 1.8tradke2008-01-23
| | | | darcs-hash:20080123132645-3fd61-ed195918c2c55889623aaf2195237e2ff7bd6e17.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
* CarpetIOHDF5: Output additional attribute "Datasets"Erik Schnetter2008-01-11
| | | | | | | | Output an additional attribute "Datasets" into the "Parameters and Global Attributes" group. This attribute is an array of strings and contains the full variable names of all variables in this file. darcs-hash:20080111111324-dae7b-895d9c619e1f2126ea367cb93b77f407d50f15b4.gz
* Temporary hack to fix hdf5-1.8.0-beta5 compatibility issuescott2007-11-30
| | | | darcs-hash:20071130052144-fff0f-57258dcf6536be5b2d8a14f2a5ef5be56d6f038f.gz
* CarpetIOHDF5: #include <cstring>Erik Schnetter2007-11-02
| | | | darcs-hash:20071102224421-dae7b-79e89575a8e23c46fea47ef043d28ab7331da985.gz
* CarpetIOHDF5: workaround for excessive HDF5-internal memory requirements ↵tradke2007-10-19
| | | | | | | | | | | | | | | | | | | | | | | during recovery Various people had reported problems of running out of memory when recovering from multiple chunked checkpoint files. It turned out that the HDF5 library itself requires a considerable amount of memory for each opened HDF5 file. When all chunked files of a checkpoint are opened at the same time during recovery (which is the default) this may cause the simulation to abort with an 'out of memory' error in extreme cases. This patch introduces a new steerable boolean parameter IOHDF5::open_one_input_file_at_a_time which, if set to "yes", will tell the recovery code to open/read/close chunked files one after another for each refinement level, thus avoiding excessive HDF5-internal memory requirements due to multiple open files. The default behaviour is (as before) to keep all input files open until all refinement levels are recovered. darcs-hash:20071019091424-3fd61-834471be8da361b235d0a4cbf3d6f16ae0b653f0.gz
* CarpetIOHDF5: fix memory leak in recovery codetradke2007-10-18
| | | | | | | The new code to collect I/O timing statistics introduced a memory leak while accumulating the number of bytes transfered. darcs-hash:20071018115734-3fd61-e087a4ad1c8fdcf8a59320b71f90b92e9fd850de.gz
* CarpetIOHDF5: Correct inconsistency in tracking I/O timingErik Schnetter2007-10-04
| | | | darcs-hash:20071004024754-dae7b-2096582f0b63bd0521d41e3eea01e74f7962bf79.gz
* CarpetIOHDF5: Record time spent in I/OErik Schnetter2007-10-03
| | | | darcs-hash:20071003194857-dae7b-d8bb68e9c4ee52559fea874b3f80a57eebf9650f.gz
* CarpetIOHDF5: Remove unused variablesErik Schnetter2007-10-03
| | | | darcs-hash:20071003194834-dae7b-f9a5ba7a3c9c3b0542a9cc316d5854d961d15baa.gz
* CarpetIOHDF5: Add a timer around OutputGHErik Schnetter2007-08-25
| | | | darcs-hash:20070825060808-dae7b-9ea6675a36f9230332067acdb705d48e75d12fd2.gz
* CarpetIOHDF5: Initialise list of variables which need to be synchronisedErik Schnetter2007-08-23
| | | | | | | Initialise the list of variables which need to be synchronised after recovery correctly. darcs-hash:20070823210422-dae7b-31da5366355d1bfbea2e4181b8639c5b4e6caf0c.gz
* CarpetIOHDF5: Synchronise after recoveringErik Schnetter2007-06-08
| | | | | | | Synchronise the recovered grid functions. This removes the need for calling the postregrid bin after recovering. darcs-hash:20070608201848-dae7b-4d2044344f7e8e9a30ca60780199f2906a58d957.gz
* CarpetIOHDF5: Add utility HDF5-to-ASCII converter againErik Schnetter2007-05-30
| | | | | | The HDF5-to-ASCII converter was accidentally removed. darcs-hash:20070530133215-dae7b-b1da3480a9a963ad78bc8cf02f5150389e19d286.gz
* CarpetIOHDF5: Remove make.configuration.defnErik Schnetter2006-08-08
| | | | | | | Remove the make.configuration.defn file. Configuration dependencies are now handled by the configuration.ccl file. darcs-hash:20060808151859-dae7b-525b7e54c2f3c771bba2acdb7b11c9fd0c1dc8c6.gz
* CarpetIOHDF5: Require capability HDF5Erik Schnetter2005-11-19
| | | | | | | Require the capability HDF5 instead of testing whether HDF5 was configured in. darcs-hash:20051119212528-dae7b-5600109d2e5fc5c89477fd1b4a978d39f3aed555.gz
* CarpetIOHDF5: Say "simulation time" instead of "physical time"Erik Schnetter2007-05-23
| | | | darcs-hash:20070523204447-dae7b-364638404dec31fbf3f0db103d930fc60c13ad65.gz
* CarpetIOHDF5: Output unsuccessful file names when reading initial dataErik Schnetter2007-05-23
| | | | | | | | | When no files can be found when reading initial data from files, then output all files names that were tried. Since the file names are constructed dynamically, this makes it easier to find errors in parameter files. darcs-hash:20070523204234-dae7b-676f945408731a162d2795ab2559b012eaf4fcaf.gz
* CarpetIOHDF5: Make use_grid_structure_from_checkpoint the defaultErik Schnetter2007-05-23
| | | | | | | Make CarpetIOHDF5::use_grid_structure_from_checkpoint=yes the default setting. darcs-hash:20070523204057-dae7b-80c06a4a883db327ce7768f3363ebccfbc3b0dd6.gz
* CarpetIOHDF5: add option to output one file per grouptradke2007-04-30
| | | | | | | | A new steerable boolean parameter IOHDF5::out_one_file_per_group was added which - if set to "true" - will cause Cactus to output all variables of a group into a single HDF5 file (useful to reduce the total number of output files). darcs-hash:20070430162902-3fd61-f8c3e4cd641c40e8afe859933e611cda50c52efe.gz
* CarpetIOHDF5: Correct error in setting up gdata communication objectErik Schnetter2007-05-01
| | | | | | Set up gdata object correctly before copying it between processors. darcs-hash:20070501163757-dae7b-55cb3575d707f88806bff70f4cfc7153de879c1f.gz
* CarpetIOHDF5: Checkpoint and restore each level's current timeErik Schnetter2007-04-19
| | | | darcs-hash:20070419021113-dae7b-baa8e7a012bddab40246f9485d5b3987fd7dc587.gz
* CarpetIOHDF5: Allow IO::out_dir to be steerableErik Schnetter2007-04-19
| | | | darcs-hash:20070419021042-dae7b-fa34acf3bf956f5b07a74e882f1cb0663f2826dd.gz
* CarpetIOHDF5: abort after I/O errors if requested by the userThomas Radke2007-04-18
| | | | | | | | | | | | By setting the new steerable boolean parameter IO::abort_on_io_errors to true in a parfile, the user can now tell the simulation to abort in case of any I/O errors while writing HDF5 output/checkpoint files. The default is to only warn about such errors and continue the simulation. This patch requires an up-to-date CVS version of thorn CactusBase/IOUtil from which the parameter IO::abort_on_io_errors is inherited. darcs-hash:20070418155052-776a0-554152ad445c5215daac96e8fa2b55f06318d0c1.gz
* CarpetIOHDF5: omit sum norms in the testsuites' reduction outputThomas Radke2007-02-23
| | | | | | | | | In order to make the recovery testsuites pass, one would have to specify a rather large absolute tolerance for the sum norms. Since this isn't possible for an individual norm, I decided to omit the output of sum norms entirely. darcs-hash:20070223165809-776a0-83dbbb59855996cec51bd6b9da945d4bf467bd4e.gz
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