aboutsummaryrefslogtreecommitdiff
path: root/Carpet/CarpetIOHDF5/src
Commit message (Collapse)AuthorAge
* CarpetIOHDF5: Do not use "map" as local variable nameErik Schnetter2007-01-12
| | | | | | | | Use "m" instead of "map" as local variable name. Remove "Carpet::" qualifier in front of variable "maps". darcs-hash:20070112224022-dae7b-0c5241b73c1f4a8ff4722e04bc70ed047d6158da.gz
* CarpetIOHDF5: support per-variable output compression levelsThomas Radke2006-11-17
| | | | | | | | | | | | | | | | | Implement variable-specific output request option 'compression_level' so that users can specify eg. IOHDF5::compression_level = 1 IOHDF5::out_vars = "admbase::metric admconstraints::hamiltonian admbase::lapse{ compression_level = 0 }" to request HDF5 dataset compression for every output variable except for the lapse. This modification also requires an update of thorn CactusBase/IOUtil. darcs-hash:20061117132206-776a0-0e1d07a85cf206fa262a94fd0dd63c6f27e50fa2.gz
* CarpetIOHDF5: support automatic gzip dataset compressionThomas Radke2006-11-17
| | | | | | | | | With the new steerable integer parameter IOHDF5::compression_level users can now request gzip dataset compression while writing HDF5 files: levels from 1-9 specify a specific compression rate, 0 (which is the default) disables dataset compression. darcs-hash:20061117115153-776a0-7aaead5d2a0216841a27e091fddb9b6c4f40eed4.gz
* CarpetIOHDF5: hdf5toascii_slicer now also provides 0D and 3D outputThomas Radke2006-10-05
| | | | darcs-hash:20061005133135-776a0-1550cde9db6e0a375b661b2ab6b0ed9c762bbe9d.gz
* CarpetIOHDF5: use aliased function Coord_GroupSystem() only optionallyThomas Radke2006-10-04
| | | | | | | If no thorn provided this aliased function, CarpetIOHDF5 assumes that no coordinate information is available. darcs-hash:20061004144616-776a0-00da12cca7d6b6ad1ae0a38a96923f771239de79.gz
* CarpetIOHDF5: Use new regridding API when recoveringErik Schnetter2006-09-25
| | | | darcs-hash:20060925220348-dae7b-303594fd2b999c93d2b816a9d3f11d0d97e391c2.gz
* CarpetIOHDF5: Cast size_t to int explicitlyErik Schnetter2006-09-25
| | | | darcs-hash:20060925220323-dae7b-040ddfb0afc83c15cd4802fe26fe4822826a2e8a.gz
* CarpetIOHDF5: Save grid structure in the output filesErik Schnetter2006-09-25
| | | | | | | Save grid structure in the output files whenever the parameters are saved, even when it is not a checkpoint file. darcs-hash:20060925220235-dae7b-09e23cc6ec48e20df0b560356f19648a67e955dd.gz
* CarpetIOHDF5: Add missing #include <cstring>Erik Schnetter2006-09-25
| | | | darcs-hash:20060925220415-dae7b-2b72aef51ae3d8b056b18221acd9989668a2864d.gz
* CarpetIOHDF5: added new option '--match <regex string>' in hdf5toascii_slicerThomas Radke2006-09-01
| | | | | | | | | | | | ../exe/wave/hdf5toascii_slicer [--match <regex string>] ... where [--match <regex string>] selects HDF5 datasets by their names matching a regex string using POSIX Extended Regular Expression syntax darcs-hash:20060901085302-776a0-3a9cfb71f9008b1a7bf93d9857195f92b67f1e25.gz
* CarpetIOHDF5: add support for integer datasets in hdf5toascii_slicerThomas Radke2006-08-31
| | | | darcs-hash:20060831174548-776a0-bf352f210d8736f48a666654309f0ad3443cf3a3.gz
* CarpetIOHDF5: hdf5toascii_slicer now allows 1D line extraction from 3D HDF5 ↵Thomas Radke2006-08-28
| | | | | | files darcs-hash:20060828173429-776a0-b231124b73645983b8ed56efa35d5ec2c9354add.gz
* CarpetIOHDF5: make hdf5toascii_slicer --help output more informativeJonathan Thornburg2006-08-22
| | | | | | | Clarify an ambiguity in the --help output: timestep selection is by cctk_time value, not by cctk_iteration darcs-hash:20060822142353-b0a3f-e0ad1ea0e2f4eca7038fc2d77b0ff3d724b97aab.gz
* CarpetIOHDF5: add missing #include to hdf5toascii_slicer utilityJonathan Thornburg2006-08-22
| | | | | | Adds a missing #include <cmath> so std::fabs() can be used darcs-hash:20060822114437-b0a3f-f85a976d02c36aa6311c7b6916aad107747954b2.gz
* CarpetIOHDF5: add timestep selection to hdf5toascii_slicer utilityThomas Radke2006-08-21
| | | | | | | The new command line parameter option '--timestep <timestep>' allows users to select an individual timestep in an HDF5 file. darcs-hash:20060821200601-776a0-8e977e93014eded2d6f6cab376209ce7d4293b94.gz
* CarpetIOHDF5: fix g++ compiler error and warnings in hdf5toascii_slicer.ccThomas Radke2006-08-21
| | | | | | | | While Intel C++ (9.0) had no problems compiling hdf5toascii_slicer.cc at all, GNU C++ generates an error when assigning -424242424242 to a long int. Also fixed some other things that g++ warns about. darcs-hash:20060821094951-776a0-84d68b511de0bbd65b212755d699a415779c9674.gz
* CarpetIOHDF5: #include <algorithm> in hdf5toascii_slicer.cc because sort() ↵Erik Schnetter2006-08-17
| | | | | | is used darcs-hash:20060817173012-dae7b-857f1313b12144e1ba997d029990a0464bb36df5.gz
* CarpetIOHDF5: added make.configuration.deps with rules to build utility programsThomas Radke2006-08-14
| | | | darcs-hash:20060814142824-776a0-1553d2404adc099fea75b546d4169f184dc5d3ab.gz
* CarpetIOHDF5: added utility program hdf5toascii_slicerThomas Radke2006-08-08
| | | | | | | This utility program extracts 2D slices from CarpetIOHDF5 output files and prints them to stdout in CarpetIOASCII format. darcs-hash:20060808123300-776a0-4088993ec64ad291510977ee5c10d521863ef2ac.gz
* CarpetIOHDF5: fix bug in deletion of recovery fileThomas Radke2006-06-26
| | | | | | | | | | | Due to bug in my previous patch, the logic for removing the checkpoint file after successful recovery was wrong: it was removed if IO::recover_and_remove was set to "false". This patch fixes this bug by reversing the logic. Thanks to Ian Hinder for noticing this and presenting the fix. darcs-hash:20060626162548-776a0-8d3ebc0c43a74cb3faa892aa2a410e13bb37825e.gz
* CarpetIOHDF5: Remove unused local variableErik Schnetter2006-06-13
| | | | darcs-hash:20060613171412-dae7b-cf8a7c6112d6c364bd7f4e7568e0df2c683c01f3.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: don't try to recover variables in groups which have no grid ↵Thomas Radke2006-05-12
| | | | | | points (zero size) darcs-hash:20060512115514-776a0-dba29d6e31a12d4cff6772e69bd1ef54e3aa2d8b.gz
* CarpetIOHDF5: fix the HDF5 library version test when determining the ↵Thomas Radke2006-05-11
| | | | | | | | | datatype for H5Sselect_hyperslab() arguments This patch lets you compile CarpetIOHDF5 also with HDF5-1.8.x (and future versions). darcs-hash:20060511172957-776a0-acbc1bd6b8d92223c0b52a43babf394c0ab9b0f4.gz
* CarpetIOHDF5: Delay check whether storage is enabledErik Schnetter2006-05-11
| | | | | | | Check whether a group has storage only after checking whether it should be output. darcs-hash:20060511203215-dae7b-20604fda3117034cccf38998561b7e3bed1e6873.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: better optimisation during recoveryThomas Radke2006-02-17
| | | | | | | | | When recovering from a checkpoint, each processor now continuously reads through all chunked files until all grid variables on this processor have been fully recovered. This should always minimise the number of individual checkpoint files necessary to open on each processor. darcs-hash:20060217160928-776a0-28c076749861c0b26d1c41a6f4ef3bdb00c23274.gz
* CarpetIOHDF5: more efficient recovery with same number of processorsThomas Radke2006-02-12
| | | | | | | | This patch introduces some optimisation for the case when recovering with the same number of processors as used during the checkpoint: each processor opens only its own chunked file and reads its metadata, skipping all others. darcs-hash:20060212200032-776a0-3dd501d20b8efb66faa715b401038218bb388b4f.gz
* CarpetIOHDF5: fix small memory leak in HDF5 outputThomas Radke2006-02-12
| | | | | | While outputting dataset attributes, an HDF5 dataspace wasn't closed properly. darcs-hash:20060212143008-776a0-41e46c61bce2dc22fbfc7093d2ad776bfae00687.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: remove deprecated I/O parametersThomas Radke2006-02-06
| | | | | | | | | | | This patch finally closes the long-standing issue of keeping both old and new CarpetIOHDF5 parameters around. Now the old parameters have been removed, only the new ones can be used further on. If you still have old-style parameter files, you must convert them now. The perl script CarpetIOHDF5/srcutil/SubstituteDeprecatedParameters.pl does that for you automatically. darcs-hash:20060206184519-776a0-29d9d612e011dda4bf2b6054cee73546beae373a.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: fix warnings about incompletely read variablesThomas Radke2006-02-01
| | | | | | | | When the filereader was used, CarpetIOHDF5 still checked all grid variables whether they had been read completely from a datafile, even those which weren't even specified in the IO::filereader_ID_vars parameter. darcs-hash:20060201174945-776a0-faa9fe295ef273ffd38308bbda7fde092503513c.gz
* CarpetIOHDF5: raise the warning level from 2 (COMPLAIN) to 1 (ALERT) for ↵Thomas Radke2006-01-27
| | | | | | warnings about the use of deprecated I/O parameters darcs-hash:20060127164814-776a0-89f59f04f6118191ba7a965cf72e3c6c548c817d.gz
* CarpetIOHDF5: fix recovery of multiple map grid variablesThomas Radke2006-01-20
| | | | | | | | | | | The recovery code didn't properly recover grid functions with multiple maps: all maps were initialised with the data from map 0. This patch fixes the problem so that checkpointing/recovery should work now also for multipatch applications. The patch only affects recovery code, meaning it will also work with older checkpoint files. darcs-hash:20060120164515-776a0-68f93cb5fb197f805beedfdc176fd8da9b7bfc49.gz
* CarpetIOHDF5: Put unique build ID into output filesErik Schnetter2005-11-19
| | | | darcs-hash:20051119212808-dae7b-023ea8552306cda54ab6204ee338809a55228a3b.gz
* CarpetIOHDF5: Remove unused local variable in Input.ccErik Schnetter2005-11-19
| | | | darcs-hash:20051119212959-dae7b-d50e2cc4c8a980720b44cfafd9504eb201e3aa8b.gz
* CarpetIOHDF5: Change #include "hdf5.h" to <hdf5.h>Erik Schnetter2005-11-19
| | | | darcs-hash:20051119212924-dae7b-3447198d7a1d4090ffc6cff4cde12ccf037c5e8f.gz
* CarpetIOHDF5: bugfix in recovery codeThomas Radke2005-11-20
| | | | | | | | Before reading a variable from a dataset, also check that its timelevel is valid. This fixes problems when recovering from a checkpoint (created with 'Carpet::enable_all_storage = true') and this boolean parameter set to 'false'. darcs-hash:20051120134642-776a0-4fe21611ca733ecb42f8e2a82bfa1fe51a5d9e81.gz
* CarpetIOHDF5: bugfix in checkpointing codeThomas Radke2005-11-16
| | | | | | | Don't remove an initial data checkpoint file if IO::checkpoint_keep is set to a value larger 0. darcs-hash:20051116133326-776a0-5fa5bd333cd26434609e920cf49434551db9ff2e.gz
* CarpetIOHDF5: implement "out_unchunked" option for individual variables to ↵Thomas Radke2005-10-05
| | | | | | | | | | be output Apart from setting the parameter IO::out_unchunked to choose the output mode for all variables, this can be overridden for individual variables in an option string appended to the variable's name in the IOHDF5::out_vars parameter. darcs-hash:20051005100152-776a0-9f6f2e4b691a46b12aefab555440625f39836aaf.gz
* CarpetIOHDF5: respect setting of out_unchunked parameter also in ↵Thomas Radke2005-09-18
| | | | | | | | | | single-processor runs For single-processor runs, CarpetIOHDF5 unconditionally wrote HDF5 output files in unchunked format. Like for multi-processor runs, the user can now choose between chunked and unchunked through the out_unchunked parameter. darcs-hash:20050918214401-776a0-882e8b1e6dcee4d25330bc11d4b6973e297f1a52.gz
* CarpetIOHDF5: don't checkpoint variables tagged as 'checkpoint="no"'Thomas Radke2005-09-13
| | | | darcs-hash:20050913162936-776a0-7b3fa7d3f08c37321b6ea836178168131fa98964.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
* Carpet*: generalise the comm_state class for collective buffer communicationsThomas Radke2005-08-15
| | | | | | | | | CarpetLib's comm_state class (actually, it's still just a struct) has been extended to handle collective buffer communications for all possible C datatypes at the same time. This makes it unnecessary for the higher-level communication routines to loop over each individual datatype separately. darcs-hash:20050815150023-776a0-dddc1aca7ccaebae872f9f451b2c3595cd951fed.gz
* CarpetIOHDF5: optimise I/O accesses for the case when all processors recover ↵Thomas Radke2005-07-28
| | | | | | | | | | | | | | from a single chunked checkpoint file The list of HDF5 datasets to process is now reordered so that processor-local components are processed first. When processing the list of datasets, only those will be reopened from which more data is to be read. The check when a variable of a given timelevel has been fully recovered was improved. This closes http://bugs.carpetcode.org/show_bug.cgi?id=87 "Single-file, many-cpu recovery very slow". darcs-hash:20050728122546-776a0-21dfceef87e12e72b8a0ccb0911c76066521e192.gz
* Carpet{IOScalar,IOHDF5,IOStreamedHDF5}: use C++ strings (rather than ↵Thomas Radke2005-07-26
| | | | | | | | | | | | Util_asprintf()) to construct C output strings There was a small memory leak in using Util_asprintf() to continuously append to an allocated string buffer. The code has now been rewritten to use C++ string class objects which are destroyed automatically. This closes http://bugs.carpetcode.org/show_bug.cgi?id=89. darcs-hash:20050726122331-776a0-874ccd0d5766b85b1110fcd6f501a7e39c35e965.gz
* CarpetIOHDF5: remove an old checkpoint only if the current one has been ↵Thomas Radke2005-07-25
| | | | | | written successfully by all output processors darcs-hash:20050725150549-776a0-fe03ace195af6a723af91ca7d0a63eaeae25b050.gz
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-02 14:34:48 +0000