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* add option "alias" to read datasets into different variablesrhaas2013-08-10
| | | | | | | | | | | | | | | Extents the file readers capabilities to not only take a cctk_iteration string but also a string alias. A value of IO::filereader_vars = "hydrobase::vel[0]{alias=admbase::shiftx}" will read the datasets admbase::shiftx into the variable hydrobase::vel[0]. The idea is to be able to read variables of evolution thorns into postprocessing thorns. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@304 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* abort run when user tries to change a non-steerable parameter during recoveryrhaas2013-07-04
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@303 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Add TODO item relating to checking the return value of CCTK_ParameterFilenamehinder2013-01-07
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@294 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Increase string buffer sizes for parameter file nameeschnett2012-12-26
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@293 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Report error when parameter file cannot be writteneschnett2012-11-20
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@292 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* IOUtil: abort IOUtil_TruncateOutputFiles if called too earlyrhaas2012-06-11
| | | | | | | | | | | | | | | | | | | | | | | currently when called before the grid extension for IOUtil has been registered (which is when IOUtils learns if the is a checkpoint recovery run or not), the routine returns -1. However the documentation in the thorn guide states that Thorn IOUtil provides an aliased function for other I/O thorns to call: CCTK_INT FUNCTION IO_TruncateOutputFiles (CCTK_POINTER_TO_CONST IN cctkGH) This function simply returns 1 or 0 if output files should or should not be truncated. Since there are thorns out there that take this to heart and test for IO_TruncateOutputFiles() being true (ie non-zero) these thorns always overwrite data during a recovery when calling IOUtils too early. This happened to Carpet in ticket #908. The attached patch makes IOUtil abort instead which seems better than silently returning the wrong (since undocumented) answer. No actual user thorn should be affected. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@289 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Remove unused variableeschnett2012-05-11
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@287 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* make checkpoint_dir steerable. This requires the checkpoint_dir to be ↵knarf2012-01-11
| | | | | | created not only at startup, and the only point in which this can be helped with in this thorn is in IOUtil_AssembleFilename() which is called by using thorns to get the file name of the checkpoint - this is repeated there now git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@286 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* IOUtil: Advertise that this is the new version of this APIschnetter2009-12-05
| | | | | | | | | | Advertise that this is the new version of this API, which has 'out_dt' arguments in certain IOUtil_* functions: #define IOUTIL_PARSER_HAS_OUT_DT 1 git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@275 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* IOUtil: Update parsing API to allow output by simulation timeschnetter2009-12-05
| | | | | | | | | Update the parsing API to allow output by simulation time (out_dt) in addition to output by iteration (out_every). This adds an additional parameter to IOUtil_ParseVarsForOutput. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@274 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Make error message clearer: mention that it does not try to read from the ↵knarf2009-08-12
| | | | | | given filename, but that what was given is only the basefilename git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@273 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Make error message clearer: mention that it does not try to read from the ↵knarf2009-08-12
| | | | | | given filename, but that what was given is only the basefilename git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@272 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* bugfix: remove correct key from options list table in routine SetOutputVar()tradke2009-05-18
| | | | | | | | so that no false warning is issued anymore about an option with unrecognized key 'reductions' git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@270 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* extend IOUtil_ParseVarsForOutput() to parse an options string for a list oftradke2009-04-21
| | | | | | | | reductions (to be used in scalar output methods) This applies patch http://www.cactuscode.org/old/pipermail/patches/2009-April/000259.html. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@269 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* preallocate buffer in IOUtil_GetAllParameters(), to prevent too many subsequenttradke2008-10-17
| | | | | | | reallocs which may cause unnecessary memory fragmentation git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@261 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Change level 1 warning about non-existing directory to info messageschnetter2008-02-29
| | | | | | | when "autoprobe" is used git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@258 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Correct signatures of scheduled functionsschnetter2008-02-29
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@257 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Correct signatures of scheduled functionsschnetter2008-02-29
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@256 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Correct small (probably inconsequential) memory leak in recoveryschnetter2008-02-15
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@255 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Explicitly convert size_t to intschnetter2008-01-28
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@254 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* check for a valid cctkGH pointer passed into IOUtil_RecoverVarsFromDatafiles()tradke2007-06-01
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@253 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Implement variable-specific output request option 'compression_level'tradke2006-11-17
| | | | | | | | | | | | | | | | 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 is currently supported only by PUGH's and Carpet's HDF5 I/O thorns. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@250 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Make only optional use of aliased function Coord_GetDefaultSystem().tradke2006-10-04
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@249 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Fixed a small memory leak in evaluation of option strings of I/O parameters.tradke2006-09-04
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@248 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Properly encode/decode non-printable characters as 3-digit octal numberstradke2006-08-30
| | | | | | | | in a parameter string to be checkpointed/recovered. Thanks to Erik Schnetter for this patch. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@247 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* In DecodeString, convert char to unsigned char before printing it asschnetter2006-08-25
| | | | | | | | | | integer. This ensures that there are no negative numbers. Check for errors, and clean up and emit a warning and return NULL in such a case. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@246 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* When encoding a non-printable character in a string, create aschnetter2006-08-25
| | | | | | | | zero-padded escape sequence ("\010") instead of a blank-padded one ("\ 10"). git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@245 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Have IOUtil_GetAllParameters() encode parameter values before concatenatingtradke2006-08-25
| | | | | | | | | | | "<parameter> = <value>" pairs by a newline delimiter, and its complement IOUtil_SetAllParameters() do the reverse. This fixes problems with checkpointing/recovery when parameter values themself contained newlines. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@244 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Create the default output directory on all processors if IO::out_mode isn't settradke2006-07-03
| | | | | | | to "onefile". git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@243 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Fix evaluation of IO::truncate_files_after_recovering and IO::truncate_filestradke2006-06-08
| | | | | | | paramters in IO_TruncateOutputFiles(). git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@242 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Introduce new boolean parameter IO::truncate_files.tradke2006-05-11
| | | | | | | | | | | | | | | | | Currently Cactus always truncates existing output files unless the simulation has been recovered from a checkpoint (in which case existing output files will get appended unless the parameter IO::truncate_files_after_recovering is set to true). Christian Ott requested that it should also be possible to always append new datasets to existing output files. The new boolean I/O parameter IO::truncate_files implements that. Its default value is true, preserving the existing Cactus behaviour. This applies patch http://www.cactuscode.org/old/pipermail/patches/2006-May/000169.html. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@240 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Introduce new boolean parameter IO::require_empty_output_directorytradke2006-05-11
| | | | | | | | | | | | | | | | which can be used to test if IO::out_dir points to either a non-existing or empty directory at simulation startup. If this parameter is set to "yes" and an already existing IO::out_dir is found to have any contents (eg. output files from a previous simulation which was using the same output directory) Cactus will print an appropriate error message and abort, as opposed to continuing and (potentially by accident) overwriting existing files. The default for IO::require_empty_output_directory is "no". This applies patch http://www.cactuscode.org/old/pipermail/patches/2006-May/000168.html. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@239 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Remove old unused test code.tradke2006-05-08
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@238 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Auto-recovery from an unchunked checkpoint file got broken in my last commit.tradke2006-02-13
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@237 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* When searching for a list of checkpoint files in recovery modetradke2006-02-13
| | | | | | | | | | | | IO::recover = "{auto|autoprobe}": check for a '.file_<processor>' suffix for chunked output files (and not only for '.file_0' as processor 0's output). This allows for recovery from a chunked checkpoint in auto mode even if not all the chunked checkpoint files are visible to all processors (eg. if the checkpoint directory is local on a compute node on a cluster). git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@236 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* The general routine to parse the value of IO*::out_vars parameters now alsotradke2005-10-05
| | | | | | | | | checks for the option "out_unchunked = 'true|false|yes|no'" which can be used to overwrite the general output mode (as defined by IO::out_unchunked) on a per-variable basis. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@230 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Check for valid variable index in IOUtil_DefaultIORequest().tradke2005-07-25
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@228 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Set the default slice centre for 1D/2D output to be the centre of the boxtradke2005-06-16
| | | | | | | if the user specified invalid values in the parfile. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@226 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Parse option "refinement_levels" in an I/O parameter option string.tradke2005-02-04
| | | | | | | | If specified, it must be an array of positive integers selecting individual refinement levels to output. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@223 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Do not recover accumulator parameters.tradke2005-01-13
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@222 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Add missing #include <stdio.h> statementschnetter2004-12-29
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@221 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Decreased warning level for "existing parameter file will not be overwritten"tradke2004-12-08
| | | | | | | messages from 1 to 2. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@220 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Provide an aliased function IO_TruncateOutputFiles() for other I/O thornstradke2004-11-17
| | | | | | | | | to check whether or not to truncate existing output files. The default is to not truncate after recovering. This can be overwritten by the new boolean parameter IO::truncate_files_after_recovering. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@219 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Removed definition of deprecated routine IOUtil_PrepareFilename().tradke2004-11-15
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@218 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Changed non-standard snprintf to Cactus Util_snprintf for portability.goodale2004-10-29
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@216 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* assert fixyye002004-08-12
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@215 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Erik preferred filereader_ID_dir to filereader_dirswhite2004-07-28
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@214 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Added new parameter IO::filereader_dirswhite2004-07-28
| | | | | | | | | | | | See bug 1809 doc/documentation.tex: Ran through spellchecker Fixed a little grammar Changed square brackets to curly ones in doc for filereader_ID_vars git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@213 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Added new routine IOUtil_AssembleFilename() to generate a checkpoint/filereadertradke2004-06-30
| | | | | | | | | | | filename and returns the pointer to that (allocated) string. This routine is meant to replace IOUtil_PrepareFilename() which is now marked as deprecated. This closes PR IO/1791: "IOUtil_PrepareFilename does not check buffer length". git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@212 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
* Don't generate separate checkpoint filenames for different refinement levels.tradke2004-06-28
| | | | | | | PUGH doesn't care, and Carpet stores everything into a single checkpoint file. git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@211 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a
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