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* IOHDF5Util doesn't need to inherit from Hyperslab anymore.tradke2004-04-23
| | | | | | | Instead it REQUIRES the hyperslab functions to be provided. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@113 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Clean up the check for HDF5schnetter2004-04-10
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@112 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Do not require Hyperslab any more.schnetter2004-04-02
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@111 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Use the capability Hyperslab instead of inheriting from theschnetter2004-04-01
| | | | | | | implementation Hyperslab. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@110 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Updated configuration.ccl files. In Beta14 some of these willgoodale2004-03-27
| | | | | | | | | | | | | | disappear as function aliasing will be updated to have aliased functions either be optional or required, as opposed to optional as they are at the moment. This will thus remove the configuration.ccl files which are merely there to ensure that certain aliased functions are actually provided. Also far more stuff will be done via function aliasing which should remove some more of these dependencies. Tom git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@108 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Do not check for PUGH, because this is handled by theschnetter2004-03-10
| | | | | | | configuration.ccl file. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@107 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Write all the Cactus parameters into a dataset rather than a single stringtradke2004-02-04
| | | | | | | | attribute. This fixes a problem with very many parameters to dump as HDF5 has a 16k size limit on attributes. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@106 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Renamed some aliased hyperslab functions to comply with the maximum lengthtradke2004-01-22
| | | | | | | | | | | | | | for names of Fortran routines (31 characters): Hyperslab_DefineGlobalMappingByPhys -> Hyperslab_GlobalMappingByPhys Hyperslab_DefineGlobalMappingByIndex -> Hyperslab_GlobalMappingByIndex Hyperslab_DefineLocalMappingByPhys -> Hyperslab_LocalMappingByPhys Hyperslab_DefineLocalMappingByIndex -> Hyperslab_LocalMappingByIndex Also renamed the providing functions accordingly. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@105 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* When looping over all groups for checkpointing: skip groups with no variablestradke2003-11-24
| | | | | | | | attached to them (eg. vector groups with vector length 0) and zero-sized groups (grid arrays with SIZE=<parameter> and parameter = 0). git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@104 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Correct inter-thorn dependencies.schnetter2003-11-19
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@103 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* For checkpointing: set the with_ghostzones flag in the ioRequest structure ↵tradke2003-11-17
| | | | | | | | | to true. Note: you will need to update IOUtil also. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@102 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Be backwards compatible for group type codes when reading old checkpoint files.schnetter2003-10-29
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@101 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Change the way in which pointers are passed to and from Fortran.schnetter2003-10-28
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@100 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Fixed a problem with recovering small distributed grid arraystradke2003-10-24
| | | | | | | which have zero size on some processors. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@99 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Fix for recovery of grid scalars: their rank should be compared against 0 now.tradke2003-10-23
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@98 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Introduce the new Cactus variable type CCTK_INT1.schnetter2003-10-13
| | | | | | | Extend routines to handle the new type. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@97 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* PUGHIO* thorns now require the thorns they depend upon (PUGH, IOHDF5Util,tradke2003-09-04
| | | | | | | FlexIO) to be compiled in and activated. No need to inherit from them anymore. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@96 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Fixed prototype for the hyperslab conversion function parameter totradke2003-09-01
| | | | | | | Hyperslab_DefineGlobalMappingByIndex() / Hyperslab_DefineLocalMappingByIndex(). git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@95 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Change to CCTK_MaxTimeLevelsallen2003-07-16
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@94 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Use CCTK_GroupStorageIncrease() to get the number of active timelevels fortradke2003-07-14
| | | | | | | checkpointing. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@93 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Better wording in warning message which is issued if the reduction operationtradke2003-07-14
| | | | | | | | failed while dumping the value of a grid scalar during a multiprocessor run. This closes BetaThorns/1564. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@92 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Checkpoint active timelevels only. This closes PR BetaThorns/1564.tradke2003-07-14
| | | | | | | | Currently the number of active timelevels is determined by calling PUGH_NumTimeLevels() because there is no such flesh counterpart. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@91 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Fix for checkpointing grid arrays which don't have any points on a processor.tradke2003-06-27
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@90 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Another fix for the bounding box attributes of hyperslab output.tradke2003-06-13
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@89 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Fix the bounding box attributes "origin", "min_ext", "max_ext", and "delta"tradke2003-06-12
| | | | | | | which weren't taking hyperslab parameters into account. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@88 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Fixed argument types for hyperslab function aliases.tradke2003-05-28
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@87 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Support for new aliased function specification format.rideout2003-05-02
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@86 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Removed an ugly artefact where a union was used to convert a 'const cGH*'tradke2003-03-10
| | | | | | | | pointer into 'cGH *' which was required by the old flesh's reduction API. This API has been fixed now. You need to update the flesh for this. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@85 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* New specification for describing aliased functions. (from Thomas Radke)rideout2003-02-26
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@84 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Added missing includes and fixed structure name when compiling with parallel ↵tradke2002-12-05
| | | | | | | | | HDF5. This fixes PR CactusPUGHIO/1329. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@83 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Pass the cGH pointer as a CCTK_POINTER_TO_CONST.tradke2002-11-12
| | | | | | | You will need to update the flesh also. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@82 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Including "Hyperslab.h" isn't neccessary anymore since we are using functiontradke2002-11-06
| | | | | | | aliases now. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@81 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Use the "Hyperslab_*" function aliases.tradke2002-11-06
| | | | | | | You must also update CactusPUGH/PUGHSlab now. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@80 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* When called by the filereader API, check whether to read in a dataset by nametradke2002-09-18
| | | | | | | even before opening a dataset and verifying its attributes. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@79 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Shortcutting H5Giterate() after a dataset has been successfully recovered.tradke2002-09-17
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@78 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* During checkpointing, also check individual timelevels if they have storagetradke2002-09-04
| | | | | | | assigned. This closes PR BetaThorns/1224. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@77 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Broadcast recovered cctk_time as a CCTK_REAL (instead CCTK_REAL4).tradke2002-08-16
| | | | | | | This fixes precision problems when advancing by very small delta times. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@76 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* For filereader: report the restored variables also with default setting fortradke2002-07-05
| | | | | | | IO::verbose. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@75 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Fixed a resource leak in the recovery routines.tradke2002-07-05
| | | | | | | Also print the iteration number of a recovered variable. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@74 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Extended the routine registered as IOHDF5's filereader to select variablestradke2002-07-01
| | | | | | | | with a specific iteration number (see IOUtil's thorn documentation for an example). You must also update thorn IOUtil now. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@73 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Needs the Hyperslab.h headerallen2002-06-27
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@72 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Fixed potential malloc() of zero bytes. Thanks to efence.tradke2002-06-24
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@71 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* changing the documentation.tex files to use our cactus style fileikelley2002-06-04
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@69 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Give a more verbose warning if datasets cannot be recovered.tradke2002-05-30
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@68 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Allow the 'out_every' option in option strings to set the output frequencytradke2002-05-28
| | | | | | | | | | | | for individual variables. Allow hyperslab options 'origin', 'direction', 'extent', and 'downsample' in option strings to specify hyperslab selections for individual variables. You also need to update CactusBase/IOUtil now. See the thornguide for a description and an example. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@67 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Fixed a syntax error (added missing closing bracket).tradke2002-05-22
| | | | git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@66 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Added '-s' as an option to grep when checking for LFS in the HDF5 installation.tradke2002-05-13
| | | | | | | This prevents a warning from grep if the HDF5 configuration file doesn't exist. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@65 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Parameter names changes as announced in today's mail to users@cactuscode.org.tradke2002-05-06
| | | | | | | | | You must also update thorn IOUtil now. This thorn will be moved from BetaThorns to CactusPUGHIO now. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@64 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Values for CCTK_SCALAR variables are taken only from processor 0.tradke2002-04-30
| | | | | | | If other processors have different values a warning will be issued. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@63 7842ec3a-9562-4be5-9c5b-06ba18f2b668
* Moved the I/O request description and parsing routines to IOUtil so that theytradke2002-04-26
| | | | | | | can be shared by all I/O thorns. git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@62 7842ec3a-9562-4be5-9c5b-06ba18f2b668
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