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path: root/Carpet/CarpetIOHDF5/src/Output.cc
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* 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: 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: 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: 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: 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
* 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: add "cctk_bbox" and "cctk_nghostzones" attributes to each datasetThomas Radke2005-06-28
| | | | darcs-hash:20050628113206-776a0-3ed3eae73dcc785de93273c16df556c3c6531de3.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: resolve conflictErik Schnetter2005-06-06
| | | | darcs-hash:20050606164745-891bb-bfdba5217c624e406550ea12d38969eed76c51ed.gz
* CarpetIOHDF5: API for H5Sselect_hyperslab() has changed in HDF5 1.6.4Thomas Radke2005-05-12
| | | | | | | The second argument to H5Sselect_hyperslab must be a 'const hsize_t start[]' in the latest release 1.6.4. It used to be 'const hssize_t start[]' in all previous releases. darcs-hash:20050512101748-776a0-068b805f7e8c6399e96c38d8689d0e246b708cf9.gz
* CarpetIOHDF5: Put unique simulation ID into each fileErik Schnetter2005-06-05
| | | | | | Add the unique simulation ID as attribute to each dataset. darcs-hash:20050605221351-891bb-05a025dbdefc60c7dc476e4b7b50ff608bdacd61.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: API for H5Sselect_hyperslab() has changed in HDF5 1.6.4Thomas Radke2005-05-12
| | | | | | | The second argument to H5Sselect_hyperslab must be a 'const hsize_t start[]' in the latest release 1.6.4. It used to be 'const hssize_t start[]' in all previous releases. darcs-hash:20050512101740-776a0-3581a3be23f057105585cf57b384a166f30aec29.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: pass vartype in comm_state constructor tto make use of ↵Thomas Radke2005-03-31
| | | | | | collective communication buffers darcs-hash:20050331080034-776a0-629822f876800af1b76d5d43ca131f5373e991a4.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
* CarpetIOHDF5: Use positive timelevelsErik Schnetter2005-02-07
| | | | darcs-hash:20050207131924-891bb-0dbd85d6ac494fcac9aef96ad00c37025a4891e1.gz
* CarpetIOHDF5: output individual refinement levels if requestedThomas Radke2005-02-04
| | | | | | | | | | | | | After updating CactusBase/IOUtil, one can now choose refinement levels for individual grid functions to be output, simply by using an options string, eg.: IOHDF5::out_vars = "wavetoy::phi{refinement_levels = {1 2}}" If no such option is given, output defaults to all refinement levels. Note that the parsing routine (in IOUtil) does not check for invalid refinement levels (>= max_refinement_levels). darcs-hash:20050204181016-776a0-4d1d74a64c2869ffc4a16846146e1a0b7fd98638.gz
* global: Change the way in which the grid hierarchy is storedErik Schnetter2005-02-01
| | | | | | | | | | | | | | | | | | | | Change the way in which the grid hierarchy is stored. The new hierarchy is map mglevel reflevel component timelevel i.e., mglevel moved from the bottom to almost the top. This is because mglevel used to be a true multigrid level, but is now meant to be a convergence level. Do not allocate all storage all the time. Allow storage to be switched on an off per refinement level (and for a single mglevel, which prompted the change above). Handle storage management with CCTK_{In,De}creaseGroupStorage instead of CCTK_{En,Dis}ableGroupStorage. darcs-hash:20050201225827-891bb-eae3b6bd092ae8d6b5e49be84c6f09f0e882933e.gz
* global: Turn CarpetLib templates into classesErik Schnetter2005-01-01
| | | | | | | | | | | | | | | | | | | Turn most of the templates in CarpetLib, which used to have the form template<int D> class XXX into classes, i.e., into something like class XXX by setting D to the new global integer constant dim, which in turn is set to 3. The templates gf and data, which used to be of the form template<typename T, int D> class XXX are now of the form template<typename T> class XXX The templates vect, bbox, and bboxset remain templates. This change simplifies the code somewhat. darcs-hash:20050101182234-891bb-c3063528841f0d078b12cc506309ea27d8ce730d.gz
* CarpetIOHDF5/src/Output.cc: fix calculation of "origin" attribute; don't ↵Thomas Radke2005-01-10
| | | | | | output "cctk_bbox" and "cctk_nghostzones" attributes for unchunked data darcs-hash:20050110105925-776a0-610cbdb983ac67dcb5a28bf558cba4937d20fe60.gz
* CarpetIOHDF5/src/Output.cc: write bbox attributes only if a variable has a ↵Thomas Radke2005-01-03
| | | | | | coordinate system associated with it darcs-hash:20050103174917-776a0-29c425b306db7d85ff60d91496bd4db5895a0a0f.gz
* global: Remove $Header$ keywords from Carpet arrangementErik Schnetter2005-01-01
| | | | darcs-hash:20050101162121-891bb-ac9d070faecc19f91b4b57389d3507bfc6c6e5ee.gz
* CarpetIOHDF5: Only add "m=" to dataset name for grid functionsErik Schnetter2004-12-25
| | | | darcs-hash:20041225152539-891bb-24fd38d3792883217dbd102df99bda9255c9c0e2.gz
* CarpetIOHDF5: Correct typo in commentErik Schnetter2004-12-25
| | | | darcs-hash:20041225152403-891bb-65b7df424b36f544260bdd82db2f7a3f2353e911.gz
* CarpetIOHDF5: Use bool instead of int for some logical variablesErik Schnetter2004-12-25
| | | | darcs-hash:20041225145321-891bb-28ca9adbd7601709dc0c75158eab8013ee863ef9.gz
* CarpetIOHDF5: Add semicolons after DECLARE_* macrosErik Schnetter2004-12-25
| | | | darcs-hash:20041225145224-891bb-03520cc5f5fa997d7bb6aeccebf3b1b32bfcfdf1.gz
* CarpetIOHDF5/src/Output.cc: changed warning level for deprecated parameters ↵tradke2004-12-07
| | | | | | from 1 to 2; don't sleep(3) after such warnings darcs-hash:20041207163828-3fd61-dac602f5c3a0285ed05e79046d3fde3c57e22c33.gz
* CarpetIOHDF5/src/Output.cc: forgot to include <unistd.h> to get sleep(3)tradke2004-12-06
| | | | darcs-hash:20041206152516-3fd61-1dec08523b8094b4decabed463b37188d85914a6.gz
* CarpetIOHDF5: fix output of DISTRIB=CONSTANT arraystradke2004-12-06
| | | | | | | | | | | | DISTRIB=CONSTANT grid variables (including scalars) are assumed to have the same values across all processors. Therefore only the portion on processor 0 will be output. The portions from other processors are compared against this processor's portion, and a level-1 warning will be issued if they don't match. During recovery, the DISTRIB=CONSTANT array portion from the checkpoint file is distributed across all processors (independently of how many there are). darcs-hash:20041206151054-3fd61-5a47be7936480027c1e6f4419a4051d223e10c7d.gz
* CarpetIOHDF5/src/Output.cc: if deprecated parameters were set in the ↵tradke2004-12-03
| | | | | | parfile, wait 5 seconds after the warning(s) before scrolling on darcs-hash:20041203155935-3fd61-8bf992a86bf39e6cbc1abe21351c571815730f7e.gz
* CarpetIOHDF5/src/Output.cc: check for already existing datasets in an output ↵tradke2004-12-03
| | | | | | | | | | | file After recovery, it may happen that HDF5 output is requested at the same iteration when it had been done before. Therefore the code must check for this case, and remove an already existing dataset from the output file before it can be created anew. darcs-hash:20041203152858-3fd61-7703c468af4f84b6a737f9fa9a5272f4d2313724.gz
* CarpetIOHDF5: deprecate all parameters with '3D' in their namestradke2004-12-03
| | | | | | | | | | | | | | | | | | | | | CarpetIOHDF5 does output for grid variables of any dimensions, not only 3D. Therefore parameters with '3D' in their names have been marked deprecated now and should not be used anymore. They are still valid though but you will get a level-1 warning if you still use them. At some point in the future those deprecated parameters will be removed. So you should eventually fix your parameter files to substitute their occurances by their newly introduced counterparts (parameters of the same name but without the '3D'). CarpetIOHDF5/src/util/ contains a small perl script which can be applied to parfiles to automatically substitute old parameter names: ~/cactus/arrangements/Carpet/CarpetIOHDF5/src/util> ./SubstituteDeprecatedParameters.pl This perl script automatically substitutes deprecated parameter names in a parfile. Usage: ./SubstituteDeprecatedParameters.pl <parameter file> darcs-hash:20041203134032-3fd61-5d49fdff6c13f19772c6b441d5d558708dd88c71.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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