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base: H5hut/src:H5Part-1.3.3
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H5hut/src:master H5hut/src:int8 H5hut/src:1.99.x H5hut/src:1.99 H5hut/src:1.6 H5hut/src:1.4 H5hut/src:1.2 H5hut/src:1.0
H5hut/src:H5hut-2.0.0rc7 H5hut/src:H5hut-2.0.0rc6 H5hut/src:H5hut-2.0.0rc5 H5hut/src:H5hut-2.0.0rc4 H5hut/src:H5hut-2.0.0rc1 H5hut/src:H5hut-2.0.0rc3 H5hut/src:H5hut-2.0.0rc2 H5hut/src:1.99.13 H5hut/src:1.99.12 H5hut/src:1.99.11 H5hut/src:1.99.10 H5hut/src:1.99.9 H5hut/src:1.99.8 H5hut/src:1.99.7 H5hut/src:H5Part-1.6.5 H5hut/src:1.99.6 H5hut/src:H5Part-1.6.4 H5hut/src:1.99.5 H5hut/src:H5Part-1.6.3 H5hut/src:1.99.4 H5hut/src:1.99.3 H5hut/src:1.99.2 H5hut/src:H5hut-1.99.1 H5hut/src:1.99.0 H5hut/src:H5Part-1.6.2 H5hut/src:H5Part-1.6.1 H5hut/src:H5Part-1.6.0 H5hut/src:H5Part-1.4 H5hut/src:H5Part-1.3.3 H5hut/src:H5Part-1.3.2 H5hut/src:H5Part-1.3.1
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compare: H5hut/src:1.99.x
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H5hut/src:master H5hut/src:int8 H5hut/src:1.99.x H5hut/src:1.99 H5hut/src:1.6 H5hut/src:1.4 H5hut/src:1.2 H5hut/src:1.0
H5hut/src:H5hut-2.0.0rc7 H5hut/src:H5hut-2.0.0rc6 H5hut/src:H5hut-2.0.0rc5 H5hut/src:H5hut-2.0.0rc4 H5hut/src:H5hut-2.0.0rc1 H5hut/src:H5hut-2.0.0rc3 H5hut/src:H5hut-2.0.0rc2 H5hut/src:1.99.13 H5hut/src:1.99.12 H5hut/src:1.99.11 H5hut/src:1.99.10 H5hut/src:1.99.9 H5hut/src:1.99.8 H5hut/src:1.99.7 H5hut/src:H5Part-1.6.5 H5hut/src:1.99.6 H5hut/src:H5Part-1.6.4 H5hut/src:1.99.5 H5hut/src:H5Part-1.6.3 H5hut/src:1.99.4 H5hut/src:1.99.3 H5hut/src:1.99.2 H5hut/src:H5hut-1.99.1 H5hut/src:1.99.0 H5hut/src:H5Part-1.6.2 H5hut/src:H5Part-1.6.1 H5hut/src:H5Part-1.6.0 H5hut/src:H5Part-1.4 H5hut/src:H5Part-1.3.3 H5hut/src:H5Part-1.3.2 H5hut/src:H5Part-1.3.1

715 Commits
H5Part-1.3.3 ... 1.99.x

Author SHA1 Message Date
gsell 1c8a5dd0d1 MPIPOSIX removed, this has been removed in hdf5 1.8.13, so we cannot use it any more 2015-06-12 14:49:10 +02:00
gsell 64f8552443 src/h5core/h5b_readwrite.c: 
- fix early return in  _select_hyperslab_for_writing()
 2015-06-12 14:44:31 +02:00
gsell da1ceec4f5 configure.ac: 
- set version to 1.99.14
 2015-04-16 18:21:35 +02:00
gsell b12b39dedf src/h5core/h5b_model.c: 
- bugfix in serial code of h5b_3d_set_view()
 2015-04-16 18:21:09 +02:00
gsell aac94b38e8 version 1.99.13 released 2013-11-22 16:35:13 +01:00
gsell 3e918f8001 ignore file edited 2013-11-22 15:56:23 +01:00
Gsell Achim 0be5518252 option to shift mesh added 2013-11-22 15:54:46 +01:00
gsell 9fa5becf1e ignore file edited 2013-11-15 17:08:09 +01:00
gsell 8d04bca079 libpthread and libdl added to link command (required for serial builds) 2013-11-15 17:07:16 +01:00
gsell fda65e5527 bugfixes in autotool configuration 2013-08-28 10:17:00 +02:00
gsell 5d6a9a9ac9 ignore list edited 2013-06-14 12:48:05 +00:00
gsell bdbeb061c5 fixed problem with install of header files 2013-06-14 12:27:45 +00:00
gsell 6ff8067ba8 fixes to get 'make dest' working 2013-06-14 09:35:20 +00:00
gsell 47c80a05b7 ignore list edited 2013-06-14 07:11:19 +00:00
gsell 20d5b95d59 version fixed 2013-06-13 15:23:24 +00:00
gsell 095df28103 functions h5_close_hdf5() and hdf5_close() backported from trunk 2013-06-13 15:21:15 +00:00
gsell b16054d590 Fortran API backported from trunk 2013-06-13 15:20:06 +00:00
gsell 406375687b Fortran API backported from trunk 2013-06-13 15:19:38 +00:00
gsell bbf2cc335f bugfixes 2013-06-13 15:17:08 +00:00
gsell 13cc544fc1 fixed library order for Linux linker 2013-06-13 12:24:31 +00:00
gsell d8880dfcb9 to be linked libraries fixed 2013-06-13 12:14:46 +00:00
gsell 26d8508984 bugfix in H5.h 2013-06-04 11:40:45 +00:00
gsell 0bb516ecbd new Makefile.am in includes added 2013-05-16 12:47:33 +00:00
gsell 72fa424a51 outside source build now possible, C API with inline functions, examples moved from 'test' directory to new 'example' directory 2013-05-16 12:46:37 +00:00
gsell 22421d8d88 new updated 2013-04-15 09:12:37 +00:00
gsell f15fcacc68 bugfixes in autotools files 2013-04-15 09:11:56 +00:00
gsell 55aa93e6d6 autotool files: INCLUDE replaced by AM_CPPFLAGS 2013-02-15 14:34:02 +00:00
gsell 465152e58b bugfix: wrong number of leaf elements on level 0 in some cases 2013-02-15 14:32:50 +00:00
gsell 6e03a3ca17 bugfix in vtk2h5grid 2013-02-15 14:29:57 +00:00
gsell 55171d3b14 VTK to H5grid converter added 2013-01-30 16:06:47 +00:00
gsell 173b09c39d warnings on 32bit systems and with gcc 4.7.2 fixed 2013-01-30 14:23:24 +00:00
gsell fca85a787d toplevel patch branch created 2013-01-30 09:18:43 +00:00
gsell e27bdb592e tools/h5PartDcToVtk tools/h5PartSurfaceToVtk removed from BUILD_TOOLS 2012-03-14 15:41:40 +00:00
gsell 9becc99e02 bugfix in get_option() 2012-03-14 15:40:53 +00:00
gsell 556fe9b8a6 Fortran API fixed 2011-11-02 17:23:31 +00:00
gsell bc84ce205a API to retrieve local neighbor indicies of an element added 2011-10-27 12:16:24 +00:00
gsell c45c1e9bb9 trimesh_2gnuplot added to test/H5Fed 2011-10-27 11:46:07 +00:00
gsell 4085a1c30c ignore list modified 2011-10-27 11:45:14 +00:00
gsell ce8b6dae77 bugfix in H5OpenFile() 2011-10-27 11:43:14 +00:00
gsell 29888601b8 bugfix in open with O_CREAT 2011-10-27 11:42:47 +00:00
gsell d82e7143ed branch 1.99 created 2011-10-27 11:35:06 +00:00
gsell 3569a12376 link problem on Linux fixed 2011-10-05 08:44:02 +00:00
gsell 4a33578c8f changes merged from r3753 2011-09-09 10:36:52 +00:00
gsell 72920b2cbd define PARALLEL_IO only if H5_HAVE_PARALLEL is defined and but not PARALLEL_IO 2011-09-08 12:24:22 +00:00
gsell 9de08ab78f define PARALLEL_IO if H5_HAVE_PARALLEL is defined 2011-09-08 12:20:47 +00:00
gsell cba9c17dff don't output MPI_Comm and MPI_Info params in debug output to avoid problems with different MPI implementations 2011-09-08 12:19:22 +00:00
gsell 318bf9140a alloc cleared memory for mesh structure 2011-09-08 11:36:48 +00:00
gsell 431782f85e format error fixed in debug output 2011-09-08 11:34:57 +00:00
gsell 99464ac39d several bugfixes in parallel code 2011-08-23 15:13:22 +00:00
gsell 0d37e27db2 missing type cast added 2011-08-23 15:11:01 +00:00
gsell dafcdc6879 merge errors fixed 2011-08-23 15:08:50 +00:00
gsell ff35718467 print used C++ compiler in summary 2011-08-23 07:59:14 +00:00
gsell 8860a72e65 changesets -3740 merged from sandbox 2011-08-18 16:19:28 +00:00
gsell aacd90c1cc bugfix 2011-08-16 09:16:34 +00:00
gsell 060f4b0029 changesets 3713,3714,3725 merged from sandbox 2011-08-15 15:04:14 +00:00
gsell c3f6a51426 functions to flush data to disk added 2011-08-12 14:24:19 +00:00
adelmann 5a31c58c41 cleanup 2011-08-12 11:18:33 +00:00
adelmann 63bfd8a516 cleanup 2011-08-12 11:16:41 +00:00
adelmann 826ec5491c rewriting for H5hut 2011-08-12 08:48:43 +00:00
adelmann b1e8e15b90 fix more stuff 2011-08-12 07:05:54 +00:00
adelmann 8862acd04f fixes ... 2011-08-11 15:51:02 +00:00
gsell 2b3a3fdafb ignore list updated 2011-08-11 15:23:48 +00:00
gsell a29d3c894a flush step after writing dataset 2011-08-11 15:04:14 +00:00
gsell f9710938f2 target 'clean-local' added 2011-08-11 15:02:33 +00:00
adelmann 33f3e8a24d more tools must later go to OPAL 2011-08-11 15:01:16 +00:00
adelmann 95903d2711 fix tools makefile 2011-08-11 14:31:55 +00:00
adelmann e23aeea0ef remove dbg output 2011-08-11 11:24:26 +00:00
gsell 7dc3981621 install static libs in src/lib via all-local rule 2011-08-05 14:54:49 +00:00
gsell 2954499875 libtoolize naming problem on Mac OS X fixed 2011-08-05 14:54:04 +00:00
gsell 339c86404c fix problems with autogen.sh on ScientificLinux 5 and new autotools 2011-08-04 11:22:50 +00:00
gsell d2a55f9a90 missing error handling fixed 2011-08-02 14:51:44 +00:00
gsell 92d0cc5ae5 write zero-particle bug fixed 2011-08-02 13:34:10 +00:00
Marc Howison 329a72fa82 1.6.3 release 2011-07-25 14:09:43 +00:00
gsell 2921aa87d5 adaptions for libtools on Mac, work around to use env.varibales removed 2011-07-19 13:10:36 +00:00
Marc Howison be103949eb new build system for both H5hut and H5Part; preparing 1.6.3 release of H5Part 2011-07-16 18:30:25 +00:00
gsell df552265bc debug output added to MPI wrapper and some small fixes 2011-07-08 14:52:14 +00:00
gsell ffe7b30b02 Oops 2011-07-01 14:34:50 +00:00
gsell 154c03bbbe missing 'static inline' fixed 2011-07-01 14:28:16 +00:00
gsell 259e4b1ff0 implemented NDEBUG for __FUNC_ARGSx and __FUNC_RETURN 2011-06-30 14:41:53 +00:00
gsell a4f95fa4db implement all private functions as inline 2011-06-30 14:40:35 +00:00
gsell d8c84a3bff bugfix in read function 2011-06-30 09:13:52 +00:00
gsell 30cf451716 some adaptions to coding style 2011-06-30 09:12:56 +00:00
gsell c1eadeb678 issues with Intel C 11.1 fixed 2011-06-24 10:10:20 +00:00
gsell 8030a7246b H5Fed C-API inlined 2011-06-17 15:03:14 +00:00
gsell 81f7f7716f smal docu change 2011-06-17 15:02:35 +00:00
gsell 7baf635bef bugfixes 2011-06-17 13:04:36 +00:00
gsell 87eae5c238 functions in 'C/H5Fed.c' are no inline 2011-06-17 13:03:43 +00:00
gsell 562f9ac3e3 set absolute path in CC and CXX 2011-06-16 14:06:51 +00:00
gsell cfc13be3af add function to output coordinates of all elements 2011-06-16 14:05:07 +00:00
gsell ade15f37ca obsolete file 'h5t_errorhandling.c' removed 2011-06-15 13:30:11 +00:00
gsell ad6bcf73d7 include mpi.h on paralell I/O 2011-06-15 13:29:27 +00:00
gsell 601bebc183 readjust to API changes 2011-05-25 08:21:16 +00:00
gsell ad7c1cf026 test for mpicc/mpicxx in AC_PROG_CC if parallel is enabled 2011-05-25 08:16:01 +00:00
gsell 375132fac9 pre-refine code fixed 2011-05-24 15:45:37 +00:00
gsell b47448390e extern "C" wrapper added 2011-05-24 15:30:03 +00:00
gsell 91eeefb9d2 more warnings fixed 2011-05-24 15:28:32 +00:00
gsell 9bdff77a00 use mpicc/mpicxx in AC_PROG_{CC,CXX} if --enable-parallel is set 2011-05-24 14:23:33 +00:00
gsell bb5bbb4216 several warnings with Intel-C/GCC -Wall fixed 2011-05-24 12:59:35 +00:00
gsell 2a2c461f71 several format warnings fixed 2011-05-23 14:51:55 +00:00
gsell 87feccada8 several format warnings fixed 2011-05-23 14:50:00 +00:00
gsell ed913eaa0f experimental code added fot adding named triangle meshes 2011-05-23 14:34:57 +00:00
gsell 0b94f58cc9 proc rank is now printed by h5priv_vprintf 2011-05-23 14:33:41 +00:00
gsell 4818fa0efb 'mesh_label' removed from 'struct h5_file' 2011-05-23 14:31:37 +00:00
gsell 5b6e145e87 pre-refine implemented as mesh specific function 2011-05-20 14:02:05 +00:00
gsell 22c45153a8 bugfixes 2011-05-20 14:01:00 +00:00
gsell a7b9621850 h5t_openclose* renamed to h5t_model*, some functions moved from file to files 2011-05-20 13:01:14 +00:00
gsell f79b06ef4d h5t_const.c and h5t_const_private.h removed 2011-05-20 11:55:19 +00:00
gsell 1a8433681f API changed: now we have explicit function to open/add meshes of specific type 2011-05-20 11:53:49 +00:00
gsell 0dbb8f22e3 dedicated function to add triangle and tetrahedral meshes added 2011-05-13 11:04:57 +00:00
gsell 532da439a6 svn:ignore edited 2011-05-13 11:02:43 +00:00
gsell 7075ab7712 'h5_attach_test.c' added 2011-05-13 11:01:37 +00:00
gsell 5bd6ab7109 svn:ignore edited 2011-05-13 10:59:04 +00:00
gsell f3517f3775 code added for parallel compilation 2011-05-13 10:53:40 +00:00
Marc Howison 30ea30603e created code generator for H5_attribs_F.c 2011-05-06 13:28:37 +00:00
Marc Howison 1f8f6cddde updated Fortran interfacae to use new macros 2011-05-06 13:28:02 +00:00
Marc Howison 11fd3c10c5 updated h5_lustre.c to user new macros; changed library targets to ../lib/lib*.a to avoid the mv and mkdir hacks in Makefile.am; fixed problem in h5u_test with H5PartSetViewIndices; OPEN BUG with h5u_test for >1 MPI task (strange pthread setfault?) 2011-05-05 17:58:05 +00:00
gsell c676222a03 output of debug information added to all private API functions 2011-05-05 07:36:47 +00:00
gsell 09cad98413 src/lib added 2011-05-05 07:29:19 +00:00
gsell 53b8850329 output of debug information added to all API and core-API functions 2011-05-03 09:30:30 +00:00
gsell 808d489564 fixed bug in h5_get_num_steps() 2011-04-18 12:30:40 +00:00
gsell ecb23b66dd libH5hutC.a added to ignore list 2011-04-07 11:05:22 +00:00
gsell 64de405353 libH5hut.a added to ignore list 2011-04-07 11:04:45 +00:00
gsell 0cce74dadb H5PartTest.cc adapted to H5hut API 2 2011-04-01 14:33:07 +00:00
gsell aa3462472d added include of stdarg.h 2011-04-01 14:29:43 +00:00
gsell af3601d2d9 test/H5Part/Makefile added to AC_CONFIG_FILES() 2011-04-01 14:27:56 +00:00
gsell 407bbe4d0c implementation of attachments continued 2011-03-31 15:30:16 +00:00
gsell 6661eca765 added extern "C" wrapper for C++ 2011-03-25 14:53:31 +00:00
gsell 1000240374 work in progress 2011-03-25 14:51:46 +00:00
gsell cea4a22f9b fixed warnings 2011-03-25 14:49:46 +00:00
gsell e4e78f713c attachment implementation 2011-03-24 09:07:12 +00:00
gsell 4b0d303ceb - h5_attachments.c added 2011-03-11 16:12:17 +00:00
gsell 4d348dbe0d - function hdf5_get_dataset_info_by_name() added 
- args of function hdf5_get_npoints_of_dataset_by_name() are now const
 2011-03-11 16:11:23 +00:00
gsell 745e2229e7 use function hdf5_get_datasetinfo_by_idx() in h5u_get_dataset_info() 2011-03-11 15:29:29 +00:00
gsell b0c321dd54 - renamed functions: 
h5_get_num_hdf5_groups() -> hdf5_get_num_groups()
  h5_get_num_hdf5_groups_matching_prefix() -> hdf5_get_num_groups_matching_prefix()
  h5_get_hdf5_groupname_by_idx() -> h5_get_hdf5_groupname_by_idx()
  h5_get_hdf5_groupname_by_idx() -> hdf5_get_num_datasets()
  h5_get_hdf5_datasetname_by_idx() -> hdf5_get_name_of_dataset_by_idx()
  h5_get_objname() -> hdf5_get_objname()
- added functions:
  hdf5_get_dataset_info_by_idx()
- changed args:
  h5_get_dataset_type(): file handle removed
 2011-03-11 15:08:02 +00:00
gsell a8dd08c5bf - added functions: H5Block3d{G,S}etFieldOrigin(), H5Block3d{G,S}etSpacing() 2011-02-24 16:34:51 +00:00
gsell 427c550993 - fixes for Intel C on Linux 2011-02-24 09:59:15 +00:00
gsell d3c09a61b2 - removed "h5_file_t f" argument where we don't need need (but not in API) 
- removed arguments from macros h5_error_internal() h5_error_not_implemented()
- some coding style issues fixed
 2011-02-24 08:18:45 +00:00
gsell 7e93a7ab2f - improved debugging 
- abort error handler now terminates all processes in MPI_COMM_WORLD
- some formating issues fixed
- some minor (cosmetic) changes
 2011-02-18 10:33:44 +00:00
gsell 05772223f5 - use specific data types for local IDs and indices (instead of h5_id_t) 2011-02-03 10:51:28 +00:00
gsell 2bc7cc1024 - local IDs and indices are now 32bit (in the future it will be possible 
to compile the library with 32bit or 64bit IDs/indices.
- bugfixes
 2011-02-03 10:40:40 +00:00
gsell d0ce31c8c0 - more generic private functions added to attrib API 2011-02-03 09:17:05 +00:00
gsell ea09184d53 output entities as n-tuple of vertex indices, not their ID 2011-01-21 13:15:13 +00:00
gsell eb5c31e80f build of trimesh_adjacencies added 2011-01-21 10:33:01 +00:00
gsell 607c084ac4 added 2011-01-21 10:32:19 +00:00
gsell b9eed5630c - reference elements revisited (extensions, bugfixes...) 
- adjacency computation reviewed, bug fixes
- some reformating and refactoring
 2011-01-21 10:27:48 +00:00
gsell 212c9b86a1 label in macro H5_API_RETURN renamed 2011-01-21 10:23:36 +00:00
gsell f6eeeca9b0 label in macro H5_API_RETURN renamed 2011-01-21 10:21:37 +00:00
gsell 54aaf846e7 - hash functions reviewed and optimzed 2011-01-06 12:05:20 +00:00
gsell a6ef33d66c - label "exit" renamed to "done" (as in hdf5) 2011-01-06 12:04:03 +00:00
gsell 4fdfc6e4dc - add -std=c99 to CFLAGS if compiler is gcc 
- bugfix in AIX test
 2011-01-06 12:02:40 +00:00
gsell 27c19efe59 bugfixes 2011-01-04 08:32:14 +00:00
gsell 12a2c7ef27 ID-list structure changed 2011-01-03 14:48:05 +00:00
gsell 6b4a664546 hcompute_loc_id_keyed() optimized 2011-01-03 14:45:53 +00:00
gsell f59fd40b34 'h5priv_alloc_idlist_items()' renamed to 'alloc_idlist_items()' 2010-12-16 15:27:39 +00:00
gsell db5fd1b01e 'h5priv_free_idlist_items()' removed from priv core API 2010-12-16 15:24:35 +00:00
gsell 81b488a8d2 changed 'marked_entities' to ptr type 2010-12-16 15:16:20 +00:00
gsell d1f6efa8c0 - missing memory release for te and td structure implemented 2010-12-16 15:09:28 +00:00
gsell ec8258e902 'num_levels', 'cur_level' and related functions refactored to 'num_leaf_levels' etc 2010-12-16 14:25:15 +00:00
gsell cb35755cf5 - refactored 'num_elems_on_level' to 'num_elems_on_leaf_level' 
- introduced new refinement level
 2010-12-16 12:25:28 +00:00
gsell b8a7e0686d - introduced macros for enter and return from API functions 
- iterators revisited
 2010-12-16 10:37:33 +00:00
gsell 2c865deb88 refactor memory allocation function as public core functions 2010-12-15 14:12:53 +00:00
gsell 912b776b83 core iterator API refactored 2010-12-15 10:14:31 +00:00
gsell aec44637d7 trimesh_write_dunetest added 2010-12-14 10:35:51 +00:00
gsell 8d21236264 - boundary mesh iterators implemented 
- #pragma replaced with macro
- several minor changes
 2010-12-14 10:24:33 +00:00
Christian Engwer f5ace232e8 - export h5tpriv_find_te2 via h5core/h5t_adjacencies.h 
- method is called h5t_find_te2
 2010-12-10 08:40:08 +00:00
gsell edcdd4ce0f h5b_test added to ignore list 2010-11-12 08:29:04 +00:00
gsell bd993eadf2 - boundary facets iterator added 2010-11-12 08:25:51 +00:00
gsell 0de4641ec5 - introducing types for local and globale IDs and indices 
- different structurs for local elements and stored elements in file
- interator for border facets added
 2010-11-12 08:23:00 +00:00
Marc Howison 1dd75f48e6 fixed problems with compiling on my Mac 2010-11-08 01:56:45 +00:00
gsell 6dc020da64 - introduced types for local and global indices and ID's 
- bugfixes
 2010-10-18 16:12:41 +00:00
gsell b6a5823e23 - bug fixed in write_tagset(): wrong limit in for loop 2010-09-06 15:47:51 +00:00
gsell 441915f443 - Removed some parallel tests from serial code 
- fix some warnings
 2010-09-06 15:45:47 +00:00
gsell 031cd58999 bugfixes 2010-08-25 16:32:54 +00:00
gsell de20cdd032 bugfixes 2010-08-25 16:32:35 +00:00
gsell 6d0600febf - handling of imported env.vars revised 2010-08-20 15:55:55 +00:00
gsell c47c0cfc6e - neighbor information management added to elements 
- prefix 'global' removed form global element struct
- global and local element data now have the same struct
- and several other changes
 2010-08-20 15:54:01 +00:00
gsell 21ba443bcd - new adjacency API implemented 
- some minor fixes
 2010-08-20 15:47:40 +00:00
gsell d745498f3c - use of type h5_size_t in H5Block functions 
- several fixes to get rid of warnings with icc -Wall
 2010-08-20 15:46:28 +00:00
gsell e5aa8e5703 added install-libs-local target 2010-08-20 15:42:25 +00:00
gsell 77d5f4feb8 - type casts added to printf args 
- changed to new adjacency API
 2010-08-20 15:41:07 +00:00
gsell 982bf089ac lib added to ignore list 2010-07-29 11:33:42 +00:00
gsell 0137e7ac2a use 'idx' in element structure as global index for global elements and level idx for local elements. We don't need to save the level index for globale elements and it makes no sense to store the local index of a local element. 2010-07-29 11:33:29 +00:00
gsell b0bacdc6a7 function h5t_map_global_elem_indices2local() added 2010-07-29 11:19:00 +00:00
gsell 5da74b94df some entries added to ignore list 2010-07-29 11:15:28 +00:00
Marc Howison 6568099f62 fixed errors found by regression tests: 
the H5Fed file data structure can't be created by >1 MPI task, so it is disabled in parallel mode (for now)
the H5Block3dSetHalo function was inverting the halo radii
the h5b_test wasn't writing the correct data in the halo case
 2010-07-28 21:55:00 +00:00
Marc Howison 377af10fb0 tested out packaging a tarball and compiling/install on Franklin 
fixed several issues with the build system
 2010-07-24 00:10:41 +00:00
Marc Howison 421a92630a refactored Fortran interface to use h5core calls instead of C API calls 2010-07-22 20:32:52 +00:00
gsell b920c0f9e8 - level_idx removed from element structure 
- mesh type specific read methods
 2010-07-22 20:02:48 +00:00
Marc Howison a1a90c8af0 corrections for IASDS paper 2010-07-22 18:52:40 +00:00
gsell 4a20cd715e - neighborhood informations added to elements (to be continued) 
- several name changes in struct h5t_fdata
- refactoring according changes in struct h5t_fdata
 2010-07-22 14:43:17 +00:00
gsell 56b1be9ddb define sub-dirs for src/Makefile via configure 2010-07-22 14:36:41 +00:00
gsell 3e1d5fbff0 ignore-list edited 2010-07-22 14:29:39 +00:00
gsell ff4fbc0835 ignore-list edited 2010-07-22 14:28:53 +00:00
gsell 64585bfcc2 ignore-list edited 2010-07-22 14:27:48 +00:00
gsell fb78efc6fa ignore-list edited 2010-07-22 14:27:26 +00:00
gsell 0960b906a9 ignore-list edited 2010-07-22 14:25:37 +00:00
gsell 1fd9ae1406 h5t_access_{tetm,trim}.c added to sources, h5t_XYZ_{tetm,trim}_private.h merged with h5t_XYZ_private.h 2010-07-22 12:53:14 +00:00
gsell 4ccd632e54 deleted 2010-07-22 12:39:07 +00:00
gsell 8c8de6e523 added 2010-07-22 12:06:06 +00:00
gsell b56c4246c9 reference element type renamed 2010-07-22 10:16:22 +00:00
Marc Howison 5f6808947a added h5hutcc wrapper 
updated documentation
finished merging the Fortran interface and refactoring H5Block
started an H5Block regression test
 2010-07-20 18:23:48 +00:00
Marc Howison 7ea00c38f8 Integrated H5Part regression test and fixed numerous errors that it discovered. 
Finished integrating H5Block and the Fortran interface (untested).
Started adding an H5Block regression test with a few simple tests (all pass).
Added automatic detection of stripe information on lustre, and config option to compile against lustre API.
Moved buffers for H5Block ghost zone disolving out of the file handle and into the h5b_3d_set_view function.
Fixed bug with pointers in the H5Fed file data not being initialized to NULL.
 2010-07-15 19:44:48 +00:00
Marc Howison 2c267f173a continued working on Fortran interface 2010-07-10 00:00:54 +00:00
Marc Howison 9f3fd3b053 continued merging H5Block: still some functionality missing (attribs, read, write); added H5Part regression tests; simplified several Makefile.am files and configure.ac; began merging new Fortran interface 2010-07-09 16:24:57 +00:00
gsell b2dbc55839 added 2010-07-08 10:09:06 +00:00
gsell 16738fdd6f fixed error in documentation 2010-07-08 10:08:29 +00:00
gsell 2a47df9875 removed obsolete H5PartSomeThing() declaration 2010-07-08 10:06:57 +00:00
gsell 77b1198151 h5_{s,g}et_debug_level() renamed to h5_{s,g}et_debuglevel() 2010-07-08 10:05:10 +00:00
gsell 362bb8d9a2 define ULLONG_MAX if not already defined 2010-07-06 15:17:44 +00:00
gsell c32853c3d4 h5priv_te_find() now return H5_NOK, if element not found 2010-07-02 11:54:39 +00:00
gsell 2f55e95381 typo fixed in call of H5Pset_fapl_mpiposix() 2010-07-02 08:25:13 +00:00
gsell 7a977e3cd1 leading underscore removed from static functions 2010-07-01 13:11:12 +00:00
gsell aaf37f791f typo in call of h5_get_debug_level() fixed 2010-07-01 13:01:02 +00:00
gsell fb557952e9 some type-cast added to fix Intel C warnings 2010-07-01 13:00:07 +00:00
Marc Howison e06dc187c7 added const to pass-by-value function parameters; worked more to attributes API 2010-06-29 15:27:25 +00:00
Marc Howison fa806cf273 forgot to add a file 2010-06-26 17:31:45 +00:00
Marc Howison 8783ac2cf2 first part of LBL merge: h5core and H5Part 2010-06-26 17:29:37 +00:00
gsell 6ea921eba4 - append Float64 to H5Block read/write function 
- function H5Block3dReadScalarField() removed
- forgoten refactoring of h5priv_mpi_allgather() fixed
 2010-06-24 13:45:53 +00:00
gsell 6ab3025c9f define ERR_XYZ as macro 2010-06-24 13:42:18 +00:00
gsell d76db8511c 2010-06-24 13:38:02 +00:00
gsell 0c5dd6cff3 more binaries added to ignore list 2010-06-24 13:36:23 +00:00
gsell c313f3da2a refactoring of H5hut types 2010-06-24 13:35:24 +00:00
gsell ff5aaf08a5 more binaries added to ignore list 2010-06-24 13:34:05 +00:00
gsell 04d8d30ed0 refactoring of H5hut types 2010-06-24 13:33:16 +00:00
gsell 06caa6dcb1 2010-06-10 21:00:25 +00:00
gsell 816b81a1c1 2010-06-10 15:46:08 +00:00
gsell 3a87865fc3 rename several variables, functions and struct members to make clear that deal with indices and not IDs 2010-05-28 15:55:39 +00:00
gsell 15455ad905 several files renamed to more consistent names 2010-05-28 14:23:57 +00:00
gsell 2f30c9fcb8 - update of internal data structures reviewed 2010-05-28 14:09:08 +00:00
gsell cb37690b83 renamed 'h5t_open_level()' to 'h5t_set_level()' 2010-05-28 09:43:00 +00:00
gsell 93c43c7cdd renamed 'h5t_open_level()' to 'h5t_set_level()' 2010-05-28 09:42:52 +00:00
gsell 47a7bab09f adapted to coding style 2010-05-28 09:39:31 +00:00
gsell 052041715d renamed 'rebuild_internal_structs()' to 'update_internal_structs()' 2010-05-28 09:12:40 +00:00
gsell d526ebb484 underscore prefix removed from static functions 2010-05-28 07:50:07 +00:00
gsell 22e45ec997 adapted to coding style 2010-05-28 07:43:38 +00:00
gsell 27763974e1 type fixed 2010-05-27 14:07:37 +00:00
gsell 6a9398ed19 adapted to coding style 2010-05-27 14:06:09 +00:00
gsell 2755e69636 adapted to coding style 2010-05-27 14:05:45 +00:00
gsell 010a605a3b removed, replacement functions are in h5_hdf5.c 2010-05-27 13:40:46 +00:00
gsell 4e7eb421c1 - obsolete hdf5_xyz() functions replaced 2010-05-27 13:40:02 +00:00
gsell 45637df399 - obsolete hdf5_xyz() functions replaced 
- adapted to coding style
 2010-05-27 13:38:57 +00:00
gsell f8f1590df8 adapted to coding style 2010-05-27 13:27:30 +00:00
gsell d3dc68d045 adapted to coding style 2010-05-27 13:26:51 +00:00
gsell 0ce6476aa6 adapted to coding style 2010-05-27 13:26:33 +00:00
gsell bd4908eeba adapted to coding style 2010-05-27 13:26:22 +00:00
gsell 01c729b290 adapted to coding style 2010-05-27 13:25:30 +00:00
gsell 7d91ce9b73 adapted to coding style 2010-05-27 13:25:05 +00:00
gsell 10f406da47 adapted to coding style 2010-05-27 13:24:37 +00:00
gsell e32b897b7a adapted to coding style 2010-05-27 13:23:40 +00:00
gsell e1767b3189 adapted to coding style 2010-05-27 13:15:30 +00:00
gsell eed6021c71 adapted to coding style 2010-05-27 13:14:40 +00:00
gsell eef07ed9ea adapted to coding style 2010-05-27 13:14:18 +00:00
gsell ff91c08950 adapted to coding style 2010-05-27 13:13:50 +00:00
gsell 3d2a804c63 adapted to coding style 2010-05-27 13:13:37 +00:00
gsell 3d1569ab01 adapted to coding style 2010-05-27 13:12:20 +00:00
gsell d084b153d8 adapted to coding style 2010-05-27 13:11:44 +00:00
gsell c1137a6e32 adapted to coding style 2010-05-27 13:10:43 +00:00
gsell 6db56d9f5b cleanup #include's 2010-05-21 13:04:58 +00:00
gsell 5d94a6ccd8 adapted to coding style 2010-05-21 11:59:11 +00:00
gsell 7e6e819ad9 - DUNE-style refinement implemented 2010-05-21 10:14:42 +00:00
gsell 4243deb2c4 ignore list edited 2010-05-19 07:37:35 +00:00
gsell 493ca7ab49 - use abort error handler 
- polishing
- adapted to coding style
 2010-05-19 07:35:02 +00:00
gsell 5ce0374892 h5t_close_mesh() is a public API function now 2010-05-19 07:31:45 +00:00
gsell 6bdf9d2117 h5t_openclose_private.h added to EXTRA_HEADERS 2010-05-19 07:30:44 +00:00
gsell 7010c7b864 declaration of private open/close function moved to this file 2010-05-19 07:29:34 +00:00
gsell c6cd77b523 - files added 
- implement traversal function with iterators
 2010-05-12 20:32:49 +00:00
gsell 538b0989eb - iterators implemented/debugged 
- traversal functions with iterators debugged for triangle meshes
 2010-05-12 19:51:57 +00:00
gsell 1c41ca12ce update ignore prop 2010-05-06 11:50:35 +00:00
gsell 0edf356fb4 - Use new travere/iterate functions 
- Use new H5FedGetVertexIndicesOfXXX() functions
 2010-05-06 11:49:38 +00:00
gsell bbc480fc80 - trimesh_read/_write added to Makefile.am 2010-05-06 11:47:56 +00:00
gsell f9111871fe - H5Fed_map.[ch] removed 2010-05-06 11:45:17 +00:00
gsell dda3cb98a4 - H5FedGetVertexIndicesOfEntity() added 
- H5FedLMapXXX() renamed to H5FedGetVertexIndicesOfXXX
- function in H5Fed_map.c moved to H5Fed_retrieve.c
 2010-05-06 11:42:13 +00:00
gsell 339c8b95db update ignore prop 2010-05-03 13:21:53 +00:00
gsell bde5ef3624 - adapted to new iterate/traverse functions 2010-05-03 13:19:37 +00:00
gsell 8a5afeae31 - argument types for partition definition changed from 'h5_int64_t' to 'h5_size_t' 2010-05-03 13:18:42 +00:00
gsell 24565cab22 - '--enable-64' removed 
- bug in CFLAGS handling fixed
 2010-05-03 13:16:30 +00:00
gsell c2539b6120 fixed wrong #include for reference elements 2010-05-03 07:27:38 +00:00
gsell e013cc9c31 - traverse function replaced with iterator functions 2010-05-02 21:25:22 +00:00
gsell fa2fdf2640 - rename h5t_get_local_vids_of_xxx() to h5t_get_vertex_indices_of_xxx() 2010-05-02 21:24:41 +00:00
gsell d8ba18d662 H5Fed_retrieve.c added 2010-05-02 21:23:14 +00:00
gsell 920a661d37 - traverse function replaced with iterator functions 2010-05-02 21:22:16 +00:00
gsell c72e04b302 added 2010-05-02 21:21:20 +00:00
gsell c9a9ebfc96 - h5t_get_vertex_indices_of_entity() added 
- specific function declaration revised
 2010-05-02 21:20:22 +00:00
gsell b0c436cb14 - typo in include of stdarg.h fixed 
- H5_OID_MAX add to enum h5_oid
 2010-05-02 21:18:00 +00:00
gsell dd21d78ce4 - definition of h5tpriv_get_face_id() renamed to h5tpriv_get_face_idx() 2010-05-02 21:16:41 +00:00
gsell 5c9a6fe9c2 - traverse function replaced with iterator functions 2010-05-02 21:16:06 +00:00
gsell 20e3399294 - definition of h5_error_not_implemented() and h5_error_internal() moved from private header 2010-05-02 21:14:53 +00:00
gsell 2375429556 reference elemets introduced 2010-05-02 21:12:57 +00:00
gsell 39df27c36a - traverse function replaced with iterator functions 2010-05-02 21:09:42 +00:00
gsell 5e8147a575 - change function name: h5tpriv_get_face_id() -> h5tpriv_get_face_idx() 2010-05-02 21:08:43 +00:00
gsell 60a67092ae - use reference element to determine number of vertices 
- return an internal error if buffer to small
 2010-05-02 21:07:12 +00:00
gsell 061778a800 - adaptions to changed h5t_find/search_xxx() functions 
- use of reference elements where reasonable
 2010-05-02 21:04:18 +00:00
gsell cdaf8ce6c9 - traverse function replaced with new iterator functions 2010-05-02 21:01:08 +00:00
gsell a35b845a80 - type of return argument changed to h5_idlist_t in h5t_find/search_xxx functions 
- h5tpriv_get_face_id() renamed to h5tpriv_get_face_idx()
- face_id renamed to face_idx
 2010-05-02 20:59:44 +00:00
gsell 4005b30e8e get number of vertices from reference element 2010-05-02 20:53:16 +00:00
gsell 88e146442c bugfix in function h5priv_hresize(), some comments added 2010-05-02 20:52:08 +00:00
gsell 612bc12796 definition of struct h5t_entity_iterator moved to other header file, build-in iterators removed, ptr to reference element added to struct h5t_fdata 2010-05-02 20:49:00 +00:00
gsell 8960d5c365 definition of h5_error_not_implemented() and h5_error_internal() to public header file 2010-05-02 20:45:52 +00:00
gsell 8a3840baae change return type of result to h5_id_list in h5t_find_xxx and h5t_search_xxx , use face_idx and elem_idx for face and element indices 2010-05-02 20:44:17 +00:00
gsell e44c3b5857 change return type of result to h5_id_list in h5t_find_xxx and h5t_search_xxx , use face_idx and elem_idx for face and element indices 2010-05-02 20:42:02 +00:00
gsell 55d81d3afa include of stdargs.h added 2010-04-28 15:35:15 +00:00
gsell c02c5f3666 prepended underscore removed from static function names 2010-04-23 09:13:59 +00:00
gsell 9be719e66d @H5P_LIB_LOC@ replaced with ${abs_top_builddir} 2010-04-22 15:38:48 +00:00
gsell a7e4cacd3c H5P_LIB_LOC removed, H5PartTest removed from TPTARGET if not parallel 2010-04-22 15:37:34 +00:00
gsell be01b8fa82 update ignore prop 2010-04-22 15:36:11 +00:00
gsell ab139ea9dc update ignore prop 2010-04-22 15:35:13 +00:00
gsell 46202cf1c3 @H5P_LIB_LOC@ replaced with ${abs_top_builddir} 2010-04-22 15:34:13 +00:00
gsell 2bfcfcac51 update ignore prop 2010-04-22 15:33:20 +00:00
gsell ecc22ea489 @H5P_LIB_LOC@ replaced with ${abs_top_builddir}, libstdc++ added to target H5test 2010-04-22 15:32:35 +00:00
gsell 5168a7ea04 change 'all' rule to build library in ../lib 2010-04-22 14:48:10 +00:00
gsell f2d3a7bbaa add 'all' rule to copy library to ../lib 2010-04-22 14:42:36 +00:00
gsell 3875c7c7ff Makefile.am for src dir added 2010-04-22 14:12:18 +00:00
gsell 239b2b632f update ignore prop 2010-04-22 14:09:37 +00:00
gsell dc3df38658 move license/copyright to file COPYING 2010-04-22 14:07:03 +00:00
gsell 5e9d7f56c1 update ignore prop 2010-04-22 14:01:52 +00:00
gsell 9b0c49ca52 path adapted 2010-04-22 14:00:56 +00:00
gsell 08fe1e8dfc update ignore prop 2010-04-22 13:59:13 +00:00
gsell f7ca3bdac5 path adapted 2010-04-22 13:58:17 +00:00
gsell bf5d529160 moved 2010-04-22 13:17:47 +00:00
gsell 63287b8fb6 header file renamed 2010-04-22 13:15:00 +00:00
gsell 6c9b34c9d5 update ignore prop 2010-04-22 12:08:27 +00:00
gsell 149f50628c rename h5_core to h5core 2010-04-22 12:07:19 +00:00
gsell f61185ddc4 public header files moved to ../include 2010-04-22 11:50:41 +00:00
gsell d24ae27e47 public header files moved to ../include/h5core 2010-04-22 11:49:38 +00:00
gsell 17426706fc paths adapted 2010-04-22 11:48:59 +00:00
gsell 0399e82580 moved 2010-04-22 11:47:17 +00:00
gsell 3b587676ef moved 2010-04-22 11:47:04 +00:00
gsell 7db65fab6e reorganize language bindings 2010-04-22 11:07:35 +00:00
gsell 50ba923191 reorganize language bindings 2010-04-22 11:06:39 +00:00
gsell 33f6fca514 reorganize language bindings 2010-04-22 11:04:59 +00:00
gsell 2a0211cb19 update ignore prop 2010-04-22 11:01:26 +00:00
gsell aa2c42a56b update ignore prop 2010-04-22 10:59:38 +00:00
gsell e3212420b4 update ignore prop 2010-04-22 10:59:01 +00:00
gsell 96683751bc update ignore prop 2010-04-22 10:58:05 +00:00
gsell 9df74f2f6a update ignore prop 2010-04-22 10:57:27 +00:00
gsell 7164fd6479 added 2010-04-22 10:56:47 +00:00
gsell a13e413fa5 rename Graphs to Examples 2010-04-22 10:55:19 +00:00
gsell b454e1fd93 rename Graphs to Examples 2010-04-22 10:51:51 +00:00
gsell 7062737caf update ignore prop 2010-04-22 10:42:13 +00:00
gsell b754c790a2 update ignore prop 2010-04-22 10:36:23 +00:00
gsell ea79d93e63 update ignore prop 2010-04-22 10:34:30 +00:00
gsell 1607ada0b7 files removed 2010-04-15 16:07:11 +00:00
gsell f027b16757 2010-04-15 16:06:07 +00:00
gsell 2bb4d67749 files added 2010-04-15 16:05:34 +00:00
gsell d2b696959c files removed 2010-04-15 16:05:16 +00:00
gsell 462fb26ba4 2010-04-15 16:00:41 +00:00
gsell 4cb0c1bcfe 2010-01-22 15:00:25 +00:00
gsell e833b1fd16 2009-12-08 00:03:44 +00:00
gsell 6e9cfa47e1 mesh examples added 2009-12-04 16:28:11 +00:00
gsell ce9205c368 tetmesh_write2.c added 2009-11-13 21:52:57 +00:00
gsell 5584086e40 tag test added 2009-11-13 21:51:38 +00:00
gsell 65186f2186 tag implementation, bugfixes ... 2009-11-13 21:50:38 +00:00
gsell 5eb841ecdf tag implementation, bugfixes ... 2009-11-13 21:48:01 +00:00
gsell 57a9c11948 tag implementation, bugfixes ... 2009-11-13 21:46:53 +00:00
gsell 22a1fa33eb tag implementation, bugfixes ... 2009-11-13 21:46:15 +00:00
gsell c4961753a9 Adapted to new API 2009-08-14 13:20:49 +00:00
gsell 75fcb2f68f Adapted to new API 2009-08-14 13:20:16 +00:00
gsell ee0f09de43 Some type cast warning fixed 2009-08-14 13:18:57 +00:00
gsell 9f189e7146 2009-08-14 13:18:04 +00:00
gsell 2ec6aad172 See H5Fed_inquiry.c 2009-08-14 13:15:45 +00:00
gsell 7e39956a36 - Query current level only 
- Documentation updated
 2009-08-14 13:15:08 +00:00
gsell 1665bc9703 H5FedStoreBoundaryfaceGlobalID() removed 2009-08-14 13:13:13 +00:00
gsell 3eac0d6264 see H5Fed_retrieve.c 2009-08-14 13:12:23 +00:00
gsell 3e4028de84 some type cast warning fixed 2009-08-14 13:10:18 +00:00
gsell 0cb95e9683 - Function for traversing elements now returns local ID and local vertex IDs only 
- Function for traversing vertices returns local ID and coordinates only
- Doxygen documentation updated
 2009-08-14 13:08:52 +00:00
gsell 4f78beabde added 2009-08-14 13:04:39 +00:00
gsell 0228c69cfa - refactored variable names local_ prefix removed in some files 
- test existence of vertices while refining via adjecencies
 2009-08-14 13:03:48 +00:00
gsell e047595885 set error handler to abort programm and removed all error checks 2009-07-27 15:17:51 +00:00
gsell 12722cebaf set error handler to abort programm and removed all error checks 2009-07-27 15:17:22 +00:00
gsell 0b9dcea258 set error handler to abort programm and removed all error checks 2009-07-27 15:16:30 +00:00
gsell 05061e09ae fixed empty line follows backslash warning 2009-07-27 15:15:08 +00:00
gsell da80c1736d binary tree replaced with hash-tables and several fixes 2009-07-27 15:12:34 +00:00
gsell 92a24b8890 bugfixes in start traverse functions 2009-07-16 08:42:53 +00:00
gsell 5b45cbce7a bugfixes in pointer calculation 2009-07-16 08:41:44 +00:00
gsell a65496cea3 include for hash search functions added 2009-07-16 08:40:30 +00:00
gsell 92adaf3509 _h5_calloc added 2009-07-16 08:39:35 +00:00
gsell f70dce9acc hash funktions added 2009-07-16 08:38:09 +00:00
gsell a4036b7b5d formating fix 2009-07-16 08:36:49 +00:00
gsell e38e7d1c8e error handler added 2009-07-16 08:35:32 +00:00
gsell d0daec98fa renamed 2009-07-11 08:07:44 +00:00
gsell 38a9e2ee90 renamed 2009-07-11 08:06:50 +00:00
gsell 3978da3963 renamed 2009-07-11 08:05:59 +00:00
gsell f4ea22a702 write TWiki-friendly output 2009-07-11 08:05:24 +00:00
gsell f1239351eb some tests added 2009-07-11 08:03:31 +00:00
gsell 5485eb2661 write TWiki-friendly output 2009-07-11 08:02:27 +00:00
gsell 639d91ee4e renamed 2009-07-03 12:40:38 +00:00
gsell 8f98ff0165 print all up- and downward adjacencies 2009-07-01 19:18:54 +00:00
gsell b6f2894ddb - up- and downward adjacencies implemented 2009-07-01 19:17:38 +00:00
gsell 607894f565 - read everything while opening mesh 
- upward and downward adjacencies added
 2009-07-01 19:16:24 +00:00
gsell 35bbbfb1a9 added 2009-07-01 19:15:14 +00:00
gsell 91b0543866 edge traversing added 2009-06-12 23:56:07 +00:00
gsell b3187bed21 edge traversing added 2009-06-12 23:55:29 +00:00
gsell 584ff25f33 some API function has been renamed 2009-06-11 23:14:27 +00:00
gsell 17556cbfab added 2009-06-11 23:12:24 +00:00
gsell eccbfc5a42 added 2009-06-11 23:11:06 +00:00
gsell 255da882f7 bugfixes, implementation of adjacency functions 2009-06-11 23:10:11 +00:00
gsell 5bd0617f59 bugfixes, implementation of adjacency functions 2009-06-11 23:09:47 +00:00
gsell 48618f0028 removed 2009-06-08 22:54:25 +00:00
gsell bf9dbef0c9 adapted to changed API 2009-05-14 16:41:29 +00:00
gsell 6f8757a27d bugfixes 2009-05-14 16:40:16 +00:00
gsell 6b5d9181e4 adaptions to element structurs: insteed of storeing the refinement level we save the global id of the first child 2009-05-14 16:39:17 +00:00
gsell e40565f8f0 macros to (dis-)assemble edge and triangle ids added 2009-05-14 16:35:04 +00:00
gsell 12a7988abc use macro to extract element id 2009-05-14 16:33:46 +00:00
gsell 8442f85127 same basic functionality added 2009-05-14 16:28:53 +00:00
gsell e0221ae1b7 member "global_child_eid" added to hdf5 datatype 2009-05-14 16:27:43 +00:00
gsell 9012551834 bugfixes in traversing refined elements 2009-05-14 16:26:06 +00:00
gsell 526e4cfc10 bugfixes, use macro to extract element id from triangle/edge id 2009-05-14 16:24:41 +00:00
gsell bf851824a2 bugfixes in refinement 2009-05-14 16:22:56 +00:00
gsell 6a60e90a43 bugfix in H5FedRefineElem() 2009-05-14 16:20:25 +00:00
gsell 8c22590be2 API changes 2009-04-16 15:24:29 +00:00
gsell e206c259a5 API changes 2009-04-16 15:23:57 +00:00
gsell 533f2d083b added 2009-04-16 15:22:50 +00:00
gsell 90b075b911 2009-04-16 15:22:00 +00:00
gsell 035ef4655c added 2009-04-16 15:21:31 +00:00
gsell 6623cc38ad 2009-04-16 15:20:53 +00:00
gsell 6231364157 API adaptions 2009-03-26 16:34:50 +00:00
gsell 0d7a0c737e API adaptions 2009-03-26 16:34:25 +00:00
gsell 09923dba23 - Bugfixes 
- API adaptions
 2009-03-26 14:24:12 +00:00
gsell b831965df9 - bugfixes 
- API adaptions
 2009-03-26 14:23:33 +00:00
gsell b3e7f433ee Added 2009-03-26 14:22:39 +00:00
gsell 25de55c54b Removed 2009-03-26 14:22:00 +00:00
gsell 6a0e624969 Added 2009-03-26 14:20:54 +00:00
gsell 6401b94f60 Adapted to new API 2009-03-26 14:18:59 +00:00
gsell a82888c2e8 configure.ac: 
- split var for test target TTARGET into TPTARGET, TBTARGET, ...
 2009-03-13 15:29:03 +00:00
gsell f405045b13 - adapted to new API 2009-03-13 15:26:04 +00:00
gsell 8921386b9b - adapted to new API 2009-03-13 15:25:27 +00:00
gsell b1b9c2190d - adapt to new API 2009-03-13 15:24:50 +00:00
gsell dc631ce508 - changes for revised API 
- bugfixes
- ...
 2009-03-13 15:23:52 +00:00
gsell 2006e4d5ff - start implementing wrappers for HDF5 calls 
- bugfixes
- ...
 2009-03-13 15:22:50 +00:00
gsell 199a9a56c2 added 2009-01-30 15:07:01 +00:00
gsell c1cec7234b 2009-01-30 15:06:15 +00:00
gsell 4fe83456f6 - do not run doxygen as default target. 2009-01-30 15:05:16 +00:00
gsell 3d0f8bab99 - moved intro from C-source to H5.dox 
- add some new input-files to Doxydoc
 2009-01-30 15:03:27 +00:00
gsell d8eb90d620 - merge changes from 1.4 branch 2009-01-30 15:00:06 +00:00
gsell 253708eab7 - several API changes 
- refactoring
- ... and more
 2009-01-30 14:57:13 +00:00
gsell caeefd811d - several API changes 
- refactoring
- ... and more
 2009-01-30 14:56:01 +00:00
gsell 35280e88e0 added 2008-10-01 15:46:06 +00:00
gsell 14ef15cf83 refactoring 2008-10-01 15:43:55 +00:00
gsell 828388c065 2008-09-25 15:52:26 +00:00
gsell c263b1557b added 2008-09-25 15:51:32 +00:00
gsell 2680653214 2008-09-25 15:50:49 +00:00
gsell b22f280da0 2008-09-25 15:50:18 +00:00
gsell a1d62018ff 2008-09-25 15:49:08 +00:00
gsell cd7ffd24e4 added 2008-09-25 15:47:55 +00:00
gsell b737d2cb14 refactoring 2008-09-25 15:47:26 +00:00
gsell ae72438ae3 added 2008-09-25 15:46:39 +00:00
gsell 07e57ff23a refactoring 2008-09-25 15:43:24 +00:00
gsell 7959742667 renamed 2008-08-27 13:56:59 +00:00
gsell de5f7c29d6 h5_core/h5_general.c 
- use function to get debug level
- use of H5_ERR_INIT insteed H5PART_ERR_INIT
- function to get/set error number
 2008-08-27 13:56:41 +00:00
gsell 0011e28251 directory h5 renamed to h5_core 2008-08-27 10:06:46 +00:00
gsell f09c47a6b2 include of H5Fed_boundaries added 2008-08-27 10:04:33 +00:00
gsell c5eb850b01 new source files H5Fed_boundaries.[ch] added 2008-08-27 10:03:33 +00:00
gsell 7465764861 declaration of function H5FedMapTriangle2GlobalID() added 2008-08-27 10:02:36 +00:00
gsell 58549852a6 files renamed: h5 prefix added 2008-08-27 09:59:36 +00:00
gsell 5b381c8def added 2008-08-27 09:56:14 +00:00
gsell 3f9da8b2bd Mappings of vertices and triangles 2008-08-27 09:54:24 +00:00
gsell 16a6792af4 file renamed 2008-08-27 09:28:55 +00:00
gsell 1a2ee0adf6 definition of H5_TET_MASK fixed 2008-08-27 09:28:07 +00:00
gsell bceb2c6b35 test map_triangle2globalid added 2008-08-20 15:08:33 +00:00
gsell 90e53a6e52 use of obsolete macro fixed 2008-08-20 15:07:45 +00:00
gsell 66f0bf6e4e use of obsolete macro fixed 2008-08-20 15:07:28 +00:00
gsell 657aee3049 autotools generated file removed 2008-08-20 14:46:44 +00:00
gsell ba01c980ac added 2008-08-20 14:37:57 +00:00
gsell 6def843cc3 renamed 2008-08-20 14:37:30 +00:00
gsell c98053870f some tests renamed and more added 2008-08-20 14:36:46 +00:00
gsell 774d60f9bb added 2008-08-20 14:35:56 +00:00
gsell 0f34916a56 mapping of tets and triangles to global and local id added 2008-08-20 14:30:57 +00:00
gsell 4f37dbe55a added 2008-08-20 14:30:31 +00:00
gsell a390b30fcb mapping of tets and triangles to global and local id added 2008-08-20 14:29:26 +00:00
Benedikt Oswald fb891c3e80 Corrected wrong directory names in automake files. 2008-08-06 09:09:51 +00:00
gsell 8175442f6b C files renamed 2008-07-30 08:26:52 +00:00
gsell 54546b8e84 h5b renamed to H5Block 2008-07-30 08:20:40 +00:00
gsell 7400597342 h5u renamed to H5Part 2008-07-30 08:20:14 +00:00
gsell a2a36999c9 h5t renamed to H5Fed 2008-07-30 08:19:23 +00:00
gsell 9681dbf3b1 mappings and bookkeeping functions we need for boundary triangles 2008-07-17 14:01:20 +00:00
gsell 5f79e622fc triangle tests added 2008-07-02 14:27:35 +00:00
gsell bd01dcc24b refactoring 2008-07-02 14:26:24 +00:00
gsell 309cf36f38 refactoring 2008-07-02 14:25:50 +00:00
gsell 1b9fb3302d added 2008-07-02 14:24:38 +00:00
gsell f6d203f6a7 added 2008-07-02 14:23:30 +00:00
gsell 55b5b5e7cc added 2008-07-02 14:22:51 +00:00
gsell 1790c475da refactoring and triangle meshes 2008-07-02 14:21:21 +00:00
gsell 5729fa420f can be recreated by autogen.sh 2008-06-19 15:37:24 +00:00
gsell 83012629ac refactoring 2008-06-19 15:34:06 +00:00
gsell 2457075f32 refactoring 2008-06-19 15:34:00 +00:00
gsell ad4ab87b6e refactoring 2008-06-19 15:33:47 +00:00
gsell 0e4151ae1f refactoring 2008-06-19 15:33:02 +00:00
gsell b55e29398f refactoring 2008-06-19 15:32:43 +00:00
gsell 0547eb1817 refactoring 2008-06-19 15:28:44 +00:00
gsell d0f262e755 refactoring 2008-06-19 15:16:48 +00:00
gsell 7829615f32 refactoring 2008-06-19 15:15:58 +00:00
gsell 11b105bc82 refactoring 2008-06-19 15:13:34 +00:00
gsell b51290f270 refactoring 2008-06-19 15:12:02 +00:00
gsell d828fb0364 refactoring 2008-06-19 15:11:23 +00:00
gsell 3efd4d64a5 refactoring 2008-06-19 15:10:43 +00:00
gsell 1d1dfdb883 refactoring 2008-06-19 15:10:29 +00:00
gsell 44d30257a4 refactoring 2008-06-19 15:10:21 +00:00
gsell e21d2af4ec refactoring 2008-06-19 15:10:15 +00:00
gsell d407f58b7c refactoring 2008-06-19 15:10:08 +00:00
gsell a768784821 refactoring 2008-06-19 15:09:00 +00:00
gsell 2e0dde14c4 refactoring 2008-06-19 15:08:10 +00:00
gsell 6781800ede refactoring 2008-06-19 15:06:16 +00:00
gsell d19eb1469e refactoring 2008-06-19 15:06:10 +00:00
gsell 13fee62afd refactoring 2008-06-19 15:06:05 +00:00
gsell b0bad95604 refactoring 2008-06-19 15:05:48 +00:00
gsell 275d279f8d refactoring 2008-06-19 15:05:43 +00:00
gsell d00ea580cd refactoring 2008-06-19 15:04:36 +00:00
gsell 4072560858 refactoring 2008-06-19 15:04:28 +00:00
gsell dddb0f8c2b refactoring 2008-06-19 15:04:07 +00:00
gsell f671df975d refactoring 2008-06-19 15:03:44 +00:00
gsell caeac4ef8b refactoring 2008-06-19 15:03:15 +00:00
gsell d06bef0854 refactoring 2008-06-19 15:03:01 +00:00
gsell 12ae632ac4 added 2008-06-05 12:48:52 +00:00
gsell fd43fea24e removed 2008-06-05 12:45:24 +00:00
gsell 0f271a745f added 2008-03-19 11:36:30 +00:00
gsell 4d4b21aac3 read_vertices() 
read_tets()
	- leave loop as soon as we have read the expected number of objects
 2008-02-22 14:39:33 +00:00
gsell 136b1df93e several funcion renamed and param types changed, read logs for include 
files for more details
 2008-02-22 14:23:19 +00:00
gsell 702a2b0398 _read_data() 
- step id from error handling removed
 2008-02-22 14:13:13 +00:00
gsell 68529915b3 H5FedGetNumMeshes() 
H5FedOpenMesh()
H5FedGetNumLevels()
H5FedSetLevel()
	- added
H5FedGetVertex()
H5FedGetTetrahedron()
	- param type changed
 2008-02-22 13:56:49 +00:00
gsell 5d5e49cd83 _h5t_init_fdata() 
* init t->num_meshes;
 2008-02-22 13:53:13 +00:00
gsell d52258a68a H5U_read_elems() 
- #ifdef INDEPENDENT_IO removed, pass xfer_prop in both cases
 2008-02-22 13:51:37 +00:00
gsell 33e37380d2 H5t_open_mesh() 
- renamed, was H5t_set_mesh
	- parm id isn't const any more
H5t_open_level()
	- renamed, was H5t_set_level
H5t_get_vertex()
	- parm P type changed
H5t_get_tet
	- parm vertex_ids type changed
 2008-02-22 13:49:03 +00:00
gsell 8cee40b22a reading of vertices and tets added 2008-02-22 13:45:25 +00:00
gsell 88ec6fd6d0 H5_ERR_INTERNAL 
- added
struct h5t_fdata
       - last_retrieved_vertex_id and last_retrieved_tet_id added
 2008-02-22 13:44:02 +00:00
gsell 17b5cf1a47 HANDLE_H5_INTERNAL_ERR 
- added
HANDLE_H5D_READ_ERR
	- do not print step id any more
 2008-02-22 13:42:34 +00:00
gsell f50381096a rules to compile read_tet added 2008-02-22 13:39:42 +00:00
gsell d7230920ed added 2008-02-22 13:38:54 +00:00
gsell 3b1b2075a5 struct vertex 
* global_id added
add_level()
	* use global vertex id defined in struct
main()
	* add error handling after calls to add_level)
 2008-02-22 13:38:28 +00:00
Benedikt Oswald 37a9b877aa Added include files. 2008-02-20 14:19:29 +00:00
gsell 6888d0cd6f - empty line removed 2008-02-20 14:07:58 +00:00
gsell 446e5dfcd8 H5t_store_tet() 
- some debug output added
 2008-02-20 14:07:18 +00:00
gsell 77ca64df60 H5t_get_num_meshes() 
H5t_get_num_meshes()
H5t_get_num_levels()
H5t_set_level()
	- added
H5t_store_tet()
	- output of error messages added
 2008-02-20 14:04:59 +00:00
gsell 6684a3cdfc - declaration of new functions added 2008-02-20 13:48:55 +00:00
gsell 5426e8267e HANDLE_H5_UNDEF_MESH_ERR 
HANDLE_H5_UNDEF_LEVEL_ERR
HANDLE_H5_OVERFLOW_ERR
HANDLE_H5_PARENT_ID_ERR
HANDLE_H5_OUT_OF_RANGE_ERR
	- macros added
 2008-02-20 13:48:13 +00:00
gsell c6dc048f25 H5FedGetNumLevels() 
- moved to H5Fed_storeretrieve.c
 2008-02-20 13:46:16 +00:00
gsell 9eb059e1ec struct h5t_fdata 
- num_meshes added
 2008-02-20 13:42:41 +00:00
gsell 8df79f3ee4 H5FedGetNumLevels() 
H5FedSetLevel()
H5FedGetNumMeshes()
H5FedSetMesh()	
	- added
 2008-02-20 13:41:12 +00:00
gsell 64b9441aed H5FedGetNumVertices() 
- call H5t_get_num_vertices()
H5FedGetVertex()
- call H5t_get_vertex()
H5FedGetNumTetrahedras()
- call H5t_get_num_tets()
H5FedGetTetrahedra()
- call H5t_get_tet()
 2008-02-20 10:32:23 +00:00
gsell 11921ff04c - declaration of new functions added 2008-02-20 10:25:54 +00:00
gsell a83d527326 _write_data() 
* write of dataset H5T_TETMESH_NUM_ELEMS_ON_LEVEL_DSNAME added
H5_add_level()
H5_store_tet()
	* handling of num_tets_on_level added
_read_vertices()
H5t_get_num_vertices()
H5t_get_vertex_ids()
H5t_get_vertex()
H5t_get_num_tets()
H5t_get_tet()
	* added
 2008-02-20 10:24:48 +00:00
gsell 3c69548d96 - macro H5T_TETMESH_NUM_ELEMS_ON_LEVEL_DSNAME added 2008-02-20 10:18:18 +00:00
gsell e1055a5241 - num_tets_on_level added to struct h5t_fdata 2008-02-20 10:17:11 +00:00
gsell 449e7b9465 trunk/src/H5Block.c 
trunk/src/H5Fed.c
trunk/src/H5Fed_storeretrieve.c
- include <stdarg.h> added
 2008-02-18 14:40:12 +00:00
gsell bac53ee2d2 test/h5t/Makefile.am 
test/h5u/Makefile.am
test/h5b/H5BlockTestAttributes.c
test/h5b/Makefile.am
src/H5Part.c
src/H5Block.c
src/H5Part.h
src/Makefile.am
src/h5/errorhandling.c
src/h5/h5_types.h
src/h5/attribs.c
src/h5/t_readwrite.c
src/h5/u_readwrite.c
src/h5/t_openclose.c
src/h5/h5_private.h
src/h5/readwrite.c
src/h5/openclose.c
src/h5/Makefile.am
- changes due to removed H5PartTypes.h, H5BlockTyes.h and H5PartPrivate.h
 2008-02-18 14:33:30 +00:00
gsell a805b54aac removed 2008-02-18 14:03:25 +00:00
gsell 91100da0d7 removed 2008-02-18 14:01:16 +00:00
gsell d658271487 removed 2008-02-18 14:00:16 +00:00
gsell 056ad4e54f added 2008-02-18 13:55:48 +00:00
gsell 1be1123b9a - typo in value of include_HEADERS fixed 2008-02-18 13:54:51 +00:00
gsell 1cec74a0b4 _h5b_open_file() 
- we cannot call H5_check_filehandle() here
H5_open_file()
- Output of info-message changed
 2008-02-18 13:52:38 +00:00
gsell 1597d075fd H5_write_data() 
- output info-message with group and dataset name we are writing to
 2008-02-18 13:45:59 +00:00
gsell 361bdbedc6 - calls of HANDLE_H5S_CREATE_SIMPLE_ERR() adapted to new definition 2008-02-18 13:43:52 +00:00
gsell 96f5a0ec45 - error handling added 2008-02-18 13:42:17 +00:00
gsell 2ab830d4f1 - error handling added 
- output of informational messages
 2008-02-18 13:41:41 +00:00
gsell 08424772cf - HANDLE_H5S_CREATE_SIMPLE_ERR() output rank now 2008-02-18 13:40:23 +00:00
gsell 551113e4a8 - H5_get_objname() added 
- some log-macros added
 2008-02-18 13:36:16 +00:00
gsell 08cb0e3e55 H5_get_objname() 
- added
 2008-02-18 13:35:16 +00:00
gsell 7651bbf900 - SET_FNAME() added to all functions 2008-02-18 13:34:26 +00:00
gsell e3f0a69e9d - reduce verbosity level to 4 2008-02-18 13:32:05 +00:00
gsell ee593dd338 src/H5Fed.c 
- includes fixed
 2008-02-14 15:43:10 +00:00
gsell 1c7df2a598 H5Part.c 
H5Block.c
h5/u_readwrite.c
h5/attribs.c
h5/t_openclose.c
h5/readwrite.c
h5/openclose.c
- includes fixed
 2008-02-14 15:41:50 +00:00
gsell bd3b9fa4f6 src/h5/t_readwrite.h 
- declaration of new functions added
 2008-02-14 15:38:56 +00:00
gsell 693c9ff72b src/h5/h5_private.h 
- include of "errorhandling_private.h" added
- macros "CHECK_FILEHANDLE", "CHECK_WRITABLE_MODE", "CHECK_READONLY_MODE" and
   "CHECK_TIMEGROUP" added
 2008-02-14 15:37:42 +00:00
gsell 99274bbec9 src/h5/t_readwrite.c 
- includes fixed
- H5t_add_level()
  H5t_add_num_vertices()
  H5t_store_vertex()
  H5t_add_num_tets()
  H5t_store_tet()
  * added
 2008-02-14 15:35:17 +00:00
gsell f163070d47 src/h5/h5_types.h 
- macro H5_ERR_NOT_IMPLEMENTED added
 2008-02-14 15:32:59 +00:00
gsell 9c48120cd9 src/h5/errorhandling.h 
- maro "H5_warn" added
- declaration of "H5_set_funcname()" fixed
 2008-02-14 15:31:53 +00:00
gsell bf9993808a src/h5/errorhandling.c 
- includes fixed
- use "h5" types insteed of obsolete "h5part" types
- H5_set_funcname()
  * fix definition of parameter "fname"
  * fix cast in assignment to "__funcname"
 2008-02-14 15:30:11 +00:00
gsell 8c35cd1bdf src/Makefile.am 
- "H5PartErrors.h" and "H5BlockErrors.h" removed from "include_HEADERS"
 2008-02-14 15:26:29 +00:00
gsell 13c206ef1a src/H5Fed_storeretrieve.c 
- include files fixed
- SET_FNAME(__func__) added to all (?) functions
- move real implementation to "h5/t_readwrite.c"
 2008-02-14 15:24:44 +00:00
gsell 4ad70757eb removed 2008-02-14 14:57:27 +00:00
gsell 35888e637f src/H5PartErrors.h 
- removed, content moved to "h5/errorhandling_private.h"
 2008-02-14 13:44:58 +00:00
gsell 4be57b410a src/H5BlockErrors.h 
- removed, content added to "h5/errorhandling_private.h"
 2008-02-14 13:41:23 +00:00
gsell 7deb9dff22 src/h5/h5.h 
- renamed, was "_h5.h"
 2008-02-14 13:22:14 +00:00
gsell a972f67eba src/h5/_h5.h 
- renamed, was "H5.h"
 2008-02-14 13:21:36 +00:00
gsell 4f28118033 src/h5/H5.h 
- include of "h5_private.h" removed
 2008-02-14 13:20:31 +00:00
gsell 091e228da1 Makefile.am 
src/Makefile.am
- clean/distclean errors fixed
 2008-02-14 09:15:08 +00:00
gsell 78c4e01ee1 removed 2008-02-14 09:13:12 +00:00
gsell 7de54ba17e src/H5Fed.c 
- includes fixed
 2008-02-13 16:11:35 +00:00
gsell a26d761d20 src/H5Fed_storeretrieve.c 
- includes fixed
 2008-02-13 16:11:05 +00:00
gsell 0561fc835e test/h5u/H5PartTest.cc 
- format type error fixed
 2008-02-13 16:09:48 +00:00
gsell ece99021bd configure.ac 
- adaptions to new hierarchy in test dir
 2008-02-13 15:42:05 +00:00
gsell 48c68c5fa7 src/H5Fed.h 
- several API changes
 2008-02-13 15:40:29 +00:00
gsell 8a39409161 src/H5PartErrors.h 
- output of step id removed
 2008-02-13 15:38:49 +00:00
gsell b7cd8ff3b6 removed 2008-02-13 15:36:57 +00:00
gsell bde413ad6c removed 2008-02-13 15:35:47 +00:00
gsell 87a40d2a73 added 2008-02-13 15:34:53 +00:00
gsell baf9487e12 removed 2008-02-13 15:33:44 +00:00
gsell b421bd27dc src/h5/H5.h 
- include of "t_openclose.h" added
 2008-02-13 15:32:07 +00:00
gsell a79bfceef8 added 2008-02-13 15:29:29 +00:00
gsell 5f40ae0ba6 src/h5/readwrite.c 
- error handling of dataset write errors: output of step-id removed
 2008-02-13 15:24:56 +00:00
gsell 29f928c69a src/h5/openclose.h 
- several declarations added
 2008-02-13 15:22:56 +00:00
gsell d42a441130 src/h5/h5_types.h 
src/h5/t_readwrite.c
src/h5/t_openclose.c
- mesh write functions implemented
 2008-02-13 15:21:51 +00:00
gsell 926723962a src/h5/openclose.c 
- minor fixes
 2008-02-13 15:18:56 +00:00
gsell 0222405291 removed 2008-02-13 15:16:47 +00:00
gsell bc10ebd64e tests moved to subdirectories 2008-02-13 15:15:11 +00:00
gsell b1f4233cb7 added 2008-02-13 15:09:50 +00:00
gsell 7cc4d11c37 added 2008-02-13 15:09:44 +00:00
gsell 69b9b6bb4b added 2008-02-13 15:09:35 +00:00
gsell 1da909b862 added 2008-02-13 15:09:26 +00:00
gsell 39be999eb6 added 2008-02-13 15:09:13 +00:00
gsell 4541d58a9c added 2008-02-13 15:09:05 +00:00
gsell b6f16a7648 added 2008-02-13 15:08:57 +00:00
gsell 25ca447c5a added 2008-02-13 15:08:36 +00:00
gsell aef14e1392 test/h5u/H5test.cc 
test/h5u/H5testF.f
test/h5u/H5PartTest.cc
test/h5u/H5ParallelTest.cc
test/h5b/H5BlockParTestScalarField.pbs
- moved
 2008-02-06 11:08:52 +00:00
gsell 1c0148668f test/h5b/H5BlockTestAttributes.c 
test/h5b/H5BlockTestAttributesF.f90
test/h5b/H5BlockParTestScalarField.c
test/h5b/H5BlockParTestScalarFieldF.f90
test/h5b/H5BlockDissolveGhosts.c
- moved
 2008-02-06 11:06:17 +00:00
gsell e7288533d6 test/h5u/Bench.c 
- moved
 2008-02-06 11:03:03 +00:00
gsell 447d800a1c added 2008-02-06 10:59:51 +00:00
gsell ca8decaf45 est/H5BlockTestAttributes.c 
- adaption to renamed elements in struct h5_file
src/H5PartErrors.h
src/H5BlockTypes.h
src/H5Part.h
src/H5Block.c
- refactoring
src/H5Fed.h
src/H5Fed_statistics.c
src/Makefile.am
src/H5BlockErrors.h
src/h5/h5_types.h
src/h5/attribs.c
src/h5/t_readwrite.c
src/h5/u_readwrite.c
src/h5/t_openclose.c
src/h5/H5.h
src/h5/readwrite.c
src/h5/openclose.c
src/h5/openclose.h
src/H5Fed.c
- H5Fed write vertices and tets
 2008-01-25 19:30:41 +00:00
gsell e581c105d6 src/H5PartErrors.h 
* adaptions to renamed members in "struct h5_file"
 2008-01-20 11:11:08 +00:00
gsell fe82dbc905 src/H5Fed.c 
* coding
 2008-01-20 11:09:20 +00:00
gsell 1dc9bd1a4b src/H5Parth 
* new macros for file access modes
 2008-01-20 11:07:55 +00:00
gsell f1400efd79 src/H5Fed_store.c 
* rudimental write functions for vertices and tets added
 2008-01-20 11:05:27 +00:00
gsell ec530077a8 src/H5Part.c 
* adaptions to renamed member in "struct h5_file"
 2008-01-20 11:01:58 +00:00
gsell 3ad5991be5 src/h5/Makefile.am 
* some C files added to library source
 2008-01-20 11:00:27 +00:00
gsell 1caf5a3a04 src/h5/t_openclose.c 
src/h5/t_readwrite.c
* added
 2008-01-20 10:58:56 +00:00
gsell ee30cb6123 src/h5/openclose.c 
* adaption to renamed members in "struct h5_file"
* several changes and additions for H5Fed
 2008-01-20 10:57:19 +00:00
gsell 720674a15f src/h5/readwrite.c 
* adaptions to renamed members in "struct h5_file"
* several changes/additions for H5Fed
 2008-01-20 10:55:19 +00:00
gsell 89b62f0306 src/h5/u_readwrite.c 
* adaption to renamed members in "struct h5_file"
 2008-01-20 10:53:59 +00:00
gsell 53d6c0cf0a src/h5/h5_types.h 
* several members in "struct h5_file" renamed
* structures for H5Fed added
 2008-01-20 10:52:34 +00:00
gsell efa9c1cd84 src/H5Block.c 
* adaption to renamed members in "struct h5_file"
 2008-01-20 10:49:28 +00:00
gsell 6df181d0c7 src/H5BlockTypes.h 
* struct h5b_fdata
  - "timestep" renamed to "step_idx"
 2008-01-20 10:45:35 +00:00
gsell 9940630e2c src/H5Fed.h 
- API changes
 2008-01-20 10:42:51 +00:00
adelmann 08d7c7fddd Full blown autogen, configure bla etc. 2008-01-08 21:37:28 +00:00
adelmann 3d2b121cf2 clean up before commit configure like H5PartMerge 2008-01-08 20:18:50 +00:00
adelmann 16615a96ba Initial commit of Christof's H5PartMerge 2008-01-05 13:52:05 +00:00
gsell c356139f6b src/h5/h5_types.h 
- definition of h5_file added
 2007-12-21 19:08:18 +00:00
gsell e46df85671 src/H5PartTypes.h 
- definition of h5_file moved to h5/h5_types.h
 2007-12-21 19:07:25 +00:00
gsell e4ed2a1ae6 src/H5Fed_adjacency.c 
src/H5Fed_dof.c
src/H5Fed_retrieve.c
src/H5Fed_statistics.c
src/H5Fed_store.c
src/H5Fed.c
	- added
 2007-12-21 19:06:25 +00:00
gsell b27695d751 src/Makefile.am 
- H5Fed files added
 2007-12-21 19:03:14 +00:00
gsell 35c5969094 src/H5Fed.h 
- some fixes (typo's  etc)
	- Doxygen doc moved to .c files
 2007-12-21 19:02:21 +00:00
gsell c1ddd1e8fc src/H5Fed.c 
- added
 2007-12-21 16:16:10 +00:00
gsell 452b1fd471 src/h5/h5_types.h 
- added
 2007-12-21 16:15:05 +00:00
gsell f7b2471701 src/H5Fed.h 
src/H5BlockTypes.h
src/H5Part.c
src/H5PartPrivate.h
src/H5Block.c
src/H5Part.h
src/h5/u_readwrite.h
src/h5/H5.h
src/h5/readwrite.c
src/h5/openclose.c
src/h5/attribs.c
src/h5/u_readwrite.c
src/h5/readwrite.h
src/h5/openclose.h
src/h5/attribs.h
src/bindings/Fortran/H5PartF.c
src/bindings/Fortran/H5BlockF.c
src/H5Block.h
src/H5PartTypes.h
	- refactoring
	  * struct H5PartFile -> struct h5_file
	  * struct H5BlockStruct -> struct h5b_fdata
 2007-12-21 16:14:08 +00:00
gsell b5b66ebed1 src/bindings/C++/Makefile.am 
- CFLAGS/Include definitions revised
 2007-12-21 16:06:41 +00:00
Benedikt Oswald 4009cb3f15 Added first write routines to C++ API of H5FED. 2007-12-19 08:59:45 +00:00
Benedikt Oswald 16a481c4fa Added first write routines to C++ API of H5FED. 2007-12-19 08:55:51 +00:00
Benedikt Oswald 3a350f975d Corrected C++ part. 2007-12-19 08:32:06 +00:00
gsell 1dd6e487be src/bindings/C++/Makefile.am 
- definition of OBJEXT added
 2007-12-17 23:18:35 +00:00
gsell 0858cca67d src/bindings/C++/Makefile.am 
- rules added to build libH5XX.a
 2007-12-17 23:16:26 +00:00
gsell 65c8f7de29 src/h5/Makefile.am 
- minor change (some blank lines removed)
 2007-12-17 23:15:14 +00:00
gsell cddb48ff47 src/Makefile.am 
- minor change (blank line added somewhere)
 2007-12-17 23:14:10 +00:00
gsell 607a398f87 configure.ac 
- code to build C++ interface added
 2007-12-17 16:37:42 +00:00
gsell fc87576807 added 2007-12-17 16:36:11 +00:00
gsell 4a6c4817ce src/Makefile.am 
- rule to build "libpH5Part.a" removed
 2007-12-17 16:35:24 +00:00
gsell 3c22a8c653 configure.ac 
- option "--with-hdf5" prefered over env.variable
	- "TOOLS_H5PART_LIB" set to "-lH5Part" in serial *and* parallel mode
 2007-12-17 14:58:59 +00:00
gsell c4c9eca143 src/h5/u_readwrite.c 
- forgot to rename "H5Part_print_debug()" to "H5_print_debug()" in some lines.
 2007-12-17 14:55:36 +00:00
gsell e919f34618 test/Makefile.am 
- "-lH5Part" and "-lpH5Part" removed from build rules
 2007-12-17 14:54:15 +00:00
Benedikt Oswald bfcacfddc8 Definition of H5Fed C++ interface, class definition and implementation, first material. 2007-12-17 12:41:37 +00:00
gsell 5e0c8a67cd src/h5/openclose.c 
- _init_block()
	  fixed: check of file handle with non-existing function
 2007-12-17 12:36:48 +00:00
gsell 69367a7713 src/h5/errorhandling.c 
- "_err_handler" initialized with non-existing function
 2007-12-17 12:35:13 +00:00
gsell 89bdeb1459 src/H5Block.c 
- H5BlockGetFieldInfo()
	  * call of non-existing function "_H5Part_get_object_name()" new name of this function
	    is "H5_get_object_name()".
 2007-12-17 12:33:16 +00:00
gsell 4e7f8be568 configure.ac 
- some "echo" calls replaced with AC_MSG_... calls
 2007-12-17 12:28:35 +00:00
Benedikt Oswald 317d1b6d9f Definition of H5Fed C++ interface, class definition and implementation, first material. 2007-12-17 11:11:00 +00:00
Benedikt Oswald 0235b61dc9 Definition of H5Fed C++ interface, class definition and implementation, first material. 2007-12-17 10:45:50 +00:00
Benedikt Oswald dfebe64c73 Definition of H5Fed C++ interface, class definition and implementation, first material. 2007-12-17 10:45:21 +00:00
gsell 921469eba8 src/H5Fed.h 
- new type 'h5_id_t' for object id's
	- new type 'h5_size_t' for size of objects
	- parameter 'parent_id' added to Get/Store functions
	- various other changes
 2007-12-16 23:56:00 +00:00
gsell 379de5735f added 2007-12-16 21:45:43 +00:00
gsell e474e78160 C API declaration for H5Fed 2007-12-10 14:28:12 +00:00
adelmann 7b43df2f79 add ierr to MPI_Finalize 2007-11-26 19:45:55 +00:00
gsell d9239fdd88 src/h5/errorhandling.c 
src/h5/u_readwrite.h
src/h5/H5.h
src/h5/errorhandling.h
src/h5/readwrite.c
src/h5/openclose.c
src/h5/attribs.c
src/h5/Makefile.am
src/h5/u_readwrite.c
src/h5/readwrite.h
src/h5/openclose.h
src/h5/attribs.h
	* added
 2007-11-22 11:08:23 +00:00
gsell 69600afb50 * Fortran bindings moved to src/bindings/Fortran 2007-11-22 11:05:10 +00:00
gsell 75de0e2754 src/bindings/Fortran 
* dirs added
	* Fortran bindings moved to bindings/Fortran
 2007-11-22 11:02:52 +00:00
gsell 535d18389c src/h5 
* added
 2007-11-22 11:01:48 +00:00
gsell 082724e233 src/H5PartTypes.h 
* entry to keep the ID of the root group added to struct H5PartFile
	* name of current step/index added to struct H5PartFile
 2007-11-22 10:52:34 +00:00
gsell b9e9b910f1 src/H5BlockErrors.h 
* function to get nam of currengt function has been renamed to H5_get_funcname()
 2007-11-22 10:48:06 +00:00
gsell 4ce50652bc src/Makefile.am 
* Fortran bindings have been moved to another directory
 2007-11-22 10:46:20 +00:00
gsell b2e2cf3b95 src/H5Block.c 
* use of H5 kernel functions
	* INIT(f) removed, Block stuff will now be initialized during file opening.
 2007-11-22 10:44:49 +00:00
gsell 698135bb91 src/H5PartErrors.h 
* _H5Part_get_funcname() has been renamed to H5_get_funcname()
 2007-11-22 10:42:19 +00:00
gsell 9a8a7a7fe9 src/H5PartPrivate.h 
* declarations moved to corresponding files in libH5
 2007-11-22 10:39:18 +00:00
gsell b4414ea058 src/H5Part.c 
* mostly everything moved to libH5.
 2007-11-22 10:36:20 +00:00
gsell 8abb105f2f configure.ac 
* set version number in AC_INIT to 1.5.0
        * set AC_PREREQ to 2.59
        * --with-hdf5path renamed to --with-hdf5
        * we don't distinguish serial and paralell version in the library name any more
	* src/h5/Makefile added to AC_CONFIG_FILES
 2007-11-22 10:34:26 +00:00
gsell 52fa2ad3ee Makefile.am 
o src/h5 added to subdirs
 2007-11-22 10:21:52 +00:00
gsell b9d3f8d2bd test/Makeffile.am 
o libH5 added to H5LIB
 2007-11-22 10:20:50 +00:00
Kurt Stockinger 607d1e86ab Corrected version number 2007-08-29 01:59:47 +00:00
Kurt Stockinger 3ebc9de7a9 Prepare new tag with updates on H5Block. 2007-08-29 01:26:50 +00:00
gsell d8ce890902 src/H5Block.c 
_normalize_partition()
	* wrong type for 'x' fixed
_open_block_group()
_open_field_group()
	* 'herr' type error fixed
_select_hyperslab_for_reading()
	* 'herr' type error fixed
	* type cast boundaries to 'hsize_t'
_create_field_group()
	* 'herr' type error fixed
H5BlockWriteFieldAttrib()
	* type cast 'attrib_type' to 'hid_t'
H5Block3dSetFieldOrigin()
H5Block3dGetFieldSpacing()
	* type cast 'H5PART_FLOAT64' to 'hid_t'
 2007-07-12 09:50:42 +00:00
gsell b191ac7a6a src/H5Part.c 
- H5PartDefineStepName()
	* type cast 'width'
- _H5Part_iteration_operator()
	* type cast error return
- _H5Part_get_object_name()
	* type cast of arg 'idx' and 'len_obj_name' added
- H5PartGetDatasetInfo()
	* type of 'herr' changed from 'herr_t' to 'h5part_int64_t'
- _get_diskshape_for_reading()
 	* 'CHECK_FILEHANDLE()' removed
	* type cast error return to 'hid_t'
- _get_memshape_for_reading()
 	* 'CHECK_FILEHANDLE()' removed
	* type cast error return to 'hid_t'
 2007-07-12 09:15:21 +00:00
gsell 356f7149c5 src/H5Part.c 
- _read_data()
	* type error fixed
- H5PartAbortErrorHandler()
	* type cast exit code
- H5PartSetVerbosityLevel()
	* type cast 'level' to 'unsigned int'
 2007-07-11 15:34:15 +00:00
gsell a0dd21b79e src/H5Part.c 
- _H5Part_set_step()
	* revert use of 'snprintf()' (Windows doesn't have it!)
 2007-07-11 15:10:06 +00:00
gsell 08ce0ee46a src/H5Part.c 
- _H5Part_get_attrib_info():
	* type cast 'attrib_type' in call to '_H5Part_write_attrib()'
- H5PartWriteStepAttrib()
	* change type of 'herr' to 'h5part_int64_t'
	* type cast 'attrib_type' in call to '_H5Part_write_attrib()'
- H5PartWriteFileAttrib()
	* change type of 'herr' to 'h5part_int64_t'
	* type cast 'attrib_type' in call to '_H5Part_write_attrib()'
- H5PartGetStepAttribInfo()
  H5PartGetFileAttribInfo()
  H5PartReadStepAttrib()
  H5PartReadFileAttrib()
	* change type of 'herr' to 'h5part_int64_t'
- _H5Part_set_step()
	* use 'snprintf()' instead of 'sprintf()'
 2007-07-11 15:06:49 +00:00
gsell 7085e22448 src/H5PartTypes.h 
- revert last change
 2007-07-11 14:58:20 +00:00
gsell 74a31f9b8f src/H5Part.c 
- several implicit type conversions fixed
 2007-07-11 14:37:39 +00:00
gsell a38a56865f src/H5PartTypes.h: 
- change type 'stepno_width' in 'struct H5PartFile' from 'int' to
  'h5part_int64-t'
 2007-07-11 14:35:51 +00:00
Kurt Stockinger 1a20e25a84 Added nSteps as command line parameter 2007-07-10 22:41:55 +00:00
gsell 43ff5d2ca0 src/H5PartF90.inc 
- declarations for open in append mode functions added
 2007-06-29 10:02:04 +00:00
gsell 8080f5e2e5 src/H5PartF.c 
- h5pt_opena() open in append mode added
- h5pt_opena_par() open in append mode paralell version added
 2007-06-29 10:01:06 +00:00
Kurt Stockinger 4f870ccbf7 Fixed H5PartGetDatasetInfo. 2007-06-27 23:12:51 +00:00
gsell e6364c637d src/H5BlockF.c 
* correct macro definition of FORTRAN library names for field spacing/origin attribute
 2007-06-16 21:35:37 +00:00
gsell 28c0ac78ad src/H5BlocF90.inc 
* declaration of h5bl_3d_{g,s}et_field_origin() added
 2007-06-14 15:13:26 +00:00
gsell a642074d85 src/H5Block.c 
* Attribute name for field spacing renamed from "Spacing" to "__Spacing__"
* Attribute name for field origin renamed from "Origin" to "__Origin__"
 2007-06-14 15:12:22 +00:00
gsell e962caf1b9 src/H5BlockF.c 
* h5b_3d_set_field_origin() and h5b_3d_get_field_origin() added
* wrong types in h5b_3d_{g,s}et_field_spacing fixed
 2007-06-14 15:10:37 +00:00
gsell 8cad5e3aea src/H5BlockF.c 
* h5b_3d_set_field_spacing() and h5b_3d_get_field_spacing() added
 2007-06-13 12:33:38 +00:00
gsell a2dfad7b69 src/H5BlockF90.inc 
* Declarations to set/get field spacing functions added
 2007-06-13 12:32:33 +00:00
Kurt Stockinger 15c2e1260a Removed trailing backslash. 2007-06-12 16:39:03 +00:00
gsell 655511a02a src/H5Block.c 
* Documentation added
 2007-06-12 09:59:35 +00:00
gsell 0231ece31b src/H5Block.h 
* Obsolete declarations removed
 2007-06-12 08:40:58 +00:00
Kurt Stockinger b64ddd03d1 Added MPI-IO for large block I/O + switch for COLLECTIVE/NON-COLLECTIVE IO. 2007-06-08 17:02:17 +00:00
Kurt Stockinger 853837477e Fixed wrong include file and variable types. 2007-06-07 00:35:31 +00:00
Kurt Stockinger 4956504d17 Fixed dataset name in _get_field_info 2007-06-06 23:47:27 +00:00
gsell e4c8f743ae src/H5Block.c 
* doxygen documentation added
 2007-06-06 09:30:05 +00:00
gsell df627138dc src/H5Part 
* _H5Part_open_file()
	- set f->comm to 0 in serial caseI_COMM_WORLD;
 2007-06-06 09:29:04 +00:00
gsell a4e77a138a doc/Makefile.am: web-pages removed 2007-05-21 13:29:31 +00:00
gsell 9a09f11631 undelete 2007-05-21 13:28:49 +00:00
gsell 783a1ce2b5 Web-pages moved to new repo "H5Webpages" 2007-05-21 12:57:37 +00:00
gsell c43f785ab0 src/H5Block.c 
- more doxygen doc added
 2007-05-17 16:30:37 +00:00
gsell e1a18b62e2 src/H5Part.h 
- function H5PartHasStep() added
 2007-05-17 16:29:08 +00:00
gsell 3ae60f8e46 src/H5Part.c 
- _H5Part_open_file()
		* allocate mem for pnparticles in any case
	- H5PartHasStep()
		* function added
 2007-05-17 16:28:24 +00:00
gsell 949505517c doc/H5X_File_Format.txt 2007-05-15 15:59:42 +00:00
gsell ae9fd98dac src/H5PartTypes.h 
- "typdef" typo fixed in WIN32 section
 2007-05-11 16:05:59 +00:00
gsell 70bc6af59f test/H5BlockTestAttributes.c 
- include mpi.h removed if PARRALLEL_IO
	- typedef MPI_Comm removed if not PARALLEL_IO
 2007-05-10 20:37:34 +00:00
gsell 825322c576 src/H5Part.c 
- some type-casts added
	- internal error variable '_errno' renamed to '_h5part_errno'
 2007-05-10 19:18:00 +00:00
gsell 58bd753fad src/H5Block.c 
- type cast all malloc's
 2007-05-10 19:15:22 +00:00
gsell 904e609377 src/H5Part.h 
- don't wrap system include files in 'extern "C"'
 2007-05-10 19:13:36 +00:00
gsell d1b594a788 src/H5Part/Types: 
- tydef of int64_t added for Windows
 2007-05-10 19:08:32 +00:00
gsell 3bafbc6029 continue writing 2007-05-10 15:03:37 +00:00
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*** Copyright Notice ***
H5hut Copyright (c) 2006-2010, The Regents of the University of California,
through Lawrence Berkeley National Laboratory (subject to receipt of any
required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
Institut (Switzerland). All rights reserved.
If you have questions about your rights to use or distribute this
software, please contact Berkeley Lab's Technology Transfer Department
at TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
NOTICE. This software was developed under partial funding from the U.S.
Department of Energy. As such, the U.S. Government has been granted for
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*** License agreement ***
H5Part Copyright (c) 2006-2009, The Regents of the University of California,
through Lawrence Berkeley National Laboratory (subject to receipt of any
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Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
(1) Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
(2) Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
(3) Neither the name of the University of California, Lawrence Berkeley
National Laboratory, U.S. Dept. of Energy, Paul Scherrer Institut
(Switzerland) nor the names of its contributors may be used to endorse
or promote products derived from this software without specific prior
written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
You are under no obligation whatsoever to provide any bug fixes,
patches, or upgrades to the features, functionality or performance of
the source code ("Enhancements") to anyone; however, if you choose to
make your Enhancements available either publicly, or directly to
Lawrence Berkeley National Laboratory, without imposing a separate
written license agreement for such Enhancements, then you hereby grant
the following license: a non-exclusive, royalty-free perpetual license
to install, use, modify, prepare derivative works, incorporate into
other computer software, distribute, and sublicense such enhancements or
derivative works thereof, in binary and source code form.
COPYRIGHT
-7
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@@ -1,7 +0,0 @@
*** Copyright Notice ***
H5Part Copyright (c) 2006, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy) and the Paul Scherrer Institut (Switzerland). All rights reserved.
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
NOTICE. This software was developed under partial funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.
GNUmakefile.orig
-133
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@@ -1,133 +0,0 @@
UNAME := $(shell uname | perl -pe 's/(sn\d\d\d\d|jsimpson)/UNICOS\/mk/')
# for host specific options
HOST := $(shell hostname)
# for processor-specific options
ifeq ($(UNAME), Linux)
PROC := $(shell uname -p)
endif
CXX = c++
CC = cc
H5HOME = /usr/local/hdf5
CFLAGS = -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# MacOS-X Serial
ifeq ($(UNAME), Darwin)
ifeq ($(PARALLEL), yes)
CXX = g++
CC = mpicc
H5HOME = /usr/local
CFLAGS = -O -g -I$(H5HOME)/include -DPARALLEL_IO
LDFLAGS = -L$(H5HOME)/lib -lmpich -lpmpich -lhdf5 -lz -lm
else
CXX = c++
CC = cc
F90 = xlf
H5HOME = /usr/local
CFLAGS = -O -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif
endif
# SGI MIPS/Irix
ifeq ($(UNAME), IRIX64)
CXX = CC
CC = cc
F90 = f90
ifeq ($(PARALLEL), yes)
H5HOME = $(HDF5_DIR)
CFLAGS = -64 -O3 -I$(H5HOME)/include -DPARALLEL_IO
LDFLAGS = -64 -O3 -L$(H5HOME)/lib -lhdf5 -lz -lmpi -lm
else
H5HOME = /usr/local
CFLAGS = -O3 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif
endif
# AIX/SP-2 Parallel/serial : Seaborg
ifeq ($(UNAME), AIX)
ifeq ($(PARALLEL), yes) # parallel
CXX = mpCC_r
CC = mpxlc_r
# H5HOME = /usr/common/usg/hdf5_64/1.4.5-post2/parallel
H5HOME = /usr/common/usg/hdf5_64/1.6.1/parallel
# /usr/common/usg/hdf5/1.4.4/parallel
H4HOME = /usr/common/usg/hdf/default
OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
CFLAGS = -q64 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lsz -lm
else # serial
CXX = xlC
CC = xlc
H5HOME = /usr/common/usg/hdf5/1.4.4/serial
H4HOME = /usr/common/usg/hdf/default
OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
CFLAGS = -g -bmaxdata:800000000 -bmaxstack:256000000 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
endif
endif
# Linux
ifeq ($(UNAME), Linux)
# if this machine is NERSC/Davinci Altix system
ifeq ($(PROC), ia64)
CC = icc
CXX = icc
ifeq ($(PARALLEL), yes)
# IA64 Linux Parallel
ifeq ($(HOST), davinci)
H5HOME = $(HDF5_PAR)
MPILIB = -lmpi
else
H5HOME = /usr/local
HDF5_PAR_LIB = -L$(H5HOME)/lib -lhdf5 -lz -lm
HDF5_PAR_INCLUDE = -I$(H5HOME)/include
MPIHOME = /usr/local
MPILIB = -lmpich
endif # HOST
CFLAGS = -O3 -DPARALLEL_IO -DH5_HAVE_PARALLEL $(HDF5_PAR_INCLUDE)
LDFLAGS = $(HDF5_PAR_LIB) $(MPILIB)
else # IA64 Linux Serial
CFLAGS = -O3 $(HDF5_INCLUDE)
LDFLAGS = $(HDF5_LIB) -lm
endif # PARALLEL
# else this is standard IA32 linux
else
ifeq ($(PARALLEL), yes)
# Linux Parallel
CC = gcc
CXX = g++
H5HOME = /usr/local
MPIHOME = /usr/local
CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
else # Linux Serial
CXX = g++
CC = gcc
CFLAGS = -O -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif # !PARALLEL
endif # PROC!ia64
endif # !Linux
ifeq ($(PARALLEL), yes) #parallel
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest
endif
else
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o
endif
endif
include rules.make
Makefile.am
+4 -4
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@@ -1,11 +1,11 @@
# Trial by Antino Kim
# Top level Makefile.am
ACLOCAL_AMFLAGS = -I m4
EXTRA_DIST = autogen.sh
SUBDIRS = \
doc \
src \
test \
tools
tools \
doc
MAINTAINERCLEANFILES = \
config.h \
Makefile.orig
-59
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@@ -1,59 +0,0 @@
# This is a very rudimentary multiarchitecture makefile
# You need to uncomment the default block of make variables you need
# Some key things to watch for are the following defines
# -DREGRESSIONTEST : enables a main(){} inside of
# the H5Part.cc file that does simple regression testing.
# -DPARALLEL_IO : If you want to use parallel HDF5, you have to
# enable this. Otherwise, you get only the serial
# implementation of the library.
# MacOS-X Serial
#CXX = c++
#CC = cc
#F90 = xlf
#H5HOME = /usr/local
#CFLAGS = -O -g -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# AIX/SP-2 Parallel : Seaborg
#CXX = mpCC_r
#CC = mpcc_r
#F90 = mpxlf
#H5HOME = /usr/common/usg/hdf5/1.4.4/parallel
#H4HOME = /usr/common/usg/hdf/default
#OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
#CFLAGS = -g -bmaxdata:800000000 -bmaxstack:256000000 -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
# Linux Serial
#CXX = g++
#CC = gcc
#F90 = g77 # or could be pgif90
#CFLAGS = -O -g -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# Linux Jacquard
CC = mpicc
CXX = mpicxx
F90 = mpif90
H5HOME = /usr/common/usg/hdf5/1.6.3/parallel
CFLAGS = -O2 -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# Linux Parallel
#CC = gcc
#CXX = g++
#F90 = g77
#H5HOME = /usr/local
# /usr/common/usg/hdf5/1.6.3/parallel
#MPIHOME = /usr/local
#CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
all: H5PartTest H5PartTest.o H5Part.o
parallel: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest # parallel regression tests
fortran: H5PartF.o # fortran bindings
include rules.make
NEWS
+260
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@@ -1,3 +1,263 @@
#### H5PART 1.99.10 ###########################################################
Bugfixes in the malloc wrappers
Converter from vtk to H5hut added.
Bugfixes in the autotools files.
#### H5PART 1.99.9 ############################################################
Bugfix in option parsing in tools/h5PartDcToVtk and tools/h5PartSurfaceToVtk
tools/h5PartDcToVtk and tools/h5PartSurfaceToVtk removed from list of tools
to be compiled. These tools should be moved to another repository anyway.
#### H5PART 1.99.8 ############################################################
Bugfixes
#### H5PART 1.99.7 ############################################################
Linking problem on Linux fixed
#### H5PART 1.99.6 ############################################################
#### H5PART 1.99.5 ############################################################
#### H5PART 1.99.4 ############################################################
#### H5PART 1.99.3 ############################################################
#### H5PART 1.99.2 ############################################################
#### H5PART 1.99.1 ############################################################
#### H5PART 1.99 ############################################################
Renamed type:
H5PartFile -> h5_file_t
h5part_int64_t -> h5_int64_t
Renamed functions:
#### H5PART 1.6.6 ############################################################
Fixed typo (Write instead of Read) in the h5bl_3d_read_scalar_field* Fortran
interface.
Added missing type normalization for int32 type.
Rewrite of h5pAttrib tool.
#### H5PART 1.6.5 ############################################################
Fixed several build errors reported by Iuri Prilepov on Ubuntu 11.04.
#### H5PART 1.6.4 ############################################################
Fixed bug where H5PartSetViewIndices was not setting an empty view when the
number of elements is 0.
Set a threshold on the HDF5 alignment parameter so that small metadata writes
are not aligned, which causes large gaps in the file.
#### H5PART 1.6.3 ############################################################
New build system uses libtool and can build shared libraries.
Fixed a bug that incorrectly identifies the number of selected points in a view
when using H5PartSetViewIndices.
Fixed bug in Fortran test reported by several people, as well as several
incorrect views set in the C test that were causing segfaults.
Fixed name mismatches in the Fortran interface, and an off-by-one indexing
problem.
#### H5PART 1.6.2 ############################################################
Removed H5PartSetViewEmpty
--------------------------
An empty view can now be selected with:
H5PartSetNumParticles(file, 0);
Bug Fixes to Attribute Calls in Fortran API
-------------------------------------------
Fixed a problem where attribute values were reverting to zero.
#### H5PART 1.6.1 ############################################################
Chunking in the H5Part API
--------------------------
There is now an H5Part equivalent H5PartSetChunkSize to the existing
H5BlockDefine3DChunkDims call. Both of these calls enable the chunking
mechanism in the underlying HDF5 layer. Chunking is used in combination
with the aligned open calls to pad datasets to alignment multiples
on disk.
All Steps Available on Write
----------------------------
Previously, existing steps in a file were only accessible in read-only mode.
Now, all steps are available in all modes, including write-truncate and
write-append. Thus, it is now possible to overwrite existing data in write
mode. To help alert the user to this possibility, a warning is issued every
time an existing dataset is written to. Warnings can be printed by setting
the verbosity to H5PART_VERB_WARN or higher.
New Throttling Routine
----------------------
Previously, a throttle factor of N meant that for P processors, the total
number of P writes were divided into N batches of P/N writes.
To better accommodate round-robin lustre striping, the new policy is to
execute P/N batches of N writes. Thus, matching N to the number of stripes
results in the desirable 1-1 matching of writers to stripes.
Other Fixes
-----------
* The configure script should correctly detect PGI compilers now.
* There was a small memory leak in the Fortran file open calls.
* There was a compile error with HDF5 1.6.x due to a missing assignment.
#### H5PART 1.6 ##############################################################
Updated Documentation
---------------------
The Fortran API has been added to the doxygen documentation. Most entries have
a reference to their respective C API call.
Regression Test Suite
---------------------
The test subdirectory has been reorganized to include a systematic series
of regression tests of common use cases for the API. The goal is to have both
complete coverage of the API (every call is exercised) and testing of some
unlikely or unsuspected values and cases.
Currently, the C test covers the entire H5Part API and the Fortran test is
still in development.
Benchmark Utilities
-------------------
Two benchmarking utilities, H5PartBench and H5BlockBench, have been added to
the tools collection. Both require the parallel library and have functionality
and syntax similar to the IOR benchmark:
http://sourceforge.net/projects/ior-sio/
File Mode Flags
---------------
Previously, the only flags used were H5PART_READ, H5PART_WRITE, and
H5PART_APPEND, and these were mutually exclusive. Additional flags have been
added to select the underlying virtual file driver (VFD) that HDF5 uses in
parallel mode and to accommodate the lustre filesystem:
H5PART_VFD_MPIPOSIX (use the MPI-POSIX driver, which bypasses MPI-IO)
H5PART_VFD_MPIIO_IND (use MPI-IO in independent mode)
H5PART_FS_LUSTRE (activate H5P tunings for the lustre stripe size)
These flags can be specified using the typical bitwise OR method, e.g.
char flag = H5PART_WRITE | H5PART_VFD_MPIPOSIX | H5PART_FS_LUSTRE;
will select write mode with these two additional options.
The parallel library now defaults to using the MPI-IO collective mode driver
(previously it used independent mode). The collective buffering algorithm in
the Cray XT4/5 environment has been substantially improved in the last year,
and defaulting to collective mode allows us to take advantage of these
improvements automatically.
There are also new open calls H5PartOpenAlign and H5PartOpenParallelAlign that
take an additional 'alignment' value. This value is passed to HDF5 and used to
pad out objects so that they align to filesystem boundaries. For instance, it
would make sense to use the stripe size as the alignment value when writing to
a lustre filesystem.
Unified 'View' Model
--------------------
Views are now supported in both read and write mode (previously only supported
in read mode). It is possible to specify non-sensical views: you could for
instance specify a read view that is larger than the dataset on disk. Or you
could create a write view that is larger than the data in memory. In those
cases, you will encounter an error when you try to perform a read or write
operation on a dataset.
There are two new methods for selecting views. H5PartSetNumParticlesStrided
selects a view with $n$ particles per processor, but such that the data in
memory is expected to have a 'stride' factor. For instance, if you have
particle data with fields $x$ and $y$ and a single array with entries
$x1,y1,x2,y2...$, then the stride factor is 2. Striding works for both reads
and writes and only affects the view of memory: individual fields are still
stored as individual arrays on disk.
The second new method is H5PartSetViewIndices, which allows for point
selections of datasets. You can pass a list of indices for the points you
want to select. This is useful, for instance, when interfacing with FastBit
to perform queries that select a small subset of non-contiguous particles.
Because views are now supported on write, it is possible to write a dataset
using multiple 'passes' or to leave some values unwritten.
Also, all views are now *inclusive*, so that a view of (0,9) corresponds
to the 10 items 0, 1, 2, ... 9.
Internal Handling of Dataspaces
-------------------------------
H5PartSetNumParticles and H5PartSetNumParticlesStrided now share the same
HDF5 dataspace state in the H5PartFile struct with the calls that modify
the view (H5PartSetView etc.). Previously, the memory and disk dataspaces
were regenerated from the view on every read access, which was unnecessary.
Autogeneration of API Calls
---------------------------
Python scripts have been added to automatically generate read/write call
variants for different data types.
Renamed Fortran Include
-----------------------
The automake system no longer greps the *F90.inc files to generate an include
called 'H5Part.inc'. Instead, the *F90.inc files have been renamed to *.f90,
and awk is used to generate an 'H5PartF.h' file (the same naming convention
as in MPI's 'mpif.h').
The change to *.f90 was necessary to facilitate integration of the Fortran
API into doxygen. Note that the *.f90 files will not compile, nor can they
be included directly. Simply use
include 'H5PartF.h'
in your Fortran code to include all the definitions for Fortran H5Part/H5Block
calls.
64 Char Limit on Dataset Names
------------------------------
Previously, a user could overrun internal buffers for dataset names. Now, a
fixed limit of 64 chars is imposed. Dataset names that are longer than this are
truncated and a warning is printed. We expect that most users are using
short canonical names like x, px, id, etc.
Changes to Existing API
-----------------------
The H5BlockGetFieldInfo and H5BlockGetFieldInfoByName calls now both include
a parameter for the 'type' of the field.
#### H5PART 1.4 ##############################################################
Error Handling
--------------
Now all functions, in which an error could occure, are returning a
README
-418
View File
@@ -1,418 +0,0 @@
==============================================================================
README file for H5Part configure
==============================================================================
+ 0. HDF5 library
-----------------
Make sure you have a working version of the HDF5 library in your computer. If you plan
to use parallel I/O you need to use a parallel HDF5 version. If you don't have the
library download the sources from http://hdf.ncsa.uiuc.edu/HDF5/
+ 1. Quick start (If you feel lucky...)
----------------------------------------
For many platforms, where compilers are installed in the "default" location
and all the environment variables are set correctly, it should be sufficient
to type:
./configure [OPTIONS] && make [install]
to have the libraries and test program compiled.
==============================================================================
+ 2. configure line options
----------------------------
(1) Enable options
--enable-fortran
--enable-parallel
--enable-tools
--enable-python
--enable-64 (only for AIX and Irix)
(2) Setting compilers related variables manually
To assign environment variables (e.g., CC, CFLAGS...), specify them as
VAR=VALUE. See below for descriptions of some of the useful variables.
Compiler environment variables:
CC C compiler command
CXX C++ compiler command
FC Fortran compiler command
(3) Setting prefix for installation manually
--prefix=PREFIX install files in PREFIX
For more information, type:
./configure --help
==============================================================================
+ 3. Platform specific settings for compiling libraries & test programs
------------------------------------------------------------------------
Building
make : builds the libraries and test programs
make install: builds and installs
make clean : removes extraneous object files
make distclean : returns configuration to unconfigured state
As tested on hosts:
(1) Davinci <davinci.nersc.gov> (Linux"SUSE"-ia64)
---------------------------------------------------
FIRST THING FIRST!! Type:
module load intel
to have the proper compilers set up for use.
module load hdf5_par
[NOTE: module load hdf5 does not work at this moment.
Possible installation error of HDF5 on Davinci.]
Brief profile:
CC = icc
CXX = icc
FC = ifort
MPICC = icc
MPICXX = icc
MPIFC = ifort
If default doesn't work, try:
For C shell:
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
For Korn or Bourne shell:
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
run:
mpirun 2 H5testFpar
mpirun 2 H5PartTestP
NOTE: Number 2 above is a arbitrary number that indicates the number of processes.
(2) Jacquard <jacquard.nersc.gov> (Linux"SUSE"-x86_64)
-------------------------------------------------------
Brief profile:
CC = pathcc
CXX = pathCC
FC = pathf90
MPICC = mpicc
MPICXX = mpicxx
MPIFC = mpif90
If default doesn't work, try:
For C shell:
env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
For Korn or Bourne shell:
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
In Jacquard, we need a script to run parallel programs, since Jacquard does not support interactive parallel processing. Instead, we need to submit the task to a queue. A sample script (run_H5testFpar.scr) may look like below:
+++++++++++++++++++++++++++++++++++++++
#!/bin/csh
#PBS -l nodes=1:ppn=2,walltime=00:05:00
#PBS -N H5testFpar
#PBS -o H5testFpar.out
#PBS -e H5testFpar.err
#PBS -q debug
#PBS -A mpccc
#PBS -V
setenv PBS_OWORKDIR /home/H5Part/test
cd $PBS_O_WORKDIR
mpirun -np 2 ./H5testFpar
+++++++++++++++++++++++++++++++++++++++
Then, we need to submit the task to a queue by running:
qsub run_H5testFpar.scr
After processed, the result will appear in H5testFpar.out, and error messages will appear in H5testFpar.err.
(3) Bassi <bassi.nersc.ogv> (AIX5.3.0.0-Power 3)
-------------------------------------------------
FIRST THING FIRST!! Type:
module load gcc
to have the proper compilers set up for use.
Brief profile:
CC = cc_r
CXX = cc_r
FC = xlf_r
MPICC = mpcc_r
MPICXX = mpcc_r
MPIFC = mpxlf_r
If default doesn't work, try:
For C shell:
env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
For Korn or Bourne shell:
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
run:
unsetenv MP_SINGLE_THREAD
poe ./H5PartTestP -procs 2 -nodes 1
poe ./H5testFpar -procs 2 -nodes 1
For more details on how to run parallel programs on Bassi, go to:
http://www.nersc.gov/nusers/resources/bassi/running_jobs/
(4) Starsky <starsky.lbl.gov> (Darwin8.5.0-PowerPC)
----------------------------------------------------
FIRST THING FIRST!! Set environment variables: (in tcsh)
setenv LD_LIBRARY_PATH /usr/local/g95/lib/gcc-lib/powerpc-apple-darwin8.5.0/4.0.3/
setenv PATH ${PATH}:/usr/local/g95/bin
NOTE: This environment variable setting is specifit to Starsky. It is to make configure find the fortran compiler.
Brief profile:
CC = gcc
CXX = g++
FC = g95
If default doesn't work, try:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(5) Linux AMD64 Visualization group workstations (Linux"SUSE"-x86_64)
---------------------------------------------------------
Brief profile:
CC = gcc
CXX = g++
FC = g95
If default doesn't work, try:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(6) Cray XT3 @ CSCS gele
1) modules/3.1.6 9) PrgEnv-pgi/1.4.26 17) xt-lustre-ss/1.4.26
2) MySQL/4.0.26 10) xt-pbs/5.3.4 18) Base-opts/1.4.26
3) acml/3.0 11) xt-service/1.4.26 19) subversion/1.3.2
4) pgi/6.1.4 12) xt-libc/1.4.26 20) zlib/1.2.3
5) totalview/7.2.0 13) xt-os/1.4.26 21) szip/2.0
6) xt-libsci/1.4.26 14) xt-catamount/1.4.26 22) hdf5/1.6.5
7) xt-mpt/1.4.26 15) xt-boot/1.4.26
8) xt-pe/1.4.26 16) xt-crms/1.4.26
CFLAGS="-I$H5HOME/include -DF77_SINGLE_UNDERSCORE" LDFLAGS="-L$H5HOME/lib -L$ZHOME/lib" ./configure --enable-parallel --enable-fortran
(7) merlin00 / merlin3
Currently Loaded Modulefiles:
1) hdf5/hdf5-1.6.5 2) root/root-5.10.00 3) mpi/mpich2-1.0.3-pgi-6.1 4) pgi/pgi_64-6.1
FC=mpif90 ./configure --enable-parallel --enable-fortran
==============================================================================
+ 4. Trouble shooting (Things to check for...)
--------------------------------------------
(0) Have you set the LD_LIBRARY_PATH?
---Some systems require the user to manually set the environment variable, LD_LIBRARY_PATH. To do so:
set the environment variable HDF5ROOT or PHDF5ROOT to point to your installation of HDF5 (serial and/or parallel respectively).
For Korn or Bourne shell:
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HDF5ROOT}/lib;export LD_LIBRARY_PATH
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:{PHDF5ROOT}/lib;export LD_LIBRARY_PATH
For C shell:
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HDF5ROOT}/lib
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${PHDF5ROOT}/lib
Note that the values of HDF5ROOT & PHDF5ROOT will be in the "summary" section when you run configure.
Not properly set LD_LIBRARY_PATH value may result in a runtime error:
./H5PartTest: error while loading shared libraries: libhdf5.so.0: cannot open shared object file: No such file or directory
(1) Are the compilers set correctly?
---Check with: which COMPILER
(2) Have you installed HDF5?
---You can get it at: http://vis.lbl.gov/Research/AcceleratorSAPP/index.html
(3) Have you loaded the proper modules?
---It is necessary in Davinci & Bassi, and configure && make install may not work without it.
autogen.sh
+26 -24
View File
@@ -1,46 +1,48 @@
#!/bin/sh
# Run this to generate all the initial makefiles, etc.
ACLOCAL_FLAGS="-I m4 $ACLOCAL_FLAGS"
LIBTOOLIZE_FLAGS="--force $LIBTOOLIZE_FLAGS"
AUTOMAKE_FLAGS="--add-missing --copy --foreign $AUTOMAKE_FLAGS"
LIBTOOLIZE=`which libtoolize`
if [ "$LIBTOOLIZE" = "" ]; then
LIBTOOLIZE=`which glibtoolize`
fi
if [ "$LIBTOOLIZE" = "" ]; then
echo "libtoolize not found" 1>&2
exit 1
fi
echo "+ making misc files ..."
touch NEWS README AUTHORS ChangeLog
echo
echo
$LIBTOOLIZE $LIBTOOLIZE_FLAGS || {
echo "libtoolize failed"
exit 1
}
echo
echo "+ running aclocal ..."
aclocal $ACLOCAL_FLAGS || {
echo
echo "aclocal failed - check that all needed development files are present on system"
exit 1
echo "aclocal failed - check that all needed development files are present on system"
exit 1
}
echo
echo
echo
echo
echo "+ running autoheader ... "
autoheader || {
echo
echo "autoheader failed"
exit 1
echo "autoheader failed"
exit 1
}
echo
echo
echo
echo "+ running autoconf ... "
autoconf || {
echo
echo "autoconf failed"
exit 1
echo "autoconf failed"
exit 1
}
echo
echo
echo
echo "+ running automake ... "
automake -a -c --foreign || {
echo
echo "automake failed"
exit 1
automake $AUTOMAKE_FLAGS || {
echo "automake failed"
exit 1
}
echo
echo
echo
config.guess
Vendored
-1469
View File
File diff suppressed because it is too large Load Diff
config.h.in
-44
View File
@@ -1,44 +0,0 @@
/* config.h.in. Generated from configure.ac by autoheader. */
/* "" */
#undef MY_BUILD_CPU
/* "" */
#undef MY_BUILD_OS
/* "" */
#undef MY_BUILD_VENDOR
/* "" */
#undef MY_GNUNAME
/* "" */
#undef MY_UNAME
/* Name of package */
#undef PACKAGE
/* Define to the address where bug reports for this package should be sent. */
#undef PACKAGE_BUGREPORT
/* Define to the full name of this package. */
#undef PACKAGE_NAME
/* Define to the full name and version of this package. */
#undef PACKAGE_STRING
/* Define to the one symbol short name of this package. */
#undef PACKAGE_TARNAME
/* Define to the version of this package. */
#undef PACKAGE_VERSION
/* Version number of package */
#undef VERSION
/* Define to 1 if on AIX 3.
System headers sometimes define this.
We just want to avoid a redefinition error message. */
#ifndef _ALL_SOURCE
# undef _ALL_SOURCE
#endif
config.sub
Vendored
-1563
View File
File diff suppressed because it is too large Load Diff
configure.ac
+290 -508
View File
@@ -1,77 +1,87 @@
# Every configure script must call AC_INIT before doing anything else.
# AC_INIT (package, version, [bug-report], [tarname])
AC_INIT([H5Part], [1.3.3], [h5part@lists.psi.ch], H5Part)
AC_INIT([H5hut], [1.99.14], [h5part@lists.psi.ch], H5hut)
AC_PREREQ(2.60)
AC_CONFIG_HEADERS(config.h)
AC_CONFIG_MACRO_DIR([m4])
AM_INIT_AUTOMAKE
# Ensure that a recent enough version of Autoconf is being used.
# If the version of Autoconf being used to create configure is earlier than version,
# print an error message to the standard error output and do not create configure.
#AC_PREREQ(2.59)
# should be called right after AC_INIT.
# configure scripts can create a C header file containing `#define' directives.
# The AC_CONFIG_HEADERS macro selects this kind of output.
AC_CONFIG_HEADER(config.h)
ENABLE_DEBUG='no'
ENABLE_C='yes'
ENABLE_FORTRAN='no'
ENABLE_PARALLEL='no'
###############################################################################
################# --enable-xxx and --with-xxx Argument ########################
###############################################################################
# --enable-xxx and --with-xxx Arguments
AC_ARG_ENABLE(
[debug],
[AS_HELP_STRING([--enable-debug], [Compile with debug flags [default=no]])],
[ENABLE_DEBUG=$enableval])
AM_CONDITIONAL([ENABLE_DEBUG], [test "$ENABLE_DEBUG" = "yes"])
AC_ARG_ENABLE(
[64],
[AC_HELP_STRING([--enable-64],
[Compile using 64-bit flags [default=no]])],
[USE_64=$enableval])
[c],
[AS_HELP_STRING([--enable-c],
[Compile the C interface [default=yes]])],
[ENABLE_C=$enableval])
AM_CONDITIONAL([ENABLE_C], [test "$ENABLE_C" = "yes"])
AC_ARG_ENABLE(
[fortran],
[AC_HELP_STRING([--enable-fortran],
[AS_HELP_STRING([--enable-fortran],
[Compile the Fortran interface [default=no]])],
[USE_FORTRAN=$enableval])
[ENABLE_FORTRAN=$enableval])
AM_CONDITIONAL([ENABLE_FORTRAN], [test "$ENABLE_FORTRAN" = "yes"])
AC_ARG_ENABLE(
[parallel],
[AC_HELP_STRING([--enable-parallel],
[AS_HELP_STRING([--enable-parallel],
[Compile the MPI/IO interface [default=no]])],
[USE_PARALLEL=$enableval])
[ENABLE_PARALLEL=$enableval])
AM_CONDITIONAL([ENABLE_PARALLEL], [test "$ENABLE_PARALLEL" = "yes"])
AC_ARG_ENABLE(
[tools],
[AC_HELP_STRING([--enable-tools],
[Compile h5part tools [default=no]])],
[USE_TOOLS=$enableval])
[large-indices],
[AC_HELP_STRING([--enable-large-indices],
[Compile with 64bit local IDs and indices [default=no]])],
[USE_LARGE_INDICES=$enableval])
AC_ARG_ENABLE(
[experimental],
[AS_HELP_STRING([--enable-experimental],
[Compile experimental code [default=no]])],
[ENABLE_EXPERIMENTAL=$enableval])
AM_CONDITIONAL([ENABLE_EXPERIMENTAL], [test "$ENABLE_EXPERIMENTAL" = "yes"])
AC_ARG_ENABLE(
[vtkconverter],
[AS_HELP_STRING([--enable-vtkconverter],
[Compile the vtk to H5hut converter for grids [default=no]])],
[ENABLE_VTKCONVERTER=$enableval])
AM_CONDITIONAL([ENABLE_VTKCONVERTER], [test "$ENABLE_VTKCONVERTER" = "yes"])
AC_ARG_WITH(
[mpipath],
[AC_HELP_STRING([--with-mpipath],
[path to MPI installation [default=""]])],
[MPIPATH=$withval], [MPIPATH=""])
AC_ARG_WITH(
[hdf5path],
[AC_HELP_STRING([--with-hdf5path],
[hdf5],
[AS_HELP_STRING([--with-hdf5],
[path to HDF5 installation [default=""]])],
[HDF5PATH=$withval], [HDF5PATH=""])
[HDF5_PREFIX=$withval], [])
###############################################################################
################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
###############################################################################
AC_ARG_WITH(
[mpi],
[AS_HELP_STRING([--with-mpi],
[path to MPI installation [default=""]])],
[PATH=$MPI_PREFIX/bin:$PATH])
AC_ARG_WITH(
[lustre],
[AS_HELP_STRING([--with-lustre],
[path to lustre user API [default=""]])],
[LUSTREPATH=$withval], [LUSTREPATH=""])
AC_ARG_WITH(
[parmetis],
[AC_HELP_STRING([--with-parmetis],
[path to ParMETIS API [default=""]])],
[PARMETISPATH=$withval], [PARMETISPATH=""])
SAVE_CC=$CC
SAVE_CXX=$CXX
SAVE_FC=$FC
SAVE_MPICC=$MPICC
SAVE_MPICXX=$MPICXX
SAVE_MPIFC=$MPIFC
SAVE_MPILIB=$MPILIB
SAVE_MPIINC=$MPIINC
SAVE_CFLAGS=$CFLAGS
CFLAGS=''
SAVE_FFLAGS=$FFLAGS
SAVE_MPIROOT=$MPIROOT
SAVE_HDF5ROOT=$HDF5ROOT
SAVE_LDFLAGS=$LDFLAGS
###############################################################################
############### PATH SERACH FUNCTION - to be used later... ####################
@@ -85,117 +95,92 @@ SAVE_LDFLAGS=$LDFLAGS
# @enddesc
#@@*/
PATH_Search()
{
eval $1=""
if test $# -lt 4 ; then
h5part_basedir=""
else
h5part_basedir="$4/"
fi
for h5part_place in $2
do
echo -n "looking in $h5part_place ... $ac_c" #1>&6
if test -r "$h5part_basedir$h5part_place/$3" ; then
echo "$ac_t"" found" #1>&6
eval $1="$h5part_place"
break
fi
if test -d "$h5part_basedir$h5part_place/$3" ; then
echo "$ac_t"" found" #1>&6
eval $1="$h5part_place"
break
fi
echo "$ac_t"" no" #1>&6
done
return
PATH_Search() {
eval $1=""
if test $# -lt 4 ; then
h5part_basedir=""
else
h5part_basedir="$4/"
fi
for h5part_place in $2; do
AC_MSG_CHECKING([looking in $h5part_place ... ])
if test -r "$h5part_basedir$h5part_place/$3" ; then
AC_MSG_RESULT([found])
eval $1="$h5part_place"
break
fi
AC_MSG_RESULT([no])
done
return
}
###############################################################################
############# MISC SETTINGS INCLUDING C & C++ COMPILER SETTING ################
###############################################################################
# Compute the canonical host-system type variable, host, and its three
# individual parts host_cpu, host_vendor, and host_os.
# MISC SETTINGS INCLUDING C & C++ COMPILER SETTING
AC_CANONICAL_HOST
AC_PROG_MAKE_SET
uname=`uname -s`
if test $uname = "AIX"; then
AC_MSG_CHECKING([if system is AIX])
AC_MSG_RESULT([OK])
# If on AIX, define _ALL_SOURCE. Allows the use of some BSD functions.
# Should be called before any macros that run the C compiler.
AC_AIX
# debug enabled?
AC_MSG_CHECKING([if debug is enabled])
if test "X$ENABLE_DEBUG" = "Xyes"; then
AC_MSG_RESULT([yes])
CFLAGS="$CFLAGS -g -Wall"
CXXFLAGS="$CFLAGS -g -Wall"
FFLAGS="$FFLAGS -g"
else
AC_MSG_RESULT([no])
fi
# DAVINCI SPECIFIC!!!
if test `uname -n` = "davinci"; then
echo "DAVINCI SPECIFIC TESTING FOR STDC++ LIBRARY!"
PATH_Search STDCXX_CHECK '/usr/lib64 /usr/lib' libstdc++.a
# if STDCXX_CHECK is set...
if test "$STDCXX_CHECK" = "/usr/lib64"; then
echo "STDCXX setting ..."
echo "STDCXX_CHECK = $STDCXX_CHECK ..."
STDCXX="-L/usr/lib64 -lstdc++"
echo "STDCXX = $STDCXX ..."
elif test "$STDCXX_CHECK" = "/usr/lib"; then
echo "STDCXX setting ..."
echo "STDCXX_CHECK = $STDCXX_CHECK ..."
STDCXX="-L/usr/lib -lstdc++"
echo "STDCXX = $STDCXX ..."
fi
# Determine a C/C++ compiler to use.
if test "x$ENABLE_PARALLEL" = "xyes"; then
CCOMPILERS="mpicc"
CXXCOMPILERS="mpic++"
else
CCOMPILERS="pgcc pathcc icc gcc cc_r cc"
CXXCOMPILERS="pgcc pathcc icc g++ cc_r c++"
fi
AC_PROG_CC($CCOMPILERS)
CC=`which $CC`
AC_PROG_CXX($CXXCOMPILERS)
CXX=`which $CXX`
# Determine a C compiler to use.
# If CC is not already set in the environment, check for gcc and cc, then
# for other C compilers.
# Set output variable CC to the name of the compiler found.
AC_PROG_CC(pathcc icc cc_r gcc cc)
AC_PROG_CC_C99
if test "x$ac_cv_prog_cc_c99" = "xno"; then
AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
exit 1
fi
# AC_PROG_CC doesn't pick up cc_r in Bassi. The following AC_PATH_PROGS
# is the fix.
AC_PATH_PROGS([BAS_CC], [cc_r], [], [$PATH])
# if BAS_CC not empty
if test -n "$BAS_CC"; then
echo "CC setting for Bassi ..."
CC=$BAS_CC
echo "CC = $CC ..."
fi
# Determine a C++ compiler to use.
# Check if the environment variable CXX or CCC (in that order) is set;
# if so, then set output variable CXX to its value.
# Otherwise, if the macro is invoked without an argument,
# then search for a C++ compiler under the likely names (first g++ and c++
# then other names).
# If none of those checks succeed, then as a last resort set CXX to g++.
AC_PROG_CXX(pathCC icc cc_r g++ gcc cc)
# Set output variable INSTALL to the path of a BSD-compatible install program,
# if one is found in the current PATH.
# Otherwise, set INSTALL to `dir/install-sh -c`
AC_PROG_INSTALL
AC_PROG_AWK
# AM_INIT_AUTOMAKE is required to use autoconf with automake
AM_INIT_AUTOMAKE()
AC_PROG_RANLIB
# Disable shared libraries by default: can be enabled with --enable-shared
LT_INIT([disable-shared])
AC_PROG_LIBTOOL
# Default prefix for bindir, etc... (eg >> ./build/bin)
AC_PREFIX_DEFAULT(`pwd`/build)
# Checks for header files.
AC_CHECK_HEADERS([fcntl.h limits.h stdint.h stdlib.h string.h sys/ioctl.h unistd.h])
# Checks for typedefs, structures, and compiler characteristics.
AC_HEADER_STDBOOL
AC_C_INLINE
AC_TYPE_INT16_T
AC_TYPE_INT32_T
AC_TYPE_INT64_T
AC_TYPE_SIZE_T
AC_TYPE_SSIZE_T
AC_TYPE_UINT16_T
AC_TYPE_UINT32_T
AC_TYPE_UINT64_T
AC_CHECK_TYPES([ptrdiff_t])
# Checks for library functions.
AC_FUNC_MALLOC
AC_FUNC_REALLOC
AC_CHECK_FUNCS([memmove memset pow strchr strdup strerror strstr])
# AC_DEFINE_UNQUOTED (variable, value, [description])
# Define the C preprocessor variable variable to value
@@ -207,401 +192,198 @@ AC_DEFINE_UNQUOTED(MY_GNUNAME, "${host_cpu}-${host_vendor}-${host_os}", "")
AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
###############################################################################
######################## CONFIGURE LINE OPTIONS ###############################
###############################################################################
# PROCESS ARGUMENTS
###################### 64-bit compilation enabled #############################
AC_MSG_CHECKING([if 64-bit compilation is enabled])
# If --enable-64 is set in the configure line
if test "X$USE_64" = "Xyes"; then
AC_MSG_RESULT([yes])
if test $uname = "AIX"; then
CFLAGS="$CFLAGS -q64"
FFLAGS="$FFLAGS -q64"
fi
if test $uname = "IRIX64"; then
CFLAGS="$CFLAGS -64"
FFLAGS="$FFLAGS -64 -fPIC -fno-second-underscore"
fi
# C enabled?
AC_MSG_CHECKING([if C interface enabled])
if test "X$ENABLE_C" = "Xyes"; then
AC_MSG_RESULT([yes])
else
AC_MSG_RESULT([no])
AC_MSG_RESULT([no])
fi
############################ fortran enabled ##################################
# fortran enabled?
AC_MSG_CHECKING([if fortran interface enabled])
if test "X$USE_FORTRAN" = "Xyes"; then
AC_MSG_RESULT([yes])
if test "X$ENABLE_FORTRAN" = "Xyes"; then
AC_MSG_RESULT([yes])
AC_PROG_FC(ifort xlf_r pathf90 g95 g90 ftn gfortran)
if test -z "$FC" ; then
AC_MSG_ERROR([Cannot find a fortran compiler!!!])
exit 1
fi
if test "X$ENABLE_PARALLEL" = "Xyes"; then
AC_PROG_FC(mpif90 mpif77)
else
AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
fi
FC=`which $FC`
if test -z "$FC" ; then
AC_MSG_ERROR([Cannot find a Fortran compiler!])
exit 1
fi
if test ! $uname = "AIX"; then
FFLAGS="${FFLAGS} -fPIC -fno-second-underscore"
fi
if test $FC = "g90"; then
FFLAGS="${FFLAGS} -fno-second-underscore"
fi
AC_MSG_CHECKING([symbol convention in object files])
`cd src && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
`cd src && ${FC} ${FFLAGS} -c TestUnderscore.f`
`cd src && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
`cd src && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o -lc`
if test $FC = "g95"; then
FFLAGS="${FFLAGS} -fno-second-underscore"
fi
AC_MSG_CHECKING([symbol convention in object files])
`cd src/Fortran && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
`cd src/Fortran && ${FC} ${FFLAGS} -c TestUnderscore.f`
`cd src/Fortran && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
`cd src/Fortran && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
if test -f src/Fortran/TestUnderscore ; then
`cd src/Fortran && ./TestUnderscore > Underscore.h`
AC_MSG_RESULT([ok])
else
AC_MSG_RESULT([nok])
AC_MSG_ERROR([Cannot determine the symbol convention for Fortran object files!])
exit 1
fi
if test -f src/TestUnderscore ; then
UNDERSCORE_H=Underscore.h
`cd src && ./TestUnderscore > Underscore.h`
AC_MSG_RESULT([ok])
else
AC_MSG_RESULT([nok])
AC_MSG_ERROR([Cannot build fortran executables!!!])
exit 1
fi
else
AC_MSG_RESULT([no])
AC_MSG_RESULT([no])
fi
######################## large indices enabled ###########################
AC_MSG_CHECKING([if large indices are enabled])
if test "X$USE_LARGE_INDICES" = "Xyes"; then
AC_MSG_RESULT([yes])
CFLAGS="${CFLAGS} -DUSE_LARGE_INDICES"
else
AC_MSG_RESULT([no])
fi
######################## parallel interface enabled ###########################
AC_MSG_CHECKING([if parallel interface enabled])
if test "X$USE_PARALLEL" = "Xyes"; then
AC_MSG_RESULT([yes])
CFLAGS="${CFLAGS} -DPARALLEL_IO -DH5_HAVE_PARALLEL -DMPICH_IGNORE_CXX_SEEK"
AC_MSG_CHECKING([if we can compile MPI code without setting flags])
AC_TRY_LINK([#include "mpi.h"], [
MPI_Comm comm;
int n;
MPI_Comm_size( comm, &n ); ],
[echo 'yes'; r='yes'], [echo "no"; r='no'] )
if test "X$r" = "Xno"; then
AC_PATH_PROGS([MPICC], [mpicc mpcc_r], [], [$PATH])
AC_PATH_PROGS([MPICXX], [mpicxx mpcc_r], [], [$PATH])
if test -z "$MPICC" -o -z "$MPICXX"; then
AC_MSG_CHECKING([for MPI root ])
AC_MSG_RESULT([])
if test -n "$MPIROOT"; then
P=${MPIROOT}
elif test -n "$MPIHOME"; then
P=${MPIHOME}
elif test -n "$MPIPATH"; then
P=${MPIPATH}
else
P=''
P="$P /usr"
P="$P /usr/local"
P="$P /usr/local/mpi"
P="$P /usr/local/packages/mpi"
P="$P /usr/local/mpich2"
P="$P /usr/local/mpich"
P="$P /opt/xt-mpt/default/mpich2-64/P2"
fi
PATH_Search MPIROOT "$P" include/mpi.h
if test ! -n "$MPIROOT"; then
AC_MSG_ERROR([Cannot determine MPI root!!!])
exit 1
fi
if test -e "${MPIROOT}/bin/mpicc"; then
MPICC=${MPIROOT}/bin/mpicc
fi
if test -e "${MPIROOT}/bin/mpicxx"; then
MPICXX=${MPIROOT}/bin/mpicxx
fi
fi
if test -z "$MPICC" -o -z "$MPICXX"; then
MPIINC="${MPIINC} -I${MPIROOT}/include"
FFLAGS="${FFLAGS} -I${MPIROOT}/include"
AC_MSG_CHECKING([for name of MPI lib ])
if test -e ${MPIROOT}/lib/libmpi.a; then
MPILIB="-L${MPIROOT}/lib -lmpi"
elif test -e ${MPIROOT}/lib/libmpi.so; then
MPILIB="-L${MPIROOT}/lib -lmpi"
elif test -e ${MPIROOT}/lib/libmpich.a; then
MPILIB="-L${MPIROOT}/lib -lmpich"
elif test -e ${MPIROOT}/lib/libmpich.so; then
MPILIB="-L${MPIROOT}/lib -lmpich"
else
AC_MSG_RESULT([not found])
exit 1
fi
AC_MSG_RESULT([${MPILIB}])
fi
if test -n "$MPICC"; then
CC=${MPICC}
fi
if test -n "$MPICXX"; then
CXX=${MPICXX}
fi
fi
MTARGET="libpH5Part.a"
TTARGET="H5PartTestP H5PartAndreasTest Bench"
TTARGET="${TTARGET} H5BlockTestAttributes"
TTARGET="${TTARGET} H5BlockParTestScalarField"
# parallel + fortran
if test "X$USE_FORTRAN" = "Xyes"; then
AC_PATH_PROGS([MPIFC], [mpxlf_r mpif90], [], [$PATH])
if test -z "${MPIFC}" ; then
if test -e "${MPIROOT}/bin/mpif90"; then
MPIFC=${MPIROOT}/bin/mpif90
fi
fi
# if MPIFC empty
if test ! -n "$MPIFC"; then
AC_MSG_CHECKING([ No MPIFC detected. Setting MPIFC to FC.])
MPIFC=$FC
echo "MPIFC = $MPIFC ..."
fi
if test -n "$MPIFC"; then
FC=${MPIFC}
fi
MTARGET="${MTARGET} libpH5PartF.a"
TTARGET="${TTARGET} H5testFpar"
TTARGET="${TTARGET} H5BlockParTestScalarFieldF"
fi
else # --enable-parallel=no
AC_MSG_RESULT([no])
MTARGET="libH5Part.a"
TTARGET="H5PartTest H5test"
TTARGET="${TTARGET} H5BlockTestAttributes"
if test "X$USE_FORTRAN" = "Xyes"; then
MTARGET="${MTARGET} libH5PartF.a"
TTARGET="${TTARGET} H5testF"
TTARGET="${TTARGET} H5BlockTestAttributesF"
fi
fi
AC_MSG_CHECKING([wheter tools are enabled])
if test "X$USE_TOOLS" = "Xyes"; then
AC_MSG_RESULT([yes])
BUILD_TOOLS="h5pAttrib h5pToGNUplot # homdynToH5p"
else
AC_MSG_RESULT([no])
fi
###############################################################################
######################### PATH CHECKING & SETTING #############################
###############################################################################
AC_MSG_CHECKING([for HDF5 root ])
AC_MSG_RESULT([])
if test -n "${HDF5ROOT}"; then
P=${HDF5ROOT}
elif test -n "${HDF5HOME}" ; then
P=${HDF5HOME}
elif test -n "${HDF5PATH}" ; then
P=${HDF5PATH}
else
P=''
P="$P /usr"
P="$P /usr/local"
P="$P /usr/local/hdf5"
P="$P /usr/local/packages/hdf5"
P="$P /apps/hdf5"
if test "X$USE_PARALLEL" = "Xyes"; then
P="$P /usr/local/phdf5"
P="$P /usr/local/hdf5/hdf5_par"
if test "X$USE_64" = "Xyes"; then
P="$P /usr/common/usg/hdf5/64/default/parallel"
else
P="$P /usr/common/usg/hdf5/32/default/parallel"
fi
else
P="$P /usr/local/hdf5/hdf5_serial"
if test "X$USE_64" = "Xyes"; then
P="$P /usr/common/usg/hdf5/64/default/serial"
else
P="$P /usr/common/usg/hdf5/32/default/serial"
fi
fi
fi
PATH_Search HDF5ROOT "$P" include/hdf5.h
if test -z "$HDF5ROOT"; then
AC_MSG_ERROR([Cannot determine HDF5 root!!!])
exit 1
fi
AC_MSG_CHECKING([if we need to link to libsz ])
if test -n "$HDF5ROOT"; then
if test -f $HDF5ROOT/lib/libsz.a; then
if test "X$ENABLE_PARALLEL" = "Xyes"; then
AC_MSG_RESULT([yes])
SZLIB="-L$HDF5ROOT/lib/ -lsz"
else
CPPFLAGS="${CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
if test "X$ENABLE_EXPERIMENTAL" = "Xyes"; then
AC_MSG_CHECKING([for ParMETIS])
if test "X$PARMETISPATH" != "X"; then
CPPFLAGS="$CPPFLAGS -I$PARMETISPATH/include"
LDFLAGS="$LDFLAGS -L$PARMETISPATH/lib"
fi
LIBS="$LIBS -lparmetis -lmetis"
AC_TRY_LINK([#include <parmetis.h>], [
ParMETIS_V3_PartGeom (NULL, NULL, NULL, NULL, NULL);],
[AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
if test "X$r" = "Xno"; then
AC_MSG_ERROR([ParMETIS])
exit 1
fi
fi
else # --enable-parallel=no
AC_MSG_RESULT([no])
SZLIB=""
fi
fi
AC_MSG_CHECKING([for static zlib root ])
echo
PATH_Search ZLIBROOT '/apps/zlib' lib/libz.a
if test -n "$ZLIBROOT"; then
LDFLAGS="$LDFLAGS -L$ZLIBROOT/lib"
fi
###############################################################################
#################### MISC SETTINGS - path, flags, etc #########################
###############################################################################
H5P_LIB_LOC=`pwd`/src
###############################################################################
################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
###############################################################################
#if there was an external input for the variable...
if test -n "$SAVE_CC"; then
CC=$SAVE_CC
# LIBRARY PATHS
if test -z "${HDF5_PREFIX}"; then
# alternatives to HDF5_PREFIX
if test -n "${HDF5_DIR}"; then
HDF5_PREFIX=${HDF5_DIR}
fi
fi
if test -n "$SAVE_CXX"; then
CXX=$SAVE_CXX
if test -n "${HDF5_PREFIX}"; then
CPPFLAGS="$CPPFLAGS -I$HDF5_PREFIX/include"
LDFLAGS="$LDFLAGS -L$HDF5_PREFIX/lib"
fi
AC_CHECK_LIB([z], [compress2])
AC_CHECK_LIB([hdf5], [H5open])
AS_IF([test "x$ac_cv_lib_hdf5_H5open" != xyes],
[AC_MSG_ERROR([Cannot compile and link a HDF5 program]);
exit 1])
if test -n "$SAVE_FC"; then
FC=$SAVE_FC
fi
if test -n "$SAVE_MPICC"; then
MPICC=$SAVE_MPICC
fi
if test -n "$SAVE_MPICXX"; then
MPICXX=$SAVE_MPICXX
fi
if test -n "$SAVE_MPIFC"; then
MPIFC=$SAVE_MPIFC
fi
if test -n "$SAVE_MPILIB"; then
MPILIB=$SAVE_MPILIB
fi
if test -n "$SAVE_MPIINC"; then
MPIINC=$SAVE_MPIINC
fi
if test -n "$SAVE_CFLAGS"; then
CFLAGS="$SAVE_CFLAGS ${CFLAGS}"
fi
if test -n "$SAVE_FFLAGS"; then
FFLAGS=$SAVE_FFLAGS
fi
if test -n "$SAVE_MPIROOT"; then
MPIROOT=$SAVE_MPIROOT
fi
if test -n "$SAVE_HDF5ROOT"; then
HDF5ROOT=$SAVE_HDF5ROOT
fi
if test -n "$SAVE_LDFLAGS"; then
LDFLAGS=$SAVE_LDFLAGS
fi
if test -n "$MPICXX"; then
TOOLS_CXX=$MPICXX
TOOLS_H5PART_LIB="-lpH5Part"
TOOLS_HDFLIB="-L$HDF5ROOT/lib -lhdf5"
AC_MSG_CHECKING([for lustre API ])
AC_MSG_RESULT([])
if test -n "${LUSTREPATH}"; then
P=${LUSTREPATH}
elif test -n "${LUSTREROOT}" ; then
P=${LUSTREROOT}
elif test -n "${LUSTREHOME}" ; then
P=${LUSTREHOME}
elif test -n "${LUSTRE_DIR}" ; then
P=${LUSTRE_DIR}
else
TOOLS_CXX=$CXX
TOOLS_H5PART_LIB="-lH5Part"
TOOLS_HDFLIB="-L$HDF5ROOT/lib -lhdf5"
P=''
P="$P /usr"
P="$P /usr/local"
P="$P /usr/local/lustre"
P="$P /opt/lustre"
fi
PATH_Search LUSTREROOT "$P" usr/include/lustre/liblustreapi.h
if test -z "$LUSTREROOT"; then
AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
else
CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
CPPFLAGS="$CPPFLAGS -I$LUSTREROOT/usr/include"
LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
LIBS="$LIBS -llustreapi"
fi
LIBS="$LIBS -lm"
###############################################################################
# TOOLS
AC_MSG_CHECKING([if we have to compile the VTK to H5hut grid converter])
if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
AC_MSG_RESULT([yes])
# :TODO: add test whether we can compile/link a prog with vtk
else
AC_MSG_RESULT([no])
fi
###############################################################################
############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
###############################################################################
# AC_SUBST (variable, [value])
# Create an output variable from a shell variable.
# Make AC_OUTPUT substitute the variable variable into output files (typically one or more `Makefile's).
# This means that AC_OUTPUT will replace instances of `@variable@' in input files with the value that
# the shell variable variable has when AC_OUTPUT is called.
# This value of variable should not contain literal newlines.
# If value is given, in addition assign it to variable.
AC_SUBST(MPIROOT)
AC_SUBST(HDF5ROOT)
AC_SUBST(MPIINC)
AC_SUBST(MPILIB)
AC_SUBST(MPICC)
AC_SUBST(MPICXX)
AC_SUBST(MPIFC)
AC_SUBST(MTARGET)
AC_SUBST(TTARGET)
AC_SUBST(SZLIB)
# EXPORTING VARIABLES & CREATING OUTPUT FILES
AM_CPPFLAGS=$CPPFLAGS
AM_LDFLAGS=$LDFLAGS
AC_SUBST(HDF5_PREFIX)
AC_SUBST(CFLAGS)
AC_SUBST(FFLAGS)
AC_SUBST(STDCXX)
AC_SUBST(H5P_LIB_LOC)
AC_SUBST(UNDERSCORE_H)
AC_SUBST(BUILD_TOOLS)
AC_SUBST(LDFLAGS)
AC_SUBST(TOOLS_CXX)
AC_SUBST(TOOLS_H5PART_LIB)
AC_SUBST(TOOLS_HDFLIB)
AC_SUBST(AM_CPPFLAGS)
AC_SUBST(AM_LDFLAGS)
# Make AC_OUTPUT create each `file' by copying an input file (by default `file.in'),
# substituting the output variable values.
AC_CONFIG_FILES([
Makefile
doc/Makefile
src/Makefile
test/Makefile
tools/Makefile
Makefile
src/Makefile
src/h5core/Makefile
src/include/Makefile
src/include/h5core/Makefile
src/C/Makefile
src/Fortran/Makefile
test/Makefile
doc/Makefile
tools/Makefile
tools/h5hutcc
tools/vtk2h5grid/Makefile
])
AC_OUTPUT
###############################################################################
########################## PRINTING SUMMARY ###################################
###############################################################################
echo
echo
echo "Summary for `(hostname || uname -n) 2>/dev/null | sed 1q`:"
echo
echo "Host OS: $host_os"
echo "Host CPU: $host_cpu"
echo "Host vendor: $host_vendor"
echo "Build libraries: $MTARGET"
echo "Build test programs: $TTARGET"
echo "Build tools: $BUILD_TOOLS"
echo "CC = $CC"
echo "CXX = $CXX"
echo "FC = $FC"
echo "MPICC = $MPICC"
echo "MPICXX = $MPICXX"
echo "MPIFC = $MPIFC"
echo "CFLAGS = $CFLAGS"
echo "FFLAGS = $FFLAGS"
echo "MPILIB = $MPILIB"
echo "MPIINC = $MPIINC"
echo "MPIROOT = $MPIROOT"
echo "HDF5ROOT = $HDF5ROOT"
echo "LDFLAGS = $LDFLAGS"
echo
# PRINTING SUMMARY
AC_MSG_RESULT([ ])
AC_MSG_RESULT([Summary:])
AC_MSG_RESULT([ ])
AC_MSG_RESULT([Host OS: $host_os])
AC_MSG_RESULT([Host CPU: $host_cpu])
AC_MSG_RESULT([Host vendor: $host_vendor])
AC_MSG_RESULT([CC = $CC])
AC_MSG_RESULT([CXX = $CXX])
AC_MSG_RESULT([FC = $FC])
AC_MSG_RESULT([CFLAGS = $CFLAGS])
AC_MSG_RESULT([FFLAGS = $FFLAGS])
AC_MSG_RESULT([AM_CPPFLAGS = $AM_CPPFLAGS])
AC_MSG_RESULT([AM_LDFLAGS = $AM_LDFLAGS])
AC_MSG_RESULT([LIBS = $LIBS])
AC_MSG_RESULT([HDF5_PREFIX = $HDF5_PREFIX])
AC_MSG_RESULT([LUSTREROOT = $LUSTREROOT])
AC_MSG_RESULT([ ])
depcomp
-529
View File
@@ -1,529 +0,0 @@
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
scriptversion=2005-02-09.22
# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
# 02111-1307, USA.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.
case $1 in
'')
echo "$0: No command. Try \`$0 --help' for more information." 1>&2
exit 1;
;;
-h | --h*)
cat <<\EOF
Usage: depcomp [--help] [--version] PROGRAM [ARGS]
Run PROGRAMS ARGS to compile a file, generating dependencies
as side-effects.
Environment variables:
depmode Dependency tracking mode.
source Source file read by `PROGRAMS ARGS'.
object Object file output by `PROGRAMS ARGS'.
DEPDIR directory where to store dependencies.
depfile Dependency file to output.
tmpdepfile Temporary file to use when outputing dependencies.
libtool Whether libtool is used (yes/no).
Report bugs to <bug-automake@gnu.org>.
EOF
exit $?
;;
-v | --v*)
echo "depcomp $scriptversion"
exit $?
;;
esac
if test -z "$depmode" || test -z "$source" || test -z "$object"; then
echo "depcomp: Variables source, object and depmode must be set" 1>&2
exit 1
fi
# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
depfile=${depfile-`echo "$object" |
sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
rm -f "$tmpdepfile"
# Some modes work just like other modes, but use different flags. We
# parameterize here, but still list the modes in the big case below,
# to make depend.m4 easier to write. Note that we *cannot* use a case
# here, because this file can only contain one case statement.
if test "$depmode" = hp; then
# HP compiler uses -M and no extra arg.
gccflag=-M
depmode=gcc
fi
if test "$depmode" = dashXmstdout; then
# This is just like dashmstdout with a different argument.
dashmflag=-xM
depmode=dashmstdout
fi
case "$depmode" in
gcc3)
## gcc 3 implements dependency tracking that does exactly what
## we want. Yay! Note: for some reason libtool 1.4 doesn't like
## it if -MD -MP comes after the -MF stuff. Hmm.
"$@" -MT "$object" -MD -MP -MF "$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
mv "$tmpdepfile" "$depfile"
;;
gcc)
## There are various ways to get dependency output from gcc. Here's
## why we pick this rather obscure method:
## - Don't want to use -MD because we'd like the dependencies to end
## up in a subdir. Having to rename by hand is ugly.
## (We might end up doing this anyway to support other compilers.)
## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
## -MM, not -M (despite what the docs say).
## - Using -M directly means running the compiler twice (even worse
## than renaming).
if test -z "$gccflag"; then
gccflag=-MD,
fi
"$@" -Wp,"$gccflag$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
echo "$object : \\" > "$depfile"
alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
## The second -e expression handles DOS-style file names with drive letters.
sed -e 's/^[^:]*: / /' \
-e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
## This next piece of magic avoids the `deleted header file' problem.
## The problem is that when a header file which appears in a .P file
## is deleted, the dependency causes make to die (because there is
## typically no way to rebuild the header). We avoid this by adding
## dummy dependencies for each header file. Too bad gcc doesn't do
## this for us directly.
tr ' ' '
' < "$tmpdepfile" |
## Some versions of gcc put a space before the `:'. On the theory
## that the space means something, we add a space to the output as
## well.
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
hp)
# This case exists only to let depend.m4 do its work. It works by
# looking at the text of this script. This case will never be run,
# since it is checked for above.
exit 1
;;
sgi)
if test "$libtool" = yes; then
"$@" "-Wp,-MDupdate,$tmpdepfile"
else
"$@" -MDupdate "$tmpdepfile"
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
echo "$object : \\" > "$depfile"
# Clip off the initial element (the dependent). Don't try to be
# clever and replace this with sed code, as IRIX sed won't handle
# lines with more than a fixed number of characters (4096 in
# IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
# the IRIX cc adds comments like `#:fec' to the end of the
# dependency line.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
tr '
' ' ' >> $depfile
echo >> $depfile
# The second pass generates a dummy entry for each header file.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
>> $depfile
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
aix)
# The C for AIX Compiler uses -M and outputs the dependencies
# in a .u file. In older versions, this file always lives in the
# current directory. Also, the AIX compiler puts `$object:' at the
# start of each line; $object doesn't have directory information.
# Version 6 uses the directory in both cases.
stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'`
tmpdepfile="$stripped.u"
if test "$libtool" = yes; then
"$@" -Wc,-M
else
"$@" -M
fi
stat=$?
if test -f "$tmpdepfile"; then :
else
stripped=`echo "$stripped" | sed 's,^.*/,,'`
tmpdepfile="$stripped.u"
fi
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
if test -f "$tmpdepfile"; then
outname="$stripped.o"
# Each line is of the form `foo.o: dependent.h'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile"
sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile"
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
icc)
# Intel's C compiler understands `-MD -MF file'. However on
# icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
# ICC 7.0 will fill foo.d with something like
# foo.o: sub/foo.c
# foo.o: sub/foo.h
# which is wrong. We want:
# sub/foo.o: sub/foo.c
# sub/foo.o: sub/foo.h
# sub/foo.c:
# sub/foo.h:
# ICC 7.1 will output
# foo.o: sub/foo.c sub/foo.h
# and will wrap long lines using \ :
# foo.o: sub/foo.c ... \
# sub/foo.h ... \
# ...
"$@" -MD -MF "$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
# Each line is of the form `foo.o: dependent.h',
# or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
# Some versions of the HPUX 10.20 sed can't process this invocation
# correctly. Breaking it into two sed invocations is a workaround.
sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
tru64)
# The Tru64 compiler uses -MD to generate dependencies as a side
# effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
# At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
# dependencies in `foo.d' instead, so we check for that too.
# Subdirectories are respected.
dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
test "x$dir" = "x$object" && dir=
base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
# With Tru64 cc, shared objects can also be used to make a
# static library. This mecanism is used in libtool 1.4 series to
# handle both shared and static libraries in a single compilation.
# With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
#
# With libtool 1.5 this exception was removed, and libtool now
# generates 2 separate objects for the 2 libraries. These two
# compilations output dependencies in in $dir.libs/$base.o.d and
# in $dir$base.o.d. We have to check for both files, because
# one of the two compilations can be disabled. We should prefer
# $dir$base.o.d over $dir.libs/$base.o.d because the latter is
# automatically cleaned when .libs/ is deleted, while ignoring
# the former would cause a distcleancheck panic.
tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
tmpdepfile2=$dir$base.o.d # libtool 1.5
tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
"$@" -Wc,-MD
else
tmpdepfile1=$dir$base.o.d
tmpdepfile2=$dir$base.d
tmpdepfile3=$dir$base.d
tmpdepfile4=$dir$base.d
"$@" -MD
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
exit $stat
fi
for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
do
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
# That's a tab and a space in the [].
sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
else
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
#nosideeffect)
# This comment above is used by automake to tell side-effect
# dependency tracking mechanisms from slower ones.
dashmstdout)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout, regardless of -o.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
test -z "$dashmflag" && dashmflag=-M
# Require at least two characters before searching for `:'
# in the target name. This is to cope with DOS-style filenames:
# a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
"$@" $dashmflag |
sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
tr ' ' '
' < "$tmpdepfile" | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
dashXmstdout)
# This case only exists to satisfy depend.m4. It is never actually
# run, as this mode is specially recognized in the preamble.
exit 1
;;
makedepend)
"$@" || exit $?
# Remove any Libtool call
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# X makedepend
shift
cleared=no
for arg in "$@"; do
case $cleared in
no)
set ""; shift
cleared=yes ;;
esac
case "$arg" in
-D*|-I*)
set fnord "$@" "$arg"; shift ;;
# Strip any option that makedepend may not understand. Remove
# the object too, otherwise makedepend will parse it as a source file.
-*|$object)
;;
*)
set fnord "$@" "$arg"; shift ;;
esac
done
obj_suffix="`echo $object | sed 's/^.*\././'`"
touch "$tmpdepfile"
${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
sed '1,2d' "$tmpdepfile" | tr ' ' '
' | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile" "$tmpdepfile".bak
;;
cpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
"$@" -E |
sed -n '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
sed '$ s: \\$::' > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
cat < "$tmpdepfile" >> "$depfile"
sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
msvisualcpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout, regardless of -o,
# because we must use -o when running libtool.
"$@" || exit $?
IFS=" "
for arg
do
case "$arg" in
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
set fnord "$@"
shift
shift
;;
*)
set fnord "$@" "$arg"
shift
shift
;;
esac
done
"$@" -E |
sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
. "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
echo " " >> "$depfile"
. "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
rm -f "$tmpdepfile"
;;
none)
exec "$@"
;;
*)
echo "Unknown depmode $depmode" 1>&2
exit 1
;;
esac
exit 0
# Local Variables:
# mode: shell-script
# sh-indentation: 2
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-end: "$"
# End:
doc/Building.html
-262
View File
@@ -1,262 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<head>
<title>Building H5Part</title>
</head>
<body bgcolor="#F0F0F0">
<font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
<UL>
<LI><a href="#Quickstart">Quickstart guide for the impatient.</a>
<LI><a href="#Details">Details of the Configuration Script</a>
<!-- <LI><a href="UsingC++.html">Using the C++ interface</a> -->
<LI><a href="#ConfigOptions">Important Configure Options</a>
<LI><a href="#EnvVariables">Important Environment Variables</a>
</UL>
<hr>
<a name="Quickstart">
<h2>Quickstart <i>for the impatient</i></h2>
</a>
<OL>
<LI><b>Configure</b>:<br>
For the serial implementation
<pre>
./configure
</pre>
For the parallel implementation configure with
<pre>
./configure --enable-parallel
</pre>
If you also want to build fortran bindings, add the
<code>--enable-fortran</code> flag to the configure line.
</LI><p>
<LI><b>Make the Library</b>:<br>
Type <code>make</code> to build the library. The libraries are
named accordingly.
<UL>
<LI>libH5Part.a: Serial C/C++ Library.</LI>
<LI>libpH5Part.a: Parallel C/C++ library.</LI>
<LI>libH5PartF.a: Serial F77/F90 library.</LI>
<LI>libpH5PartF.a: Parallel F77/F90 library.</LI>
</UL>
</LI><p>
<LI><b>Make Regression Tests and Examples</b>:<br>
Just type <code>make tests</code> to build regression tests
and/or example programs for H5Part. These tests are
<UL>
<LI>H5PartF: Fortran example (only build if --enable-fortran
is specified).</LI>
<LI>H5PartFpar: Parallel Fortran example (only built if both
--enable-fortran and --enable-parallel are specified).</LI>
<LI>H5PartTest: Serial C example. This test writes a sample
datafile and then reopens it for reading. It demonstrates
the most basic reading/writing capabilities.</LI>
<LI>H5PartTestP: Parallel C example (only built if
--enable-parallel is specified). This program only works
as an MPI/parallel program.</LI>
<LI>Bench: This program will only be built if
--enable-parallel is specified. It compares the
performance of raw binary
I/O (one file per processor), raw binary MPI-IO based
parallel I/O to a single file, and the parallel H5Part/HDF5 to
a single file. Generally, H5Part should be very close to the
MPI-IO implementation in terms of performance, but slower
than one-file-per-processor. If HDF5 is slower the
MPI-IO, it would indicate that some performance tuning
will be required for your platform (contact us, and we will
see what we can do!).</LI>
</UL>
</LI><p>
<LI><b>Building Your Own Programs</b>:<br>
There are many different subtleties to linking on various
computer platforms, but typically one does the following.
<UL>
<LI>C/C++ Serial:
<br><code>#include
&lt H5Part.h &gt </code> into your
source file.
<br><code>$CC -I<i>path_to_H5Part.h</i>
-I<i>path_to_hdf5.h</i> -o outfile
MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
</LI>
<LI>C/C++ Parallel:
<br><code>#include
&lt H5Part.h &gt </code> into your
source file.
<br><code>$MPICC -I<i>path_to_H5Part.h</i>
-I<i>path_to_hdf5.h</i> -DPARALLEL_IO
-DH5_HAVE_PARALLEL -o outfile
MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
</LI>
<LI>Fortran Serial:
<br><code>include
'H5Part.inc'</code> into your
source file.
<br><code>$FC -I<i>path_to_H5Part.h</i>
-I<i>path_to_hdf5.h</i> -o outfile
MyFile.cc -L<i>path_to_libH5PartF.a</i> -lH5PartF
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
</LI>
<LI>Fortran Parallel:
<br><code>include
'H5Part.inc'</code> into your
source file.
<br><code>$MPIF90 -I<i>path_to_H5Part.h</i>
-o outfile
MyFile.cc -L<i>path_to_libpH5PartF.a</i> -lpH5PartF
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
</LI><p>
</UL>
</OL>
<hr>
<a name="Details">
<h1>Details for H5Part Configure and Build</h1>
</a>
<a name="ConfigOptions">
<h2>Configure Options</h2>
</a>
H5Part uses GNU Autoconf to generate a Makefile from the makefile
template called <code>Makefile.in</code>.
The configure script pays attention to the following
configure options;<p>
<UL>
<LI><b>--prefix=PREFIX</b> Install files in PREFIX</LI>
<LI><b>--enable-fortran</b> By default H5part will make no attempt to
build Fortran bindings. If you add the
<code>--enable-fortran</code> flag to the ./configure line, it
will create a small test program to determine how to generate
the fortran bindings and then create a library that includes
those bindings. You may need to set the fortran compiler by
setting the <code>FC</code> environment variable in your shell.</LI>
<LI><b>--enable-parallel</b> The version of HDF5 that you build for
Parallel I/O differs from the library you would build for
serial I/O. Consequently, the H5Part libraries must be built
specifically for the kind of I/O you have in mind (parallel or
serial). The configure script will attempt to find an
<code>mpicc</code> if it is available. If no
<code>mpicc</code> is available it will use the regular
C-compiler and will try to locate the location of the MPI
include files and libraries. You can assist the configure
program in its search by setting the <code>MPIROOT</code>
environment variable.</LI>
<LI><b>--enable-tools</b> Builds the currently available tools
<br>
<b>h5pAttrib</b>, an inspection tool that prints the number of timesteps in a file
the file attributes, the step attributes, the dataset names and their values.
<br>
<b>h5pToGNUplot</b>, a converter to two column ASCII format to load in GNUplot.
</LI>
<LI><b>--enable-python</b><font color=red> Under construction</font> Option to build python bindings. It has not been tested.
</LI>
<LI><b>--help</b> Prints configure options.
</LI>
</UL>
<p>
<a name="MakeOptions">
<h2>Make Options</h2>
</a>
<UL>
<LI>make</LI>builds the libraries and test programs
<LI>make install</LI>builds and installs
<LI>make clean</LI>removes extraneous object files
<LI>make distclean</LI>returns configuration to unconfigured state
</UL>
<a name="EnvVariables">
<h2>Environment Variables for Configure</h2>
</a>
The
configuration script is of limited intelligence. Sometimes, you
have to define the following environment variables in order to
help it on its way. You will often only need to tell it where to
find the HDF5 libraries (<code>H5ROOT</code> for serial or
<code>PHDF5ROOT</code> for parallel builds). All of these
environment variables can also be overidden in the Makefile that
is generated by the autoconfigure script.
The configure script pays attention to the following
environment variables;
<p>
<UL>
<LI><b>CC</b>: Use the <code>CC</code> environment variable to tell the
configure script where to find the C compiler. You can
also directly modify this variable in the
<code>Makefile</code> that is generated by the autoconfigure</LI>
<LI><b>CXX</b>: Use the <code>CXX</code> environment variable to tell the
configure script where to find the C++ compiler. You can
also directly modify this variable in the
<code>Makefile</code> that is generated by the autoconfigure</LI>
<LI><b>FC</b>: Use the <code>FC</code> environment variable to tell the
configure script where to find the fortran compiler. You can
also directly modify this variable in the
<code>Makefile</code> that is generated by the autoconfigure</LI>
<LI><b>MPICC</b>: If you are building for parallel C I/O, then it is
useful to tell the configure script where to find the
<code>mpicc</code> script. Normally, <code>mpicc</code> is
merely a wrapper script for a build using a regular C-compiler.
If no <code>mpicc</code> is available, then the
<code>configure</code> script will attempt to locate the mpi
header files and libraries. In that case, it may be useful to
define the <code>MPI_HOME</code> environment variable.</LI>
<LI><b>MPICXX</b>If you are building for parallel C++</LI>
<LI><b>MPIFC</b>: If you are building for parallel Fortran I/O, then it is
useful to tell the configure script where to find the parallel fortran compiler.
<LI><b>MPIROOT</b>: Set this environment variable to help the
configure script to locate the MPI libraries that should be
used to build the parallel version of the libraries. This
variable will be ignored if configured only to build the
serial implementation of the library.</LI>
<LI><b>HDF5ROOT</b>: Find the path to your serial HDF5 installation. If you
are building the serial version of H5part, then you should set
the <code>PHDF5ROOT</code> environment variable.</LI>
</UL><p>
<h3>Common compiler environemt variables for NERSC platforms</h3>
<UL>
<LI><b>DaVinci</b>: Linux ia64 </LI>
CC=icc CXX=icc F90=ifort MPICC=icc MPIFC=ifort MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include
<LI><b>Bassi</b>: AIX</LI>
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r
<LI><b>Jacquard</b>: Linux x86_64</LI>
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90
<LI><b>Starsky.lbl.gov:</b> (Darwin) PowerPC</LI>
CC=gcc CXX=g++ FC=g95
</UL>
<br>
NOTE: You might need to set the MPI library path (MPILIB) and MPI includes (MPIIINC) if they are in non standard places. For example: <br>
MPILIB=-L/usr/lpp/ppe.poe/lib -lmpi_r MPIINC=-I/usr/lpp/ppe.poe/include/thread
<h3>How to set the variables for configure:</h3>
It is very simple just call env with the variables together with configure. Notice the quotes in MPILIB.
<pre>
% env CC=icc CXX=icc F90=ifort MPICC=icc MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include ./configure (configure options follow here)
</pre>
In the worst case, you can edit the <code>src/Makefile.am</code> and <code>test/Makefile.am</code> as
needed to perform the proper build.
</div>
doc/BuildingHDF5.html
-64
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@@ -1,64 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<head>
<title>Building HDF5</title>
</head>
<body>
<font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
<UL>
<LI><a href="#ConfigOptions">Configure Options</a>
<LI><a href="#EnvVariables">Important Environment Variables</a>
</UL>
<hr>
<a name="ConfigOptions">
<h2>Configure options</h2></a>
</a>
To set the installation path configure with
<pre>
./configure --prefix=your hdf5 installation full path, e.g.--prefix=/usr/local/hdf5
</pre>
For the serial implementation configure with
<pre>
./configure
</pre>
For the parallel implementation configure with
<pre>
./configure --enable-parallel
</pre>
To enable shared objects configure with
<pre>
./configure --enable-shared
</pre>
<a name="EnvVariables">
<h2>Environment Variables</h2></a>
</a>
To add HDF5 to your PATH and LD_LIBRARY_PATH edit your
.tcshr, or .cshrc depending on the shell you are using and add
<pre>
setenv HDF5 "your hdf5 installation full path"
setenv PATH ${PATH}:${HDF5}/bin
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HDF5}/lib
</pre>
if you are using bash, add to your .bashrc
<pre>
export HDF5="your hdf5 installation full path"
export PATH=$PATH:${HDF5}/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HDF5}/lib
</pre>
Open a new terminal or do a
source .tcshr (.cshrc, .bashrc) in the one that you are using.
You can <a href="http://vis.lbl.gov/Research/AcceleratorSAPP/Downloading.html">continue <a/>downloading and installing H5Part.
</div>
doc/Downloading.html
-37
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@@ -1,37 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Downloading HDF5 and H5Part</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<head>
<title>Downloading HDF5 and H5Part</title>
</head>
<body>
<font face="arial,helvetica" size="+2" color="#555588"><h2>Downloading H5Part</h2></font>
<UL>
<LI><a href="#hdf5">Downloading HDF5</a>
<LI><a href="#h5part">Downloading H5Part</a>
</UL>
<hr>
<a name="hdf5">
<h2>Downloading HDF5</h2></a>
You will need to download and install the HDF5 library and link H5Part with it.
<UL>
<LI><a href="ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.6.5.tar.gz">ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.6.5.tar.gz</a></LI>
<LI><a href="http://www.zlib.net/zlib-1.2.3.tar.gz">http://www.zlib.net/zlib-1.2.3.tar.gz</a></LI>
<LI><a href="ftp://ftp.hdfgroup.org/lib-external/szip/2.0/src/szip-2.0.tar.gz">ftp://ftp.hdfgroup.org/lib-external/szip/2.0/src/szib-2.0.tar.gz</a></LI>
</UL>
<P>
Note: you might already have libz in your system and you will not need libsz unless you build hdf5 with support for it.
</P>
<h2 id="h5part">Downloading H5Part</h2>
H5Part is available for download from Berkeley Labs Codeforge system <a href="https://codeforge.lbl.gov/projects/h5part/">https://codeforge.lbl.gov/projects/h5part</a>.
</div>
doc/Doxyfile
+33 -31
View File
@@ -3,8 +3,8 @@
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
PROJECT_NAME = H5Part
PROJECT_NUMBER = 1.3.3
PROJECT_NAME = H5hut
PROJECT_NUMBER = 1.9.9
OUTPUT_DIRECTORY = ./ReferencePages
CREATE_SUBDIRS = NO
OUTPUT_LANGUAGE = English
@@ -35,7 +35,7 @@ INHERIT_DOCS = YES
SEPARATE_MEMBER_PAGES = NO
TAB_SIZE = 8
ALIASES =
OPTIMIZE_OUTPUT_FOR_C = NO
OPTIMIZE_OUTPUT_FOR_C = YES
OPTIMIZE_OUTPUT_JAVA = NO
BUILTIN_STL_SUPPORT = NO
DISTRIBUTE_GROUP_DOC = NO
@@ -57,7 +57,7 @@ CASE_SENSE_NAMES = YES
HIDE_SCOPE_NAMES = NO
SHOW_INCLUDE_FILES = NO
INLINE_INFO = YES
SORT_MEMBER_DOCS = YES
SORT_MEMBER_DOCS = NO
SORT_BRIEF_DOCS = NO
SORT_BY_SCOPE_NAME = NO
GENERATE_TODOLIST = YES
@@ -67,7 +67,7 @@ GENERATE_DEPRECATEDLIST= YES
ENABLED_SECTIONS =
MAX_INITIALIZER_LINES = 30
SHOW_USED_FILES = NO
SHOW_DIRECTORIES = YES
SHOW_DIRECTORIES = NO
FILE_VERSION_FILTER =
#---------------------------------------------------------------------------
# configuration options related to warning and progress messages
@@ -82,20 +82,22 @@ WARN_LOGFILE =
#---------------------------------------------------------------------------
# configuration options related to the input files
#---------------------------------------------------------------------------
INPUT += ../src/H5Part.c
INPUT += ../src/H5Block.c
FILE_PATTERNS =
RECURSIVE = YES
EXCLUDE =
EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS =
EXAMPLE_PATH =
EXAMPLE_PATTERNS = *
EXAMPLE_RECURSIVE = NO
IMAGE_PATH =
INPUT_FILTER =
FILTER_PATTERNS =
FILTER_SOURCE_FILES = NO
INPUT += H5.dox
INPUT += ../src/h5core/
INPUT += ../src/C/
INPUT += ../src/Fortran/
FILE_PATTERNS =
RECURSIVE = YES
EXCLUDE =
EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS =
EXAMPLE_PATH =
EXAMPLE_PATTERNS = *
EXAMPLE_RECURSIVE = NO
IMAGE_PATH =
INPUT_FILTER =
FILTER_PATTERNS =
FILTER_SOURCE_FILES = NO
#---------------------------------------------------------------------------
# configuration options related to source browsing
#---------------------------------------------------------------------------
@@ -118,8 +120,8 @@ IGNORE_PREFIX =
GENERATE_HTML = YES
HTML_OUTPUT = .
HTML_FILE_EXTENSION = .html
HTML_HEADER =
HTML_FOOTER = doxyfooter
HTML_HEADER =
HTML_FOOTER =
HTML_STYLESHEET =
HTML_ALIGN_MEMBERS = YES
GENERATE_HTMLHELP = NO
@@ -191,13 +193,13 @@ EXPAND_ONLY_PREDEF = NO
SEARCH_INCLUDES = YES
INCLUDE_PATH =
INCLUDE_FILE_PATTERNS =
PREDEFINED =
PREDEFINED = PARALLEL_IO
EXPAND_AS_DEFINED =
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration::additions related to external references
#---------------------------------------------------------------------------
TAGFILES = YES
TAGFILES =
GENERATE_TAGFILE =
ALLEXTERNALS = NO
EXTERNAL_GROUPS = YES
@@ -205,21 +207,21 @@ PERL_PATH = /usr/bin/perl
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
CLASS_DIAGRAMS = YES
CLASS_DIAGRAMS = NO
HIDE_UNDOC_RELATIONS = YES
HAVE_DOT = YES
CLASS_GRAPH = YES
COLLABORATION_GRAPH = YES
GROUP_GRAPHS = YES
HAVE_DOT = NO
CLASS_GRAPH = NO
COLLABORATION_GRAPH = NO
GROUP_GRAPHS = NO
UML_LOOK = NO
TEMPLATE_RELATIONS = NO
INCLUDE_GRAPH = NO
INCLUDED_BY_GRAPH = NO
CALL_GRAPH = NO
GRAPHICAL_HIERARCHY = YES
DIRECTORY_GRAPH = YES
GRAPHICAL_HIERARCHY = NO
DIRECTORY_GRAPH = NO
DOT_IMAGE_FORMAT = png
DOT_PATH = /Applications/Graphviz.app/Contents/MacOS
DOT_PATH =
DOTFILE_DIRS =
MAX_DOT_GRAPH_WIDTH = 1024
MAX_DOT_GRAPH_HEIGHT = 1024
doc/Examples/meshexample.dxf
+47962
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File diff suppressed because it is too large Load Diff
doc/Examples/meshexample.txt
+77
View File
@@ -0,0 +1,77 @@
NumLevels: 2
NumVerticesOnLevel: 11 20 29
Vertices:
1 0.0 0.0
2 60.0 -70.0
3 90.0 -10.0
4 140.0 -70.0
5 180.0 -10.0
6 240.0 -60.0
7 220.0 60.0
8 140.0 90.0
9 200.0 120.0
10 130.0 150.0
11 50.0 80.0
12 115.0 40.0
13 95.0 85.0
14 70.0 35.0
15 160.0 -40.0
16 135.0 -10.0
17 115.0 -40.0
18 200.0 25.0
19 180.0 75.0
20 160.0 40.0
21 125.0 15.0
22 112.5 -10.0
23 102.5 15.0
24 147.5 15.0
25 137.5 40.0
26 150.0 65.0
27 127.5 65.0
28 117.5 87.5
29 105.0 62.5
NumElemsOnLevel: 12 24 36
NumElems: 12 28 44
Elements:
ID PID CID VertexIDs Adj Translation Tbl (dim num lvls - 1)
1 -1 -1 1 2 3 2 11 -1 1
2 -1 -1 2 3 4 3 -1 1 2
3 -1 12 3 4 5 4 12 2 -1
4 -1 -1 4 5 6 5 -1 3 3
5 -1 -1 5 7 6 -1 4 6 4
6 -1 17 8 5 7 5 7 12 -1
7 -1 -1 8 9 7 -1 6 8 5
8 -1 -1 10 8 9 7 -1 9 6
9 -1 -1 11 10 8 8 10 -1 7
10 -1 25 11 3 8 12 9 11 -1
11 -1 -1 1 11 3 10 1 -1 8
12 -1 21 3 8 5 6 3 10 -1
13 3 -1 3 14 13 16 21 2 9
14 3 -1 14 4 12 4 16 2 10
15 3 -1 13 12 5 4 23 16 11
16 3 -1 14 13 12 15 14 13 12
17 6 -1 8 17 16 20 5 22 13
18 6 -1 17 5 15 5 20 23 14
19 6 -1 16 15 7 5 7 20 15
20 6 -1 17 16 15 19 18 17 16
21 12 -1 3 18 13 24 13 26 17
22 12 -1 18 8 17 17 24 27 18
23 12 -1 13 17 5 18 15 24 19
24 12 -1 18 13 17 23 22 21 20
25 10 -1 11 20 19 28 9 11 21
26 10 -1 20 3 18 21 28 11 22
27 10 -1 19 18 8 22 9 28 23
28 10 -1 20 3 18 27 26 25 24
3,0 3,1 4,2 2,3 16,4
1 2 -1 3 4
1 2 3
1 3 6
2 11 1 13 14
doc/Examples/simple_tet.vtk
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# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 18 90
4 0 3 2 1
4 0 4 3 1
4 0 5 6 7
4 5 3 8 9
4 6 8 2 10
4 7 9 10 1
4 5 6 7 9
4 5 6 8 9
4 6 7 9 10
4 6 8 9 10
4 0 11 12 13
4 11 5 14 15
4 12 14 6 16
4 13 15 16 7
4 11 12 13 15
4 11 12 14 15
4 12 13 15 16
4 12 14 15 16
CELL_TYPES 18
10
10
10
10
10
10
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10
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10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
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4
5
6
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8
9
10
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12
13
14
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CELL_DATA 18
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
0
1
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doc/Examples/simple_tet_level0.vtk
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# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 2 10
4 0 3 2 1
4 0 4 3 1
CELL_TYPES 2
10
10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
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CELL_DATA 2
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
0
1
doc/Examples/simple_tet_level1.vtk
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@@ -0,0 +1,80 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 9 45
4 0 4 3 1
4 0 5 6 7
4 5 3 8 9
4 6 8 2 10
4 7 9 10 1
4 5 6 7 9
4 5 6 8 9
4 6 7 9 10
4 6 8 9 10
CELL_TYPES 9
10
10
10
10
10
10
10
10
10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
CELL_DATA 9
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
0
1
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4
5
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7
8
doc/Examples/simple_tet_level2.vtk
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@@ -0,0 +1,101 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 16 80
4 0 4 3 1
4 5 3 8 9
4 6 8 2 10
4 7 9 10 1
4 5 6 7 9
4 5 6 8 9
4 6 7 9 10
4 6 8 9 10
4 0 11 12 13
4 11 5 14 15
4 12 14 6 16
4 13 15 16 7
4 11 12 13 15
4 11 12 14 15
4 12 13 15 16
4 12 14 15 16
CELL_TYPES 16
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
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8
9
10
11
12
13
14
15
16
CELL_DATA 16
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
1
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
doc/Examples/trimesh_dgraph_level0.metis
+13
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@@ -0,0 +1,13 @@
12 14
2 11
1 3
2 4 12
3 5
4 6
5 7 12
6 8
7 9
8 10
9 11 12
1 10
3 6 10
doc/Examples/trimesh_dgraph_level0.metis.part.2
+12
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@@ -0,0 +1,12 @@
0
1
1
1
1
1
0
0
0
0
0
1
doc/Examples/trimesh_dgraph_level0.metis.part.3
+12
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@@ -0,0 +1,12 @@
1
1
2
2
2
0
0
0
0
1
1
2
doc/Examples/trimesh_dnode_level1.metis
+49
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@@ -0,0 +1,49 @@
24 35
%1
2 8
%2
1 9 10
%3
4 10 11
%4
3 14 15
%5
6 13 15
%6
5 7
%7
6 21 23
%8
1 21 22
%9
2 12 17
%10
2 3 12
%11
3 12 19
%12
9 10 11
%13
5 16 18
%14
4 16 19
%15
4 5 16
%16
13 14 15
%17
9 20 22
%18
13 20 23
%19
11 14 20
%20
17 18 19
%21
7 8 24
%22
8 17 24
%23
7 18 24
%24
21 22 23
doc/Examples/trimesh_dnode_level1.metis.part.2
+24
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@@ -0,0 +1,24 @@
1
1
0
0
0
0
1
1
1
1
0
1
0
0
0
0
1
0
0
0
1
1
1
1
doc/Examples/trimesh_level0.metis
+13
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@@ -0,0 +1,13 @@
12 1
1 2 3
2 3 4
3 4 6
4 5 6
5 6 7
6 7 8
7 8 11
8 10 11
8 9 10
3 8 9
1 3 9
3 6 8
doc/Examples/trimesh_level0.metis.epart.2
+12
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@@ -0,0 +1,12 @@
1
1
1
1
0
0
0
0
0
0
1
1
doc/Examples/trimesh_level0.metis.ngraph
+12
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@@ -0,0 +1,12 @@
11 22
2 3 9
1 3 4
1 2 4 6 8 9
2 3 6 5
4 6 7
3 4 5 7 8
5 6 8 11
6 7 11 10 9 3
8 10 3 1
8 11 9
7 8 10
doc/Examples/trimesh_level0.metis.npart.2
+11
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@@ -0,0 +1,11 @@
1
1
1
1
1
0
0
0
0
0
0
doc/Examples/trimesh_level1.metis
+41
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@@ -0,0 +1,41 @@
20 43
%1
2 3 11
%2
1 3 4
%3
1 2 14 13 18 20
%4
2 14 12 6
%5
12 6 15 17 13
%6
4 5 7
%7
6 15 16 9
%8
9 10 19 18 17 16
%9
7 8 10
%10
8 9 11
%11
1 20 19 10
%12
4 14 13 5
%13
3 14 12 5 17 18
%14
3 13 12 4
%15
5 17 17 7
%16
7 8 17 15
%17
5 15 16 8 18 13
%18
3 13 17 8 19 20
%19
8 11 20 18
%20
3 18 19 11
doc/Examples/trimesh_level1.metis.part.2
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@@ -0,0 +1,20 @@
1
1
1
0
0
0
0
1
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1
0
0
0
0
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0
1
1
1
doc/H5.dox
+139
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@@ -0,0 +1,139 @@
/*!
\mainpage H5hut: A High-Performance I/O Library for Particle-based Simulations
Particle-based simulations running on large high-performance computing systems
over many time steps can generate an enormous amount of particle- and
field-based data for post-processing and analysis. Achieving high-performance
I/O for this data, effectively managing it on disk, and interfacing it with
analysis and visualization tools can be challenging, especially for domain
scientists who do not have I/O and data management expertise. We present the
H5hut library, an implementation of several data models for particle-based
simulations that encapsulates the complexity of HDF5 and is simple to use, yet
does not compromise performance.
Developers:
<UL>
<LI> Andreas Adelmann (PSI) </LI>
<LI> Achim Gsell (PSI) </LI>
<LI> Benedikt Oswald (PSI) </LI>
<LI> Mark Howison (NERSC/LBNL) </LI>
<LI> Prabhat (NERSC/LBNL) </LI>
<LI> Wes Bethel (NERSC/LBNL) </LI>
</UL>
Previous developers:
<UL>
<LI> John Shalf (NERSC/LBNL)</LI>
<LI> Cristina Siegerist (NERSC/LBNL)</LI>
</UL>
For more information, please contact the <a href="mailto:h5part@lists.psi.ch">h5part</a> mailing list.
*/
/*!
\defgroup h5hut_c_api H5hut C API
*/
/*!
\ingroup h5hut_c_api
\defgroup h5hut_file File Handling
*/
/*!
\ingroup h5hut_c_api
\defgroup h5hut_error Error Handling
*/
/*!
\ingroup h5hut_c_api
\defgroup h5hut_model Setting up the Data Model
*/
/*!
\ingroup h5hut_c_api
\defgroup h5hut_attrib Reading and Writing Attributes
*/
/*!
\defgroup h5part_c_api H5Part C API
*/
/*!
\ingroup h5part_c_api
\defgroup h5part_model Setting up the Data Model
*/
/*!
\ingroup h5part_c_api
\defgroup h5part_data Reading and Writing Datasets
*/
/*!
\defgroup h5block_c_api H5Block C API
*/
*/!
\ingroup h5block_c_api
\defgroup h5block_model Setting up the Data Model
*/
\ingroup h5block_c_api
\defgroup h5block_data Reading and Writing Datasets
*/
\ingroup h5block_c_api
\defgroup h5block_attrib Reading and Writing Attributes
*/
/*!
\defgroup h5fed_c_api H5Fed C API
*/
/*!
\defgroup h5hut_f90_api H5hut F90 API
*/
/*!
\ingroup h5hut_f90_api
\defgroup h5hut_file_f File Handling
*/
/*!
\ingroup h5hut_f90_api
\defgroup h5hut_model_f Setting up the Data Model
*/
/*!
\ingroup h5hut_f90_api
\defgroup h5hut_attrib_f Reading and Writing Attributes
!<
/*!
\defgroup h5part_f90_api H5Part F90 API
*/
/*!
\ingroup h5part_f90_api
\defgroup h5part_model_f Setting up the Data Model
*/
/*!
\ingroup h5part_f90_api
\defgroup h5part_data_f Reading and Writing Datasets
*/
/*!
\defgroup h5block_f90_api H5Block F90 API
*/
/*!
\ingroup h5block_f90_api
\defgroup h5block_model_f Setting up the Data Model
*/
/*!
\ingroup h5block_f90_api
\defgroup h5block_data_f Reading and Writing Datasets
*/
/*!
\ingroup h5block_f90_api
\defgroup h5block_attrib_f Reading and Writing Attributes
*/
doc/H5PartExpress.html
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@@ -1,14 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
Under construction, will be here soon.
</div>
doc/H5PartIDL.html
-15
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@@ -1,15 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
Under construction, will be here soon.
</div>
doc/H5PartParaview.html
-15
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@@ -1,15 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
Under construction, will be here soon.
</div>
doc/H5PartTools.html
-94
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@@ -1,94 +0,0 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<head>
<title>H5Part Utility Tools</title>
</head>
<body>
<font face="arial,helvetica" size="+2" color="#555588"><h2>H5Part Utility Tools</h2></font>
<UL>
<LI><a href="h5pAttrib">h5pAttrib</a>
<LI><a href="h5pToGNUplot">h5pToGNUplot</a>
</UL>
<hr>
<a name="h5pAttrib">
<h2>h5pAttrib</h2>
</a>
<b>h5pAttrib</b> is an inspection tool that prints to stdout the number of timesteps in a file
the file attributes, the step attributes, the dataset names and their values. It's simpler to use than h5dump.
Usage options are given by typing:
<br><br>
<PRE>
% ./h5pAttrib -h
usage: h5pAttrib [OPTIONS] file
OPTIONS
-h, --help Print help page
-n, --nstep Print number of steps
-A, --fileA Print file attributes
-a, --stepA Print step attributes & values for time step n
-d, --dataset Print data sets names & values for time step n
-H, --header Print shorter version without the values
</PRE>
<h3>Examples</h3>
<OL>
<LI>
Show file attribute names & values of sample.h5part
</LI>
h5pAttrib -A sample.h5part
<LI>
Show step attribute names for time step 5 of sample.h5part
</LI>
h5pAttrib -a 5 -H sample.h5part
</OL>
<a name="h5pToGNUplot">
<h2>h5pToGNUplot</h2>
</a>
<b>h5pToGNUplot</b> is a converter from H5Part to two column ASCII text format for loading into GNUplot. Usage options are given by typing:
<br><br>
<PRE>
% ./h5pToGNUplot -h
usage: h5pToGNUplot -t TIMESTEP -1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]
FLAGS
-h, --help Print help page
-1, --1var (REQUIRED) Takes first variable parameter
-2, --2var (REQUIRED) Takes second variable parameter
-i, --input (REQUIRED) Takes input file name
-t, --timestep (REQUIRED) Sets the timestep (Value -1 will result in dumping values of all timesteps.)
-o, --output (OPTIONAL) Takes output file name (without this flag, the program will print to stdout)
-n, --number (OPTIONAL) Sets number of output points
-s, --start (OPTIONAL) Sets the starting particle index
</PRE>
<h3>Examples</h3>
<OL>
<LI>
Create a GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54
</LI>
h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt
<LI>
Create a GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54
using 1200 points from particle index 76
</LI>
h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt -s 76 -n 1200
</OL>
</div>
doc/H5PartVisIt.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>H5Part: VisIt Plugins</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<font face="arial,helvetica"><h1>H5Part: VisIt Plugins</h1></font>
<font face="arial,helvetica" color="#555588"><h2>Introduction</h2></font>
<P>
<a href="http://www.llnl.gov/visit">VisIt</a> is an open source point-and-click 3D scientific visualization application that supports most of the common visualization techniques on structured and unstructured grids. One of its advantages is that it employs a distributed and parallel architecture in order to handle extremely large data sets interactively. VisIt's rendering and data processing capabilities are split into viewer and engine components that may be distributed across multiple machines. See this link for <a href="http://vis.lbl.gov/NERSC/Software/visit/">details</a> on how to run VisIt in NERSC.
</P>
<P>
VisIt achieves extensibility through the use of dynamically loaded plugins. All of VisIt's plots, operators, and database readers are implemented as plugins and are loaded at run-time from the plugin directory. New plugins can be added simply by installing them in this directory. VisIt comes with a graphical plugin creation tool, which greatly simplifies the process of creating new plugins. The user describes the properties of the plugin and then the tool generates most of the code necessary to implement the plugin. For example, in the case of an operator, the plugin creation tool creates the code necessary for the graphical user interface attribute window; the C++, Python, and Java interfaces; and the code necessary to interface to VisIt. The only code you need to write is the C++ code that actually performs the operation.
</P>
<font face="arial,helvetica" color="#555588"><h2>H5Part in VisIt</h2></font>
<font face="arial,helvetica" color="#555588"><h3>Database Reader Plugin</h3></font>
<P>
We wrote a Multiple Time Step Multiple Domain database reader to read H5Part data into VisIt. H5Part datasets should be named with the extension <font color=red>".h5part"</font> to be recognized by the reader since VisIt does not have a format selection mechanism at the time of reading. Figure 1 shows a Pseudocolor plot of a data set and Figure 2 shows a Scatter plot x-y (any combination of x, px, y, py, z, pz, id are possible).
</P>
<P>
<TABLE>
<TR>
<TD>
<a href="H5PartVisIt/cloud_visit.png"><img src="H5PartVisIt/cloud_visit.s.png" width=400 height=300></a>
</TD
></TR>
<TR>
<TD width=300>
Figure 1. VisIt User interface showing an H5Part particle file rendered as spheres using the Pseudocolor plot.
</TD>
</TR>
<TR>
<TD>
<a href="H5PartVisIt/cloud_visit_2D.png"><img src="H5PartVisIt/cloud_visit_2D.s.png" width=300 height=300></a>
</TD>
</TR>
<TR>
<TD>
Figure 2. A Scatter plot of the x-y projection of the particles.
</TD>
</TR>
</TABLE>
</P>
<P>
VisIt provides a Query interface, for single time steps and for time series. Figure 3 shows the query interace over time for the sum of the x position and the z position of the particoes.
</P>
<P>
<TABLE>
<TR>
<TD>
<a href="H5PartVisIt/visit_query1.png"><img src="H5PartVisIt/visit_query1.s.png" width=400 height=300></a>
</TD
></TR>
<TR>
<TD width=300>
Figure 3. VisIt's Time Query Output.
</TD>
</TR>
</TABLE>
</p>
<font face="arial,helvetica" color="#555588"><h2>Operator Plugins</h2></font>
<P>
<font face="arial,helvetica" color="#555588"><h3>Particle Random Sampler</h3></font>
</P>
<P>
<font face="arial,helvetica" color="#555588"><h3>Particle Binner</h3></font>
</P>
</div>
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doc/H5X_File_Format.txt
+26 -7
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@@ -28,9 +28,10 @@ top of HDF5: A H5X file is a very special HDF5 file.
2.1.1 File attributes
Attributes of the HDF5 root group are called "file attributes". There
are no restrictions on file attribute names. Supported values are
scalars and arrays of 64bit integer and 64bit floating point number as
well as string values, but not arrays of strings.
are no restrictions on file attribute names. Names with "__" as prefix and
postfix are intended for internal use. Supported values for file attributes
are scalars and arrays of 64bit integer and 64bit floating point number as
well as string values. Arrays of strings are not supported.
2.1.1.1 Predefined file attributes
@@ -63,18 +64,28 @@ Example: With __stepnumwidth__ := 5 the name of the step group with
number 42 is "Step#00042", with __stepnumwidth__ := 0 the name is
"Step#42".
Step groups may be unsorted in the HDF5 file und may not be number
Step groups may be unsorted in the HDF5 file und needn't be number
consecutively.
2.1.3 Other members of the root group
Other sub-groups of the root group are allowed, but the group names are restricted
to names not matching "Step#.*".
2.2 Format of a step group
2.2.1 Step attributes
Step attributes are HDF5 attributes asigned to a step group. There
are no restrictions on file attribute names. Supported values are
scalars and arrays of 64bit integer and 64bit floating point number as
well as string values, but not arrays of strings.
are no restrictions on step attribute names. As with file attributes names
enclosed in "__" are intended for internal use. Supported values are the same
as for file attributes:
* 64bit integer value
* arrays of 64bit integer values
* 64bit floating point number
* array of 64bit floating point number
* strings
Note that array of strings are not supported!
2.2.2 Predefined step attributes
@@ -147,5 +158,13 @@ n-dimensional vector values with n := 1.
2.3 Step properties [NEW]
Why? Much faster than step attributes if you need to access consecutive values
Group of root group with name "StepProperties"
Members are datasets
Supported values are the same as for step attributes
Mapping of value to step via object index of step group
doc/H5tools/H5tools.html
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<html><head><title>H5Part Tools How-to</title>
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<table border="0" cellpadding="0" cellspacing="0" width="987">
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<div id="mainleft"><font face="Arial, Helvetica, sans-serif"><a name="TOP"></a>
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<div id="maincenter"> <font face="arial,helvetica">
<h1 align="center"><font face="Arial, Helvetica, sans-serif"><b><font color="#666699">H5Part
Tools How-to</font></b></font></h1>
</font><font color="#555588" face="arial,helvetica">
<h2><font color="#666699" face="Arial, Helvetica, sans-serif">Table
of Contents</font></h2>
</font>
<p><font face="Arial, Helvetica, sans-serif"><b><a href="#Quick%20Guide">
[1] Quick Guide</a></b> </font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pAttrib</font></b></font><font face="Arial, Helvetica, sans-serif"><br>
<b><br>
<a href="#timesteps">[2] To see number of timesteps in a h5part file</a><br>
<br>
<a href="#file%20attributes">[3] To see file attributes in a h5part
file</a><br>
<br>
<a href="#step%20attributes"> [4] To see step attributes in a h5part
file</a><br>
<br>
<a href="#dataset">[5] To see dataset in a h5part file</a><br>
<br>
<a href="#flags">[6] Providing more than one flag at once for h5pAttrib</a></b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pToGNUplot</font></b></font><font face="Arial, Helvetica, sans-serif"><br>
<br>
<b><a href="#parameters">[7] What parameters to provide</a><br>
<br>
<a href="#input%20file">[8] How to create an input file to GNUplot</a></b></font></p>
<p>&nbsp;</p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p>&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="Quick Guide">[1]
Quick Guide</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif">Executing the program with
-h option will display a concise help page.</font></p>
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono">./h5pAttrib
-h</font></font></p>
<p><font face="Courier New, Courier, mono">usage: h5pAttrib [OPTIONS]
file</font></p>
<p><font face="Courier New, Courier, mono"> OPTIONS<br>
-h, --help Print help page<br>
-n, --nstep Print number of steps<br>
-A, --fileA Print file attributes<br>
-a n, --stepA n Print step attributes &amp; values for time step n<br>
-d n, --dataset n Print data sets names &amp; values for time step
n<br>
-H, --header Print shorter version without the values</font></p>
<p><font face="Courier New, Courier, mono"> Examples:</font></p>
<p><font face="Courier New, Courier, mono"> 1) Show file attribute names
&amp; values of sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"> h5pAttrib -A sample.h5part<br>
OR<br>
h5pAttrib --fileA sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"> 2) Show step attribute names
for time step 5 of sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"> h5pAttrib -a 5 -H sample.h5part<br>
OR<br>
h5pAttrib --stepA 5 -H sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"><br>
<b><font size="+1">$&gt;</font></b> ./h5pToGNUplot -h</font></p>
<p><font face="Courier New, Courier, mono">usage: h5pToGNUplot -t TIMESTEP
-1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]</font></p>
<p><font face="Courier New, Courier, mono"> FLAGS<br>
-h, --help Print help page</font><br>
<font face="Courier New, Courier, mono">-1 par, --1var par (REQUIRED)
Takes first variable parameter to "par"<br>
-2 par, --2var par (REQUIRED) Takes second variable parameter to "par"<br>
-i file, --input file (REQUIRED) Takes input file name to "file"<br>
</font><font face="Courier New, Courier, mono">-t step, --timestep
step (REQUIRED) Sets the timestep to "step" (Value -1 will
result in dumping values of all timesteps.)<br>
-o file, --output file (OPTIONAL) Takes output file name to "file"
(without this flag, the program will print to stdout)<br>
-n num, --number num (OPTIONAL) Sets number of output points to "num"<br>
-s idx, --start idx (OPTIONAL) Sets the starting particle index to
"idx"</font></p>
<p><font face="Courier New, Courier, mono"><br>
Examples:</font></p>
<p><font face="Courier New, Courier, mono"> 1) Create GNU plot file
output.txt from sample.h5part by ploting x vs px for timestep 54</font></p>
<p><font face="Courier New, Courier, mono"> h5pToGNUplot -t 54 -1 x
-2 px -i sample.h5part -o output.txt</font></p>
<p><font face="Courier New, Courier, mono"> 2) Create GNU plot file
output.txt from sample.h5part by ploting x vs px for timestep 54<br>
using 1200 points from particle index 76</font></p>
<p><font face="Courier New, Courier, mono"> h5pToGNUplot -t 54 -1 x
-2 px -i sample.h5part -o output.txt -s 76 -n 1200</font></p>
<p>&nbsp;</p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p>&nbsp;</p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pAttrib</font></b></font></p>
<p>&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="timesteps">[2]
To see number of timesteps in a h5part file</a></font></h2>
<p>Executing the program h5pAttrib with -n flag will display the number
of timesteps in the file.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -n sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing number of timesteps
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">There are total 252 number
of timesteps.<br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font><font face="Arial, Helvetica, sans-serif"><br>
</font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<h2><font color="#666699" face="Arial, Helvetica, sans-serif"><br>
<font color="#555588"><a name="file attributes">[3] To see file attributes
in a h5part file</a></font></font></h2>
<p>File attribute contains information about the file. (file description
etc...) Executing the program h5pAttrib with -A flag will display
the file attributes in the file.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -A sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing file attributes
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of file attributes
for file sample.h5part is 0 ...<br>
There are no file attributes.<br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p><font face="Arial, Helvetica, sans-serif"><br>
<i>NOTE: -H option will omit the list of values of file attributes.</i></font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p align="center">&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="step attributes">[4]
To see step attributes in a h5part file</a></font></h2>
<p>Step attribute contains information that belongs to a specific step.
(step name, timestep number, etc...) Executing the program h5pAttrib
with -a flag will display the step attributes in the file.<br>
Note that the timestep index should follow -a flag.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono">
./h5pAttrib -a 2 sample.h5part</font></font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing step attributes
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of step attributes
for timestep #2 is 10 ...</font></p>
<p><font face="Courier New, Courier, mono">Attribute #0 = Step<br>
There are 1 elements in the attribute<br>
Attribute Type is H5T_NATIVE_INT64<br>
Printing 1 element value(s):<br>
COUNT[0]: 2</font></p>
<p><font face="Courier New, Courier, mono">Attribute #1 = Spos<br>
There are 1 elements in the attribute<br>
Attribute Type is H5T_NATIVE_DOUBLE<br>
Printing 1 element value(s):<br>
COUNT[0]: 0.143580</font></p>
<p><font face="Courier New, Courier, mono">Attribute #2 = structLen<br>
There are 1 elements in the attribute<br>
Attribute Type is H5T_NATIVE_DOUBLE<br>
Printing 1 element value(s):<br>
COUNT[0]: 2.393000</font></p>
<p><font face="Courier New, Courier, mono">.<br>
.<br>
.</font></p>
<p><font face="Courier New, Courier, mono"><br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p><font face="Arial, Helvetica, sans-serif"><br>
<i>NOTE: -H option will omit the list of values of step attributes.</i></font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><br>
<a name="dataset">[5] To see dataset in a h5part file</a></font></h2>
<p>Executing the program h5pAttrib with -d flag will display the datasets
information in the file. (dataset name, type, number of elements,
etc...) Executing the program h5pAttrib with -d flag will display
the datasets information in the file.<br>
Note that the timestep index should follow -d flag.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -d 2 -H sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing names of datasets
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of datasets for
timestep #2 is 7 ...</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #0 = id<br>
Dataset Type is H5T_NATIVE_INT64<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #1 = px<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #2 = py<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #3 = pz<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #4 = x<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #5 = y<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #6 = z<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p><font face="Arial, Helvetica, sans-serif"><br>
<i>NOTE: -H option will omit the list of values of datasets.</i></font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p>&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="flags">[6]
Providing more than one flag at once</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif">When more than one flags
are provided, one result after another will be displayed.</font></p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -H -a 1 -d 1 sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing step attributes
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of step attributes
for timestep #1 is 10 ...</font></p>
<p><font face="Courier New, Courier, mono">Attribute #0 = Step<br>
Attribute #1 = Spos<br>
Attribute #2 = structLen<br>
Attribute #3 = org<br>
Attribute #4 = maxX<br>
Attribute #5 = minX<br>
Attribute #6 = maxP<br>
Attribute #7 = minP<br>
Attribute #8 = centroid<br>
Attribute #9 = nloc<br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono"><br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing names of datasets
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of datasets for
timestep #1 is 7 ...</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #0 = id<br>
Dataset Type is H5T_NATIVE_INT64<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #1 = px<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #2 = py<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #3 = pz<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #4 = x<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #5 = y<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #6 = z<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p>&nbsp;</p>
<div align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></div>
</div>
</div>
</td>
</tr>
<tr>
<td height="80"></td>
<td colspan="3" valign="top">
<h2><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pToGNUplot</font></b></font></h2>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="parameters">[7]
What parameters to provide</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif">When you execute the program
with -h option, it displays what flags are necessary and what flags are
optional.</font></p>
</td>
</tr>
<tr>
<td height="200"></td>
<td valign="top" width="137">
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Short Version</font></b></p>
<p><font face="Arial, Helvetica, sans-serif">-h<br>
-1<br>
-2<br>
-i<br>
-t<br>
-o<br>
-n<br>
-s </font></p>
</td>
<td valign="top" width="144">
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Long Version</font></b></p>
<p><font face="Arial, Helvetica, sans-serif">--help<br>
--1var<br>
--2var<br>
--input<br>
--timestep<br>
--output<br>
--number<br>
--start </font></p>
</td>
<td valign="top" width="679">
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Meanings</font></b></p>
<p><font face="Arial, Helvetica, sans-serif">Print help page<br>
(REQUIRED) Takes first variable parameter<br>
(REQUIRED) Takes second variable parameter<br>
(REQUIRED) Takes input file name<br>
(REQUIRED) Sets the timestep (Value -1 will result in dumping values of
all timesteps.)<br>
(OPTIONAL) Takes output file name (without this flag, the program will
print to stdout)<br>
(OPTIONAL) Sets number of output points<br>
(OPTIONAL) Sets the starting particle index</font> </p>
</td>
</tr>
<tr>
<td height="1786"></td>
<td colspan="3" valign="top">
<p>&nbsp;</p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><br>
<a name="input file">[8] How to create an input file to GNUplot</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b><br>
<i>Create input file to GNUplot that plots x vs. y.</i></font></p>
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono">
./h5pToGNUplot -1 x -2 y -t 1 -i sample.h5part -o output.txt<br>
<b><font size="+1">$&gt;</font></b> cat output.txt<br>
-0.390779 -0.254793<br>
-0.396527 -0.252781<br>
-0.375362 -0.285137<br>
-0.396527 -0.252781<br>
-0.379917 -0.283147<br>
-0.390779 -0.254793<br>
-0.387536 -0.287346<br>
-0.371787 -0.319797<br>
-0.379917 -0.283147<br>
-0.378967 -0.326058<br>
-0.378976 -0.326078<br>
-0.387536 -0.287346<br>
-0.378957 -0.326069<br>
-0.379917 -0.283147<br>
-0.388762 -0.265390<br>
-0.371787 -0.319797<br>
-0.390779 -0.254793<br>
-0.376825 -0.266804<br>
-0.379917 -0.283147<br>
-0.375362 -0.285137<br>
...</font></font></p>
<p><font face="Courier New, Courier, mono"><i>Then run GNUplot...</i></font></p>
<p><font face="Courier New, Courier, mono"><b><font size="+1">$&gt;</font></b>
gnuplot</font></p>
<p><font face="Courier New, Courier, mono"> G N U P L O T<br>
Version 4.0 patchlevel 0<br>
last modified Thu Apr 15 14:44:22 CEST 2004<br>
System: Linux 2.6.11.4-21.11-smp</font></p>
<p><font face="Courier New, Courier, mono"> Copyright (C) 1986 - 1993, 1998,
2004<br>
Thomas Williams, Colin Kelley and many others</font></p>
<p><font face="Courier New, Courier, mono"> This is gnuplot version 4.0.
Please refer to the documentation<br>
for command syntax changes. The old syntax will be accepted<br>
throughout the 4.0 series, but all save files use the new syntax.</font></p>
<p><font face="Courier New, Courier, mono"> Type `help` to access the on-line
reference manual.<br>
The gnuplot FAQ is available from<br>
http://www.gnuplot.info/faq/</font></p>
<p><font face="Courier New, Courier, mono"> Send comments and requests for
help to<br>
&lt;gnuplot-info@lists.sourceforge.net&gt;<br>
Send bugs, suggestions and mods to<br>
&lt;gnuplot-bugs@lists.sourceforge.net&gt;</font></p>
<p><font face="Courier New, Courier, mono"><br>
Terminal type set to 'x11'<br>
<font size="+1"><b>gnuplot&gt;</b></font> plot "output.txt"</font></p>
<p><font face="Arial, Helvetica, sans-serif"><i>This will open a GNUplot
window that plots output.txt.</i></font></p>
<p align="center"><img src="H5tools_files/snapshot1.jpg" height="541" width="672"><br>
<font face="Arial, Helvetica, sans-serif">&lt;Sample screen shot of GNUplot
with input datafile generated by h5pToGNUplot&gt;</font></p>
</td>
</tr>
<tr>
<td height="44"></td>
<td></td>
<td></td>
<td></td>
</tr>
</tbody></table>
</body></html>
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>H5Part, Logical Internal HDF5 File Layout</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<font face="arial,helvetica"><h1>H5Part: Logical Internal HDF5 File Layout</h1></font>
<P>
HDF5 is extremely flexible in the sense that it allows the user to define a higher level data model to describe domain-specific data relationships. This flexibility however makes it necessary to develop an agreement on the logical layout of the data. The H5Part data model consists of Particle groups corresponding to the simulation time steps, each with seven datasets corresponding to x, px, y, py, z, pz, id for each particle. Attributes can be added to the file and to the datasets.
</P>
<center><img src="layout.png"></center>
<PRE>
HDF5 "parttest.h5" {
GROUP "/" {
GROUP "Particles#0" {
DATASET "id" {
DATATYPE H5T_STD_I64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "px" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "py" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "pz" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "x" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "y" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "z" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
}
</PRE>
<P>
See <a href="http://www-vis.lbl.gov/Publications/2002/hdf5.pdf">hdf5.pdf</a> for an introduction on the use of HDF5.
</P>
</div>
doc/Makefile.am
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EXTRA_DIST = \
Doxyfile doxyfooter \
$(wildcard *.html) \
$(wildcard *.png) \
$(wildcard H5PartVisIt/*.png) \
$(wildcard H5tools/*.html) \
$(wildcard H5tools/H5tools_files/*.jpg)
EXTRA_DIST = \
Doxyfile \
H5.dox \
Makefile.in
all:
doc:
doxydoc:
doxygen
clean:
${RM} -rf ReferencePages TWiki
doc/UsingC.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>H5Part, the C/C++ API</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<h1>The C/C++ Application Programming Interface (API)</h1>
<UL>
<LI><a href="#Opening">Opening, Closing, and Validating Datafiles</a>
<LI><a href="#SetStep">Setting the Simulation Timestep</a>
<LI><a href="#SetNumParticles">Setting the Number of Particles</a>
<LI><a href="#Writing">Writing Datasets</a>
<LI><a href="#ReadingNumTimeSteps">Reading the Number of Time Steps</a>
<LI><a href="#ReadingNumParticles">Reading the Number of Particles</a>
<LI><a href="#Reading">Reading Datasets</a>
<LI><a href="#DatasetsInfo">Reading the Number and the Names of Datasets</a>
<LI><a href="#AttributesInfo">Attributes Interface</a>
<LI><a href="#WriteAttribs">Writing Additional Attributes</a>
<LI><a href="#ReadAttribs">Reading Attributes</a>
</UL>
<br>
<a href="ReferencePages/index.html">Reference Manual (Doxygen)</a>
<br>
<hr>
<a name="Opening"><h2>Opening Datafiles</h2></a>
<P>
Just like the familiar <code>FILE*</code> type for C stdio operations, all
H5Part file operations require a file handle. The type of this handle is
<code>(H5PartFile*)</code>.
<br>
<code>H5PartOpenFile()</code> is
used to open a serial file and
<code>HDFPartOpenFileParallel()</code> is used to open a file for
Parallel I/O (in an MPI program).
After you open the file handle you can use the same set of
subroutines for operations on the file regardless of whether the
file is a parallel or serial I/O file.
The libraries manage all of this internally.<p>
</P>
<b>C Prototypes</b><br>
<P>
<b>Serial File</b><br>
<code>H5PartFile *H5PartOpenFile(const char *filename, unsigned
accessmode);</code><br>
<b>Parallel File</b><br>
<code>H5PartFile *H5PartOpenFileParallel(char *filename,int
accessmode,MPI_Comm communicator);</code><br>
<DT><i>filename</i>: </DT><DD>The name of the IEEEIO data file to
open. The typical extension for these files is <i>.h5</i></DD>
<DT><i>accessmode</i>: </DT><DD>The accessmode for the file. This is
one of 2 different access modes<br>
<code>H5PART_READ</code> : Opens a file in read-only mode.</DT><br>
<code>H5PART_WRITE</code> : Opens a file in write-only mode.
If the
file does not exist, it will be created. If it does
exist, it will be
truncated.
<DT><i>communicator</i>: </DT>
<DD>This argument is only available if the program has been
compiled with the <code>PARALLEL_IO</code> C-preprocessor flag
defined. It is used to pass in the communicator that will be
used for all collective I/O operations that target the same
file on disk.</DD>
<DT><i>Returns</i>:</DT><DD>A new filehandle with an open file or NULL if error.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
. . . code . . .
/* Open an HDF5 file for writing */
H5PartFile *writer = H5PartOpenFile("datafileout.h5",H5PART_WRITE);
/* Open an HDF5 file for Parallel I/O */
H5PartFile *writer = H5PartOpenFileParallel("datafileout.h5",H5PART_WRITE,MPI_COMM_WORLD);
/* open HDF5 file for reading */
H5PartFile *reader = H5PartOpenFile("datafilein.h5",H5PART_READ);
/* open HDF5 file for parallel reads */
H5PartFile *reader = H5PartOpenFileParallel("datafilein.h5",H5PART_READ,MPI_COMM_WORLD);
. . . more code . . .
</pre> <br>
<hr>
<h2>Closing Datafiles</h2>
<P>
To close the file, you simply use H5PartCloseFile() for both
parallel and serial files. You must call H5PartCloseFile() on any
file descriptor created by H5PartFileOpen() regardless of
whether the file turns out to be valid or not.
</P>
<b>C Prototypes</b><br>
<P>
<code>void H5PartCloseFile(H5PartFile *fileID);</code>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
H5PartOpenFile() or H5PartOpenFileParallel().</DD>
<DT><i>Returns</i>:</DT><DD>void.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *file;
... code ...
file=H5PartOpenFileParallel("parttest.h5",H5PART_WRITE,comm);
... more code ...
H5PartCloseFile(file);
</pre>
<br>
<hr>
<h2>Validating Datafiles</h2>
<P>
You can test if the file was opened successfully using the
H5PartFileIsValid() function. It returns 1 if valid, 0 if invalid.<p>
</P>
<b>C Prototype</b><br>
<P>
<code>int H5PartFileIsValid(H5PartFile *fileID);</code>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
H5PartOpenFile() or H5PartOpenFileParallel().</DD>
<DT><i>Returns</i>:</DT><DD>1 if valid, 0 if invalid.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<P>
Here is an example of validating a newly opened file. Even if
the file is invalid, you must use H5PartCloseFile() to reclaim
the file handle.
</P>
<pre>
#include &lt H5Part.h &gt
. . . code . . .
H5PartFile *fileID = H5PartOpenFile("datafileout.h5",H5PART_WRITE);
if(!H5PartFileIsValid(fileID)){
puts("The file you specified does not exist or is not in a
readable format");
H5PartClose(fileID); /* must reclaim fileID even if file is invalid */
. . . do other cleanup . . .
}
. . . more code . . .
</pre><br>
<hr>
<a name="SetStep">
<h2>Setting the Timestep</h2>
</a>
<P>
When writing data to a file the current time step must be set (even if there is only one). In a file with N time steps, the steps are numbered from 0 to N-1.
</P>
<b>C Prototype</b><br>
<P>
<code>void H5PartSetStep((H5PartFile *fileID,int step);</code>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
H5PartOpenFile() or H5PartOpenFileParallel().</DD>
<DT><i>step</i>: </DT><DD>An integer time step.
</DD>
<DT><i>Returns</i>: </DT><DD>void.</DD>
</DL>
<br><b>Example Use</b><br>
</P>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
int timeStep;
....
H5PartSetStep(fileID,timeStep);
....
</pre>
<hr>
<a name="SetNumParticles">
</a>
<h2>Setting the Number of Particles</h2>
<P>
H5PartSetNumParticles: This function's sole purpose is to
prevent needless creation of new HDF5 DataSpace handles if
the number of particles is invariant throughout the sim.
That's its only reason for existence. After you call this
subroutine, all subsequent operations will assume this
number of particles will be written.
</P>
<b>C Prototype</b><br>
<P>
<code>void H5PartSetNumParticles(H5PartFile *fileID,long long nparticles);</code>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
H5PartOpenFile() or H5PartOpenFileParallel().</DD>
<DT><i>nparticles</i>: </DT><DD>A long long integer specifying the number of particles.
</DD>
<DT><i>Returns</i>: </DT><DD>void.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
long long nparticles;
....
H5PartSetStep(fileID,nparticles);
....
</pre>
<hr>
<a name="Writing">
<h2>Writing Datasets</h2>
</a>
<P>
After setting the number of particles with
<a href="#SetNumParticles">H5PartSetNumParticles()</a>
and the current timestep using
<a href="#SetStep">H5PartSetStep()</a>, you can start
writing datasets into the file. Each dataset has a name
associated with it (chosen by the user) in order to facilitate
later retrieval. The writing routines also implicitly store
the datatype of the array so that the array can be
reconstructed properly on other systems with incompatible type
representations. The data is committed to disk before the
routine returns. All data that is written after setting the
timestep is associated with that timestep. While the number of
particles can change for each timestep, you cannot change the
number of particles in the middle of a given timestep.
</P>
<b>C Prototypes</b><br>
<P>
<code>int H5PartWriteDataFloat64(H5PartFile *fileID,char
*name,double *array);</code></br>
<code>int H5PartWriteDataInt64(H5PartFile *fileID,char
*name,double *array);</code>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string for the
name of the array. When retrieving datasets from disk,
you ask for them by name. There are no restrictions on
naming of arrays, but it is useful to arrive at some common
naming convention when sharing data with other groups.</DD>
<DT><i>array</i>: </DT><DD>A buffer containing an array of
particle data to commit to disk. The datatype for
elements in the buffer is implicit in the name of the
subroutine call.</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
double *x,*y,*z;
int timeStep;
long long nparticles;
...
H5PartSetStep(fileID,timeStep); /* must set the current timestep in file */
H5PartSetNumParticles(fileID,nparticles); /* then set number of particles to store */
/* now write different tuples of data into this timestep of the file */
H5PartWriteDataFloat64(fileID,"x",x);
H5PartWriteDataFloat64(fileID,"y",y);
H5PartWriteDataFloat64(file,"z",z);
..
</pre>
<hr>
<a name="ReadingNumTimeSteps">
<h2>Reading the Number of Time Steps</h2>
</a>
<P>
This reads the number of datasteps that are
currently stored in the datafile.
It works for both reading and writing of files, but is probably
only typically used when you are reading.
</P>
<b>C Prototype</b><br>
<P>
<code>int H5PartGetNumSteps (H5PartFile *fileID);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by <a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>Returns</i>: </DT><DD>The number of timesteps currently stored in the file.
</DL>
</P>
<hr>
<a name="ReadingNumParticles">
<h2>Reading the Number of Particles</h2>
</a>
<P>
This reads the number of particles that are
currently stored in the current time step.
It will arbitrarily select a timestep if you haven't
already set the timestep with H5PartSetStep().
</P>
<b>C Prototype</b><br>
<P>
<code>long long H5PartGetNumParticles (H5PartFile *fileID);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by <a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>Returns</i>: </DT><DD>The number of particles in current timestep.
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
int timeStep;
long long nparticles;
H5PartSetStep(fileID,0);
nparticles=H5PartGetNumParticles(fileID);
...
</pre>
<hr>
<a name="Reading">
<h2>Reading Datasets</h2>
</a>
<P>
After setting the time step and getting the number of particles to allocate the data arrays, you can start to read the data.
</P>
<b>C Prototypes</b><br>
<P>
<code>int H5PartReadDataFloat64(H5PartFile *fileID,char *name,double *array);</code><br>
<code>int H5PartReadDataInt64(H5PartFile *fileID,char *name,long long *array);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string for the
name of the array. When retrieving datasets from disk,
you ask for them by name. There are no restrictions on
naming of arrays, but it is useful to arrive at some common
naming convention when sharing data with other groups.</DD>
<DT><i>array</i>: </DT><DD>A buffer to which the particle data will be read.i
The datatype for
elements in the buffer is implicit in the name of the
subroutine call.</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
double *x,*y,*z;
int timeStep;
long long nparticles;
H5PartSetStep(fileID,0);
nparticles=H5PartGetNumParticles(fileID);
...
H5PartReadDataFloat64(file,"x",x);
H5PartReadDataFloat64(file,"y",y);
H5PartReadDataFloat64(file,"z",z);
...
</pre>
<hr>
<a name="DatasetsInfo"><h2>Reading the Number and Names of Datasets</h2></a>
<P>
H5Part provides funtions to find out how many datasets are stored at a particular timestep
and what their names are if you don't know what they are a-priori.
</P>
<b>C Prototypes</b><br>
<P>
<code>int H5PartGetNumDatasets(H5PartFile *fileID);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>Returns</i>: </DT><DD>The number of datasets.</DD>
</DL>
</P>
<P>
<code>int H5PartGetDatasetName(H5PartFile *fileID,int index,char *name,int maxlen);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>index</i>:</DT><DD> integer specifying the index of the dataset. If the number of datasets is
nds, the range of index is 0 to nds-1.</DD>
<DT><i>name</i>:</DT><DD> A null-terminated string for the name of the dataset.</DD>
<DT><i>maxlen</i>:</DT><DD> An integer specifying the maximum length of the name array.</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
char name[64];
int index, nds;
...
nds=H5PartGetNumDatasets(fileID);
for(index=0;index&lt nds;index++){
H5PartGetDatasetName(fileID,index,name,64);
printf("\tDataset[%u] name=[%s]\n", index,name);
}
...
</pre>
<hr>
<a name="AttributesInfo">
<h2>Attributes Interface</h2></a>
<P>
In the current H5Part implemtation there are two types of attributes: file attributes which are bound to the file
and step attributes which are bound to the current timestep. You
must set the timestep explicitly before writing the attributes (just
as you must do when you write a new dataset. Currently there are no
attributes that are bound to a particular data array, but this could
easily be done if required.
</P>
<P>H5PartGetNumStepAttribs and H5PartGetNumFileAttribs return the number of attributes bound to a step and to a file respectively. H5PartGetStepAttribInfo and H5PartGetFileAttribInfo return the name, type and number of elements of type "type" bound to a step and a file respectively.
</P>
<b>C Prototypes:</b><br>
<code>int H5PartGetNumStepAttribs(H5PartFile *fileID);
</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>Returns</i> </DT><DD> The number of step attributes for the current step.</DD>
</DL>
<code>int H5PartGetNumFileAttribs(H5PartFile *fileID);
</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>Returns</i> </DT><DD> The number of file attributes.</DD>
</DL>
<code>void H5PartGetStepAttribInfo(H5PartFile *fileID,int idx, char *name,size_t maxnamelen,hid_t *type,int *nelem);
</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>idx</i>: </DT><DD>Index of the attribute.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string with the name of the attribute.</DD>
<DT><i>maxnamelen</i></DT><DD>the length of the name of the attribute.</DD>
<DT><i>type</i>: </DT><DD>One of the following: H5T_NATIVE_DOUBLE H5T_NATIVE_INT64 H5T_NATIVE_CHAR.</DD>
<DT><i>nelem</i>: </DT><DD>Number of elements of type "type".</DD>
<DT><i>Returns</i> </DT><DD> void.</DD>
</DL>
<code>void H5PartGetFileAttribInfo(H5PartFile *fileID,int idx, char *name,size_t maxnamelen, hid_t *type,int *nelem);
</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>idx</i>: </DT><DD>Index of the attribute.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string with the name of the attribute.</DD>
<DT><i>maxnamelen</i></DT><DD>the length of the name of the attribute.</DD>
<DT><i>type</i>: </DT><DD>One of the following: H5T_NATIVE_DOUBLE H5T_NATIVE_INT64 H5T_NATIVE_CHAR.</DD>
<DT><i>nelem</i>: </DT><DD>Number of elements of type "type".</DD>
<DT><i>Returns</i> </DT><DD> void.</DD>
</DL>
<a name="WriteAttribs">
<h2>Writing Attributes</h2>
</a>
<P>
An attribute can be bound to the file or after setting the time step to this time step.
</P>
<b>C Prototypes: Generic Attributes</b><br>
<P>
<code>int H5PartWriteFileAttrib(H5PartFile *fileID,char *name, hid_t type,void *value,int nelem);</code><br>
<code>int H5PartWriteStepAttrib(H5PartFile *fileID,char *name, hid_t type,void *value,int nelem);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string for the
name of the array. When retrieving datasets from disk,
you ask for them by name. There are no restrictions on
naming of arrays, but it is useful to arrive at some common
naming convention when sharing data with other groups.</DD>
<DT><i>type</i>: One of H5T_NATIVE_DOUBLE, H5T_NATIVE_INT64, H5T_NATIVE_CHAR.</DD>
<DT><i>value</i>: value of the attribute.</DD>
<DT><i>nelem</i>: number of elements of type "type".</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
double actPos;
...
H5PartWriteStepAttrib(file_m,"Spos",H5T_NATIVE_DOUBLE,&actPos,1);
...
</pre>
<b>C Prototypes: String Attributes</b><br>
<P>
<code>int H5PartWriteStepAttribString(H5PartFile *fileID,char *name, char *attrib);</code><br>
<code>int H5PartWriteFileAttribString(H5PartFile *fileID,char *name, char *attrib);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string for the
name of the array. When retrieving datasets from disk,
you ask for them by name. There are no restrictions on
naming of arrays, but it is useful to arrive at some common
naming convention when sharing data with other groups.</DD>
<DT><i>attrib</i>: the attribute character string.</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
char *newattrib;
char *newname;
...
H5PartWriteFileAttribString(fileID, newname,newattrib);
...
</pre>
<hr>
<a name="ReadAttribs">
<h2>Reading Attributes</h2>
</a>
<P>
<P>
As with the writing of attributes, there are two basic reading interfaces one that reads file bound attributes and one that reads
step bound attributes. If the step is not set the current one will be used.
</P>
</P>
<b>C Prototypes</b><br>
<P>
<code>void H5PartReadStepAttrib(H5PartFile *fileID,char *name,void *value);</code><br>
<code>void H5PartReadAttrib(H5PartFile *fileID,char *name,void *value);</code><br>
<code>int H5PartReadFileAttrib(H5PartFile *fileID,char *name,void *value);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string for the
name of the array. When retrieving datasets from disk,
you ask for them by name. There are no restrictions on
naming of arrays, but it is useful to arrive at some common
naming convention when sharing data with other groups.</DD>
<DT><i>value</i>: value of the attribute.</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br>
NOTE: H5PartReadAttrib has been superseeded by H5PartSetStep.
<br>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
int step;
char name[MAXNAME];
...
H5PartSetStep(fileID, step);
if (H5PartReadStepAttrib(file, "filename", &name[0]) == 1){
printf("Read step from file: %s\n", name);
}
...
</pre>
</div>
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>H5part, the Fortran API</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<h1>The FORTRAN Application Programming Interface (API)</h1>
<P>
These references contain the information on how to access the H5Part API using FORTRAN bindings. All pointers are cast to haddr_t (a unint64_t) within the C/C++ code. In fortran, these pointers (handles) are carried as INTEGER*8
</P>
<UL>
<LI><a href="#Opening">Opening, Closing, and Validating Datafiles</a>
<LI><a href="#SetStep">Setting the Simulation Timestep</a>
<LI><a href="#SetNumParticles">Setting the Number of Particles</a>
<LI><a href="#Writing">Writing Datasets</a>
<LI><a href="#ReadingNumTimeSteps">Reading the Number of Time Steps</a>
<LI><a href="#ReadingNumTimeSteps">Reading the Number of Particles</a>
<LI><a href="#Reading">Reading Datasets</a>
<LI><a href="#DatasetsInfo">Reading the Number and the Names of Datasets</a>
<LI><a href="#AttributesInfo">Attributes Interface</a>
<LI><a href="#WriteAttribs">Writing Additional Attributes</a>
<LI><a href="#ReadAttribs">Reading Attributes</a>
</UL>
<hr>
<a name="Opening"><h2>Opening Datafiles</h2></a>
<P>
Like the familiar OPEN in FORTRAN files can be opened to read and write. Different functions are used for the serial and parallel case.
</P>
<b>FORTRAN Prototypes</b><br>
<P>
<b>Serial File</b><br>
<code>INTEGER*8 h5pt_openr</code><br>
<code>FUNCTION h5pt_openw(file)<br>
in CHARACTER file(*) : the filename to open for writing </code><br>
returns INTEGER*8 : and open filehandle for serial reads</code><br>
<br>
<code>INTEGER*8 h5pt_openw</code><br>
<code>FUNCTION h5pt_openw(file)<br>
in CHARACTER file(*) : the filename to open for writing<br>
returns INTEGER*8 : and open filehandle for serial writes</code><br>
<br>
<b>Parallel File</b><br>
<code>INTEGER*8 h5pt_openr_par</code><br>
<code>FUNCTION h5pt_openr_par(file,mpi_communicator)<br>
in CHARACTER file(*) : the filename to open for writing<br>
in INTEGER mpi_communicator : the MPI_Communicator used by the program<br>
returns INTEGER*8 : and open filehandle for parallel reads</code><br>
<br>
<code>INTEGER*8 h5pt_openw_par</code><br>
<code>FUNCTION h5pt_openw_par(file,mpi_communicator)<br>
in CHARACTER file(*) : the filename to open for writing<br>
in INTEGER mpi_communicator : the MPI_Communicator used by the program<br>
returns INTEGER*8 : and open filehandle for parallel reads</code><br>
</P>
<P>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
...
file = h5pt_openw("testfilef.h5")
...
</pre>
</P>
<hr>
<h2>Closing Datafiles</h2>
<P>
To close the file, you simply use h5pt_close() for both parallel and serial files. You must call h5pt_close() on any file descriptor created by h5pt_open*() regardless of whether the file turns out to be valid or not.</P>
<b>FORTRAN Prototype</b><br>
<code>EXTERNAL h5pt_close</code><br>
<code>SUBROUTINE h5pt_close(filehandle)<br>
in INTEGER*8 filehandle : close this open filehandle</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
...
call h5pt_close(file)
...
</pre>
</P>
<hr>
<h2> Validating Datafiles</h2>
<P>
You can test if the file was opened successfully using the
h5p_isvalid() function. It returns 1 if valid, 0 if invalid.
</P>
<b>FORTRAN Prototype</b><br>
<code>INTEGER h5pt_isvalid</code><br>
<code>FUNCTION h5pt_isvalid(filehandle)<br>
in INTEGER*8 filehandle: an open filehandle <br>
returns INTEGER : 1 if the file is valid, 0 if it is not</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER status
...
status = h5pt_isvalid(file)
...
</pre>
</P>
<hr>
<a name="SetStep">
<h2>Setting the Timestep</h2>
</a>
<P>
When writing data to a file the current time step must be set (even if there is only one). In a file with N time steps, the steps are numbered from 0 to N-1.
</P>
<b>FORTRAN Prototype</b><br>
<code>EXTERNAL h5pt_setstep</code><br>
<code>SUBROUTINE h5pt_setstep(filehandle,step)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in INTEGER step : Set the current timestep in the file to this
</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER I
INTEGER nstep
...
do I=1,nstep
call h5pt_setstep(file,I)
... more code ...
enddo
</pre>
</P>
<hr>
<a name="SetNumParticles">
</a>
<h2>Setting the Number of Particles</h2>
<P>
This function's sole purpose is to
prevent needless creation of new HDF5 DataSpace handles if
the number of particles is invariant throughout the sim.
That's its only reason for existence. After you call this
subroutine, all subsequent operations will assume this
number of particles will be written.
</P>
<b>FORTRAN Prototype</b><br>
<code>EXTERNAL h5pt_setnpoints</code><br>
<code>SUBROUTINE h5pt_setnpoints(filehandle,npoints)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in INTEGER*8 npoints : The number of particles on *this* processor</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER*8 npoints
...
call h5pt_setnpoints(file,npoints)
...
</pre>
<hr>
<a name="Writing">
<h2>Writing Datasets</h2>
</a>
<P>
After setting the number of particles with
<a href="#SetNumParticles">h5pt_setnpoints()</a>
and the current timestep using
<a href="#SetStep">h5pt_setstep()</a>, you can start
writing datasets into the file. Each dataset has a name
associated with it (chosen by the user) in order to facilitate
later retrieval. The writing routines also implicitly store
the datatype of the array so that the array can be
reconstructed properly on other systems with incompatible type
representations. The data is committed to disk before the
routine returns. All data that is written after setting the
timestep is associated with that timestep. While the number of
particles can change for each timestep, you cannot change the
number of particles in the middle of a given timestep.
</P>
<b>FORTRAN Prototypes</b><br>
<P>
The two data types supported for the moment are REAL*8 and INTEGER*8 (float64 and int64).
</P>
<code>EXTERNAL h5pt_writedata_r8</code><br>
<code>SUBROUTINE h5pt_writedata_r8(filehandle,name,data)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the data we are writing eg. "X" or "Y" or "PX" etc...<br>
in REAL*8 data(*) : The dataarray to write</code><br>
<br>
<code>EXTERNAL h5pt_writedata_i8</code><br>
<code>SUBROUTINE h5pt_writedata_i8(filehandle,name,data)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the data we are writing eg. "X" or "Y" or "PX" etc...<br>
in INTEGER*8 data(*) : The dataarray to write</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER nstep
INTEGER I
REAL*8,ALLOCATABLE:: X(:)
...
do I=1,nstep
call h5pt_setstep(file,I)
call h5pt_writedata_r8(file,"x",X)
enddo
...
</pre>
<hr>
<a name="ReadingNumTimeSteps">
<h2>Reading the Number of Time Steps</h2>
</a>
<P>
This reads the number of datasteps that are
currently stored in the datafile.
It works for both reading and writing of files, but is probably
only typically used when you are reading.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_getnsteps</code><br>
<code>FUNCTION h5pt_getnsteps(filehandle)<br>
in INTEGER*8 filehandle : an open filehandle<br>
returns INTEGER : number of timesteps stored in the file</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER nstep
file = h5pt_openr("testfilef.h5")
nstep = h5pt_getnsteps(file)
</pre>
<hr>
<a name="ReadingNumParticles">
<h2>Reading the Number of Particles</h2>
</a>
<P>
This reads the number of particles that are currently stored in the current time step. It will arbitrarily select a timestep if you haven't already set the timestep with H5PartSetStep().
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_getnpointss</code><br>
<code>FUNCTION h5pt_getnpoints(filehandle)<br>
in INTEGER*8 filehandle : an open filehandle<br>
returns INTEGER : number of particles in the current time step</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER*8 npoints
INTEGET step;
file = h5pt_openr("testfilef.h5")
call h5pt_setstep(file,0)
npoints = h5pt_getnpoints(file)
...
</pre>
<hr>
<a name="Reading">
<h2>Reading Datasets</h2>
</a>
<P>
After setting the time step and getting the number of particles to allocate the data arrays, you can start to read the data.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_readdata_r8</code><br>
<code>FUNCTION h5pt_readdata_r8(filehandle,name,data)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the data we are writing, eg. "X" or "Y" or "PX" etc...<br>
out REAL*8 data(*) : The data array to read. The number of points to read is either the number within
the view setby h5pt_setview() or the default (the total number of particles in the file).<br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER err
INTEGER*8,ALLOCATABLE:: ID(:)
...
call h5pt_setstep(file,step)
err=h5pt_readdata_i8(file,"id",ID)
...
</pre>
<hr>
<a name="DatasetsInfo"><h2>Reading the Number and Names of Datasets</h2></a>
<P>
H5Part provides funtions to find out how many datasets are stored at a particular timestep
and what their names are if you don't know what they are a-priori.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_getndatasets</code><br>
<code>FUNCTION h5pt_getndatasets(filehandle)<br>
in INTEGER*8 filehandle : an open filehandle<br>
returns INTEGER*8 : number of datasets stored per timestep</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER ndata
...
call h5pt_setstep(file,1)
ndata = h5pt_getndatasets(file)
...
</pre>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_getdatasetname</code><br>
<code>FUNCTION h5pt_getdatasetname(filehandle,index,name)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in INTEGER index : Index for a given dataset name<br>
out CHARACTER name(*) returns the name of the dataset at that index<br>
returns INTEGER, 1 on success 0 on failure.</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER err
CHARACTER,ALLOCATABLE:: name(:)
...
err=h5pt_getdatasetname(file, 1, name)
...
</pre>
<hr>
<a name="AttributesInfo">
<h2>Attributes Interface</h2></a>
<P>
In the current H5Part implemtation there are two types of attributes: file attributes which are bound to the file
and step attributes which are bound to the current timestep. You
must set the timestep explicitly before writing the attributes (just
as you must do when you write a new dataset. Currently there are no
attributes that are bound to a particular data array, but this could
easily be done if required.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_getnstepattribs</code><br>
<code>FUNCTION h5pt_getnstepattribs(filehandle)<br>
in INTEGER*8 filehandle : an open filehandle<br>
returns INTEGER : number of attributes bound to this particular step<br>
</code>
<br>
<code>INTEGER h5pt_getnfileattribs</code><br>
<code>FUNCTION h5pt_getnfileattribs(filehandle)<br>
in INTEGER*8 filehandle : an open filehandle<br>
returns INTEGER : number of attributes bound to the file<br>
</code>
<br>
<code>INTEGER h5pt_getstepattribinfo</code><br>
<code>FUNCTION h5pt_getstepattribinfo(filehandle,idx,attribname,nelem)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in INTEGER idx : index of the attribute being queried<br>
out CHARACTER name(*) : The name of the attribute<br>
out INTEGER nelem : Number of elements in the attrib array<br>
returns INTEGER, 1 on success 0 on failure.<br>
</code>
<br>
<code>INTEGER h5pt_getfileattribinfo</code><br>
<code>FUNCTION h5pt_getfileattribinfo(filehandle,idx,attribname,nelem)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in INTEGER idx : index of the attribute being queried<br>
out CHARACTER name(*) : The name of the attribute<br>
out INTEGER nelem : Number of elements in the attrib array<br>
returns INTEGER, 1 on success 0 on failure.
</code>
<br>
<hr>
<a name="WriteAttribs">
<h2>Writing Attributes</h2>
</a>
<P>
An attribute can be bound to the file or after setting the time step to this time step.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_writefileattrib_r8</code><br>
<code>
FUNCTION h5pt_writefileattrib_r8(filehandle,name,attrib,nelem)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in REAL*8 attrib(*) : The array of data to write into the attribute<br>
in INTEGER nelem : Number of elements in the attrib array<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_writefileattrib_i8</code><br>
<code>FUNCTION h5pt_writefileattrib_i8(filehandle,name,attrib,nelem)<br>
in INTEGER*8 filehandle : The filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in INTEGER*8 attrib(*) : The array of data to write into the attribute<br>
in INTEGER nelem : Number of elements in the attrib array<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_writefileattrib_string</code><br>
<code>FUNCTION h5pt_writefileattrib_string(filehandle,name,string)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in CHARACTER*8 attrib(*) : The array of data to write into the attribute<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_writestepattrib_r8</code><br>
<code>FUNCTION h5pt_writestepattrib_r8(filehandle,name,attrib,nelem)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in REAL*8 attrib(*) : The array of data to write into the attribute<br>
in INTEGER nelem : Number of elements in the attrib array
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_writestepattrib_i8</code><br>
<code>FUNCTION h5pt_writestepattrib_i8(filehandle,name,attrib,nelem)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in INTEGER*8 attrib(*) : The array of data to write into the attribute<br>
in INTEGER nelem : Number of elements in the attrib array<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_writestepattrib_string</code><br>
<code>FUNCTION h5pt_writestepattrib_string(filehandle,name,string)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in CHARACTER*8 attrib(*) : The array of data to write into the attribute<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
REAL*8 REALTIME
INTEGER err
...
err=h5pt_writefileattrib_string(file,"Annotation","Testing 1 2 3")
err=h5pt_writestepattrib_r8(file,"RealTime",REALTIME,1)
...
</pre>
<hr>
<a name="ReadAttribs">
<h2>Reading Attributes</h2>
</a>
<P>
As with the writing of attributes, there are two basic reading interfaces one that reads file bound attributes and one that reads
step bound attributes. If the step is not set the current one will be used.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_readstepattrib</code><br>
<code>FUNCTION h5pt_readstepattrib(filehandle,name,data)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER attributename(*) : name of the attribute to read<br>
out <anytype> data(*) : the attribute data will be read into this array<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_readfileattrib</code><br>
<code>FUNCTION h5pt_readfileattrib(filehandle,name,data)<br>
in INTEGER*8 filehandle an open filehandle<br>
in CHARACTER attributename(*) : name of the attribute to read<br>
out <anytype> data(*) : the attribute data will be read into this array<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
REAL*8 REALTIME
...
call h5pt_setstep(file,0)
err=h5pt_readstepattrib(file,"RealTime",data)
...
</pre>
</div>
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<html>
<head>
<title>H5Part: a Portable High Performance Parallel Data Interface to HDF5</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<font face="arial,helvetica"><h1>H5Part: a Portable High Performance Parallel Data Interface to HDF5</h1></font>
<!--<h2><font color="red"> THESE PAGES ARE UNDER CONSTRUCTION, September 2006</h2></font>-->
<font face="arial,helvetica" color="#555588"><h2>Motivation</h2></font>
<P>
<TABLE>
<TR>
<TD>
<a href="collision_6.png"><img src="collision_6.s.png" width=300 height=300></a>
</TD
></TR>
<TR>
<TD>
Beam-beam collision simulation.
</TD>
</TR>
</TABLE>
</P>
<P>
Particle based simulations of accelerator beam-lines, especially in
six dimensional phase space, generate vast amounts of data. Even
though a subset of statistical information regarding phase space
or analysis needs to be preserved, reading and writing such
enormous restart files on massively parallel supercomputing
systems remains challenging.<p>
</P>
<P>
H5Part is a very simple data storage schema and provides an
API that simplifies the reading/writing of the data to the HDF5
file format. An important foundation for a stable visualization and data
analysis environment is a stable and portable file storage format and
its associated APIs. The presence of a "common file storage format,"
including associated APIs, will help foster a fundamental level of
interoperability across the project's software infrastructure. It will
also help ensure that key data analysis capabilities are present
during the earliest phases of the software development effort.
</P>
<P>
H5Part is built on top of the <a href="http://hdf.ncsa.uiuc.edu/HDF5">HDF5 (Hierarchical Data Format).</a>
HDF5 offers a self-describing machine-independent
binary file format that supports scalable parallel I/O
performance for MPI codes on a variety of supercomputing
systems, and works equally well on laptop computers. The API is
available for C, C++, and Fortran codes. The H5Part file format and APIs
enable disparate research groups with different simulation
implementations to transparently share datasets and data
analysis tools. For instance, the common file format will enable
groups that depend on completely different simulation
implementations to share data analysis tools.
</P>
<font face="arial,helvetica" color="#555588"><h2>H5Part file organization and API</h2></font>
<P>
The proposed file storage format uses HDF5 for the lowlevel
file storage and a simple API to provide a high-level
interface to that file format. A programmer can either use
the H5Part API to access the data files or write directly to
the file format using some simple conventions for organizing
and naming the objects stored in the file.
</P>
<P>
In order to store Particle Data in the HDF5 file format,
we have formalized the hierarchical arrangement of the
datasets and naming conventions for the groups and associated
datasets. The sample H5Part API formally encodes
these conventions in order to provide a simple and uniform
way to access these files from C, C++, and Fortran codes.
The API makes it easier to write very portable data adaptors
for visualization tools in order to expand the number of
tools available to access the data. Even so, anyone can use
the HDF5 h5ls utility to examine the organization of the
H5Part files and even write their own HDF5-based interface
for reading and writing the file format. The standards
offered by the sample API are completely independent of
the standard for organizing data within the file.The file
format supports the storage of multiple timesteps
of datasets that contain multiple fields.
</P>
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<font face="arial,helvetica" color="#555588"><h2>Requirements Specification</h2></font>
<UL>
<LI><a href="H5PartSpecs.html">H5Part API specifications
</UL>
</a>
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<font face="arial,helvetica" color="#555588"><h2>Downloading and Installing H5Part</h2></font>
<UL>
<LI><a href="Downloading.html">Downloading HDF5 and H5Part
<LI><a href="BuildingHDF5.html">Building the HDF5 Library</a>
<LI><a href="Building.html">Building the H5Part Library</a>
</UL>
<font face="arial,helvetica" color="#555588"><h2>Bindings</h2></font>
<UL>
<LI><a href="UsingC.html">Using the C/C++ interface</a>
<LI><a href="UsingF.html">Using the F77/F90 interface</a>
<LI><a href="InternalLayout.html">Logical Internal HDF5 File</a>
<LI><a href="H5PartTools.html">H5Part Utility Tools</a>
<LI><a href="ReferencePages/index.html">Reference Manual</a> (Note: Requires doxygen
to be run in the directory /doc)
</UL>
<font face="arial,helvetica" color="#555588"><h2>H5Part Visualization Tools</h2></font>
<UL>
<!--<LI><a href="H5PartExpress.html">H5Part Express Reader</a>-->
<LI><a href="H5PartVisIt.html">H5Part VisIt Reader</a>
<!--<LI><a href="H5PartIDL.html">H5Part IDL Reader</a>-->
<LI><a href="http://www.cscs.ch/a-display.php?id=170">H5Part sparticles Reader: developed at CSCS, Switzerland</a>
<LI><a href="http://vis.lbl.gov/Vignettes/PartView/index.html">PartView Visualization Application</a>
</UL>
</div>
doc/html2twiki
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#!/bin/bash
shopt -s nullglob
function html2twiki() {
declare -rx infile=$1
declare -rx outdir=$2
declare -rx fname=$( sed -n 's/.* member="\([a-zA-Z0-9_.]*\)::\([_a-zA-Z0-9]*\)" .*/\2/p' "${infile}" )
declare -rx outfile="${outdir}/${fname}.txt"
grep -q " member=" "${infile}" || return 0
sed '/Generated by/,/anchor/d' "${infile}" > "${outfile}"
}
mkdir -p TWiki/h5_core
mkdir -p TWiki/H5
mkdir -p TWiki/H5Part
mkdir -p TWiki/H5Block
mkdir -p TWiki/H5Fed
for f in ReferencePages/group__h5__core_*.html; do
html2twiki $f TWiki/h5_core
done
for f in ReferencePages/group__h5__c__api_*.html; do
html2twiki $f TWiki/H5
done
for f in ReferencePages/group__h5part__c__api_*.html; do
html2twiki $f TWiki/H5Part
done
for f in ReferencePages/group__h5block__c__api_*.html; do
html2twiki $f TWiki/H5Block
done
for f in ReferencePages/group__h5fed__c__api_*.html; do
html2twiki $f TWiki/H5Fed
done
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doc/tetrahedron_refinements/1-edge/edge_01_refined/01.txt
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TET no. 0:
0.5, 0.5, 0.0
0.0, 0.0, 1.0
0.0, 0.0, 0.0
0.0, 1.0, 0.0
TET no. 1:
0.5, 0.5, 0.0
0.0, 0.0, 0.0
0.0, 0.0, 1.0
1.0, 0.0, 0.0
doc/tetrahedron_refinements/1-edge/edge_01_refined/01.vtk
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# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 5 DOUBLE
0.5 0.5 0.0
0.0 0.0 1.0
0.0 0.0 0.0
0.0 1.0 0.0
1.0 0.0 0.0
CELLS 2 10
4 0 1 2 3
4 0 2 1 4
CELL_TYPES 2
10
10
CELL_DATA 2
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
doc/tetrahedron_refinements/1-edge/edge_01_refined/01_smal.png
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doc/tetrahedron_refinements/1-edge/edge_12_refined/12.txt
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TET no. 0:
0.0, 0.5, 0.5
0.0, 0.0, 0.0
1.0, 0.0, 0.0
0.0, 1.0, 0.0
TET no. 1:
0.0, 0.5, 0.5
1.0, 0.0, 0.0
0.0, 0.0, 0.0
0.0, 0.0, 1.0
doc/tetrahedron_refinements/1-edge/edge_12_refined/12.vtk
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# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 5 DOUBLE
0.0 0.5 0.5
0.0 0.0 0.0
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
CELLS 2 10
4 0 1 2 3
4 0 2 1 4
CELL_TYPES 2
10
10
CELL_DATA 2
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
doc/tetrahedron_refinements/1-edge/edge_12_refined/12_small.png
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TET no. 0:
0.5, 0.0, 0.5
0.0, 0.0, 0.0
0.0, 1.0, 0.0
0.0, 0.0, 1.0
TET no. 1:
0.5, 0.0, 0.5
0.0, 1.0, 0.0
0.0, 0.0, 0.0
1.0, 0.0, 0.0
doc/tetrahedron_refinements/1-edge/edge_20_refined/20.vtk
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# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 5 DOUBLE
0.5 0.0 0.5
0.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
1.0 0.0 0.0
CELLS 2 10
4 0 1 2 3
4 0 2 1 4
CELL_TYPES 2
10
10
CELL_DATA 2
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
doc/tetrahedron_refinements/1-edge/edge_20_refined/20_small.png
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TET no. 0:
0.0, 0.0, 0.5
1.0, 0.0, 0.0
0.0, 1.0, 0.0
0.0, 0.0, 0.0
TET no. 1:
0.0, 0.0, 0.5
0.0, 1.0, 0.0
1.0, 0.0, 0.0
0.0, 0.0, 1.0
doc/tetrahedron_refinements/1-edge/edge_23_refined/23.vtk
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# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 5 DOUBLE
0.0 0.0 0.5
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 0.0
0.0 0.0 1.0
CELLS 2 10
4 0 1 2 3
4 0 2 1 4
CELL_TYPES 2
10
10
CELL_DATA 2
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
doc/tetrahedron_refinements/1-edge/edge_23_refined/23_small.png
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TET no. 0:
0.5, 0.0, 0.0
0.0, 1.0, 0.0
0.0, 0.0, 1.0
0.0, 0.0, 0.0
TET no. 1:
0.5, 0.0, 0.0
0.0, 0.0, 1.0
0.0, 1.0, 0.0
1.0, 0.0, 0.0
doc/tetrahedron_refinements/1-edge/edge_30_refined/30.vtk
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# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 5 DOUBLE
0.5 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
0.0 0.0 0.0
1.0 0.0 0.0
CELLS 2 10
4 0 1 2 3
4 0 2 1 4
CELL_TYPES 2
10
10
CELL_DATA 2
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
doc/tetrahedron_refinements/1-edge/edge_30_refined/30_small.png
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TET no. 0:
0.0, 0.5, 0.0
0.0, 0.0, 1.0
1.0, 0.0, 0.0
0.0, 0.0, 0.0
TET no. 1:
0.0, 0.5, 0.0
1.0, 0.0, 0.0
0.0, 0.0, 1.0
0.0, 1.0, 0.0
doc/tetrahedron_refinements/1-edge/edge_31_refined/31.vtk
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# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 5 DOUBLE
0.0 0.5 0.0
0.0 0.0 1.0
1.0 0.0 0.0
0.0 0.0 0.0
0.0 1.0 0.0
CELLS 2 10
4 0 1 2 3
4 0 2 1 4
CELL_TYPES 2
10
10
CELL_DATA 2
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
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TET no. 0:
0.5, 0.5, 0.0
0.0, 1.0, 0.0
0.0, 0.5, 0.5
0.0, 0.0, 0.0
TET no. 1:
0.0, 0.5, 0.5
1.0, 0.0, 0.0
0.5, 0.5, 0.0
0.0, 0.0, 0.0
TET no. 2:
1.0, 0.0, 0.0
0.0, 0.5, 0.5
0.0, 0.0, 1.0
0.0, 0.0, 0.0
doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12.vtk
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# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 6 DOUBLE
0.5 0.5 0.0
0.0 1.0 0.0
0.0 0.5 0.5
0.0 0.0 0.0
1.0 0.0 0.0
0.0 0.0 1.0
CELLS 3 15
4 0 1 2 3
4 2 4 0 3
4 4 2 5 3
CELL_TYPES 3
10
10
10
CELL_DATA 3
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
2
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