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base: H5hut/src:H5Part-1.3.1
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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
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compare: H5hut/src:H5hut-2.0.0rc7
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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

341 Commits
H5Part-1.3.1 .. H5hut-2.0.0rc7

Author SHA1 Message Date
gsell c41bd6ec54 Merge branch '21-hdf5-1-12-and-newer-support' into 'master' 
Resolve "hdf5 1.12 and newer support"

Closes #21

See merge request H5hut/src!6
 2024-10-02 14:58:27 +02:00
gsell a69a88c49c version bumped to 2.0.0rc7 2024-10-02 14:57:51 +02:00
gsell 4088d02f55 hdf5 >=1.12.0 support added 2024-10-02 14:48:53 +02:00
gsell 5f57c23499 Merge branch '20-unknown-macro-ac_msg_erro' into 'master' 
Resolve "unknown macro AC_MSG_ERROR"

Closes #20

See merge request H5hut/src!5
 2020-08-18 09:52:31 +02:00
gsell b71fa8c9dc LT_INIT added to configure.ac, should fix unknown AC_MSG_ERROR 2020-08-18 09:51:44 +02:00
gsell 7e7a85f14f Merge branch '19-release-2-0-0rc6' into 'master' 
Resolve "release 2.0.0rc6"

Closes #19

See merge request H5hut/src!4
 2019-06-20 20:49:00 +02:00
gsell fc1322432c version set to 2.0.0rc6 2019-06-20 20:48:48 +02:00
gsell f5778e0197 Merge branch '18-memory-leaks-in-h5part' into 'master' 
Resolve "memory leaks in H5Part"

Closes #18

See merge request H5hut/src!3
 2019-06-20 20:42:33 +02:00
gsell fb084fdff4 memory leaks in H5Port core functions fixed 2019-06-20 20:42:42 +02:00
gsell be7cd1d471 Merge branch '17-in-configure-ac-exit-after-ac_msg_error-is-not-required' into 'master' 
Resolve "in configure.ac: exit after AC_MSG_ERROR is not required"

Closes #17

See merge request H5hut/src!2
 2019-06-20 19:01:02 +02:00
gsell f7b7a45a28 configure.ac: exit calls after ASC_MSG_ERROR removed 2019-06-20 19:01:17 +02:00
gsell e41db835eb Merge branch '15-move-dissolving-ghost-zones-into-dedicated-function' into 'master' 
Resolve "move dissolving ghost-zones into dedicated function"

Closes #15

See merge request H5hut/src!1
 2019-06-20 18:57:49 +02:00
gsell 8140378213 H5Block3dSetView() does not dissolve ghost-zones any more 
- new API function H5Block3dSetViewDissolveGhostZones() added
 2019-06-20 18:52:02 +02:00
gsell 6a4d711b99 test: use independent IO in h5u_test_{read,write}3() for hdf5 > 1.8.12 
Since MPI-POSIX VFD has been removed from hdf5 > 1.8.12, but a test
with stride data should be performed, we use independent IO instead for
hdf5 > 1.8.12
 2018-11-19 17:08:48 +01:00
gsell 2ae76250e6 src/h5core/h5u_model.c: bug fixed in h5_set_view() 
In h5_set_view() u->shape was created two times.
 2018-11-19 17:01:08 +01:00
gsell f1cb1c981e Merge branch 'master' of gitlab.psi.ch:H5hut/src 2018-11-19 14:51:52 +01:00
gsell 627d6673e1 src/include/h5core/h5_log.h: bugfix: declaration of 'h5_initialized()' declared insite 'extern C' 2018-11-19 14:51:28 +01:00
gsell ed85fb32b7 changes merged from upstrean 2018-11-19 14:47:57 +01:00
gsell df2be38428 examples/H5Part/write_setview.c 
- include of "mpi.h" removed. There is no need for it and this breaks the serial case
 2018-11-08 16:42:03 +01:00
gsell d423367d4f most warnings fixed if compiling with NDEBUG defined 2018-11-08 15:34:32 +01:00
gsell 1985a0a2e0 src/h5core/h5u_model.c: 
- h5u_get_totalnum_particles_by_idx():
  - comment added
  - definition of 'total' and 'dmax' moved
 2018-11-05 16:47:48 +01:00
gsell 24533c4c2e examples/H5/openclose.c: 
- set DEBUGMASK to all
 2018-11-05 16:43:47 +01:00
Achim Gsell 72365540a3 src/include/h5core/h5_log.h: missing backslashes in definition of macro 'H5_API_ENTER()' if NDEBUG is set fixed 2018-11-02 23:56:27 +01:00
Gsell Achim 4daf9b786c * C-API 
- H5PartSetNumPoints() renamed to H5PartSetNumItems()
- H5PartGetNumPoints() renamed to H5PartGetNumItems()
- Dataset names longer then 64 bytes are handled as error.
- Same for step/iteration names.
* core API
- we use the term 'iteration' instead of 'step'
- we use the term 'item' instead of 'point'
- re-factor function and variable names
- in printing messages/debug output fixed
- do not flush (sync to disk) after writing a dataset by default,
  can be controlled by a property
 2018-09-14 16:46:40 +02:00
gsell 072a2781fc configure.ac 
- set version to 2.0.0rc5
 2018-09-04 10:34:04 +02:00
gsell 9c9bfda054 src/Python/Makefileam 
- print message if Python is disabled
 2018-09-04 10:33:44 +02:00
gsell 604dade2a1 src/h5core/h5b_model.c 
- warning in 'h5b_3d_set_grid()' if compiled serial fixed
 2018-09-04 10:33:09 +02:00
gsell 2da69d1095 error in logging/debug output fixed, see issue #13 2018-09-04 10:32:04 +02:00
gsell 15317a9bb0 do not include 'h5_init.h' where not required 2018-09-04 10:30:13 +02:00
gsell c5f3b7fa02 src/h5core/{h5_file.c,h5_init.c,private/h5_init.h} 
- refactor 'h5_initialize()' and 'h5_finalize()'
 2018-09-04 10:28:08 +02:00
gsell a81c79e5c4 src/h5core/Makefile.am: 
- adapt to moved h5_init
 2018-09-04 10:21:38 +02:00
gsell 664cee709b src/h5core/h5_init.c: 
- moved from 'private'
 2018-09-04 10:17:47 +02:00
gsell ecc4618bd4 close data types in with H5Finalize() 2018-02-02 11:10:18 +01:00
gsell 8bdebd0c55 src/h5core/private/h5t_types.h 
- in definition of 'struct h5_dta_types': define type for parallel H5Grid only if enabled
 2018-02-01 17:51:09 +01:00
gsell 5baed631b7 examples/H5/openclose.c 
- call to H5Finalize() added
 2018-02-01 17:48:28 +01:00
gsell 65109b73a9 example/H5/openclose.c 
- call to H5SetDebugMask() added
 2018-02-01 15:26:14 +01:00
gsell 792e86e01e src/h5core/h5_log.c 
- warning in initialization of 'h5_rfmts' fixed
 2018-02-01 15:25:27 +01:00
gsell 11ab169164 src/h5core/private/h5t_ref_elements.c 
- bug in initialization of h5t_tet_ref_elem fixed
 2018-02-01 15:24:44 +01:00
gsell 7c899f99ce src/include/H5_log.h 
- H5_DEBUG_NONE added to documentation of H5SetDebugMask()
 2018-02-01 15:23:32 +01:00
gsell 12ef028ed2 src/include/h5core/h5_log.h 
- macro H5_DEBUG_NONE added
 2018-02-01 15:21:30 +01:00
gsell 094117a631 src/h5core/h5_file.c: 
- memory leak fixed
 2018-02-01 15:10:18 +01:00
gsell acc8b75ad9 - several "duplicate const" warnings fixed 
- some useless tests whether an unsigned int is less than zero removed
 2018-02-01 14:25:29 +01:00
gsell 078a51d60d examples/H5/openclose.c: explizit set verbosity of output 2018-01-05 12:16:15 +01:00
gsell 06a941eb2c configure.ac 
- test whether we are using the right hdf5 flavor added:
  parallel if we request parallel otherwise non-parallel
 2017-07-27 18:36:30 +02:00
gsell 269c5efbde src/include/h5core/h5file.h 
- no need to include 'mpi.h' and 'hdf5.h' here
 2017-07-27 18:34:00 +02:00
gsell e7a60fbe9f src/include/h5core/h5b_module.h 
- the function to define a grid are now available as dummy function in the serial version
 2017-07-27 18:33:14 +02:00
gsell 2ed8ad093c use the H5_HAVE_PARALLEL macro from hdf5 instead of the macro PARALLEL_IO 2017-07-27 18:31:34 +02:00
gsell 3a9e0e4153 src/include/h5core/h5_types.h 
- define dummy MPI data-types only if MPI_VERSION is not set.
  According to the MPI specification, this macro must be set after
  including the header MPI header file 'mpi.h'
 2017-07-27 18:29:21 +02:00
gsell aa1f4eacc8 examples/H5Part/read_stridedf.f90 
- bugfix in parallel version
 2017-07-26 17:00:03 +02:00
gsell c33ef6d390 serial H5hut can now be used with MPI, resolving #12 
src/h5core/private/h5_init.h:
- remove definition of MPI dummies for serial version
src/h5core/private/h5_types.h:
- define the MPI communicator in 'struct h5_prop_file' only in parallel version
src/h5core/h5_file.c
- adapt to above changes
 2017-07-26 16:59:16 +02:00
gsell 9a32a0b7f1 examples/H5/Makefile.am 
- do not use GNU extension for pattern rules
 2017-06-30 18:25:39 +02:00
gsell 22d6893770 autotool configuration: 
- changes to support VTK 8.0
- better check for Fortran compiler
 2017-06-30 18:24:56 +02:00
gsell 6e0f0eeedd we have to call cmake in configure to determine VTK headers and libs. 
This call creates the directory 'CMakeFiles' which we want to ignore.
 2017-06-30 18:23:05 +02:00
gsell 542daf7fc2 C examples: 
- define dummy MPI macros to be used in serial compilation, closing #10
- cleanup some "unused variable" warnings
- fix some format warnings, using C99 format macros
 2017-06-23 15:37:46 +02:00
gsell f79c808e8d src/h5core/h5_err.c 
- include stdlib.h added, closing #9
 2017-06-23 15:31:56 +02:00
gsell b6e482f56a src/h5core/h5t_store.c 
- comments edited
 2017-06-23 15:27:53 +02:00
gsell 6d3014bad5 Fortran examples: 
- adapted for serial compilation, closing #8
 2017-06-23 15:27:19 +02:00
gsell 20424235e8 configure.ac 
- set Fortran compiler with AC_PROG_FC, closing #7
 2017-06-23 15:22:33 +02:00
gsell 7d73439b10 Makefile.am 
- 'ax_pkg_swig.m4' added to 'EXTRADIST'
 2017-03-18 09:49:37 +01:00
gsell e447d536a3 configure.ac: 
- set version to 2.0.0rc3
 2017-03-18 09:27:11 +01:00
gsell 74df1bc676 src/h5core/h5_attribs.c: bugfixes 2016-09-23 17:03:20 +02:00
gsell 9e4c8bd5a4 src/h5core/h5u_io.h 
- conditional flushing step data removed, for the time being we flush anyway
 2016-09-23 16:45:20 +02:00
gsell bb1cd9c860 src/h5core/h5_file.c 
- prototype of a 'h5_set_prop_file_flush_step()' function added
 2016-09-23 16:44:30 +02:00
gsell ad52833022 configure.ac 
- set version to 2.0.0rc2
 2016-09-23 13:05:59 +02:00
gsell 3425a30068 src/include/h5core/Makefile.am 
- we have to use 'otherinclude_HEADER' instead of 'include_HEADERS'
 2016-09-23 13:05:37 +02:00
gsell 9f3a677ea6 src/h5core/Makefile.am 
- private/h5_const.h added to EXTRA_HEADERS
 2016-09-23 13:04:16 +02:00
gsell 23807ff972 examples/H5/write_file_attribs.py 
- added
 2016-07-28 17:34:56 +02:00
gsell 93d4f60116 src/Python 
- wrappers for reading/writing attributes
 2016-07-28 17:34:22 +02:00
gsell 20cd5aae98 src/h5core/h5t_io.c 
- adapted to changed 'h5priv_write_attrib()'
 2016-07-28 17:32:13 +02:00
gsell cae3b00855 implement proper handling of append-only file mode for attributes 2016-07-28 17:31:06 +02:00
gsell 2a462733ca src/h5core/private/h5_file.h 
- is_writable() is now static inline not a macro
- macro CHECK_READABLE_MODE() added
 2016-07-28 17:29:13 +02:00
gsell 6fb8b77baa src/h5core/h5_attachements.c 
- h5_add_attachment(): check file mode, return error if read-only
- adapted to new function 'h5priv_create_group()'
 2016-07-28 17:27:05 +02:00
gsell c26d6a84e3 adapted to new/changed function: 
h5priv_open_group(): open existing group
h5priv_create_group(): create or open existing group
h5priv_open_group_with_intermediates(): open existing group
h5priv_create_group_with_intermediates(): create or open existing group
 2016-07-28 17:24:34 +02:00
gsell 54ccc3b576 src/inlcude/H5_step_attribs() 
- H5GetStepAttribName() added
- use const types where applicable
 2016-07-28 17:17:18 +02:00
gsell 8ffe944519 test/Makefile.am 
- link static if debug is enabled
 2016-07-28 17:15:39 +02:00
gsell 2bb3d688ae test/h5{b,u}_{read,write}.c 
- fixes for serial version
- h5u_test_write4(): bugfix: we have to write new attributes since we are in append-only mode
 2016-07-28 16:05:36 +02:00
gsell 647af5847e src/include/H5_file_attrib.h 
- H5ReadFileAttribString(): bugdix in format of H5_API_ENTER(), print pointer value not string
 2016-07-28 16:01:11 +02:00
gsell aa4f40ee3d src/h5core/private/h5_model.h 
- h5priv_normalize_type(): bugfix: wrong type in H5_PRIV_API_ENTER() set
 2016-07-28 15:59:35 +02:00
gsell f1daa56cb8 src/h5core/private/h5_model.c 
- h5u_set_num_points(): set step to '0' if not already set
- h5u_set_chunk(): CHECK_TIMEGROUP(f) removed. The step must not be set before setting a chunk size
 2016-07-28 15:57:34 +02:00
gsell 2ea8245bba src/h5core/h5b_io.c 
- write_data():
  - bugfix: convert passed type is from H5hut to HDF5 type
  - parameter 'field_name' removed
- read_data():
  - bugfix: convert passed type is from H5hut to HDF5 type
  - compare type passed as parameter and type of dataset
- remove prefixing underscore from static functions
- adaptions to coding style
 2016-07-28 15:54:52 +02:00
gsell 04fe7fdd9e configure.ac: 
- do not ignore CC an CXX
 2016-07-28 12:18:25 +02:00
gsell 075b2f39da src/Python/H5hut.i 
- towards a more usable wrapper
 2016-07-15 17:46:02 +02:00
gsell 7b05c32ad9 src/h5core/private/h5_attrib.h 
- get_attrib_info(): wrong length was return for string attributes
 2016-07-15 17:43:59 +02:00
gsell 825ee8ac5f examples/H5/Makefile.am 
- build static executables if debug is enabled
 2016-07-15 17:40:37 +02:00
gsell 9d70c07476 src/Python/H5hut.i 
- some issues with inquiring file-attributes and datasets fixed
 2016-07-08 17:13:18 +02:00
gsell 03986b00ac src/include/g5core/h5_{file.types}.h 
- enum used for file modes instead of macros
 2016-07-08 17:11:28 +02:00
gsell ad83c3841b C-API: 
- declare more args as const
- H5GetFileAttribName() added
 2016-07-08 17:09:16 +02:00
gsell 73fabd043b src/h5core/h5b_modules.c 
- check file-handle and opened step
- h5b_3d_has_view(): debug output added
 2016-07-08 17:07:18 +02:00
gsell 0aa44727c6 src/h5core/h5_file.c 
- check file-handle and opened step
- h5_open_file2(): bugfix: move setting of step name format to the end of the function
- h5_flush_step(): bugfix: flush step data only, if a step is open
 2016-07-08 17:06:07 +02:00
gsell babd19ddd4 core API: 
- add checks for file-handle and opened step
 2016-07-08 17:03:18 +02:00
gsell c80f6f5679 use new macro H5_RETURN_ERROR where possible 2016-07-01 17:59:12 +02:00
gsell 7b1079ae5f example/H5Fed/Makefile.am 
- compile static if ENABLE_DEBUG is set. This makes life simpler if we build shared libs
 2016-07-01 16:29:10 +02:00
gsell ecd2723419 examples/H5Fed/tetmesh_{adjacencies,read_tags}.c 
- cleanup
 2016-07-01 16:18:17 +02:00
gsell c9044d8e1b src/h5core/private/h5_init.{c,h} 
- initialize MPI if not yet done
 2016-07-01 16:10:37 +02:00
gsell 5b57bedade examples/H5Fed/dump_field_attributes.c: 
- bugfix in printing string attributes
 2016-07-01 16:07:02 +02:00
gsell 222789a1cf examples/H5Block: 
- inline function changed to static inline (otherwise gcc >= 5.3 complains)
 2016-07-01 15:36:30 +02:00
gsell 21dd57c9c6 Fortran-API: 
- use enumeration for data-types
 2016-07-01 15:34:31 +02:00
gsell fc29f7b6f0 src/h5core/private/h5_hdf5.h 
- cleanup and minor changes
- more wrapper functions added
 2016-07-01 15:33:53 +02:00
gsell e56872ce92 src/include/H5_err.h: 
- remove debug output from H5AbortOnError()
 2016-07-01 15:32:54 +02:00
gsell 85ecf4c387 core API/C-API: use enumeration for data-types 2016-07-01 15:31:55 +02:00
gsell 6979a358ae .gitignore: 
- exclude all files matching *.h5
 2016-06-24 16:40:43 +02:00
gsell 9fc3b233bc examples/H5Part: 
- include of stdlib.h added
 2016-06-24 16:37:59 +02:00
gsell f5eb26d2ec examples/H5Part/query.c: 
- added examples to query dataset in steps
 2016-06-24 16:36:54 +02:00
gsell 6af129b338 examples/H5Block/read_write_scalar_field.c: 
- include stdlib.h added
 2016-06-24 16:35:43 +02:00
gsell 215d1a7d79 examples/H5/read_step_attribs: 
- include required stdlib.h
 2016-06-24 15:55:20 +02:00
gsell 8bb22e4400 exampkes/H5/read_file_attribs.c 
- use macros to define verbosity and debug mask
 2016-06-24 15:54:40 +02:00
gsell caad81996a examples/H5/attache_file.c: 
- use macros for verbosity level and debug mask
- open file rw in second part
 2016-06-24 15:53:36 +02:00
gsell f97e3c8f2d core API: 
- debugging macros simplified
- cleanup
- h5_delete_attachment(): check of file mode added
 2016-06-24 15:51:39 +02:00
gsell fba78db1c0 test/h5u_read.c: 
- h5u_test_read3(): bugfix
 2016-06-24 15:45:26 +02:00
gsell 291328b997 src/h5core/private/h5_init.h 
- cosmetic change
 2016-06-22 16:15:03 +02:00
gsell 2c1bca01aa src/include/H5Block_model.h 
- break down some longer lines
 2016-06-22 16:14:18 +02:00
gsell a633b362a6 src/include/H5Part_model.h: 
- break down some long lines
- H5PartGetDatasetName(): pass pointer to dataset name as const pointer
 2016-06-22 16:13:16 +02:00
gsell a12908ed90 src/include/h5core/h5_err.h: 
- declaration of h5_error() moved to this file
 2016-06-22 16:10:20 +02:00
gsell b83d9cc8a7 src/include/h5core/h5_log.h 
- hh5_{warn,info,debug} are not static inline any more
 2016-06-22 16:08:46 +02:00
gsell 6ad9ae50e0 src/include/h5core/h5_types.h 
- H5T_COMPOUND removed from enum h5_types_t
src/h5core/private/h5_init.c
- use H5T_COMPOUND in creation of compound types
 2016-06-22 16:05:21 +02:00
gsell 9ac7e09423 src/include/h5core/h5_file_attribs.h 
src/include/h5core/h5_step_attribs.h
src/include/h5core/h5b_attribs.h:
- use new H5hut enum type for attribute data-types
 2016-06-22 16:01:46 +02:00
gsell 66452a274b src/include/h5core/h5b_io.h 
src/include/h5core/h5u_io.h:
- pass data-type as H5hut enum
 2016-06-22 15:40:32 +02:00
gsell d947f51c2d src/h5core/...: 
- introduce/implement new H5hut types
 2016-06-22 15:38:24 +02:00
gsell f5729f6f07 src/h5core/h5_model.c 
src/h5core/h5b_attribs.c:
- cleanup/review header file we have to include
 2016-06-22 15:24:05 +02:00
gsell a64f2ce03a src/h5core/h5_err.c 
src/h5core/h5_log.c:
- define args as const where possible
- h5_verror() is now in h5_err.c
- h5priv_vprintf() is now in h5_log.c
 2016-06-22 15:19:23 +02:00
gsell b880bd397f C-API: 
- use new H5hut type enumeration, not HDF5 types
 2016-06-22 14:52:02 +02:00
gsell cd2c9031b9 src/h5core/h5_attribs.c: 
- define args as const where possible
 2016-06-22 14:48:19 +02:00
gsell fb5e55990f src/h5core/h5file 
src/h5core/h5b_io.h:
- define args as const where possible
 2016-06-22 14:38:09 +02:00
gsell 25dff9257c src/h5core/Makefile.am 
- h5_init.h is now in 'private'
 2016-06-22 14:34:44 +02:00
gsell ac37d5fc2f Fortran API: 
- use new enumeration of types for I/O. HDF5 types are not used any more in the high level API
 2016-06-22 14:33:48 +02:00
gsell 983496104b src/h5core/h5_log.c 
src/h5core/h5_init.h
src/h5core/h5_log.h:
- cleanup, minor changes
 2016-06-22 14:24:54 +02:00
gsell aaeca8b6b7 examples/H5/read_file_attribs.c: 
- call MPI_Init() before any H5hut functions
 2016-06-22 13:47:53 +02:00
gsell 0182d60835 src/h5core/h5_init.c: 
- moved to src/h5core/private
 2016-06-22 13:46:40 +02:00
gsell f75ef09cf9 consolidation of log/debug message interface 2016-06-17 13:50:07 +02:00
gsell c831a90a2e src/h5core/h5_errorhandling.c: 
- renamed to h5_err.c
 2016-06-17 13:49:35 +02:00
gsell bdcc8f2089 this commits includes several changes which should have been done in 
multiple steps:
- the functions for inquiring datasets and attributes do not return
  an HDF5 type any more but an enum of type h5_types_t. This change
  was required for the Python module.
- bugfix in reading attributes: See https://git.psi.ch/H5hut/src/issues/4
- several consts and macros have been moved from the public C-API to
  the core API
- more consitent file naming
- several 'private' function have been moved to their 'private' header
  files as 'static inline'.
- minor formatting changes
 2016-06-17 10:44:25 +02:00
gsell bbbaa6a21b src/h5core/h5t_octree.c: 
- definition of 'h5_oct_dta_types' moved from header file to this file
 2016-06-03 17:25:48 +02:00
gsell 4c5b16169d src/Fortran/Makefile.am: 
- bugfix: H5Block_attribs.f90 were listed twice
 2016-06-03 17:24:36 +02:00
gsell cc46b433e1 .gitignore: some files added 2016-06-03 17:23:43 +02:00
gsell a8e209a7d3 src/Python: 
- file and step attributes added
- all attribute i/o function have exactly 3 arguments now
- string attributes are handled the same way as attributes of other type
 2016-06-03 17:23:15 +02:00
gsell 80cf35e807 src/Python: ignore file added 2016-06-03 17:18:00 +02:00
gsell d53c5b3171 tools/vtk2h5grid/Makefile.am: use AM_LDFLAGS not LDFLAGS 2016-05-20 18:12:00 +02:00
gsell 8edb48aff8 src/Python/Makefile.am: use same name for serial and parallel version 2016-05-20 18:10:30 +02:00
gsell 24af2ae2a3 src/Makefile.am: Python sub-dir added 2016-05-20 18:09:28 +02:00
gsell 7fbd5c5de1 configure.ac: set version to 2.0.0rc1; correct indentation 2016-05-20 18:08:44 +02:00
gsell 18611991a5 Python support added 2016-05-12 13:19:51 +02:00
gsell 603366bcd6 src/h5t_io.c 
- format errors fixed
- bugfixes
 2016-04-29 18:10:25 +02:00
gsell 17317bb261 ignore file changed 2016-04-29 16:34:33 +02:00
gsell 52d44e3b3c - re-organize file hierarchy 
- years in copyright changed
 2016-04-29 16:34:07 +02:00
gsell 3d6230629c some missing query function implemented, see issue#1 in Gitlab 2016-04-22 18:06:58 +02:00
gsell 44ffea4fd5 examples/H5Block/write_field.c: H5hut file renamed to example_field.h5 2016-04-15 19:02:15 +02:00
gsell 97516866c7 examples/H5Block: attach_field_attribs and dump_field_attribs added 2016-04-15 19:01:00 +02:00
gsell 1dfcd9f876 fixes for hdf5 1.10.x 2016-04-15 18:58:10 +02:00
gsell 2dd2c625b7 .gitignore: has_field added 2016-04-08 19:07:52 +02:00
gsell 3137063d22 example/H5Block: 
- has_field.c added
 2016-04-08 19:06:42 +02:00
gsell 9a16fa090a example/H5Block/write_field.c: 
- slice in Z direction
 2016-04-08 19:06:15 +02:00
gsell df0750df4c examples/H5Block/read_write_scalar_field.c: 
- cleanup
 2016-04-07 11:11:00 +02:00
gsell b69aa9b92d example/H5Block 
- write_field added
 2016-04-07 11:10:22 +02:00
gsell 99699d4bf7 documentation updated 2016-04-01 19:12:34 +02:00
gsell 9df1a57778 src/h5core/h5b_model.c: 
- h5b_has_field() added
 2016-04-01 19:12:15 +02:00
gsell 1ed4f3985b src/include/H5Block_attribs.h: documentation updated 2016-03-30 18:05:15 +02:00
gsell 2c850612ab functions added to query existence of file-, step-. field-attributes amd to get information by name 2016-03-29 17:49:32 +02:00
gsell bc528f27e6 more cleanup on header files 2016-03-29 15:30:30 +02:00
gsell 5444b0e0ef .gitignore: vtk2h5grid added 2016-03-29 14:57:09 +02:00
gsell ae9e4cee01 C header files: 
- cleanup
 2016-03-29 14:55:35 +02:00
gsell 7490eed535 tools/vtk2h5grid/Makefile.am: 
- libH5hut library path changed
 2016-03-29 14:49:09 +02:00
gsell 84fa4a0b0a Merge branch 'master' of git.psi.ch:H5hut/src 2016-03-29 10:47:23 +02:00
gsell 718ef785f8 doc/H5.dox: re-structured 2016-03-29 10:46:35 +02:00
gsell 7002b73e82 src/{Fortran,h5core}/Makefile.am: 
- do not install the libs in src/lib
 2016-03-23 22:01:55 +01:00
gsell 2a8a43af39 src/include/H5_debug.f90: 
- h5_set_debug_mask(): bugfix
 2016-03-23 21:51:00 +01:00
gsell f0c2f29091 src/include/H5hut.f90: 
- bugfix in included files
 2016-03-23 21:50:10 +01:00
gsell 5362498a95 src/include/H5_const.f90: 
- bugfix in definition of H5_FAILED
 2016-03-23 21:49:34 +01:00
gsell 851905361d src/Fortran/H5.c: 
- h5_setprop_file_corevfd(): bugfix
 2016-03-23 21:47:40 +01:00
gsell 3c8b11f9eb src/{C,Fortran}/Makefile.am: 
- include_HEADERS fixed
 2016-03-23 21:46:37 +01:00
gsell 4dde2b61d2 COPYING: 
- year in copyright changed to 2016
 2016-03-23 21:45:25 +01:00
gsell d980f4d2b9 header files and documentation reorganized and reviewed 2016-03-18 17:58:30 +01:00
gsell 3f7c84dbf5 header files and documentation reorganized 2016-03-18 16:37:13 +01:00
gsell c5a05a1261 year in copyright changed 2016-03-18 14:25:30 +01:00
gsell 230f9a7b90 year in copyright changed 2016-03-18 14:23:49 +01:00
gsell 2cd718b7a1 src/include/h5core/h5.h: 
- h5_open_file1() return type is 'h5_file_p' not 'h5_file_t'
 2016-03-18 11:29:36 +01:00
gsell c73d10ffb7 src/include/H5Fed_model.h: 
- syntax errors fixed
 2016-03-18 11:28:40 +01:00
gsell 6209bc6cf9 src/include/H5.h: 
- bugfixes in H5OpenFile1() and H5GetVerbosityLevel1()
 2016-03-18 11:27:29 +01:00
gsell a013d43075 src/h5core/h5_openclose.c: 
- h5_open_file1(): fix return type
 2016-03-18 11:26:21 +01:00
gsell f151a24796 examples/H5Part/{read,write}_core_vfd.c: 
- missing 'incr' argument added to H5SetPropFileCoreVFD() call
 2016-03-18 11:25:25 +01:00
gsell 9d37783868 examples/H5Block/fields.c: 
- include H5hut.h
- write dims in right order
 2016-03-18 11:24:08 +01:00
gsell a8444e041b examples/H5/read_file_attribs(): 
- type cast fixed
 2016-03-18 11:22:38 +01:00
gsell dc9723dfe2 examples/H5/openclose.c 
- H5SetPropFileMPIO() renamed to H5SetFileMPIOCollective()
 2016-03-18 11:21:53 +01:00
gsell 91e7ed8c5b test/*: 
- H5SetPropFileMPIO() renamed to H5SetPropFileMPIOCollective()
 2016-03-18 11:04:11 +01:00
gsell b284ad9776 src/h5core/h5_attach.c: 
- in h5_get_attachment(): redundant check of file mode removed
 2016-03-17 17:55:41 +01:00
gsell f965ed4f18 src/h5core/*: 
- all *_has_* functions: return TRUE, FALSE or H5_FAILURE
 2016-03-17 17:53:32 +01:00
gsell 91316f314d src/include/*: 
- update/review documentation
- re-introduce old API functions
 2016-03-17 17:50:42 +01:00
gsell 538c9cdd76 src/h5core/h5u_model.c: 
- h5u_has_view() now returns H5_SUCCESS or H5_NOK
 2016-03-11 17:54:54 +01:00
gsell 28fc118118 src/h5core/h5b_model.c: 
- h5b_3d_has_view() now returns H5_SUCCESS or H5_NOK
 2016-03-11 17:53:30 +01:00
gsell 59fd8ea6c6 increment can now be specified for the core vfd driver 2016-03-11 17:51:17 +01:00
gsell 1273baf99e src/include/*: 
- doxgen documentation reviewed
 2016-03-11 17:49:09 +01:00
gsell befaccddaf doc/H5.dox: 
- document structure reviewed
 2016-03-11 17:48:37 +01:00
gsell 5204cb532b sdoc/Doxyfile 
- reviewed
 2016-03-11 17:47:59 +01:00
gsell 9917f12d96 .gitignore: 
- ignore doxygen output
 2016-03-11 17:46:54 +01:00
gsell 4b1d719d6c src/include/H5.h,H5Block_attribs.h: 
- add/review documentation
 2016-02-12 17:39:46 +01:00
gsell 43bc72b7d0 src/h5core/h5_openclose.c: 
- typo fixed
 2016-02-12 17:31:47 +01:00
gsell 64b4a3be09 doc/H5.dox: 
- update author list
- minor changes in overall structure
 2016-02-12 17:31:19 +01:00
gsell f4e7defffa doc/DoxygenLayout.xml: 
- deleted
 2016-02-12 17:30:38 +01:00
gsell 320fd77398 doc/Doxyfile: 
- changes required by new Doxygen version
- parse only files in src/include
- enable static function
 2016-02-12 17:29:32 +01:00
gsell 5714c390ec examples/*: 
- type cast malloc() result
 2016-02-09 10:10:57 +01:00
gsell a07d4101a2 examples/H5Block/read_write_scalar_field.c: 
- type cast malloc(2) return value to make C++ happy
 2016-02-09 09:55:17 +01:00
gsell 56787866fb test wheter I can commit again 2016-01-18 13:22:28 +01:00
gsell fb3b876f78 ignore zipped tar-balls 2016-01-18 13:18:55 +01:00
gsell e4ebb0f453 Makefiles.am's: 
- missing head-files added
 2015-10-16 18:39:35 +02:00
gsell 51f2210ff1 test/h5b_test.c: 
- run  tests 'write2' and 'read2' only in parallel case
 2015-10-16 18:16:27 +02:00
gsell 511fbb89de src/h5core/h5b_model.c: 
- h5b_3d_set_view(): bugfix in serial code
 2015-10-16 18:14:27 +02:00
gsell 87fcc4930b h5core: 
- H5_VER_STRING defined from PACKAGE_VERSION as const char*
 2015-10-16 18:13:18 +02:00
gsell 49460b62c3 examples: 
- compile Fortran examples only if parallel is enabled
 2015-10-16 18:11:56 +02:00
gsell 8ae12f7ee9 configure.ac 
- copyright notice added
- set version to 1.99.15rc1
 2015-10-16 18:10:46 +02:00
gsell ca7dd3b99c examples/H5Part/read_strided{.c,f.f90} 
- compute and set a canonical view
 2015-10-16 16:02:17 +02:00
gsell 6efdfce033 examples/H5Part/read_setnparticles{.c,f.f90} 
- changes in comment lines
 2015-10-16 16:01:32 +02:00
gsell 55cc6bb7d0 src/h5core/h5u_model.c 
- h5u_set_num_points(): print start index of view if debug enabled
 2015-10-16 15:59:24 +02:00
gsell 4fcc1ed3b3 .gitignore 
- *.dSYM added
 2015-10-16 15:58:12 +02:00
gsell 23bb1ced99 examples/H5Part/read_strided.c 
- bugfix in printing data
 2015-10-16 13:57:20 +02:00
gsell 1f629ee7f8 examples: 
- output format warnings fixed
 2015-10-15 17:29:18 +02:00
gsell 3c825fc71d src/Fortran/h5_private.h 
- we do not have Underscore.h any more
 2015-10-15 17:28:31 +02:00
gsell 089dc3e1ba src/Fortran: 
- debug output warnings fixed
 2015-10-15 17:27:51 +02:00
gsell 158fc17a2b src/h5core/h5t_octree_private.h 
- include 'mpi.h' if PARALLEL_IO is set
 2015-10-08 17:51:03 +02:00
gsell 149c144eee examples 
- several simple fixes
 2015-10-08 16:58:05 +02:00
gsell 4e42972ebb src/include/h5core/h5.h 
- typedef MPI_Comm to int if we compile serial code
- suppress warning about unused variables in definition of MPI_Comm_size() and MPI_Comm_rank()
 2015-10-08 16:57:12 +02:00
gsell 73c07240c2 .gitignore 
- more to ignore
 2015-10-08 16:28:47 +02:00
gsell e637522073 example/H5Fed 
- fixes
- adapted to new API
 2015-10-08 16:28:23 +02:00
gsell ec9626a0e5 src/h5core/h5t_xyz 
- get serial mesh working again
 2015-10-08 16:26:35 +02:00
gsell 86755932d9 src/h5core/h5_maps_private.h 
- indentation fixes
 2015-10-08 16:24:48 +02:00
gsell 95e21118e4 src/h5core/h5t_map_private.h 
- bugfix: we have to use a signed type for 'low', 'mid' and ' high'
 2015-10-08 16:23:46 +02:00
gsell 3fe0cc74be src/h5core/h5u_readwrite.c 
- include 'h5core/h5.h' added
 2015-10-08 16:19:23 +02:00
gsell 40c2c7d498 src/include/H5Fed_retrieve.h 
- bugfix in allocating iterators
 2015-10-08 16:17:48 +02:00
gsell cf067f7c56 src/include/h5core/h5.h 
- definition of UNUSED_ARGUMENTS() moved to 'src/h5core/h5_private.h'
 2015-10-08 16:14:09 +02:00
gsell 33129a4793 src/h5core/Makefile.am 
- bugfix: we have to compile grid stuff in any case
 2015-10-08 16:12:36 +02:00
gsell 41f2e87fc7 src/h5core/h5_module_private-h: 
- bugfix in serial version of h5priv_end_throttle()
 2015-10-08 16:11:01 +02:00
gsell 347a447302 configure.ac 
- fix problem with AC_PROG_CC/CXX
- define 'WITH_PARALLEL_H5GRID' on '--enable-experimental'
 2015-10-08 16:09:00 +02:00
gsell 03531ab4af src/h5core 
- h5priv_start_throttle() and h5priv_end_throttle() are now inline
  functions, whereby the serial version is just a dummy
 2015-09-11 14:41:52 +02:00
gsell 3d8ce28609 src/h5core/h5t_* 
- cleanup
 2015-09-11 14:12:01 +02:00
gsell cc719d116c src/h5core/h5u_models.c 
- correct error message in h5u_set_num_points()
 2015-09-11 14:11:23 +02:00
gsell 748eb1b3ab src/h5core/h5t_module.c: 
- compile error fixed in h5t_close_mesh()
 2015-09-11 14:10:25 +02:00
gsell f430c71d06 configure.ac and related Makefile.am's: 
- conditionally compile examples
 2015-09-11 14:09:05 +02:00
gsell 4a1d4d2d10 test/Makefile.am: 
- unused h5_attach_test stuff removed
 2015-09-11 14:04:53 +02:00
gsell 937d3f9c0e examples/H5Part/* 
- cleanup and fixes
 2015-09-11 14:04:12 +02:00
gsell 4d9d3dc879 examples/H5Part/... 
- bugfixes
 2015-09-09 18:25:27 +02:00
gsell 106be817d9 examples/H5Part 
- reviewed
 2015-09-08 20:53:07 +02:00
gsell ec3a29d7e4 src/Fortran/H5Part_model.c 
- adapted to refactored h5u_get_num_points()
 2015-09-08 20:52:19 +02:00
gsell c5ce2f06ac src/include/H5.f90: 
- typo fixed in function name h5_setprop_file_corevfd()
 2015-09-08 20:50:44 +02:00
gsell 992e8cf58e src/include/H5_const.f90 
- H5_DEBUG_* masks added
 2015-09-08 20:49:29 +02:00
gsell a618acf686 src/h5core/h5_errorhandling.c 
src/include/h5core/h5_errorhandling.h
- h5_error(), h5_warn(), h5_info(): print message if debug-level > 3
 2015-09-08 20:48:26 +02:00
gsell 47bee153ba src/h5core/h5_hdf5_private.h 
- minor changes in debug output
 2015-09-08 20:46:21 +02:00
gsell 390a4296b4 src/h5core/h5_hdf5.c 
- hdf5_get_name_of_dataset_by_idx(): bugfix, return H5_NOK, if dataset are in step
 2015-09-08 20:45:27 +02:00
gsell 4f7c666b1f src/h5core/h5u_module.c 
- refactore "*num_particles*" to "*num_points*"
- h5u_set_view() can now be used for writing, there are still some limitations
 2015-09-08 20:43:38 +02:00
gsell a620715ccc src/include/H5Part_io.h: 
- documentation update
 2015-09-08 17:50:06 +02:00
gsell 37bf9b35a6 src/h5core/h5_mpi_private.h: 
- all mpi wrappers are now inline
 2015-09-08 17:47:39 +02:00
gsell 2a7628c1e2 examples/H5Block/read_write_scalar_field.c: 
- write of 32-bit values added
 2015-09-03 17:27:47 +02:00
gsell 5a588415d0 Fortran H5Part examples: 
- read_canonicalviewf.f90 read_setnparticlesf.f90, read_setviewf.f90, read_stridedf.f90 implemented
 2015-09-03 17:26:54 +02:00
gsell d5fce5b2a0 examples/H5Part/write_{setviewf,stridedf}.f90: 
- bugfixes: take Fortran indexing into account
 2015-09-03 17:24:37 +02:00
gsell 7bf3985219 examples/H5Block/read_write_scalar_fieldf-f90: 
- bugfix: open file read-only
 2015-09-03 17:23:09 +02:00
gsell d939354990 example/H5/write_step_attribsf.f90: 
- bugfix
 2015-09-03 17:22:10 +02:00
gsell 8fb9834d3b C examples: 
- fix some comments
 2015-09-03 17:21:12 +02:00
gsell 2fd5d52125 src/Fortran/H5_modeul.c: 
- h5_hasstep(), h5_setstep(): decrement step number by 1
 2015-09-03 17:20:08 +02:00
gsell a1226feafd copyright notice fixed in examples 2015-09-03 13:31:29 +02:00
gsell cc7c558065 src/Fortran/H5.c: 
- conditionally compile h5_setprop_file_mpio_posix()
 2015-07-27 10:20:25 +02:00
gsell 51f90df374 Testprogramms for Fortran symbol name mangling removed 2015-07-24 18:38:58 +02:00
gsell 62c2d53324 Fortran symbol mangling simplified 2015-07-24 18:36:31 +02:00
gsell 8e9e0d84f3 change year in copyright 2015-07-23 14:59:43 +02:00
gsell d9daf9f0c7 src/h5core/h5u_module.c: 
- bugfix in h5u_set_canonical_view()
 2015-07-23 14:54:23 +02:00
gsell 559f2d8d9c test/*: 
- fix some warning if compiled serial
 2015-07-17 17:14:31 +02:00
gsell 403e535a50 ignore file edited. 2015-07-17 16:53:45 +02:00
gsell 14aa4fbd15 test/testframe.h: 
- set VERBO_HI to 65535
 2015-07-03 17:48:47 +02:00
gsell 319d7b4324 test/h5u_test.c: 
- cleanup
 2015-07-03 17:48:16 +02:00
gsell 4511fde9d1 bugfix: throttle only if VFD is MPIO independent or POSIX 2015-07-03 17:47:37 +02:00
gsell 707cafb2d8 src/h5core/h5u_model.c: 
- bugfix with h5u_set_view (0, -1)
 2015-07-03 17:45:49 +02:00
gsell 877b611758 test/testframe.c 
- initialize 'ret_value' in 'TestPrintf()' and 'TestErrPrintf()'
 2015-07-02 15:57:05 +02:00
gsell 9fb11ca838 no MPIO_POSIX in hdf5 > 1.8.12 2015-07-02 15:55:57 +02:00
gsell 7c2a315760 src/h5core/h5b_readwrite.c: fix early return in _select_hyperslab_for_writing() 2015-06-18 14:58:17 +02:00
gsell cc0135b4fc src/h5core/h5b_readwrite.c: 
- fix early return in  _select_hyperslab_for_writing()

# Conflicts:
#	src/h5core/h5b_readwrite.c
 2015-06-18 14:17:10 +02:00
gsell f47fbbf075 tools/vtk2h5grid/Makefile.am: fixes 2015-06-18 14:10:17 +02:00
gsell fd8c1e37b1 src/h5core/h5b_model.c: 
- bugfix in serial code of h5b_3d_set_view()

# Conflicts:
#	src/h5core/h5b_model.c
 2015-06-18 14:09:32 +02:00
Gsell Achim 4d770f8c84 option to shift mesh added 2015-06-18 13:51:40 +02:00
gsell 1f79b924df work on H5Block examples 2014-01-31 15:38:13 +01:00
gsell b1f143a5d7 src/examples/H5Block: ignore file added 2014-01-31 15:36:59 +01:00
gsell d6718bb866 examples/H5Part/read_canonicalviewf.f90: some fixes, but still broken 2014-01-31 15:34:20 +01:00
gsell 9deeacff51 copyright notice changed 2014-01-31 15:32:55 +01:00
gsell 5dbe8fb161 src/include/H5Block_attribs.f90: bugfix in declaration of h5bl_writefieldattrib_string() 2014-01-31 15:31:31 +01:00
gsell c3add7dde4 src/include/H5.f90: empty line removed 2014-01-31 15:30:46 +01:00
gsell 9d49361c43 some H5Block examples renamed 2014-01-31 15:29:10 +01:00
gsell 1a1878402c fixes in H5Part Fortran examples 2014-01-29 10:07:14 +01:00
gsell 069f9b64fc ignore file added to examples/H5Part 2014-01-29 10:05:15 +01:00
gsell ca6b4cc52d names of Fortran API header files fixed 2014-01-29 08:57:37 +01:00
gsell 60df95b10a most missing functions added to Fortran API 2014-01-28 17:31:22 +01:00
gsell d508f9e591 include/H5_attribs.h: reorder declarations 2014-01-28 17:30:00 +01:00
gsell 36702c6207 macros defining the names of internal attributes moved to public core file 2014-01-28 17:28:08 +01:00
gsell fa091cc2ab Fortran API files for H5Part data model renamed 2014-01-28 14:44:57 +01:00
gsell 1121a22956 Fortran API files for H5Block model renamed 2014-01-28 14:06:09 +01:00
gsell d5b8a4c0c8 ignore file edited 2013-11-15 16:50:32 +01:00
gsell 1cc3614c74 Fortran stubs added 2013-11-15 16:49:10 +01:00
gsell ca5f4abc7c comment for zero-sized selections reviewed 2013-11-15 16:46:36 +01:00
gsell 9d3c006409 MPI rank variable renamed to comm_rank 2013-11-15 16:45:06 +01:00
gsell d79d0ddf1a basic read_strided example implemented 2013-11-15 16:44:07 +01:00
gsell a1ad62bc74 'use_core_vfd.c' renamed to 'write_core_vfd.c' 2013-10-31 15:32:32 +01:00
gsell 950bcef057 explicit set of verbosity level to default; refactor variables for MPI communicator size and rank to 'comm_size' and 'comm_rank' 2013-10-31 15:30:43 +01:00
gsell 468a5d6871 H5Part examples reviewed 2013-10-31 13:44:06 +01:00
gsell cf09862f4b ignore file updated 2013-10-31 13:42:07 +01:00
gsell 6b6f290ebb MPI initialization added to vtk2h5grid.cc 2013-10-31 13:41:09 +01:00
gsell c8eecb51ae typo in filename 'examples/H5Part/use_core_vfd.c' fixed 2013-10-31 13:39:40 +01:00
gsell 23c2bdd189 typo in filename 'examples/H5Part/use_core_vfd.c' fixed 2013-10-31 13:38:27 +01:00
gsell 3e69059afc macro H5_VERBOSE_DEFAULT defined 2013-10-28 18:28:19 +01:00
gsell a6f81be2cd h5u_set_view() supports zero particle selections now, h5u_set_view_start_length() renamed to h5u_set_view_length() 2013-10-28 18:26:59 +01:00
gsell 89b91d6b46 --with-vtk added to configure.ac 2013-10-28 18:23:09 +01:00
gsell 4975de7a74 ignore list edited 2013-10-10 17:10:23 +02:00
gsell 3fe4c39e5e fix renamed macros in tests 2013-10-10 17:10:05 +02:00
gsell 89bb9ef48c missing set file property functions implemented, bugfixes 2013-10-10 17:08:32 +02:00
gsell d15993ecdc missing file property functions added 2013-10-10 17:03:13 +02:00
gsell da723dda5e missing file property functions added 2013-10-10 17:02:39 +02:00
gsell 0dcc666e5e more work on examples 2013-10-10 17:00:44 +02:00
gsell 61d17a352f same examples renamed 2013-10-10 16:56:25 +02:00
gsell 006e1cda4a examples Bench.c, H5test.c and H5testF.f90 removed 2013-09-26 16:47:51 +02:00
gsell 11e399b6c7 C and Fortran examples reviewed, new examples added 2013-09-26 15:59:09 +02:00
gsell e839226f2b unit tests adapted to new API 2013-09-26 15:54:47 +02:00
gsell 2702f846cb old file open API removed 2013-09-26 15:53:54 +02:00
gsell ee23c8cc4b Fortran API review 2013-09-26 15:51:49 +02:00
gsell c3a74c8ed4 functions added to query attributes by name 2013-09-26 15:47:43 +02:00
gsell 969acd3642 definition of H5_MAX_NAME_LEN moved to public API 2013-09-26 15:38:54 +02:00
gsell ee07f01abd C header files specified with full path 2013-09-26 15:23:54 +02:00
gsell 06f0a8b4e7 compile with -O3 if debug is disabled, compile with -Wall in always 2013-09-26 15:20:45 +02:00
gsell 205a1a5c37 .gitignore added 2013-09-02 11:20:16 +02:00
gsell 7174b36a20 fixes to Fortran API 2013-09-02 09:31:14 +02:00
gsell 273b1831d9 fixes to autotool files 2013-09-02 09:30:23 +02:00
gsell 83c5a66814 handle MPI compiler on NERSC system 2013-07-11 12:18:53 +00:00
gsell db81cb3d33 attachment test moved to examples 2013-07-11 07:50:57 +00:00
gsell 4a8eedd31e autotool fixes 2013-07-10 14:05:21 +00:00
gsell 11a1cc7c1e reformated 2013-07-10 14:04:53 +00:00
gsell a509000711 warnings popped up on Linux fixed 2013-07-05 14:45:47 +00:00
gsell a65ee3bbb7 bugfixes 2013-07-04 14:58:18 +00:00
gsell f69ee003f6 ignore list edited 2013-06-27 16:27:46 +00:00
gsell 0b18373f8c bugfixes 2013-06-27 16:25:09 +00:00
gsell 311cdad1c8 bugfix 2013-06-27 16:24:02 +00:00
gsell 6f84edd791 autotool cleanup and fixes 2013-06-27 16:21:18 +00:00
gsell 1614f9519b autotool cleanup and fixes 2013-06-27 16:20:43 +00:00
gsell 65757c1974 bug fixes, some private functions renamed, formating changes 2013-06-27 16:18:08 +00:00
gsell 80523c6df7 examples fixed 2013-06-27 16:14:22 +00:00
gsell f17f1d028c fixes for building outside source tree 2013-05-02 14:14:26 +00:00
gsell 78078c322e definitions for H5_VERBOSE_{NONE,ERROR,WARN,INFO} added 2013-05-02 14:12:43 +00:00
gsell 1284d545e1 ported to new API 2013-05-02 14:11:06 +00:00
gsell 96af35450a added something to NEWS (still work in progress) 2013-05-02 14:09:22 +00:00
gsell 5abb40125b new trunk merged from old trunk, Roman's master thesis and my changes in the sandbox 2013-04-12 12:32:58 +00:00
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src/h5core/h5_lustre_private.h -text
src/h5core/h5_maps.c -text
src/h5core/h5_maps_private.h -text
src/h5core/h5_model.c -text
src/h5core/h5_model_private.h -text
src/h5core/h5_mpi.c -text
src/h5core/h5_mpi_private.h -text
src/h5core/h5_openclose.c -text
src/h5core/h5_private.h -text
src/h5core/h5_qsort.c -text
src/h5core/h5_qsort_private.h -text
src/h5core/h5_qsort_r.c -text
src/h5core/h5_readwrite.c -text
src/h5core/h5_readwrite_private.h -text
src/h5core/h5_syscall.c -text
src/h5core/h5_syscall_private.h -text
src/h5core/h5_types_private.h -text
src/h5core/h5_va_macros.h -text
src/h5core/h5b_attribs.c -text
src/h5core/h5b_model.c -text
src/h5core/h5b_model_private.h -text
src/h5core/h5b_readwrite.c -text
src/h5core/h5b_readwrite_private.h -text
src/h5core/h5b_types_private.h -text
src/h5core/h5t_access_private.h -text
src/h5core/h5t_access_tetm.c -text
src/h5core/h5t_access_trim.c -text
src/h5core/h5t_adjacencies.c -text
src/h5core/h5t_adjacencies_private.h -text
src/h5core/h5t_adjacencies_tetm.c -text
src/h5core/h5t_adjacencies_trim.c -text
src/h5core/h5t_core.c -text
src/h5core/h5t_core_private.h -text
src/h5core/h5t_core_tetm.c -text
src/h5core/h5t_core_trim.c -text
src/h5core/h5t_errorhandling_private.h -text
src/h5core/h5t_map.c -text
src/h5core/h5t_map_private.h -text
src/h5core/h5t_model.c -text
src/h5core/h5t_model_private.h -text
src/h5core/h5t_model_tetm.c -text
src/h5core/h5t_model_trim.c -text
src/h5core/h5t_octree.c -text
src/h5core/h5t_octree_private.h -text
src/h5core/h5t_readwrite.c -text
src/h5core/h5t_readwrite_private.h -text
src/h5core/h5t_readwrite_tetm.c -text
src/h5core/h5t_readwrite_trim.c -text
src/h5core/h5t_ref_elements.c -text
src/h5core/h5t_ref_elements_private.h -text
src/h5core/h5t_retrieve.c -text
src/h5core/h5t_retrieve_private.h -text
src/h5core/h5t_retrieve_tetm.c -text
src/h5core/h5t_retrieve_trim.c -text
src/h5core/h5t_store.c -text
src/h5core/h5t_store_private.h -text
src/h5core/h5t_store_tetm.c -text
src/h5core/h5t_store_trim.c -text
src/h5core/h5t_tags.c -text
src/h5core/h5t_tags_private.h -text
src/h5core/h5t_types_private.h -text
src/h5core/h5u_errorhandling_private.h -text
src/h5core/h5u_model.c -text
src/h5core/h5u_readwrite.c -text
src/h5core/h5u_readwrite_private.h -text
src/h5core/h5u_types_private.h -text
src/include/H5.h -text
src/include/H5Block.h -text
src/include/H5Block_attribs.h -text
src/include/H5Block_io.h -text
src/include/H5Block_model.h -text
src/include/H5Fed.h -text
src/include/H5Fed_adjacency.h -text
src/include/H5Fed_model.h -text
src/include/H5Fed_retrieve.h -text
src/include/H5Fed_store.h -text
src/include/H5Fed_tags.h -text
src/include/H5Part.h -text
src/include/H5Part_io.h -text
src/include/H5Part_model.h -text
src/include/H5_attribs.h -text
src/include/H5_model.h -text
src/include/H5hut.h -text
src/include/Makefile.am -text
src/include/h5core/Makefile.am -text
src/include/h5core/h5.h -text
src/include/h5core/h5_attribs.h -text
src/include/h5core/h5_debug.h -text
src/include/h5core/h5_errorhandling.h -text
src/include/h5core/h5_model.h -text
src/include/h5core/h5_syscall.h -text
src/include/h5core/h5_types.h -text
src/include/h5core/h5b_attribs.h -text
src/include/h5core/h5b_io.h -text
src/include/h5core/h5b_model.h -text
src/include/h5core/h5t_adjacencies.h -text
src/include/h5core/h5t_map.h -text
src/include/h5core/h5t_model.h -text
src/include/h5core/h5t_octree.h -text
src/include/h5core/h5t_retrieve.h -text
src/include/h5core/h5t_store.h -text
src/include/h5core/h5t_tags.h -text
src/include/h5core/h5u_io.h -text
src/include/h5core/h5u_model.h -text
test/Makefile.am -text
test/h5b_read.c -text
test/h5b_test.c -text
test/h5b_write.c -text
test/h5u_read.c -text
test/h5u_test.c -text
test/h5u_write.c -text
test/params.h -text
test/testframe.c -text
test/testframe.h -text
tools/H5PartMerge/AUTHORS -text
tools/H5PartMerge/COPYING -text
tools/H5PartMerge/ChangeLog -text
tools/H5PartMerge/INSTALL -text
tools/H5PartMerge/NEWS -text
tools/H5PartMerge/README -text
tools/H5PartMerge/autogen.sh -text
tools/H5PartMerge/configure.ac -text
tools/H5PartMerge/makefile.am -text
tools/H5PartMerge/src/H5merge.cpp -text
tools/H5PartMerge/src/optparse.cpp -text
tools/H5PartMerge/src/optparse.hh -text
tools/Makefile.am -text
tools/README -text
tools/h5PartDcToVtk.cc -text
tools/h5PartSurfaceToVtk.cc -text
tools/h5hutcc.in -text
tools/h5pAttrib.cc -text
tools/h5pToGNUplot.cc -text
tools/homdynToH5p.cc -text
tools/vtk2h5grid/Makefile.am -text
tools/vtk2h5grid/vtk2h5grid.cc -text
visit_plugins/databases/H5Part/.depend -text
visit_plugins/databases/H5Part/Makefile -text
visit_plugins/databases/H5Part/README.txt -text
.gitignore
+95
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@@ -0,0 +1,95 @@
*.tar.gz
*.[oa]
*.la
*.lo
*.so
*.dSYM
*~
*.h5
.deps
.dirstamp
.libs
CMakeFiles
INSTALL
Makefile
Makefile.in
aclocal.m4
attach_field_attributes
dump_field_attributes
autom4te.cache/
compile
config.guess
config.h
config.h.in
config.log
config.status
config.sub
configure
depcomp
py-compile
examples/H5/attach_file
examples/H5/examples.h
examples/H5/h5hut.mod
examples/H5/openclose
examples/H5/openclosef
examples/H5/query
examples/H5/queryf
examples/H5/read_file_attribs
examples/H5/read_file_attribsf
examples/H5/read_step_attribs
examples/H5/read_step_attribsf
examples/H5/write_file_attribs
examples/H5/write_file_attribsf
examples/H5/write_step_attribs
examples/H5/write_step_attribsf
examples/H5Block/H5BlockExampleF
examples/H5Block/fields
examples/H5Block/read_write
examples/H5Part/Bench
examples/H5Part/H5test
examples/H5Part/H5testF
examples/H5Part/core_vfd
examples/H5Part/examples.h
examples/H5Part/h5hut.mod
examples/H5Part/particles
examples/H5Part/read_canonicalview
examples/H5Part/read_setnparticles
examples/H5Part/read_setview
examples/H5Part/read_strided
examples/H5Part/write_core_vfd
examples/H5Part/write_setnparticles
examples/H5Part/write_setnumparticles
examples/H5Part/write_setview
examples/H5Part/write_setviewf
examples/H5Part/write_strided
has_field
install-sh
libtool
ltmain.sh
m4/
missing
src/Fortran/TestUnderscore
src/Fortran/Underscore.h
src/include/H5hut.f
src/include/H5hutF.h
stamp-h1
test/h5b_test
test/h5u_test
test/h5_attach_test
tools/h5hutcc
tetmesh_adjacencies
tetmesh_read
tetmesh_read_tags
tetmesh_write
tetmesh_write1
examples/H5Fed/tetmesh_write2
examples/H5Fed/trimesh_2gnuplot
examples/H5Fed/trimesh_adjacencies
examples/H5Fed/trimesh_read
examples/H5Fed/trimesh_write
examples/H5Fed/trimesh_write_dunetest
tetmesh_write_tags
write_field
*.gch
ReferencePages
vtk2h5grid
AUTHORS
+1 -1
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@@ -7,4 +7,4 @@ Wes Bethel (NERSC/LBNL)
John Shalf (NERSC/LBNL)
Cristina Siegerist (NERSC/LBNL)
Please use h5part@lists.psi.ch for communicaion.
Please use h5part@lists.psi.ch for communication.
COPYING
+71
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@@ -0,0 +1,71 @@
*** Copyright Notice ***
H5hut Copyright (c) 2006-2016, 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.
*** License agreement ***
H5hut Copyright (c) 2006-2016, 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.
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.
ChangeLog
+15
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@@ -0,0 +1,15 @@
2018-09-14 Gsell Achim <achi.gsell@psi.ch>
* C-API
- H5PartSetNumPoints() renamed to H5PartSetNumItems()
- H5PartGetNumPoints() renamed to H5PartGetNumItems()
- Dataset names longer then 64 bytes are handled as error.
- Same for step/iteration names.
* core API
- we use the term 'iteration' instead of 'step'
- we use the term 'item' instead of 'point'
- re-factor function and variable names
- in printing messages/debug output fixed
- do not flush (sync to disk) after writing a dataset by default,
can be controlled by a property
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 ($(PARALLEL), yes) #parallel
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest
endif
else
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o
endif
endif
include rules.make
Makefile.am
+18 -12
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@@ -1,15 +1,21 @@
# Trial by Antino Kim
# Top level Makefile.am
ACLOCAL_AMFLAGS = -I m4
EXTRA_DIST = \
autogen.sh \
ax_pkg_swig.m4
SUBDIRS = \
doc \
src \
test \
tools
SUBDIRS = \
src \
test \
tools \
doc \
examples/H5 \
examples/H5Part \
examples/H5Block \
examples/H5Fed
MAINTAINERCLEANFILES = \
config.h \
config.log \
config.status \
stamp-h.in \
MAINTAINERCLEANFILES = \
config.h \
config.log \
config.status \
stamp-h.in \
stamp-h1
Makefile.orig
-59
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@@ -1,59 +0,0 @@
# This is a very rudimentary multiarchitecture makefile
# You need to uncomment the default block of make variables you need
# Some key things to watch for are the following defines
# -DREGRESSIONTEST : enables a main(){} inside of
# the H5Part.cc file that does simple regression testing.
# -DPARALLEL_IO : If you want to use parallel HDF5, you have to
# enable this. Otherwise, you get only the serial
# implementation of the library.
# MacOS-X Serial
#CXX = c++
#CC = cc
#F90 = xlf
#H5HOME = /usr/local
#CFLAGS = -O -g -I$(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
+254
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@@ -1,3 +1,257 @@
#### H5PART trunk ############################################################
* h5_file_t is now uintptr_t
* experimental version of parallel H5Fed
* new API function for file open using properties (similiar to hdf5 properties)
#### H5PART 1.99.10 ############################################################
* C99 compiler required
* C API with inline functions
#### H5PART 1.99.0 ############################################################
rudimental implementation of a grid manager
Important changes from version 1.6 to 1.99.0
Renamed type:
H5PartFile -> h5_file_t
h5part_int64_t -> h5_int64_t
h5part_float64_t -> h5_float_t
Renamed functions:
All function not related to a specific data model have been renamed from
H5PartFunction() to H5Function().
Example:
H5PartOpenFile() -> H5OpenFile()
Removed functions:
To simplify the API, there is just one function to open a file. It's the
same function for serial and parallel code.
#### 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 -I . $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 $AUTOMAKE_FLAGS || {
echo "automake failed"
exit 1
}
echo
echo
echo
ax_cxx_compile_stdcxx.m4
+982
View File
@@ -0,0 +1,982 @@
# ===========================================================================
# https://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_CXX_COMPILE_STDCXX(VERSION, [ext|noext], [mandatory|optional])
#
# DESCRIPTION
#
# Check for baseline language coverage in the compiler for the specified
# version of the C++ standard. If necessary, add switches to CXX and
# CXXCPP to enable support. VERSION may be '11' (for the C++11 standard)
# or '14' (for the C++14 standard).
#
# The second argument, if specified, indicates whether you insist on an
# extended mode (e.g. -std=gnu++11) or a strict conformance mode (e.g.
# -std=c++11). If neither is specified, you get whatever works, with
# preference for an extended mode.
#
# The third argument, if specified 'mandatory' or if left unspecified,
# indicates that baseline support for the specified C++ standard is
# required and that the macro should error out if no mode with that
# support is found. If specified 'optional', then configuration proceeds
# regardless, after defining HAVE_CXX${VERSION} if and only if a
# supporting mode is found.
#
# LICENSE
#
# Copyright (c) 2008 Benjamin Kosnik <bkoz@redhat.com>
# Copyright (c) 2012 Zack Weinberg <zackw@panix.com>
# Copyright (c) 2013 Roy Stogner <roystgnr@ices.utexas.edu>
# Copyright (c) 2014, 2015 Google Inc.; contributed by Alexey Sokolov <sokolov@google.com>
# Copyright (c) 2015 Paul Norman <penorman@mac.com>
# Copyright (c) 2015 Moritz Klammler <moritz@klammler.eu>
# Copyright (c) 2016 Krzesimir Nowak <qdlacz@gmail.com>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice
# and this notice are preserved. This file is offered as-is, without any
# warranty.
#serial 7
dnl This macro is based on the code from the AX_CXX_COMPILE_STDCXX_11 macro
dnl (serial version number 13).
AX_REQUIRE_DEFINED([AC_MSG_WARN])
AC_DEFUN([AX_CXX_COMPILE_STDCXX], [dnl
m4_if([$1], [11], [ax_cxx_compile_alternatives="11 0x"],
[$1], [14], [ax_cxx_compile_alternatives="14 1y"],
[$1], [17], [ax_cxx_compile_alternatives="17 1z"],
[m4_fatal([invalid first argument `$1' to AX_CXX_COMPILE_STDCXX])])dnl
m4_if([$2], [], [],
[$2], [ext], [],
[$2], [noext], [],
[m4_fatal([invalid second argument `$2' to AX_CXX_COMPILE_STDCXX])])dnl
m4_if([$3], [], [ax_cxx_compile_cxx$1_required=true],
[$3], [mandatory], [ax_cxx_compile_cxx$1_required=true],
[$3], [optional], [ax_cxx_compile_cxx$1_required=false],
[m4_fatal([invalid third argument `$3' to AX_CXX_COMPILE_STDCXX])])
AC_LANG_PUSH([C++])dnl
ac_success=no
AC_CACHE_CHECK(whether $CXX supports C++$1 features by default,
ax_cv_cxx_compile_cxx$1,
[AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])],
[ax_cv_cxx_compile_cxx$1=yes],
[ax_cv_cxx_compile_cxx$1=no])])
if test x$ax_cv_cxx_compile_cxx$1 = xyes; then
ac_success=yes
fi
m4_if([$2], [noext], [], [dnl
if test x$ac_success = xno; then
for alternative in ${ax_cxx_compile_alternatives}; do
switch="-std=gnu++${alternative}"
cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx$1_$switch])
AC_CACHE_CHECK(whether $CXX supports C++$1 features with $switch,
$cachevar,
[ac_save_CXX="$CXX"
CXX="$CXX $switch"
AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])],
[eval $cachevar=yes],
[eval $cachevar=no])
CXX="$ac_save_CXX"])
if eval test x\$$cachevar = xyes; then
CXX="$CXX $switch"
if test -n "$CXXCPP" ; then
CXXCPP="$CXXCPP $switch"
fi
ac_success=yes
break
fi
done
fi])
m4_if([$2], [ext], [], [dnl
if test x$ac_success = xno; then
dnl HP's aCC needs +std=c++11 according to:
dnl http://h21007.www2.hp.com/portal/download/files/unprot/aCxx/PDF_Release_Notes/769149-001.pdf
dnl Cray's crayCC needs "-h std=c++11"
for alternative in ${ax_cxx_compile_alternatives}; do
for switch in -std=c++${alternative} +std=c++${alternative} "-h std=c++${alternative}"; do
cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx$1_$switch])
AC_CACHE_CHECK(whether $CXX supports C++$1 features with $switch,
$cachevar,
[ac_save_CXX="$CXX"
CXX="$CXX $switch"
AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])],
[eval $cachevar=yes],
[eval $cachevar=no])
CXX="$ac_save_CXX"])
if eval test x\$$cachevar = xyes; then
CXX="$CXX $switch"
if test -n "$CXXCPP" ; then
CXXCPP="$CXXCPP $switch"
fi
ac_success=yes
break
fi
done
if test x$ac_success = xyes; then
break
fi
done
fi])
AC_LANG_POP([C++])
if test x$ax_cxx_compile_cxx$1_required = xtrue; then
if test x$ac_success = xno; then
AC_MSG_ERROR([*** A compiler with support for C++$1 language features is required.])
fi
fi
if test x$ac_success = xno; then
HAVE_CXX$1=0
AC_MSG_NOTICE([No compiler with C++$1 support was found])
else
HAVE_CXX$1=1
AC_DEFINE(HAVE_CXX$1,1,
[define if the compiler supports basic C++$1 syntax])
fi
AC_SUBST(HAVE_CXX$1)
m4_if([$1], [17], [AC_MSG_WARN([C++17 is not yet standardized, so the checks may change in incompatible ways anytime])])
])
dnl Test body for checking C++11 support
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_11],
_AX_CXX_COMPILE_STDCXX_testbody_new_in_11
)
dnl Test body for checking C++14 support
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_14],
_AX_CXX_COMPILE_STDCXX_testbody_new_in_11
_AX_CXX_COMPILE_STDCXX_testbody_new_in_14
)
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_17],
_AX_CXX_COMPILE_STDCXX_testbody_new_in_11
_AX_CXX_COMPILE_STDCXX_testbody_new_in_14
_AX_CXX_COMPILE_STDCXX_testbody_new_in_17
)
dnl Tests for new features in C++11
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_11], [[
// If the compiler admits that it is not ready for C++11, why torture it?
// Hopefully, this will speed up the test.
#ifndef __cplusplus
#error "This is not a C++ compiler"
#elif __cplusplus < 201103L
#error "This is not a C++11 compiler"
#else
namespace cxx11
{
namespace test_static_assert
{
template <typename T>
struct check
{
static_assert(sizeof(int) <= sizeof(T), "not big enough");
};
}
namespace test_final_override
{
struct Base
{
virtual void f() {}
};
struct Derived : public Base
{
virtual void f() override {}
};
}
namespace test_double_right_angle_brackets
{
template < typename T >
struct check {};
typedef check<void> single_type;
typedef check<check<void>> double_type;
typedef check<check<check<void>>> triple_type;
typedef check<check<check<check<void>>>> quadruple_type;
}
namespace test_decltype
{
int
f()
{
int a = 1;
decltype(a) b = 2;
return a + b;
}
}
namespace test_type_deduction
{
template < typename T1, typename T2 >
struct is_same
{
static const bool value = false;
};
template < typename T >
struct is_same<T, T>
{
static const bool value = true;
};
template < typename T1, typename T2 >
auto
add(T1 a1, T2 a2) -> decltype(a1 + a2)
{
return a1 + a2;
}
int
test(const int c, volatile int v)
{
static_assert(is_same<int, decltype(0)>::value == true, "");
static_assert(is_same<int, decltype(c)>::value == false, "");
static_assert(is_same<int, decltype(v)>::value == false, "");
auto ac = c;
auto av = v;
auto sumi = ac + av + 'x';
auto sumf = ac + av + 1.0;
static_assert(is_same<int, decltype(ac)>::value == true, "");
static_assert(is_same<int, decltype(av)>::value == true, "");
static_assert(is_same<int, decltype(sumi)>::value == true, "");
static_assert(is_same<int, decltype(sumf)>::value == false, "");
static_assert(is_same<int, decltype(add(c, v))>::value == true, "");
return (sumf > 0.0) ? sumi : add(c, v);
}
}
namespace test_noexcept
{
int f() { return 0; }
int g() noexcept { return 0; }
static_assert(noexcept(f()) == false, "");
static_assert(noexcept(g()) == true, "");
}
namespace test_constexpr
{
template < typename CharT >
unsigned long constexpr
strlen_c_r(const CharT *const s, const unsigned long acc) noexcept
{
return *s ? strlen_c_r(s + 1, acc + 1) : acc;
}
template < typename CharT >
unsigned long constexpr
strlen_c(const CharT *const s) noexcept
{
return strlen_c_r(s, 0UL);
}
static_assert(strlen_c("") == 0UL, "");
static_assert(strlen_c("1") == 1UL, "");
static_assert(strlen_c("example") == 7UL, "");
static_assert(strlen_c("another\0example") == 7UL, "");
}
namespace test_rvalue_references
{
template < int N >
struct answer
{
static constexpr int value = N;
};
answer<1> f(int&) { return answer<1>(); }
answer<2> f(const int&) { return answer<2>(); }
answer<3> f(int&&) { return answer<3>(); }
void
test()
{
int i = 0;
const int c = 0;
static_assert(decltype(f(i))::value == 1, "");
static_assert(decltype(f(c))::value == 2, "");
static_assert(decltype(f(0))::value == 3, "");
}
}
namespace test_uniform_initialization
{
struct test
{
static const int zero {};
static const int one {1};
};
static_assert(test::zero == 0, "");
static_assert(test::one == 1, "");
}
namespace test_lambdas
{
void
test1()
{
auto lambda1 = [](){};
auto lambda2 = lambda1;
lambda1();
lambda2();
}
int
test2()
{
auto a = [](int i, int j){ return i + j; }(1, 2);
auto b = []() -> int { return '0'; }();
auto c = [=](){ return a + b; }();
auto d = [&](){ return c; }();
auto e = [a, &b](int x) mutable {
const auto identity = [](int y){ return y; };
for (auto i = 0; i < a; ++i)
a += b--;
return x + identity(a + b);
}(0);
return a + b + c + d + e;
}
int
test3()
{
const auto nullary = [](){ return 0; };
const auto unary = [](int x){ return x; };
using nullary_t = decltype(nullary);
using unary_t = decltype(unary);
const auto higher1st = [](nullary_t f){ return f(); };
const auto higher2nd = [unary](nullary_t f1){
return [unary, f1](unary_t f2){ return f2(unary(f1())); };
};
return higher1st(nullary) + higher2nd(nullary)(unary);
}
}
namespace test_variadic_templates
{
template <int...>
struct sum;
template <int N0, int... N1toN>
struct sum<N0, N1toN...>
{
static constexpr auto value = N0 + sum<N1toN...>::value;
};
template <>
struct sum<>
{
static constexpr auto value = 0;
};
static_assert(sum<>::value == 0, "");
static_assert(sum<1>::value == 1, "");
static_assert(sum<23>::value == 23, "");
static_assert(sum<1, 2>::value == 3, "");
static_assert(sum<5, 5, 11>::value == 21, "");
static_assert(sum<2, 3, 5, 7, 11, 13>::value == 41, "");
}
// http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae
// Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function
// because of this.
namespace test_template_alias_sfinae
{
struct foo {};
template<typename T>
using member = typename T::member_type;
template<typename T>
void func(...) {}
template<typename T>
void func(member<T>*) {}
void test();
void test() { func<foo>(0); }
}
} // namespace cxx11
#endif // __cplusplus >= 201103L
]])
dnl Tests for new features in C++14
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_14], [[
// If the compiler admits that it is not ready for C++14, why torture it?
// Hopefully, this will speed up the test.
#ifndef __cplusplus
#error "This is not a C++ compiler"
#elif __cplusplus < 201402L
#error "This is not a C++14 compiler"
#else
namespace cxx14
{
namespace test_polymorphic_lambdas
{
int
test()
{
const auto lambda = [](auto&&... args){
const auto istiny = [](auto x){
return (sizeof(x) == 1UL) ? 1 : 0;
};
const int aretiny[] = { istiny(args)... };
return aretiny[0];
};
return lambda(1, 1L, 1.0f, '1');
}
}
namespace test_binary_literals
{
constexpr auto ivii = 0b0000000000101010;
static_assert(ivii == 42, "wrong value");
}
namespace test_generalized_constexpr
{
template < typename CharT >
constexpr unsigned long
strlen_c(const CharT *const s) noexcept
{
auto length = 0UL;
for (auto p = s; *p; ++p)
++length;
return length;
}
static_assert(strlen_c("") == 0UL, "");
static_assert(strlen_c("x") == 1UL, "");
static_assert(strlen_c("test") == 4UL, "");
static_assert(strlen_c("another\0test") == 7UL, "");
}
namespace test_lambda_init_capture
{
int
test()
{
auto x = 0;
const auto lambda1 = [a = x](int b){ return a + b; };
const auto lambda2 = [a = lambda1(x)](){ return a; };
return lambda2();
}
}
namespace test_digit_separators
{
constexpr auto ten_million = 100'000'000;
static_assert(ten_million == 100000000, "");
}
namespace test_return_type_deduction
{
auto f(int& x) { return x; }
decltype(auto) g(int& x) { return x; }
template < typename T1, typename T2 >
struct is_same
{
static constexpr auto value = false;
};
template < typename T >
struct is_same<T, T>
{
static constexpr auto value = true;
};
int
test()
{
auto x = 0;
static_assert(is_same<int, decltype(f(x))>::value, "");
static_assert(is_same<int&, decltype(g(x))>::value, "");
return x;
}
}
} // namespace cxx14
#endif // __cplusplus >= 201402L
]])
dnl Tests for new features in C++17
m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_17], [[
// If the compiler admits that it is not ready for C++17, why torture it?
// Hopefully, this will speed up the test.
#ifndef __cplusplus
#error "This is not a C++ compiler"
#elif __cplusplus <= 201402L
#error "This is not a C++17 compiler"
#else
#if defined(__clang__)
#define REALLY_CLANG
#else
#if defined(__GNUC__)
#define REALLY_GCC
#endif
#endif
#include <initializer_list>
#include <utility>
#include <type_traits>
namespace cxx17
{
#if !defined(REALLY_CLANG)
namespace test_constexpr_lambdas
{
// TODO: test it with clang++ from git
constexpr int foo = [](){return 42;}();
}
#endif // !defined(REALLY_CLANG)
namespace test::nested_namespace::definitions
{
}
namespace test_fold_expression
{
template<typename... Args>
int multiply(Args... args)
{
return (args * ... * 1);
}
template<typename... Args>
bool all(Args... args)
{
return (args && ...);
}
}
namespace test_extended_static_assert
{
static_assert (true);
}
namespace test_auto_brace_init_list
{
auto foo = {5};
auto bar {5};
static_assert(std::is_same<std::initializer_list<int>, decltype(foo)>::value);
static_assert(std::is_same<int, decltype(bar)>::value);
}
namespace test_typename_in_template_template_parameter
{
template<template<typename> typename X> struct D;
}
namespace test_fallthrough_nodiscard_maybe_unused_attributes
{
int f1()
{
return 42;
}
[[nodiscard]] int f2()
{
[[maybe_unused]] auto unused = f1();
switch (f1())
{
case 17:
f1();
[[fallthrough]];
case 42:
f1();
}
return f1();
}
}
namespace test_extended_aggregate_initialization
{
struct base1
{
int b1, b2 = 42;
};
struct base2
{
base2() {
b3 = 42;
}
int b3;
};
struct derived : base1, base2
{
int d;
};
derived d1 {{1, 2}, {}, 4}; // full initialization
derived d2 {{}, {}, 4}; // value-initialized bases
}
namespace test_general_range_based_for_loop
{
struct iter
{
int i;
int& operator* ()
{
return i;
}
const int& operator* () const
{
return i;
}
iter& operator++()
{
++i;
return *this;
}
};
struct sentinel
{
int i;
};
bool operator== (const iter& i, const sentinel& s)
{
return i.i == s.i;
}
bool operator!= (const iter& i, const sentinel& s)
{
return !(i == s);
}
struct range
{
iter begin() const
{
return {0};
}
sentinel end() const
{
return {5};
}
};
void f()
{
range r {};
for (auto i : r)
{
[[maybe_unused]] auto v = i;
}
}
}
namespace test_lambda_capture_asterisk_this_by_value
{
struct t
{
int i;
int foo()
{
return [*this]()
{
return i;
}();
}
};
}
namespace test_enum_class_construction
{
enum class byte : unsigned char
{};
byte foo {42};
}
namespace test_constexpr_if
{
template <bool cond>
int f ()
{
if constexpr(cond)
{
return 13;
}
else
{
return 42;
}
}
}
namespace test_selection_statement_with_initializer
{
int f()
{
return 13;
}
int f2()
{
if (auto i = f(); i > 0)
{
return 3;
}
switch (auto i = f(); i + 4)
{
case 17:
return 2;
default:
return 1;
}
}
}
#if !defined(REALLY_CLANG)
namespace test_template_argument_deduction_for_class_templates
{
// TODO: test it with clang++ from git
template <typename T1, typename T2>
struct pair
{
pair (T1 p1, T2 p2)
: m1 {p1},
m2 {p2}
{}
T1 m1;
T2 m2;
};
void f()
{
[[maybe_unused]] auto p = pair{13, 42u};
}
}
#endif // !defined(REALLY_CLANG)
namespace test_non_type_auto_template_parameters
{
template <auto n>
struct B
{};
B<5> b1;
B<'a'> b2;
}
#if !defined(REALLY_CLANG)
namespace test_structured_bindings
{
// TODO: test it with clang++ from git
int arr[2] = { 1, 2 };
std::pair<int, int> pr = { 1, 2 };
auto f1() -> int(&)[2]
{
return arr;
}
auto f2() -> std::pair<int, int>&
{
return pr;
}
struct S
{
int x1 : 2;
volatile double y1;
};
S f3()
{
return {};
}
auto [ x1, y1 ] = f1();
auto& [ xr1, yr1 ] = f1();
auto [ x2, y2 ] = f2();
auto& [ xr2, yr2 ] = f2();
const auto [ x3, y3 ] = f3();
}
#endif // !defined(REALLY_CLANG)
#if !defined(REALLY_CLANG)
namespace test_exception_spec_type_system
{
// TODO: test it with clang++ from git
struct Good {};
struct Bad {};
void g1() noexcept;
void g2();
template<typename T>
Bad
f(T*, T*);
template<typename T1, typename T2>
Good
f(T1*, T2*);
static_assert (std::is_same_v<Good, decltype(f(g1, g2))>);
}
#endif // !defined(REALLY_CLANG)
namespace test_inline_variables
{
template<class T> void f(T)
{}
template<class T> inline T g(T)
{
return T{};
}
template<> inline void f<>(int)
{}
template<> int g<>(int)
{
return 5;
}
}
} // namespace cxx17
#endif // __cplusplus <= 201402L
]])
ax_cxx_compile_stdcxx_11.m4
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@@ -0,0 +1,39 @@
# =============================================================================
# https://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx_11.html
# =============================================================================
#
# SYNOPSIS
#
# AX_CXX_COMPILE_STDCXX_11([ext|noext], [mandatory|optional])
#
# DESCRIPTION
#
# Check for baseline language coverage in the compiler for the C++11
# standard; if necessary, add switches to CXX and CXXCPP to enable
# support.
#
# This macro is a convenience alias for calling the AX_CXX_COMPILE_STDCXX
# macro with the version set to C++11. The two optional arguments are
# forwarded literally as the second and third argument respectively.
# Please see the documentation for the AX_CXX_COMPILE_STDCXX macro for
# more information. If you want to use this macro, you also need to
# download the ax_cxx_compile_stdcxx.m4 file.
#
# LICENSE
#
# Copyright (c) 2008 Benjamin Kosnik <bkoz@redhat.com>
# Copyright (c) 2012 Zack Weinberg <zackw@panix.com>
# Copyright (c) 2013 Roy Stogner <roystgnr@ices.utexas.edu>
# Copyright (c) 2014, 2015 Google Inc.; contributed by Alexey Sokolov <sokolov@google.com>
# Copyright (c) 2015 Paul Norman <penorman@mac.com>
# Copyright (c) 2015 Moritz Klammler <moritz@klammler.eu>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice
# and this notice are preserved. This file is offered as-is, without any
# warranty.
#serial 18
AX_REQUIRE_DEFINED([AX_CXX_COMPILE_STDCXX])
AC_DEFUN([AX_CXX_COMPILE_STDCXX_11], [AX_CXX_COMPILE_STDCXX([11], [$1], [$2])])
ax_pkg_swig.m4
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# ===========================================================================
# http://www.gnu.org/software/autoconf-archive/ax_pkg_swig.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_PKG_SWIG([major.minor.micro], [action-if-found], [action-if-not-found])
#
# DESCRIPTION
#
# This macro searches for a SWIG installation on your system. If found,
# then SWIG is AC_SUBST'd; if not found, then $SWIG is empty. If SWIG is
# found, then SWIG_LIB is set to the SWIG library path, and AC_SUBST'd.
#
# You can use the optional first argument to check if the version of the
# available SWIG is greater than or equal to the value of the argument. It
# should have the format: N[.N[.N]] (N is a number between 0 and 999. Only
# the first N is mandatory.) If the version argument is given (e.g.
# 1.3.17), AX_PKG_SWIG checks that the swig package is this version number
# or higher.
#
# As usual, action-if-found is executed if SWIG is found, otherwise
# action-if-not-found is executed.
#
# In configure.in, use as:
#
# AX_PKG_SWIG(1.3.17, [], [ AC_MSG_ERROR([SWIG is required to build..]) ])
# AX_SWIG_ENABLE_CXX
# AX_SWIG_MULTI_MODULE_SUPPORT
# AX_SWIG_PYTHON
#
# LICENSE
#
# Copyright (c) 2008 Sebastian Huber <sebastian-huber@web.de>
# Copyright (c) 2008 Alan W. Irwin
# Copyright (c) 2008 Rafael Laboissiere <rafael@laboissiere.net>
# Copyright (c) 2008 Andrew Collier
# Copyright (c) 2011 Murray Cumming <murrayc@openismus.com>
#
# 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 of the License, 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, see <http://www.gnu.org/licenses/>.
#
# As a special exception, the respective Autoconf Macro's copyright owner
# gives unlimited permission to copy, distribute and modify the configure
# scripts that are the output of Autoconf when processing the Macro. You
# need not follow the terms of the GNU General Public License when using
# or distributing such scripts, even though portions of the text of the
# Macro appear in them. The GNU General Public License (GPL) does govern
# all other use of the material that constitutes the Autoconf Macro.
#
# This special exception to the GPL applies to versions of the Autoconf
# Macro released by the Autoconf Archive. When you make and distribute a
# modified version of the Autoconf Macro, you may extend this special
# exception to the GPL to apply to your modified version as well.
#serial 11
AC_DEFUN([AX_PKG_SWIG],[
# Ubuntu has swig 2.0 as /usr/bin/swig2.0
AC_PATH_PROGS([SWIG],[swig swig2.0])
if test -z "$SWIG" ; then
m4_ifval([$3],[$3],[:])
elif test -n "$1" ; then
AC_MSG_CHECKING([SWIG version])
[swig_version=`$SWIG -version 2>&1 | grep 'SWIG Version' | sed 's/.*\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\).*/\1/g'`]
AC_MSG_RESULT([$swig_version])
if test -n "$swig_version" ; then
# Calculate the required version number components
[required=$1]
[required_major=`echo $required | sed 's/[^0-9].*//'`]
if test -z "$required_major" ; then
[required_major=0]
fi
[required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
[required_minor=`echo $required | sed 's/[^0-9].*//'`]
if test -z "$required_minor" ; then
[required_minor=0]
fi
[required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
[required_patch=`echo $required | sed 's/[^0-9].*//'`]
if test -z "$required_patch" ; then
[required_patch=0]
fi
# Calculate the available version number components
[available=$swig_version]
[available_major=`echo $available | sed 's/[^0-9].*//'`]
if test -z "$available_major" ; then
[available_major=0]
fi
[available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
[available_minor=`echo $available | sed 's/[^0-9].*//'`]
if test -z "$available_minor" ; then
[available_minor=0]
fi
[available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
[available_patch=`echo $available | sed 's/[^0-9].*//'`]
if test -z "$available_patch" ; then
[available_patch=0]
fi
# Convert the version tuple into a single number for easier comparison.
# Using base 100 should be safe since SWIG internally uses BCD values
# to encode its version number.
required_swig_vernum=`expr $required_major \* 10000 \
\+ $required_minor \* 100 \+ $required_patch`
available_swig_vernum=`expr $available_major \* 10000 \
\+ $available_minor \* 100 \+ $available_patch`
if test $available_swig_vernum -lt $required_swig_vernum; then
AC_MSG_WARN([SWIG version >= $1 is required. You have $swig_version.])
SWIG=''
m4_ifval([$3],[$3],[])
else
AC_MSG_CHECKING([for SWIG library])
SWIG_LIB=`$SWIG -swiglib`
AC_MSG_RESULT([$SWIG_LIB])
m4_ifval([$2],[$2],[])
fi
else
AC_MSG_WARN([cannot determine SWIG version])
SWIG=''
m4_ifval([$3],[$3],[])
fi
fi
AC_SUBST([SWIG_LIB])
])
config.guess
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config.h.in
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/* 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
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configure.ac
+490 -548
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depcomp
-529
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@@ -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
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<!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">
<!--#include virtual="/include/topIncludes.html"-->
<div id="maincenter">
<head>
<title>Building HDF5</title>
</head>
<body bgcolor="#F0F0F0">
<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>
<!--#include virtual="/include/dateFooter.html"-->
doc/Downloading.html
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<!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">
<!--#include virtual="/include/topIncludes.html"-->
<div id="maincenter">
<head>
<title>Downloading HDF5 and H5Part</title>
</head>
<body bgcolor="#F0F0F0">
<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.
<pre>
ftp ftp.ncsa.uiuc.edu
username: anonymous
password: your email
cd HDF/HDF5/current/src
ls
get hdf5-1.6.5.tar.gz (get the current version, this as the one on April 20th, 2006)
cd szip/src
ls
get szip-2.0.tar.gz (get the current version, this as the one on April 20th, 2006)
cd ../../
cd zlib/1.2/src
ls
get zlib-1.2.1.tar.gz (get the current version, this as the one on April 20th, 2006)
</pre>
Note: you might already have libz in your system and you will not need libsz unless you build hdf5 with support for it.
<a name="hpart">
<h2>Downloading H5Part</h2></a>
Please contact <address><a href="mailto:andreas.adelmann@psi.ch">Andreas Adelmann</a></address>.
</div>
<!--#include virtual="/include/dateFooter.html"-->
doc/Doxyfile
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doc/Examples/meshexample.dxf
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doc/Examples/meshexample.txt
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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
10
10
10
10
10
10
10
10
10
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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 18
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
0
1
2
3
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5
6
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9
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11
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17
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
14
15
16
CELL_DATA 2
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
0
1
doc/Examples/simple_tet_level1.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 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
2
3
4
5
6
7
8
doc/Examples/simple_tet_level2.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 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
7
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
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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
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0
1
1
1
1
1
0
0
0
0
0
1
doc/Examples/trimesh_dgraph_level0.metis.part.3
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1
1
2
2
2
0
0
0
0
1
1
2
doc/Examples/trimesh_dnode_level1.metis
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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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1
1
0
0
0
0
1
1
1
1
0
1
0
0
0
0
1
0
0
0
1
1
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1
doc/Examples/trimesh_level0.metis
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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
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1
1
1
1
0
0
0
0
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0
1
1
doc/Examples/trimesh_level0.metis.ngraph
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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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1
1
1
1
1
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0
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0
0
doc/Examples/trimesh_level1.metis
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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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1
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1
doc/H5.dox
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/*!
\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> Mark Howison (NERSC/LBNL) </LI>
<LI> Prabhat (NERSC/LBNL) </LI>
<LI> Wes Bethel (NERSC/LBNL) </LI>
</UL>
Previous developers:
<UL>
<LI> Benedikt Oswald (PSI) </LI>
<LI> Cristina Siegerist (NERSC/LBNL)</LI>
<LI> John Shalf (NERSC/LBNL)</LI>
</UL>
For more information, please contact the
<a href="mailto:h5part@lists.psi.ch">h5part</a> mailing list.
\defgroup c_api C API
@{
\note The C API is implemented with '\c static \c inline' functions to minimize overhead.
\defgroup h5_c_api H5
@{
\defgroup h5_file File interface
In this section we document the interface for accessing H5hut files.
\defgroup h5_model Setting up the data model
The fundamental data model of H5hut is pretty simple. There
are (time-)steps to group data, that's it. In this section we
document the interface to these (time-)steps.
\defgroup h5_file_attribs File attributes interface
File attributes are small datasets that can be used to
describe specific properties of a file. The H5hut API provides
functions to attach (write), read and inquire file attributes.
\defgroup h5_step_attribs Step attributes interface
Step attributes are similar to file attributes but are
attached to (time-)steps. They can be used to describe
specific properties of a specific step. The H5hut API provides
functions to attach (write), read and inquire step attributes.
\defgroup h5_attach Attaching files
Sometimes it is required (or at least useful) to attach
additional information to H5hut files. H5hut provides
functions to attach other files to H5hut files. The attached
files can be of any type.
\defgroup h5_log Controlling verbosity level
Controlling the verbosity level of H5hut. By default only
error messages are printed. For debugging it might be helpful
to increase the verbosity level.
\defgroup h5_debug Controlling debug output
Debug output mainly intended for developers.
\defgroup h5_error Error handling interface
H5hut comes with two error handler. The default error handler
prints an error message (which can be suppressed by setting
the verbosity level to \c 0), sets an internal error number
and returns to the calling program with the value \c
H5_FAILURE. It is up to the programmer to handle the error
properly. In certain use-cases it make sense just to abort the
program, so no additional error handling is needed. H5hut
provides an abort error-handler for this use-cases-
@}
\defgroup h5part_c_api H5Part
@{
\defgroup h5part_model Setting up the data model
The H5Part data model interface provides functions to set and
inquire (per core) views on datasets.
\defgroup h5part_io Dataset interface
The dataset interface provides functions to read and write
datasets. The following data types are supported:
- 64-bit floating point numbers (\c h5_float64_t)
- 32-bit floating point numbers (\c h5_float32_t)
- 64-bit integers (\c h5_int64_t)
- 32-bit integers (\c h5_int32_t)
\note Before you can write or read a dataset, you have to
define a "view" on the dataset for each core.
@}
\defgroup h5block_c_api H5Block
@{
\defgroup h5block_model Setting up the data model
The H5Block data model interface provides functions to set and
inquire (per core) views on fields.
\defgroup h5block_io Interface to block structured data
H5Block provides functions to store and retrieve
- 3-dimensional fields with scalar values
- 3-dimensional fields with 3-dimensional vectors as values
The following datatypes are supported:
- 64-bit floating point numbers (\c h5_float64_t)
- 32-bit floating point numbers (\c h5_float32_t)
- 64-bit integers (\c h5_int64_t)
- 32-bit integers (\c h5_int32_t)
\defgroup h5block_attrib Attaching attributes to field data
Field attributes are small datasets that can be used to
describe specific properties of a field like origin, spacing
or coordinates. The H5hut API provides functions to attach
(write), read and inquire file attributes.
@}
@}
*/
/*!
\defgroup f90_api Fortran90 API
@{
\defgroup h5_f90_api H5
@{
\defgroup h5_file_f file interface
\defgroup h5_model_f setting up the data model
\defgroup h5_file_attribs_f reading and writing file attributes
\defgroup h5_step_attribs_f reading and writing step attributes
\defgroup h5_log_f control verbosity level
\defgroup h5_debug_f control debug output
\defgroup h5_error_f error handling interface
@}
\defgroup h5part_f90_api H5Part
@{
\defgroup h5part_model_f setting up the data model
\defgroup h5part_io_f reading and writing datasets
@}
\defgroup h5block_f90_api H5Block
@{
\defgroup h5block_model_f setting up the data model
\defgroup h5block_io_f reading and writing datasets
\defgroup h5block_attrib_f reading and writing attributes
@}
@}
*/
doc/H5PartExpress.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
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<title>H5Part Utility Tools</title>
</head>
<body bgcolor="#F0F0F0">
<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>
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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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Proposal for a more general file format used by H5Part/H5Block
Authors: Achim Gsell
Status: Draft
1. Introduction
H5X is the file format used by H5Part and H5Block. H5X is designed on
top of HDF5: A H5X file is a very special HDF5 file.
+--------------------+
| Application |
+--------------------+
| H5Part/H5Block API |
+--------------------+
| H5X API |
+--------------------+
| HDF5 API |
+--------------------+
| Filesystem of OS |
+--------------------+
2. H5X file format specification
2.1 The root group
2.1.1 File attributes
Attributes of the HDF5 root group are called "file attributes". There
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
__stepname__ (optional)
See below.
__stepnumwidth__ (optional)
See below.
2.1.2 Members of the root group
Members of the root group are special formated HDF5 groups called
"step groups". The name of a step group is "<name>#<number>".
Whereby <name> is either defined by the optional file attribute
__stepname__ or set to "Step" by default. <number> is an
unsigned integer less than 2^63.
/
+- Step#0
+- Step#1
...
+- Step#n
+- StepProperties [NEW]
+- Mesh [NEW]
The optional file attribute __stepnumwidth__ defines the minimum width
of <number> in the name of the step group. The number is padded with
'0'. The minimum width defaults to zero, so that no paddings occurs.
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 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 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
No predefined step attributes exists.
2.2.3 Members of a step group
Members of a step group are HDF5 datasets and optional one HDF5 group
with the name "Block". HDF5 datasets in a step group are called "step
datasets". The optional block group is called "block data".
Mesh?!
2.2.4 Step datasets
Step datasets are arrays of rank 1. The dataset size must be the same
for all datasets inside a step. The size of the dataset may vary
from step to step. Array values are 64bit integer or 64bit floating
point numbers. No limitations (other than given by HDF5) are given on
step dataset names.
2.2.5 Block Data
The block data group is a container for an arbitrary number of field
data. A field is a data structure to store arrays of rank m with
n-dimensional vector values. Fields are represented within HDF5
groups. The HDF5 group name is the unique identifier for a field in
the current step.
2.2.5.1 m-rank fields with n-dimensional-vector values
Values are stored per dimension in separate datasets. Thus we have n
datasets for a field with n-dimensional vector values. Each dataset
corresponse to one dimension. The datasets are numbered from '0' to
'n-1'. Arrays are stored in column major order (Fortran indexing
scheme).
/ # HDF5 root group
...
+- Step#<i> # HDF5 group
|
+- Block # HDF5 group
|
+- <field name> # HDF5 group
|
+- 0 # HDF5 dataset, first dim of vector
+- 1 # HDF5 dataset, second dim of vector
...
+- n-1 # HDF5 dataset, last dim of vector
...
2.2.5.2 m-rank fields with scalar values
Fields with scalar values are stored as special case of fields with
n-dimensional vector values with n := 1.
/ # HDF5 root group
...
+- Step#<i> # HDF5 group
|
+- Block # HDF5 group
|
+- <field name> # HDF5 group
|
+- 0 # HDF5 dataset, scalar value
...
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
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<html><head><title>H5Part Tools How-to</title>
<meta http-equiv="Content-Type" content="text/html; charset=euc-kr"></head>
<body bgcolor="#ffffff" text="#000000">
<table border="0" cellpadding="0" cellspacing="0" width="987">
<tbody><tr>
<td height="6050" width="27"></td>
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<div id="body">
<div id="mainleft"><font face="Arial, Helvetica, sans-serif"><a name="TOP"></a>
</font></div>
<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>
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EXTRA_DIST = \
Doxyfile doxyfooter \
$(wildcard *.html) \
$(wildcard *.png) \
$(wildcard H5PartVisIt/*.png) \
$(wildcard H5tools/*.html) \
$(wildcard H5tools/H5tools_files/*.jpg)
Doxyfile \
H5.dox
all:
doc:
doxydoc:
doxygen
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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">
<!--#include virtual="/include/topIncludes.html"-->
<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">
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<head>
<title>H5part, the Fortran API</title>
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<meta name="keywords" content="scientific visualization">
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<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>H5/H5Part/H5Block/H5Fed API</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<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>
<!--
<font face="arial,helvetica" color="#555588"><h2>Requirements Specification</h2></font>
<UL>
<LI><a href="H5PartSpecs.html">H5Part API specifications
</UL>
</a>
-->
<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>
</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="H5PartPartView.html">PartView Visualization Application</a>
</UL>
</div>
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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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#!/usr/bin/env python
from lxml import etree
from lxml.html import builder as E
import os
import re
tree = etree.parse('tagfile')
tags = tree.xpath ('//member[@kind="function"]')
tags_per_files = {}
for tag in tags:
name = tag.find("name").text
anchor = tag.find("anchor").text
anchorfile = tag.find("anchorfile").text
if anchorfile in tags_per_files:
tags_per_files[anchorfile].append([name, anchor])
else:
tags_per_files[anchorfile] = [[name, anchor]]
prefix = None
for line in open("Doxyfile", "r"):
if re.search ("^OUTPUT_DIRECTORY", line):
prefix = line.split("=")[-1].strip()
if not prefix:
prefix = "."
parser = etree.HTMLParser()
for filename,anchors in tags_per_files.items():
print "Processing file: %s/%s" % (prefix, filename)
tree = etree.parse ("%s/%s" % (prefix, filename), parser)
for name,id in anchors:
anchor = tree.xpath ('//a[@id="%s"]' % id)
el = E.A(id="%s" % name)
anchor[0].addnext (el)
f = open ("%s/%s" % (prefix, filename), "w")
f.write (etree.tostring (tree))
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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
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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
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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
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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
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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
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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
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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
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doc/tetrahedron_refinements/1-edge/edge_30_refined/30.pvsm
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doc/tetrahedron_refinements/1-edge/edge_30_refined/30.txt
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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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doc/tetrahedron_refinements/1-edge/edge_31_refined/31.png
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doc/tetrahedron_refinements/1-edge/edge_31_refined/31.pvsm
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doc/tetrahedron_refinements/1-edge/edge_31_refined/31.txt
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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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