From 3364b54e106644d40321ea334a81e43feb31eba9 Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue, 16 Apr 2024 13:51:20 -0500 Subject: [PATCH] Use aliases for URLs (#4409) --- CONTRIBUTING.md | 2 +- README.md | 6 +- doc/parallel-compression.md | 28 +- doxygen/aliases | 225 +++++------ doxygen/dox/About.dox | 16 +- doxygen/dox/ExamplesAPI.dox | 620 +++++++++++++++---------------- doxygen/dox/IntroHDF5.dox | 4 +- doxygen/dox/IntroParExamples.dox | 16 +- doxygen/dox/IntroParHDF5.dox | 9 +- doxygen/dox/LearnBasics.dox | 20 +- doxygen/dox/LearnBasics2.dox | 2 +- doxygen/dox/LearnBasics3.dox | 18 +- doxygen/dox/LearnHDFView.dox | 16 +- doxygen/dox/UsersGuide.dox | 4 +- doxygen/dox/VOLConnGuide.dox | 4 +- doxygen/dox/ViewTools.dox | 53 +-- doxygen/dox/ViewToolsJPSS.dox | 4 +- doxygen/dox/rm-template.dox | 4 +- doxygen/examples/FileFormat.html | 2 +- doxygen/examples/intro_SWMR.html | 4 +- doxygen/hdf5doxy_layout.xml | 4 +- hl/src/H5DOpublic.h | 2 +- hl/src/H5LTpublic.h | 6 +- release_docs/INSTALL_Auto.txt | 2 +- src/H5Fmodule.h | 8 +- src/H5Ppublic.h | 20 +- src/H5VLmodule.h | 2 +- src/H5module.h | 8 +- 28 files changed, 552 insertions(+), 557 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3ffb0509eba..9264c975c0d 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -122,7 +122,7 @@ Please make sure that you check the items applicable to your pull request: * [ ] If changes were done to Autotools build, were they added to CMake and vice versa? * [ ] Is the pull request applicable to any other branches? If yes, which ones? Please document it in the GitHub issue. * [ ] Is the new code sufficiently documented for future maintenance? - * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://docs.hdfgroup.org/hdf5/v1_14/api-compat-macros.html) + * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (./api-compat-macros.html) * Documentation * [ ] Was the change described in the release_docs/RELEASE.txt file? * [ ] Was the new function documented in the corresponding public header file using [Doxygen](https://hdfgroup.github.io/hdf5/v1_14/_r_m_t.html)? diff --git a/README.md b/README.md index 98f093f83d2..7dff4158049 100644 --- a/README.md +++ b/README.md @@ -21,15 +21,15 @@ DOCUMENTATION ------------- This release is fully functional for the API described in the documentation. - https://docs.hdfgroup.org/hdf5/v1_14/_l_b_a_p_i.html + [HDF5 C API](./_l_b_a_p_i.html) Full Documentation and Programming Resources for this release can be found at - https://docs.hdfgroup.org/hdf5/v1_14/index.html + [Full Documentation](./index.html) The latest doxygen documentation generated on changes to HDF5 1.14.x is available at: - https://hdfgroup.github.io/hdf5/ + https://hdfgroup.github.io/hdf5/v1_14 See the [RELEASE.txt](release_docs/RELEASE.txt) file in the [release_docs/](release_docs/) directory for information specific to the features and updates included in this release of the library. diff --git a/doc/parallel-compression.md b/doc/parallel-compression.md index dc68ea4e081..a9bcdb2086a 100644 --- a/doc/parallel-compression.md +++ b/doc/parallel-compression.md @@ -79,7 +79,7 @@ participate in the collective write call. ## Multi-dataset I/O support The parallel compression feature is supported when using the -multi-dataset I/O API routines ([H5Dwrite_multi](https://hdfgroup.github.io/hdf5/group___h5_d.html#gaf6213bf3a876c1741810037ff2bb85d8)/[H5Dread_multi](https://hdfgroup.github.io/hdf5/group___h5_d.html#ga8eb1c838aff79a17de385d0707709915)), but the +multi-dataset I/O API routines ([H5Dwrite_multi](https://hdfgroup.github.io/hdf5/develop/group___h5_d.html#gaf6213bf3a876c1741810037ff2bb85d8)/[H5Dread_multi](https://hdfgroup.github.io/hdf5/develop/group___h5_d.html#ga8eb1c838aff79a17de385d0707709915)), but the following should be kept in mind: - Parallel writes to filtered datasets **must** still be collective, @@ -99,7 +99,7 @@ following should be kept in mind: ## Incremental file space allocation support -HDF5's [file space allocation time](https://hdfgroup.github.io/hdf5/group___d_c_p_l.html#ga85faefca58387bba409b65c470d7d851) +HDF5's [file space allocation time](https://hdfgroup.github.io/hdf5/develop/group___d_c_p_l.html#ga85faefca58387bba409b65c470d7d851) is a dataset creation property that can have significant effects on application performance, especially if the application uses parallel HDF5. In a serial HDF5 application, the default file space @@ -118,7 +118,7 @@ While this strategy has worked in the past, it has some noticeable drawbacks. For one, the larger the chunked dataset being created, the more noticeable overhead there will be during dataset creation as all of the data chunks are being allocated in the HDF5 file. -Further, these data chunks will, by default, be [filled](https://hdfgroup.github.io/hdf5/group___d_c_p_l.html#ga4335bb45b35386daa837b4ff1b9cd4a4) +Further, these data chunks will, by default, be [filled](https://hdfgroup.github.io/hdf5/develop/group___d_c_p_l.html#ga4335bb45b35386daa837b4ff1b9cd4a4) with HDF5's default fill data value, leading to extraordinary dataset creation overhead and resulting in pre-filling large portions of a dataset that the application might have been planning @@ -126,7 +126,7 @@ to overwrite anyway. Even worse, there will be more initial overhead from compressing that fill data before writing it out, only to have it read back in, unfiltered and modified the first time a chunk is written to. In the past, it was typically suggested that parallel -HDF5 applications should use [H5Pset_fill_time](https://hdfgroup.github.io/hdf5/group___d_c_p_l.html#ga6bd822266b31f86551a9a1d79601b6a2) +HDF5 applications should use [H5Pset_fill_time](https://hdfgroup.github.io/hdf5/develop/group___d_c_p_l.html#ga6bd822266b31f86551a9a1d79601b6a2) with a value of `H5D_FILL_TIME_NEVER` in order to disable writing of the fill value to dataset chunks, but this isn't ideal if the application actually wishes to make use of fill values. @@ -220,14 +220,14 @@ chunks to end up at addresses in the file that do not align well with the underlying file system, possibly leading to poor performance. As an example, Lustre performance is generally good when writes are aligned with the chosen stripe size. -The HDF5 application can use [H5Pset_alignment](https://hdfgroup.github.io/hdf5/group___f_a_p_l.html#gab99d5af749aeb3896fd9e3ceb273677a) +The HDF5 application can use [H5Pset_alignment](https://hdfgroup.github.io/hdf5/develop/group___f_a_p_l.html#gab99d5af749aeb3896fd9e3ceb273677a) to have a bit more control over where objects in the HDF5 file end up. However, do note that setting the alignment of objects generally wastes space in the file and has the potential to dramatically increase its resulting size, so caution should be used when choosing the alignment parameters. -[H5Pset_alignment](https://hdfgroup.github.io/hdf5/group___f_a_p_l.html#gab99d5af749aeb3896fd9e3ceb273677a) +[H5Pset_alignment](https://hdfgroup.github.io/hdf5/develop/group___f_a_p_l.html#gab99d5af749aeb3896fd9e3ceb273677a) has two parameters that control the alignment of objects in the HDF5 file, the "threshold" value and the alignment value. The threshold value specifies that any object greater @@ -264,19 +264,19 @@ in a file, this can create significant amounts of free space in the file over its lifetime and eventually cause performance issues. -An HDF5 application can use [H5Pset_file_space_strategy](https://hdfgroup.github.io/hdf5/group___f_c_p_l.html#ga167ff65f392ca3b7f1933b1cee1b9f70) +An HDF5 application can use [H5Pset_file_space_strategy](https://hdfgroup.github.io/hdf5/develop/group___f_c_p_l.html#ga167ff65f392ca3b7f1933b1cee1b9f70) with a value of `H5F_FSPACE_STRATEGY_PAGE` to enable the paged aggregation feature, which can accumulate metadata and raw data for dataset data chunks into well-aligned, configurably sized "pages" for better performance. However, note that using the paged aggregation feature will cause any setting from -[H5Pset_alignment](https://hdfgroup.github.io/hdf5/group___f_a_p_l.html#gab99d5af749aeb3896fd9e3ceb273677a) +[H5Pset_alignment](https://hdfgroup.github.io/hdf5/develop/group___f_a_p_l.html#gab99d5af749aeb3896fd9e3ceb273677a) to be ignored. While an application should be able to get -comparable performance effects by [setting the size of these pages](https://hdfgroup.github.io/hdf5/group___f_c_p_l.html#gad012d7f3c2f1e1999eb1770aae3a4963) to be equal to the value that -would have been set for [H5Pset_alignment](https://hdfgroup.github.io/hdf5/group___f_a_p_l.html#gab99d5af749aeb3896fd9e3ceb273677a), +comparable performance effects by [setting the size of these pages](https://hdfgroup.github.io/hdf5/develop/group___f_c_p_l.html#gad012d7f3c2f1e1999eb1770aae3a4963) to be equal to the value that +would have been set for [H5Pset_alignment](https://hdfgroup.github.io/hdf5/develop/group___f_a_p_l.html#gab99d5af749aeb3896fd9e3ceb273677a), this may not necessarily be the case and should be studied. -Note that [H5Pset_file_space_strategy](https://hdfgroup.github.io/hdf5/group___f_c_p_l.html#ga167ff65f392ca3b7f1933b1cee1b9f70) +Note that [H5Pset_file_space_strategy](https://hdfgroup.github.io/hdf5/develop/group___f_c_p_l.html#ga167ff65f392ca3b7f1933b1cee1b9f70) has a `persist` parameter. This determines whether or not the file free space manager should include extra metadata in the HDF5 file about free space sections in the file. If this @@ -300,12 +300,12 @@ hid_t file_id = H5Fcreate("file.h5", H5F_ACC_TRUNC, fcpl_id, fapl_id); While the parallel compression feature requires that the HDF5 application set and maintain collective I/O at the application -interface level (via [H5Pset_dxpl_mpio](https://hdfgroup.github.io/hdf5/group___d_x_p_l.html#ga001a22b64f60b815abf5de8b4776f09e)), +interface level (via [H5Pset_dxpl_mpio](https://hdfgroup.github.io/hdf5/develop/group___d_x_p_l.html#ga001a22b64f60b815abf5de8b4776f09e)), it does not require that the actual MPI I/O that occurs at the lowest layers of HDF5 be collective; independent I/O may perform better depending on the application I/O patterns and parallel file system performance, among other factors. The -application may use [H5Pset_dxpl_mpio_collective_opt](https://hdfgroup.github.io/hdf5/group___d_x_p_l.html#gacb30d14d1791ec7ff9ee73aa148a51a3) +application may use [H5Pset_dxpl_mpio_collective_opt](https://hdfgroup.github.io/hdf5/develop/group___d_x_p_l.html#gacb30d14d1791ec7ff9ee73aa148a51a3) to control this setting and see which I/O method provides the best performance. @@ -318,7 +318,7 @@ H5Dwrite(..., dxpl_id, ...); ### Runtime HDF5 Library version -An HDF5 application can use the [H5Pset_libver_bounds](https://hdfgroup.github.io/hdf5/group___f_a_p_l.html#gacbe1724e7f70cd17ed687417a1d2a910) +An HDF5 application can use the [H5Pset_libver_bounds](https://hdfgroup.github.io/hdf5/develop/group___f_a_p_l.html#gacbe1724e7f70cd17ed687417a1d2a910) routine to set the upper and lower bounds on library versions to use when creating HDF5 objects. For parallel compression specifically, setting the library version to the latest available diff --git a/doxygen/aliases b/doxygen/aliases index e2191cd4bd5..221d60e1a61 100644 --- a/doxygen/aliases +++ b/doxygen/aliases @@ -1,5 +1,18 @@ ALIASES += THG="The HDF Group" +################################################################################ +# Default URLs (Note that md files do not use any aliases) +################################################################################ +ALIASES += ARCURL="docs.hdfgroup.org/hdf5" +ALIASES += RFCURL="docs.hdfgroup.org/hdf5/rfc" +ALIASES += DSPURL="portal.hdfgroup.org/display/HDF5" +ALIASES += DOCURL="portal.hdfgroup.org/documentation/hdf5-docs" +ALIASES += AEXURL="support.hdfgroup.org/ftp/HDF5/examples" +# doxygen subdir (develop, v1_14) +ALIASES += DOXURL="hdfgroup.github.io/hdf5/v1_14" +#branch name (develop, hdf5_1_14) +ALIASES += SRCURL="github.com/HDFGroup/hdf5/blob/hdf5_1_14" + ################################################################################ # Styling ################################################################################ @@ -234,16 +247,16 @@ ALIASES += sa_metadata_ops="\sa \li H5Pget_all_coll_metadata_ops() \li H5Pget_co # References ################################################################################ -ALIASES += ref_cons_semantics="Enabling a Strict Consistency Semantics Model in Parallel HDF5" -ALIASES += ref_file_image_ops="HDF5 File Image Operations" -ALIASES += ref_filter_pipe="Data Flow Pipeline for H5Dread()" -ALIASES += ref_group_impls="Group implementations in HDF5" +ALIASES += ref_cons_semantics="Enabling a Strict Consistency Semantics Model in Parallel HDF5" +ALIASES += ref_file_image_ops="HDF5 File Image Operations" +ALIASES += ref_filter_pipe="Data Flow Pipeline for H5Dread()" +ALIASES += ref_group_impls="Group implementations in HDF5" ALIASES += ref_h5lib_relver="HDF5 Library Release Version Numbers" -ALIASES += ref_mdc_in_hdf5="Metadata Caching in HDF5" -ALIASES += ref_mdc_logging="Metadata Cache Logging" -ALIASES += ref_news_112="New Features in HDF5 Release 1.12" -ALIASES += ref_h5ocopy="Copying Committed Datatypes with H5Ocopy()" -ALIASES += ref_sencode_fmt_change="RFC H5Sencode() / H5Sdecode() Format Change" +ALIASES += ref_mdc_in_hdf5="Metadata Caching in HDF5" +ALIASES += ref_mdc_logging="Metadata Cache Logging" +ALIASES += ref_news_112="New Features in HDF5 Release 1.12" +ALIASES += ref_h5ocopy="Copying Committed Datatypes with H5Ocopy()" +ALIASES += ref_sencode_fmt_change="RFC H5Sencode() / H5Sdecode() Format Change" ALIASES += ref_vlen_strings="\Emph{Creating variable-length string datatypes}" ALIASES += ref_vol_doc="VOL documentation" @@ -251,103 +264,103 @@ ALIASES += ref_vol_doc="VOL documentation" # RFCs ################################################################################ -ALIASES += ref_rfc20220819="Terminal VOL Connector Feature Flags" -ALIASES += ref_rfc20210528="Multi-Thread HDF5" -ALIASES += ref_rfc20210219="Selection I/O" -ALIASES += ref_rfc20200213="VFD Sub-filing" -ALIASES += ref_rfc20200210="Onion VFD" -ALIASES += ref_rfc20190923="Virtual Object Layer (VOL) API Compatibility" -ALIASES += ref_rfc20190715="Variable-Length Data in HDF5 Sketch Design" -ALIASES += ref_rfc20190410="A Plugin Interface for HDF5 Virtual File Drivers" -ALIASES += ref_rfc20181231="Dataset Object Header Size" -ALIASES += ref_rfc20181220="MS 3.2 – Addressing Scalability: Scalability of open, close, flush CASE STUDY: CGNS Hotspot analysis of CGNS cgp_open" -ALIASES += ref_rfc20180830="Sparse Chunks" -ALIASES += ref_rfc20180829="H5FD_MIRROR Virtual File Driver" -ALIASES += ref_rfc20180815="Splitter_VFD" -ALIASES += ref_rfc20180712="Update to HDF5 References" -ALIASES += ref_rfc20180620="Chunk query functionality in HDF5" -ALIASES += ref_rfc20180610="VFD SWMR" -ALIASES += ref_rfc20180321="API Contexts" -ALIASES += ref_rfc20180125="Enhancement to the tool h5clear" -ALIASES += ref_rfc20170707="H5Sencode/H5Sdecode Format Change" -ALIASES += ref_rfc20160105="Setting Bounds for Object Creation in HDF5 1.10.0" -ALIASES += ref_rfc20150915="File Format Changes in HDF5 1.10.0" -ALIASES += ref_rfc20150709="Page Buffering" -ALIASES += ref_rfc20150615="Metadata Cache Image" -ALIASES += ref_rfc20150429="New Datatypes" -ALIASES += ref_rfc20150424="Collective Metadata Writes" -ALIASES += ref_rfc20150423="Enabling Collective Metadata Reads" -ALIASES += ref_rfc20150301="The Tool to Handle HDF5 File Format Compatibility for Chunked Datasets" -ALIASES += ref_rfc20150212="H5LTget_hardlinks – High-level API to list all the hard links to an object" -ALIASES += ref_rfc20150205="HDF5 Fortran Wrappers Maintenance: Dropping Support for Non-Fortran 2003 Standard Compliant Compilers" -ALIASES += ref_rfc20150202="New Autotools Behavior" -ALIASES += ref_rfc20141210="HDF5 Virtual Dataset" -ALIASES += ref_rfc20141201="Allocate/Free Mismatches in HDF5 Filter Code on Windows" -ALIASES += ref_rfc20140916="Virtual Object Layer" -ALIASES += ref_rfc20140827="Chunking and Compression Performance Tool Requirements" -ALIASES += ref_rfc20140729="Replacing H5Fis_hdf5() with H5Fis_accessible()" -ALIASES += ref_rfc20140722="Switching to a 64-bit hid_t Space in HDF5" -ALIASES += ref_rfc20140717="Data Analysis Extensions" -ALIASES += ref_rfc20140707="Virtual Object Layer" -ALIASES += ref_rfc20140524="HDF5 Compression Demystified" -ALIASES += ref_rfc20140318="Freeing Memory Allocated by the HDF5 Library" -ALIASES += ref_rfc20140313="Options to handle compatibility issues for HDF5 files" -ALIASES += ref_rfc20140224="Design: Metadata Cache Logging" -ALIASES += ref_rfc20131211="Fine-Grained Control of Metadata Cache Flushes" -ALIASES += ref_rfc20130930="Read Attempts for Metadata with Checksum" -ALIASES += ref_rfc20130919="Core VFD Backing Store Paged Writes" -ALIASES += ref_rfc20130630="Flush Dependency Testing" -ALIASES += ref_rfc20130316="HDF5 Dynamically Loaded Filters" -ALIASES += ref_rfc20121114="Direct Chunk Write" -ALIASES += ref_rfc20121024="HDF5 File Space Management" -ALIASES += ref_rfc20120828="New HDF5 API Routines for HPC Applications - Read/Write Multiple Datasets in an HDF5 file" -ALIASES += ref_rfc20120523="HDF5 File Space Management: Paged Aggregation" -ALIASES += ref_rfc20120501="HDF5 File Image Operations" -ALIASES += ref_rfc20120305="Enabling a Strict Consistency Semantics Model in Parallel HDF5" -ALIASES += ref_rfc20120220="h5repack: Improved Hyperslab selections for Large Chunked Datasets" -ALIASES += ref_rfc20120120="A Maintainer's Guide for the Datatype Module in HDF5 Library" -ALIASES += ref_rfc20120104="Actual I/O Mode" -ALIASES += ref_rfc20111119="New public functions to handle comparison" -ALIASES += ref_rfc20110825="Merging Named Datatypes in H5Ocopy()" -ALIASES += ref_rfc20110811="Expanding the HDF5 Hyperslab Selection Interface" -ALIASES += ref_rfc20110726="HDF5 File Space Allocation and Aggregation" -ALIASES += ref_rfc20110614=" Refactor h5dump to Improve Maintenance" -ALIASES += ref_rfc20110329="Support External Link Open File Cache in HDF5 Tools" -ALIASES += ref_rfc20110118="h5diff Attribute Comparisons" -ALIASES += ref_rfc20101122="SWMR Timeouts" -ALIASES += ref_rfc20101104="Caching Files Opened Through External Links" -ALIASES += ref_rfc20101018="HDF5 File and Object Comparison Specification" -ALIASES += ref_rfc20100902="h5edit – An HDF5 File Editing Tool" -ALIASES += ref_rfc20100727="Reserved Characters for HDF5 Applications" -ALIASES += ref_rfc20100726="High-Level HDF5 API routines for HPC Applications" -ALIASES += ref_rfc20100511="h5diff – Exclude Object(s) from Comparison" -ALIASES += ref_rfc20100422="Generating attributes into an object with a tool" -ALIASES += ref_rfc20100312="Supporting HDF5 1.8 in HDF5 Command Line Tools" -ALIASES += ref_rfc20091218="Supporting soft-link and external-link for h5diff" -ALIASES += ref_rfc20090907="HDF5 Tools Library Functions" -ALIASES += ref_rfc20090612="Default EPSILON values for comparing floating point data" -ALIASES += ref_rfc20081218="Reporting of Non-Comparable Datasets by h5diff" -ALIASES += ref_rfc20081205="External Link Traversal Callback" -ALIASES += ref_rfc20081030="Setting Raw Data Chunk Cache Parameters in HDF5" -ALIASES += ref_rfc20080915="Performance Report for Free-space Manager" -ALIASES += ref_rfc20080904="Setting File Access Property List for accessing External Link" -ALIASES += ref_rfc20080728="Native Time Types in HDF5" -ALIASES += ref_rfc20080723="Special Values in HDF5" -ALIASES += ref_rfc20080301="Dynamic Transformations to HDF5 Data" -ALIASES += ref_rfc20080209="Using SVN branching to improve software development process at THG" -ALIASES += ref_rfc20080206="Maintaining the HISTORY.txt and RELEASE.txt files in HDF5" -ALIASES += ref_rfc20071111="Addressing HDF5 file corruption issue" -ALIASES += ref_rfc20071018="NaN detection in HDF5" -ALIASES += ref_rfc20070801="Metadata Journaling to Improve Crash Survivability" -ALIASES += ref_rfc20070413="API Compatibility Strategies for HDF5" -ALIASES += ref_rfc20070115="A \"Private\" Heap for HDF5" -ALIASES += ref_rfc20060623="Performance Comparison of Collective I/O and Independent I/O with Derived Datatypes" -ALIASES += ref_rfc20060604="h5stat tool" -ALIASES += ref_rfc20060505="Simple Performance Test on Fletcher32 Filter" -ALIASES += ref_rfc20060410="Requirement Specifications of an HDF5 File Format Validation Tool" -ALIASES += ref_rfc20060317="Proposed changes to the sec2 driver " -ALIASES += ref_rfc20060124="Mapping FITS data to HDF5" -ALIASES += ref_rfc20040811="Conversion Between Text and Datatype" +ALIASES += ref_rfc20220819="Terminal VOL Connector Feature Flags" +ALIASES += ref_rfc20210528="Multi-Thread HDF5" +ALIASES += ref_rfc20210219="Selection I/O" +ALIASES += ref_rfc20200213="VFD Sub-filing" +ALIASES += ref_rfc20200210="Onion VFD" +ALIASES += ref_rfc20190923="Virtual Object Layer (VOL) API Compatibility" +ALIASES += ref_rfc20190715="Variable-Length Data in HDF5 Sketch Design" +ALIASES += ref_rfc20190410="A Plugin Interface for HDF5 Virtual File Drivers" +ALIASES += ref_rfc20181231="Dataset Object Header Size" +ALIASES += ref_rfc20181220="MS 3.2 – Addressing Scalability: Scalability of open, close, flush CASE STUDY: CGNS Hotspot analysis of CGNS cgp_open" +ALIASES += ref_rfc20180830="Sparse Chunks" +ALIASES += ref_rfc20180829="H5FD_MIRROR Virtual File Driver" +ALIASES += ref_rfc20180815="Splitter_VFD" +ALIASES += ref_rfc20180712="Update to HDF5 References" +ALIASES += ref_rfc20180620="Chunk query functionality in HDF5" +ALIASES += ref_rfc20180610="VFD SWMR" +ALIASES += ref_rfc20180321="API Contexts" +ALIASES += ref_rfc20180125="Enhancement to the tool h5clear" +ALIASES += ref_rfc20170707="H5Sencode/H5Sdecode Format Change" +ALIASES += ref_rfc20160105="Setting Bounds for Object Creation in HDF5 1.10.0" +ALIASES += ref_rfc20150915="File Format Changes in HDF5 1.10.0" +ALIASES += ref_rfc20150709="Page Buffering" +ALIASES += ref_rfc20150615="Metadata Cache Image" +ALIASES += ref_rfc20150429="New Datatypes" +ALIASES += ref_rfc20150424="Collective Metadata Writes" +ALIASES += ref_rfc20150423="Enabling Collective Metadata Reads" +ALIASES += ref_rfc20150301="The Tool to Handle HDF5 File Format Compatibility for Chunked Datasets" +ALIASES += ref_rfc20150212="H5LTget_hardlinks – High-level API to list all the hard links to an object" +ALIASES += ref_rfc20150205="HDF5 Fortran Wrappers Maintenance: Dropping Support for Non-Fortran 2003 Standard Compliant Compilers" +ALIASES += ref_rfc20150202="New Autotools Behavior" +ALIASES += ref_rfc20141210="HDF5 Virtual Dataset" +ALIASES += ref_rfc20141201="Allocate/Free Mismatches in HDF5 Filter Code on Windows" +ALIASES += ref_rfc20140916="Virtual Object Layer" +ALIASES += ref_rfc20140827="Chunking and Compression Performance Tool Requirements" +ALIASES += ref_rfc20140729="Replacing H5Fis_hdf5() with H5Fis_accessible()" +ALIASES += ref_rfc20140722="Switching to a 64-bit hid_t Space in HDF5" +ALIASES += ref_rfc20140717="Data Analysis Extensions" +ALIASES += ref_rfc20140707="Virtual Object Layer" +ALIASES += ref_rfc20140524="HDF5 Compression Demystified" +ALIASES += ref_rfc20140318="Freeing Memory Allocated by the HDF5 Library" +ALIASES += ref_rfc20140313="Options to handle compatibility issues for HDF5 files" +ALIASES += ref_rfc20140224="Design: Metadata Cache Logging" +ALIASES += ref_rfc20131211="Fine-Grained Control of Metadata Cache Flushes" +ALIASES += ref_rfc20130930="Read Attempts for Metadata with Checksum" +ALIASES += ref_rfc20130919="Core VFD Backing Store Paged Writes" +ALIASES += ref_rfc20130630="Flush Dependency Testing" +ALIASES += ref_rfc20130316="HDF5 Dynamically Loaded Filters" +ALIASES += ref_rfc20121114="Direct Chunk Write" +ALIASES += ref_rfc20121024="HDF5 File Space Management" +ALIASES += ref_rfc20120828="New HDF5 API Routines for HPC Applications - Read/Write Multiple Datasets in an HDF5 file" +ALIASES += ref_rfc20120523="HDF5 File Space Management: Paged Aggregation" +ALIASES += ref_rfc20120501="HDF5 File Image Operations" +ALIASES += ref_rfc20120305="Enabling a Strict Consistency Semantics Model in Parallel HDF5" +ALIASES += ref_rfc20120220="h5repack: Improved Hyperslab selections for Large Chunked Datasets" +ALIASES += ref_rfc20120120="A Maintainer's Guide for the Datatype Module in HDF5 Library" +ALIASES += ref_rfc20120104="Actual I/O Mode" +ALIASES += ref_rfc20111119="New public functions to handle comparison" +ALIASES += ref_rfc20110825="Merging Named Datatypes in H5Ocopy()" +ALIASES += ref_rfc20110811="Expanding the HDF5 Hyperslab Selection Interface" +ALIASES += ref_rfc20110726="HDF5 File Space Allocation and Aggregation" +ALIASES += ref_rfc20110614=" Refactor h5dump to Improve Maintenance" +ALIASES += ref_rfc20110329="Support External Link Open File Cache in HDF5 Tools" +ALIASES += ref_rfc20110118="h5diff Attribute Comparisons" +ALIASES += ref_rfc20101122="SWMR Timeouts" +ALIASES += ref_rfc20101104="Caching Files Opened Through External Links" +ALIASES += ref_rfc20101018="HDF5 File and Object Comparison Specification" +ALIASES += ref_rfc20100902="h5edit – An HDF5 File Editing Tool" +ALIASES += ref_rfc20100727="Reserved Characters for HDF5 Applications" +ALIASES += ref_rfc20100726="High-Level HDF5 API routines for HPC Applications" +ALIASES += ref_rfc20100511="h5diff – Exclude Object(s) from Comparison" +ALIASES += ref_rfc20100422="Generating attributes into an object with a tool" +ALIASES += ref_rfc20100312="Supporting HDF5 1.8 in HDF5 Command Line Tools" +ALIASES += ref_rfc20091218="Supporting soft-link and external-link for h5diff" +ALIASES += ref_rfc20090907="HDF5 Tools Library Functions" +ALIASES += ref_rfc20090612="Default EPSILON values for comparing floating point data" +ALIASES += ref_rfc20081218="Reporting of Non-Comparable Datasets by h5diff" +ALIASES += ref_rfc20081205="External Link Traversal Callback" +ALIASES += ref_rfc20081030="Setting Raw Data Chunk Cache Parameters in HDF5" +ALIASES += ref_rfc20080915="Performance Report for Free-space Manager" +ALIASES += ref_rfc20080904="Setting File Access Property List for accessing External Link" +ALIASES += ref_rfc20080728="Native Time Types in HDF5" +ALIASES += ref_rfc20080723="Special Values in HDF5" +ALIASES += ref_rfc20080301="Dynamic Transformations to HDF5 Data" +ALIASES += ref_rfc20080209="Using SVN branching to improve software development process at THG" +ALIASES += ref_rfc20080206="Maintaining the HISTORY.txt and RELEASE.txt files in HDF5" +ALIASES += ref_rfc20071111="Addressing HDF5 file corruption issue" +ALIASES += ref_rfc20071018="NaN detection in HDF5" +ALIASES += ref_rfc20070801="Metadata Journaling to Improve Crash Survivability" +ALIASES += ref_rfc20070413="API Compatibility Strategies for HDF5" +ALIASES += ref_rfc20070115="A \"Private\" Heap for HDF5" +ALIASES += ref_rfc20060623="Performance Comparison of Collective I/O and Independent I/O with Derived Datatypes" +ALIASES += ref_rfc20060604="h5stat tool" +ALIASES += ref_rfc20060505="Simple Performance Test on Fletcher32 Filter" +ALIASES += ref_rfc20060410="Requirement Specifications of an HDF5 File Format Validation Tool" +ALIASES += ref_rfc20060317="Proposed changes to the sec2 driver " +ALIASES += ref_rfc20060124="Mapping FITS data to HDF5" +ALIASES += ref_rfc20040811="Conversion Between Text and Datatype" ################################################################################ # The Usual Suspects diff --git a/doxygen/dox/About.dox b/doxygen/dox/About.dox index e60e0fbdc7a..b077bfe804c 100644 --- a/doxygen/dox/About.dox +++ b/doxygen/dox/About.dox @@ -23,7 +23,7 @@ Use Doxygen's here. +here. \subsection new_rm_entry Creating a New Reference Manual Entry @@ -33,7 +33,7 @@ Please refer to the \ref RMT for guidance on how to create a new reference manua For each HDF5 module, such as \Code{H5F}, there is an examples source file called \Code{H5*_examples.c}. For example, the \Code{H5F} API examples are located in - + H5F_examples.c. Examples are code blocks marked as Doxygen snippets. For example, the source code for the H5Fcreate() API sample is located between @@ -44,7 +44,7 @@ the //! \endverbatim comments in - + H5F_examples.c. Add a new API example by adding a new code block enclosed between matching @@ -80,7 +80,7 @@ See Doxygen's Custom Comman as a general reference. All custom commands for this project are located in the -aliases +aliases file in the doxygen subdirectory of the main HDF5 repo. @@ -91,7 +91,7 @@ ask for help if unsure! For ease of reference, we define custom commands for each RFC in the RFCs section of the -aliases +aliases file. For example the custom command \Code{ref_rfc20141210} can be used to insert a reference to "RFC: Virtual Object Layer". In other words, the markup \verbatim @@ -102,16 +102,16 @@ yields a clickable link: \ref_rfc20141210 To add a new RFC, add a custom command for the RFC to the -aliases +aliases file. The naming convention for the custom command is \Code{ref_rfcYYYYMMDD}, where \Code{YYYYMMDD} is the ID of the RFC. The URL is composed of the prefix \verbatim -https://docs.hdfgroup.org/hdf5/rfc/ +https://\RFCURL/ \endverbatim and the name of your RFC file, typically, a PDF file, i.e., the full URL would be \verbatim -https://docs.hdfgroup.org/hdf5/rfc/my_great_rfc_name.pdf +https://\RFCURL/my_great_rfc_name.pdf \endverbatim \subsection hosting How Do Updates and Changes Get Published? diff --git a/doxygen/dox/ExamplesAPI.dox b/doxygen/dox/ExamplesAPI.dox index 12b585bdeb2..92bb3b50dba 100644 --- a/doxygen/dox/ExamplesAPI.dox +++ b/doxygen/dox/ExamplesAPI.dox @@ -27,236 +27,236 @@ Languages are C, Fortran, Java (JHI5), Java Object Package, Python (High Level), Set Space Allocation Time for Dataset -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_alloc.h5 -h5ex_d_alloc.tst -h5ex_d_alloc.ddl +h5ex_d_alloc.tst +h5ex_d_alloc.ddl Read / Write Dataset using Fletcher32 Checksum Filter -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_checksum.h5 -h5ex_d_checksum.tst -h5ex_d_checksum.ddl +h5ex_d_checksum.tst +h5ex_d_checksum.ddl Read / Write Chunked Dataset -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_chunk.h5 -h5ex_d_chunk.tst -h5ex_d_chunk.ddl +h5ex_d_chunk.tst +h5ex_d_chunk.ddl Read / Write Compact Dataset -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_compact.h5 -h5ex_d_compact.tst -h5ex_d_compact.ddl +h5ex_d_compact.tst +h5ex_d_compact.ddl Read / Write to External Dataset -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_extern.h5 -h5ex_d_extern.tst -h5ex_d_extern.ddl +h5ex_d_extern.tst +h5ex_d_extern.ddl Read / Write Dataset w/ Fill Value -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_fillval.h5 -h5ex_d_fillval.tst -h5ex_d_fillval.ddl +h5ex_d_fillval.tst +h5ex_d_fillval.ddl Read / Write GZIP Compressed Dataset -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_gzip.h5 -h5ex_d_gzip.tst -h5ex_d_gzip.ddl +h5ex_d_gzip.tst +h5ex_d_gzip.ddl Read / Write Data by Hyperslabs -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_hyper.h5 -h5ex_d_hyper.tst -h5ex_d_hyper.ddl +h5ex_d_hyper.tst +h5ex_d_hyper.ddl Read / Write Dataset with n-bit Filter -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_nbit.h5 -h5ex_d_nbit.tst -h5ex_d_nbit.ddl +h5ex_d_nbit.tst +h5ex_d_nbit.ddl Read / Write Integer Dataset -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_rdwrc.h5 -h5ex_d_rdwrc.tst -h5ex_d_rdwr.ddl +h5ex_d_rdwrc.tst +h5ex_d_rdwr.ddl Read / Write Dataset w/ Shuffle Filter and GZIP Compression -C +C FORTRAN -Java +Java JavaObj MATLAB PyHigh PyLow h5ex_d_shuffle.h5 -h5ex_d_shuffle.tst -h5ex_d_shuffle.ddl +h5ex_d_shuffle.tst +h5ex_d_shuffle.ddl Read / Write Dataset using Scale-Offset Filter (float) -C +C FORTRAN -Java +Java JavaObj MATLAB PyHigh PyLow h5ex_d_sofloat.h5 -h5ex_d_sofloat.tst -h5ex_d_sofloat.ddl +h5ex_d_sofloat.tst +h5ex_d_sofloat.ddl Read / Write Dataset using Scale-Offset Filter (integer) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_soint.h5 -h5ex_d_soint.tst -h5ex_d_soint.ddl +h5ex_d_soint.tst +h5ex_d_soint.ddl Read / Write Dataset using SZIP Compression -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_szip.h5 -h5ex_d_szip.tst -h5ex_d_szip.ddl +h5ex_d_szip.tst +h5ex_d_szip.ddl Read / Write Dataset using Data Transform Expression -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_transform.h5 -h5ex_d_transform.tst -h5ex_d_transform.ddl +h5ex_d_transform.tst +h5ex_d_transform.ddl Read / Write Unlimited Dimension Dataset -C +C FORTRAN -Java +Java JavaObj MATLAB PyHigh PyLow h5ex_d_unlimadd.h5 -h5ex_d_unlimadd.tst -h5ex_d_unlimadd.ddl +h5ex_d_unlimadd.tst +h5ex_d_unlimadd.ddl Read / Write GZIP Compressed Unlimited Dimension Dataset -C +C FORTRAN -Java +Java JavaObj MATLAB PyHigh PyLow h5ex_d_unlimgzip.h5 -h5ex_d_unlimgzip.tst -h5ex_d_unlimgzip.ddl +h5ex_d_unlimgzip.tst +h5ex_d_unlimgzip.ddl Read / Write / Edit Unlimited Dimension Dataset -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_d_unlimmod.h5 -h5ex_d_unlimmod.tst -h5ex_d_unlimmod.ddl +h5ex_d_unlimmod.tst +h5ex_d_unlimmod.ddl @@ -272,105 +272,105 @@ FORTRAN Create "compact-or-indexed" Format Groups -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_g_compact.h5 -h5ex_g_.tst -h5ex_g_compact1.ddl -h5ex_g_compact2.ddl +h5ex_g_.tst +h5ex_g_compact1.ddl +h5ex_g_compact2.ddl Track links in a Group by Creation Order -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_g_corder.h5 -h5ex_g_corder.tst +h5ex_g_corder.tst h5ex_g_corder.ddl Create / Open / Close a Group -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_g_create.h5 h5ex_g_create.tst -h5ex_g_create.ddl +h5ex_g_create.ddl Create Intermediate Groups -C +C FORTRAN -Java +Java JavaObj MATLAB PyHigh PyLow h5ex_g_intermediate.h5 -h5ex_g_intermediate.tst +h5ex_g_intermediate.tst h5ex_g_intermediate.ddl Iterate over Groups w/ H5Literate -C +C FORTRAN -Java +Java JavaObj MATLAB PyHigh PyLow h5ex_g_iterate.h5 -h5ex_g_iterate.tst +h5ex_g_iterate.tst h5ex_g_iterate.ddl Set Conditions to Convert between Compact and Dense Groups -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_g_phase.h5 -h5ex_g_phase.tst +h5ex_g_phase.tst h5ex_g_phase.ddl Recursively Traverse a File with H5Literate -C +C FORTRAN -Java +Java JavaObj MATLAB PyHigh PyLow h5ex_g_traverse.h5 -h5ex_g_traverse.tst +h5ex_g_traverse.tst h5ex_g_traverse.ddl Recursively Traverse a File with H5Ovisit / H5Lvisit -C +C FORTRAN -Java +Java JavaObj MATLAB PyHigh PyLow h5ex_g_visit.h5 -h5ex_g_visit.tst +h5ex_g_visit.tst h5ex_g_visit.ddl @@ -387,347 +387,345 @@ FORTRAN Read / Write Array (Attribute) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_arrayatt.h5 -h5ex_t_arrayatt.tst -h5ex_t_arrayatt.ddl +h5ex_t_arrayatt.tst +h5ex_t_arrayatt.ddl Read / Write Array (Dataset) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_array.h5 -h5ex_t_array.tst -h5ex_t_array.ddl +h5ex_t_array.ddl Read / Write Bitfield (Attribute) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_bitatt.h5 -h5ex_t_bitatt.tst -h5ex_t_bitatt.ddl +h5ex_t_bitatt.tst +h5ex_t_bitatt.ddl Read / Write Bitfield (Dataset) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_bit.h5 -h5ex_t_bit.tst -h5ex_t_bit.ddl +h5ex_t_bit.tst +h5ex_t_bit.ddl Read / Write Compound (Attribute) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_cmpdatt.h5 -h5ex_t_cmpdatt.tst -h5ex_t_cmpdatt.ddl +h5ex_t_cmpdatt.tst +h5ex_t_cmpdatt.ddl Read / Write Compound (Dataset) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_cmpd.h5 -h5ex_t_cmpd.tst -h5ex_t_cmpd.ddl +h5ex_t_cmpd.tst +h5ex_t_cmpd.ddl Commit Named Datatype and Read Back -C +C FORTRAN -Java +Java JavaObj MATLAB PyHigh PyLow h5ex_t_commit.h5 -h5ex_t_commit.tst -h5ex_t_commit.ddl +h5ex_t_commit.tst +h5ex_t_commit.ddl Convert Between Datatypes in Memory -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow h5ex_t_convert.h5 -h5ex_t_convert.tst -h5ex_t_convert.ddl +h5ex_t_convert.tst +h5ex_t_convert.ddl Read / Write Complex Compound (Attribute) -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow h5ex_t_cpxcmpdatt.h5 -h5ex_t_cpxcmpdatt.tst -h5ex_t_cpxcmpdatt.ddl +h5ex_t_cpxcmpdatt.tst +h5ex_t_cpxcmpdatt.ddl Read / Write Complex Compound (Dataset) -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow h5ex_t_cpxcmpd.h5 -h5ex_t_cpxcmpd.tst -h5ex_t_cpxcmpd.ddl +h5ex_t_cpxcmpd.tst +h5ex_t_cpxcmpd.ddl Read / Write Enumerated (Attribute) -C -FORTRAN +C +FORTRAN Java JavaObj MATLAB PyHigh PyLow h5ex_t_enumatt.h5 -h5ex_t_enumatt.tst -h5ex_t_enumatt.ddl +h5ex_t_enumatt.tst +h5ex_t_enumatt.ddl Read / Write Enumerated (Dataset) -C -FORTRAN +C +FORTRAN Java JavaObj MATLAB PyHigh PyLow h5ex_t_enum.h5 -h5ex_t_enum.tst -h5ex_t_enum.ddl +h5ex_t_enum.tst +h5ex_t_enum.ddl Read / Write Floating Point (Attribute) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_floatatt.h5 -h5ex_t_floatatt.tst -h5ex_t_floatatt.ddl +h5ex_t_floatatt.tst +h5ex_t_floatatt.ddl Read / Write Floating Point (Dataset) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_float.h5 -h5ex_t_float.tst -h5ex_t_float.ddl +h5ex_t_float.tst +h5ex_t_float.ddl Read / Write Integer Datatype (Attribute) -C -FORTRAN -Java +C +FORTRAN JavaObj MATLAB PyHigh PyLow h5ex_t_intatt.h5 -h5ex_t_intatt.tst -h5ex_t_intatt.ddl +h5ex_t_intatt.tst +h5ex_t_intatt.ddl Read / Write Integer Datatype (Dataset) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_int.h5 -h5ex_t_int.tst -h5ex_t_int.ddl +h5ex_t_int.tst +h5ex_t_int.ddl Read / Write Object References (Attribute) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_objrefatt.h5 -h5ex_t_objrefatt.tst -h5ex_t_objrefatt.ddl +h5ex_t_objrefatt.tst +h5ex_t_objrefatt.ddl Read / Write Object References (Dataset) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_objref.h5 -h5ex_t_objref.tst -h5ex_t_objref.ddl +h5ex_t_objref.tst +h5ex_t_objref.ddl Read / Write Opaque (Attribute) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_opaqueatt.h5 -h5ex_t_opaqueatt.tst -h5ex_t_opaqueatt.ddl +h5ex_t_opaqueatt.tst +h5ex_t_opaqueatt.ddl Read / Write Opaque (Dataset) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_opaque.h5 -h5ex_t_opaque.tst -h5ex_t_opaque.ddl +h5ex_t_opaque.tst +h5ex_t_opaque.ddl Read / Write Region References (Attribute) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_regrefatt.h5 -h5ex_t_regrefatt.tst -h5ex_t_regrefatt.ddl +h5ex_t_regrefatt.tst +h5ex_t_regrefatt.ddl Read / Write Region References (Dataset) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_regref.h5 -h5ex_t_regref.tst -h5ex_t_regref.ddl +h5ex_t_regref.tst +h5ex_t_regref.ddl Read / Write String (Attribute) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_stringatt.h5 -h5ex_t_stringatt.tst -h5ex_t_stringatt.ddl +h5ex_t_stringatt.tst +h5ex_t_stringatt.ddl Read / Write String (Dataset) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_string.h5 -h5ex_t_string.tst -h5ex_t_string.ddl +h5ex_t_string.tst +h5ex_t_string.ddl Read / Write Variable Length (Attribute) -C -FORTRAN +C +FORTRAN Java JavaObj MATLAB PyHigh PyLow h5ex_t_vlenatt.h5 -h5ex_t_vlenatt.tst -h5ex_t_vlenatt.ddl +h5ex_t_vlenatt.tst +h5ex_t_vlenatt.ddl Read / Write Variable Length (Dataset) -C -FORTRAN +C +FORTRAN Java JavaObj MATLAB PyHigh PyLow h5ex_t_vlen.h5 -h5ex_t_vlen.tst -h5ex_t_vlen.ddl +h5ex_t_vlen.tst +h5ex_t_vlen.ddl Read / Write Variable Length String (Attribute) -C -FORTRAN +C +FORTRAN Java JavaObj MATLAB PyHigh PyLow h5ex_t_vlstringatt.h5 -h5ex_t_vlstringatt.tst -h5ex_t_vlstringatt.ddl +h5ex_t_vlstringatt.tst +h5ex_t_vlstringatt.ddl Read / Write Variable Length String (Dataset) -C -FORTRAN -Java +C +FORTRAN +Java JavaObj MATLAB PyHigh PyLow h5ex_t_vlstring.h5 -h5ex_t_vlstring.tst -h5ex_t_vlstring.ddl +h5ex_t_vlstring.tst +h5ex_t_vlstring.ddl @@ -743,92 +741,92 @@ FORTRAN Read / Write Dataset using Blosc Compression -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow -h5ex_d_blosc.h5 -h5ex_d_blosc.tst -h5ex_d_blosc.ddl +h5ex_d_blosc.h5 +h5ex_d_blosc.tst +h5ex_d_blosc.ddl Read / Write Dataset using Bit Shuffle Compression -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow -h5ex_d_bshuf.h5 -h5ex_d_bshuf.tst -h5ex_d_bshuf.ddl +h5ex_d_bshuf.h5 +h5ex_d_bshuf.tst +h5ex_d_bshuf.ddl Read / Write Dataset using BZip2 Compression -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow -h5ex_d_bzip2.h5 -h5ex_d_bzip2.tst -h5ex_d_bzip2.ddl +h5ex_d_bzip2.h5 +h5ex_d_bzip2.tst +h5ex_d_bzip2.ddl Read / Write Dataset using JPEG Compression -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow -h5ex_d_jpeg.h5 -h5ex_d_jpeg.tst -h5ex_d_jpeg.ddl +h5ex_d_jpeg.h5 +h5ex_d_jpeg.tst +h5ex_d_jpeg.ddl Read / Write Dataset using LZ4 Compression -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow -h5ex_d_lz4.h5 -h5ex_d_lz4.tst -h5ex_d_lz4.ddl +h5ex_d_lz4.h5 +h5ex_d_lz4.tst +h5ex_d_lz4.ddl Read / Write Dataset using LZF Compression -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow -h5ex_d_lzf.h5 -h5ex_d_lzf.tst -h5ex_d_lzf.ddl +h5ex_d_lzf.h5 +h5ex_d_lzf.tst +h5ex_d_lzf.ddl Read / Write Dataset using MAFISC Compression -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow -h5ex_d_mafisc.h5 -h5ex_d_mafisc.tst -h5ex_d_mafisc.ddl +h5ex_d_mafisc.h5 +h5ex_d_mafisc.tst +h5ex_d_mafisc.ddl Read / Write Dataset using ZFP Compression -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow -h5ex_d_zfp.h5 -h5ex_d_zfp.tst -h5ex_d_zfp.ddl +h5ex_d_zfp.h5 +h5ex_d_zfp.tst +h5ex_d_zfp.ddl Read / Write Dataset using ZStd Compression -C +C FORTRAN Java JavaObj MATLAB PyHigh PyLow -h5ex_d_zstd.h5 -h5ex_d_zstd.tst -h5ex_d_zstd.ddl +h5ex_d_zstd.h5 +h5ex_d_zstd.tst +h5ex_d_zstd.ddl @@ -842,66 +840,66 @@ FORTRAN Create/Read/Write an Attribute -Java +Java JavaObj -HDF5AttributeCreate.txt +HDF5AttributeCreate.txt Create Datasets -Java +Java JavaObj -HDF5DatasetCreate.txt +HDF5DatasetCreate.txt Read/Write Datasets -Java +Java JavaObj -HDF5DatasetRead.txt +HDF5DatasetRead.txt Create an Empty File -Java +Java JavaObj -HDF5FileCreate.txt +HDF5FileCreate.txt Retrieve the File Structure -Java +Java JavaObj -HDF5FileStructure.txt +HDF5FileStructure.txt Create Groups -Java +Java JavaObj -HDF5GroupCreate.txt +HDF5GroupCreate.txt Select a Subset of a Dataset -Java +Java JavaObj -HDF5SubsetSelect.txt +HDF5SubsetSelect.txt Create Two Datasets Within Groups -Java +Java JavaObj -HDF5GroupDatasetCreate.txt +HDF5GroupDatasetCreate.txt @@ -917,8 +915,8 @@ FORTRAN Creating and Accessing a File -C -FORTRAN +C +FORTRAN MATLAB PyHigh PyLow ph5_.h5 @@ -927,8 +925,8 @@ FORTRAN Creating and Accessing a Dataset -C -FORTRAN +C +FORTRAN MATLAB PyHigh PyLow ph5_.h5 @@ -937,8 +935,8 @@ FORTRAN Writing and Reading Contiguous Hyperslabs -C -FORTRAN +C +FORTRAN MATLAB PyHigh PyLow ph5_.h5 @@ -947,8 +945,8 @@ FORTRAN Writing and Reading Regularly Spaced Data Hyperslabs -C -FORTRAN +C +FORTRAN MATLAB PyHigh PyLow ph5_.h5 @@ -957,8 +955,8 @@ FORTRAN Writing and Reading Pattern Hyperslabs -C -FORTRAN +C +FORTRAN MATLAB PyHigh PyLow ph5_.h5 @@ -967,8 +965,8 @@ FORTRAN Writing and Reading Chunk Hyperslabs -C -FORTRAN +C +FORTRAN MATLAB PyHigh PyLow ph5_.h5 @@ -977,7 +975,7 @@ FORTRAN Using the Subfiling VFD to Write a File Striped Across Multiple Subfiles -C +C FORTRAN MATLAB PyHigh PyLow ph5_.h5 @@ -986,7 +984,7 @@ FORTRAN Write to Datasets with Filters Applied -C +C FORTRAN MATLAB PyHigh PyLow ph5_.h5 @@ -995,7 +993,7 @@ FORTRAN Collectively Write Datasets with Filters and Not All Ranks have Data -C +C FORTRAN MATLAB PyHigh PyLow ph5_.h5 diff --git a/doxygen/dox/IntroHDF5.dox b/doxygen/dox/IntroHDF5.dox index 89adb4662f1..50253ab4573 100644 --- a/doxygen/dox/IntroHDF5.dox +++ b/doxygen/dox/IntroHDF5.dox @@ -617,10 +617,10 @@ For information on compiling in C, C++ and Fortran, see: \ref LBCompiling IDL, MATLAB, and NCL Examples for HDF-EOS Examples of how to access and visualize NASA HDF-EOS files using IDL, MATLAB, and NCL. -Miscellaneous Examples +Miscellaneous Examples These (very old) examples resulted from working with users, and are not fully tested. Most of them are in C, with a few in Fortran and Java. -Using Special Values +Using Special Values These examples show how to create special values in an HDF5 application. */ diff --git a/doxygen/dox/IntroParExamples.dox b/doxygen/dox/IntroParExamples.dox index 9d148f59d64..cdab44f35a5 100644 --- a/doxygen/dox/IntroParExamples.dox +++ b/doxygen/dox/IntroParExamples.dox @@ -95,7 +95,7 @@ Below is the example program:
-hyperslab_by_row.c +hyperslab_by_row.c
@@ -205,7 +205,7 @@ Below is the F90 example program which illustrates how to write contiguous hyper
-hyperslab_by_col.F90 +hyperslab_by_col.F90
@@ -275,7 +275,7 @@ Below is an example program for writing hyperslabs by column in Parallel HDF5:
-hyperslab_by_col.c +hyperslab_by_col.c
@@ -346,7 +346,7 @@ Below is the example program for writing hyperslabs by column in Parallel HDF5:
-hyperslab_by_row.F90 +hyperslab_by_row.F90
@@ -431,12 +431,12 @@ Below are example programs for writing hyperslabs by pattern in Parallel HDF5:
-hyperslab_by_pattern.c +hyperslab_by_pattern.c
-hyperslab_by_pattern.F90 +hyperslab_by_pattern.F90
@@ -530,12 +530,12 @@ Below are example programs for writing hyperslabs by pattern in Parallel HDF5:
-hyperslab_by_chunk.c +hyperslab_by_chunk.c
-hyperslab_by_chunk.F90 +hyperslab_by_chunk.F90
diff --git a/doxygen/dox/IntroParHDF5.dox b/doxygen/dox/IntroParHDF5.dox index 0e30249f50d..414a186af89 100644 --- a/doxygen/dox/IntroParHDF5.dox +++ b/doxygen/dox/IntroParHDF5.dox @@ -145,8 +145,8 @@ Following is example code for creating an access template in HDF5: \endcode The following example programs create an HDF5 file using Parallel HDF5: -C: file_create.c -F90: file_create.F90 +C: file_create.c +F90: file_create.F90 \subsection subsec_pintro_create_dset Creating and Accessing a Dataset with PHDF5 @@ -226,8 +226,8 @@ The following code demonstrates a collective write using Parallel HDF5: \endcode The following example programs create an HDF5 dataset using Parallel HDF5: -C: dataset.c -F90: dataset.F90 +C: dataset.c +F90: dataset.F90 \subsubsection subsec_pintro_hyperslabs Hyperslabs @@ -264,7 +264,6 @@ HDF5 by contiguous hyperslab, by regularly spaced data in a column/row, by patte -
Navigate back: \ref index "Main" / \ref GettingStarted diff --git a/doxygen/dox/LearnBasics.dox b/doxygen/dox/LearnBasics.dox index 2847be7f778..bbdf4224c09 100644 --- a/doxygen/dox/LearnBasics.dox +++ b/doxygen/dox/LearnBasics.dox @@ -59,7 +59,7 @@ These examples (C, C++, Fortran) are provided in the HDF5 source code and (Unix) Create a file -C Fortran C++ Java Python +C Fortran C++ Java Python @@ -67,7 +67,7 @@ These examples (C, C++, Fortran) are provided in the HDF5 source code and (Unix) Create a dataset -C Fortran C++ Java Python +C Fortran C++ Java Python @@ -75,7 +75,7 @@ These examples (C, C++, Fortran) are provided in the HDF5 source code and (Unix) Read and write to a dataset -C Fortran C++ Java Python +C Fortran C++ Java Python @@ -83,7 +83,7 @@ These examples (C, C++, Fortran) are provided in the HDF5 source code and (Unix) Create an attribute -C Fortran C++ Java Python +C Fortran C++ Java Python @@ -91,7 +91,7 @@ These examples (C, C++, Fortran) are provided in the HDF5 source code and (Unix) Create a group -C Fortran C++ Java Python +C Fortran C++ Java Python @@ -99,7 +99,7 @@ These examples (C, C++, Fortran) are provided in the HDF5 source code and (Unix) Create groups in a file using absolute and relative paths -C Fortran C++ Java Python +C Fortran C++ Java Python @@ -107,7 +107,7 @@ These examples (C, C++, Fortran) are provided in the HDF5 source code and (Unix) Create datasets in a group -C Fortran C++ Java Python +C Fortran C++ Java Python @@ -115,7 +115,7 @@ These examples (C, C++, Fortran) are provided in the HDF5 source code and (Unix) Create a file and dataset and select/read a subset from the dataset -C Fortran C++ Java Python +C Fortran C++ Java Python Also see examples to Write by row (and column) below. @@ -123,7 +123,7 @@ These examples (C, C++, Fortran) are provided in the HDF5 source code and (Unix) Create an extendible (unlimited dimension) dataset -C Fortran C++ Java Python +C Fortran C++ Java Python Also see examples to Extend by row (and column) below @@ -131,7 +131,7 @@ These examples (C, C++, Fortran) are provided in the HDF5 source code and (Unix) Create a chunked and compressed dataset -C Fortran C++ Java Python +C Fortran C++ Java Python diff --git a/doxygen/dox/LearnBasics2.dox b/doxygen/dox/LearnBasics2.dox index ed2810c59bf..8eda57bc0c2 100644 --- a/doxygen/dox/LearnBasics2.dox +++ b/doxygen/dox/LearnBasics2.dox @@ -468,7 +468,7 @@ If the offset were 1x1 (instead of 1x2), then the selection can be made: The selections above were tested with the -h5_subsetbk.c +h5_subsetbk.c example code. The memory dataspace was defined as one-dimensional. \subsection subsecLBDsetSubRWProgRem Remarks diff --git a/doxygen/dox/LearnBasics3.dox b/doxygen/dox/LearnBasics3.dox index 67a4b12e106..65c873d63f0 100644 --- a/doxygen/dox/LearnBasics3.dox +++ b/doxygen/dox/LearnBasics3.dox @@ -156,9 +156,9 @@ Specifically look at the \ref ExAPI. There are examples for different languages. The C example to create a chunked dataset is: -h5ex_d_chunk.c +h5ex_d_chunk.c The C example to create a compact dataset is: -h5ex_d_compact.c +h5ex_d_compact.c \section secLBDsetLayoutChange Changing the Layout after Dataset Creation The dataset layout is a Dataset Creation Property List. This means that once the dataset has been @@ -166,7 +166,7 @@ created the dataset layout cannot be changed. The h5repack utility can be used t to a new with a new layout. \section secLBDsetLayoutSource Sources of Information -Chunking in HDF5 +Chunking in HDF5 (See the documentation on Advanced Topics in HDF5) \see \ref sec_plist in the HDF5 \ref UG. @@ -184,7 +184,7 @@ certain initial dimensions, then to later increase the size of any of the initia HDF5 requires you to use chunking to define extendible datasets. This makes it possible to extend datasets efficiently without having to excessively reorganize storage. (To use chunking efficiently, -be sure to see the advanced topic, Chunking in HDF5.) +be sure to see the advanced topic, Chunking in HDF5.) The following operations are required in order to extend a dataset: \li Declare the dataspace of the dataset to have unlimited dimensions for all dimensions that might eventually be extended. @@ -224,7 +224,7 @@ Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics \section secLBComDsetCreate Creating a Compressed Dataset HDF5 requires you to use chunking to create a compressed dataset. (To use chunking efficiently, -be sure to see the advanced topic, Chunking in HDF5.) +be sure to see the advanced topic, Chunking in HDF5.) The following operations are required in order to create a compressed dataset: \li Create a dataset creation property list. @@ -294,12 +294,12 @@ Specifically look at the \ref ExAPI. There are examples for different languages, where examples of using #H5Literate and #H5Ovisit/#H5Lvisit are included. The h5ex_g_traverse example traverses a file using H5Literate: -\li C: h5ex_g_traverse.c -\li F90: h5ex_g_traverse_F03.f90 +\li C: h5ex_g_traverse.c +\li F90: h5ex_g_traverse_F03.f90 The h5ex_g_visit example traverses a file using H5Ovisit and H5Lvisit: -\li C: h5ex_g_visit.c -\li F90: h5ex_g_visit_F03.f90 +\li C: h5ex_g_visit.c +\li F90: h5ex_g_visit_F03.f90
Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics diff --git a/doxygen/dox/LearnHDFView.dox b/doxygen/dox/LearnHDFView.dox index 2916db841e6..7624e42c40d 100644 --- a/doxygen/dox/LearnHDFView.dox +++ b/doxygen/dox/LearnHDFView.dox @@ -8,7 +8,7 @@ any programming experience. \section sec_learn_hv_install HDFView Installation \li Download and install HDFView. It can be downloaded from the Download HDFView page. -\li Obtain the storm1.txt text file, used in the tutorial. +\li Obtain the storm1.txt text file, used in the tutorial. \section sec_learn_hv_begin Begin Tutorial Once you have HDFView installed, bring it up and you are ready to begin the tutorial. @@ -113,11 +113,11 @@ Datatype information as is):
  • Double left click on the Storm dataset in the tree view. A window with an empty spreadsheet pops open.
    • -
  • Copy the data from the storm1.txt file into the dataset. +
  • Copy the data from the storm1.txt file into the dataset. -If you downloaded storm1.txt, +If you downloaded storm1.txt, then click on the Import/Export Data menu and select Import Data from -> Text File. -Specify a location, select storm1.txt +Specify a location, select storm1.txt and click on the Open button. Answer Yes in the dialog box that pops up (which asks if you wish to paste the selected data). @@ -246,7 +246,7 @@ in the file). Please note that the chunk sizes used in this topic are for demonstration purposes only. For information on chunking and specifying an appropriate chunk size, see the -Chunking in HDF5 documentation. +Chunking in HDF5 documentation. Also see the HDF5 Tutorial topic on \ref secLBComDsetCreate.
    • diff --git a/doxygen/dox/UsersGuide.dox b/doxygen/dox/UsersGuide.dox index 3dd26f1a40a..13f4edbe3f5 100644 --- a/doxygen/dox/UsersGuide.dox +++ b/doxygen/dox/UsersGuide.dox @@ -374,7 +374,7 @@ These documents provide additional information for the use and tuning of specifi -

    HDF5 Dynamically Loaded Filters

    +

    HDF5 Dynamically Loaded Filters

    Describes how an HDF5 application can apply a filter that is not registered with the HDF5 Library.

    @@ -382,7 +382,7 @@ These documents provide additional information for the use and tuning of specifi -

    HDF5 File Image Operations

    +

    HDF5 File Image Operations

    Describes how to work with HDF5 files in memory. Disk I/O is not required when file images are opened, created, read from, or written to.

    diff --git a/doxygen/dox/VOLConnGuide.dox b/doxygen/dox/VOLConnGuide.dox index 7a03ab1590d..e30a48428a8 100644 --- a/doxygen/dox/VOLConnGuide.dox +++ b/doxygen/dox/VOLConnGuide.dox @@ -92,7 +92,7 @@ Public header Files you will need to be familiar with include: Many VOL connectors are listed on The HDF Group's VOL plugin registration page, located at: -Registered VOL Connectors. +Registered VOL Connectors. Not all of these VOL connectors are supported by The HDF Group and the level of completeness varies, but the connectors found there can serve as examples of working implementations @@ -195,7 +195,7 @@ contact help@hdfgroup.org for help with this. We name you've chosen will appear on the registered VOL connectors page. As noted above, registered VOL connectors will be listed at: -Registered VOL Connectors +Registered VOL Connectors A new \b conn_version field has been added to the class struct for 1.13. This field is currently not used by the library so its use is determined by the connector author. Best practices for this field will be determined diff --git a/doxygen/dox/ViewTools.dox b/doxygen/dox/ViewTools.dox index 6502b7f9676..0a13daf0268 100644 --- a/doxygen/dox/ViewTools.dox +++ b/doxygen/dox/ViewTools.dox @@ -54,9 +54,9 @@ HDF5 files can be obtained from various places such as \ref HDF5Examples and . Specifically, the following examples are used in this tutorial topic: \li HDF5 Files created from compiling the \ref LBExamples \li HDF5 Files on the \ref ExAPI page -\li NPP JPSS files, SVM01_npp.. (gzipped) -and SVM09_npp.. (gzipped) -\li HDF-EOS OMI-Aura file +\li NPP JPSS files, SVM01_npp.. (gzipped) +and SVM09_npp.. (gzipped) +\li HDF-EOS OMI-Aura file \section secViewToolsCommandTutor Tutorial Topics A variety of command-line tools are included in the HDF5 binary distribution. There are tools to view, @@ -196,44 +196,29 @@ The following h5dump options can be helpful in viewing the content and structure Comment --n, --contents - -Displays a list of the objects in a file - -See @ref subsubsecViewToolsViewContent_h5dumpEx1 - +-n, --contents +Displays a list of the objects in a file +See @ref subsubsecViewToolsViewContent_h5dumpEx1 --n 1, --contents=1 - -Displays a list of the objects and attributes in a file - -See @ref subsubsecViewToolsViewAttr_h5dumpEx6 - +-n 1, --contents=1 +Displays a list of the objects and attributes in a file +See @ref subsubsecViewToolsViewAttr_h5dumpEx6 --H, --header - -Displays header information only (no data) - -See @ref subsubsecViewToolsViewContent_h5dumpEx2 - +-H, --header +Displays header information only (no data) +See @ref subsubsecViewToolsViewContent_h5dumpEx2 --A 0, --onlyattr=0 - -Suppresses the display of attributes - -See @ref subsubsecViewToolsViewContent_h5dumpEx2 - +-A 0, --onlyattr=0 +Suppresses the display of attributes +See @ref subsubsecViewToolsViewContent_h5dumpEx2 --N P, --any_path=P - -Displays any object or attribute that matches path P - -See @ref subsubsecViewToolsViewAttr_h5dumpEx6 - +-N P, --any_path=P +Displays any object or attribute that matches path P +See @ref subsubsecViewToolsViewAttr_h5dumpEx6 @@ -997,7 +982,7 @@ In other words, it is an array of four elements, in which each element is a 3 by This dataset is much more complex. Also note that subsetting cannot be done on Array datatypes. -See this section for more information on the Array datatype. +See this section for more information on the Array datatype. \subsubsection subsubsecViewToolsViewDtypes_objref Object Reference An Object Reference is a reference to an entire object (dataset, group, or named datatype). diff --git a/doxygen/dox/ViewToolsJPSS.dox b/doxygen/dox/ViewToolsJPSS.dox index 9c153956797..18c8ccefa0f 100644 --- a/doxygen/dox/ViewToolsJPSS.dox +++ b/doxygen/dox/ViewToolsJPSS.dox @@ -11,8 +11,8 @@ Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand This tutorial illustrates how to use the HDF5 tools to examine NPP files from the JPSS project. The following files are discussed: \code -SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5 (gzipped file) -SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5 (gzipped file) +SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5 (gzipped file) +SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5 (gzipped file) \endcode \section secViewToolsJPSSDeter Determining File Contents diff --git a/doxygen/dox/rm-template.dox b/doxygen/dox/rm-template.dox index f2e48d18d1f..003d5c4b862 100644 --- a/doxygen/dox/rm-template.dox +++ b/doxygen/dox/rm-template.dox @@ -2,9 +2,9 @@ We treat documentation like code and use Doxygen to -markup +markup comments in the code or create -stand-alone pages. +stand-alone pages. Every RM entry consists of a subset of the elements listed below. Not every RM entry warrants the full set. More is better, and we can, perhaps, distinguish diff --git a/doxygen/examples/FileFormat.html b/doxygen/examples/FileFormat.html index 30428e3cad2..eff1aead0a3 100644 --- a/doxygen/examples/FileFormat.html +++ b/doxygen/examples/FileFormat.html @@ -36,7 +36,7 @@

  • Background Reading:

    -
    HDF5 File Format Specification +
    HDF5 File Format Specification
    This describes the current HDF5 file format.
    diff --git a/doxygen/examples/intro_SWMR.html b/doxygen/examples/intro_SWMR.html index f4cd586f5f8..b1adb62bdb5 100644 --- a/doxygen/examples/intro_SWMR.html +++ b/doxygen/examples/intro_SWMR.html @@ -17,8 +17,8 @@

    Documentation

    SWMR User's Guide

    HDF5 Library APIs