diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index b4f74326efe..3df587e74da 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_4/api-compat-macros.html) + * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://docs.hdfgroup.org/hdf5/v1_14/v1_14_4/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_4/_r_m_t.html)? diff --git a/README.md b/README.md index 474211f44ed..46356c6d523 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_4/_l_b_a_p_i.html + https://docs.hdfgroup.org/hdf5/v1_14/v1_14_4/_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_4/index.html + https://docs.hdfgroup.org/hdf5/v1_14/v1_14_4/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..7cc2443797d 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/v1_14_4/group___h5_d.html#gaf6213bf3a876c1741810037ff2bb85d8)/[H5Dread_multi](https://hdfgroup.github.io/hdf5/v1_14_4/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/v1_14_4/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/v1_14_4/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/v1_14_4/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/v1_14_4/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/v1_14_4/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/v1_14_4/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/v1_14_4/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/v1_14_4/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/v1_14_4/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/v1_14_4/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/v1_14_4/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/v1_14_4/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/v1_14_4/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/test/API/README.md b/test/API/README.md index 3491b71c9d2..3e6ce7f3dc6 100644 --- a/test/API/README.md +++ b/test/API/README.md @@ -1,7 +1,7 @@ # HDF5 API Tests This directory contains several test applications that exercise HDF5's -public API and serve as regression tests for HDF5 [VOL Connectors](https://docs.hdfgroup.org/hdf5/v1_14_4/_h5_v_l__u_g.html). +public API and serve as regression tests for HDF5 [VOL Connectors](https://docs.hdfgroup.org/hdf5/v1_14/v1_14_4/_h5_v_l__u_g.html). ## Build Process and options @@ -42,7 +42,7 @@ Currently unsupported These API tests currently only support usage with the native HDF5 VOL connector and HDF5 VOL connectors that can be loaded dynamically as a plugin. For information on how to build a VOL -connector in this manner, refer to section 2.3 of the [HDF5 VOL Connector Author Guide](https://docs.hdfgroup.org/hdf5/v1_14_4/_v_o_l__connector.html). +connector in this manner, refer to section 2.3 of the [HDF5 VOL Connector Author Guide](https://docs.hdfgroup.org/hdf5/v1_14/v1_14_4/_v_o_l__connector.html). TODO: section on building VOL connectors alongside HDF5 for use with tests