From 29c268444cb04d6e4410e50c06f536fd20f9e9b9 Mon Sep 17 00:00:00 2001 From: Binh-Minh Date: Mon, 8 Apr 2024 03:05:09 -0400 Subject: [PATCH] Fix dead links Added img/images_to_copy.dox as a temporary solution because doxygen didn't copy the images used in the examples/*.html files - will investigate more. This was necessary for the links to intro_SWMR.html and intro_VDS.html. A few pages left to recreate then GH-3881 can be closed. --- doxygen/aliases | 2 +- doxygen/examples/intro_SWMR.html | 6 +++++- doxygen/examples/intro_VDS.html | 6 ++++-- doxygen/img/images_to_copy.dox | 11 +++++++++++ src/H5Fmodule.h | 2 +- 5 files changed, 22 insertions(+), 5 deletions(-) create mode 100644 doxygen/img/images_to_copy.dox diff --git a/doxygen/aliases b/doxygen/aliases index 0f5a4a4ed8f..ff8db78ff6d 100644 --- a/doxygen/aliases +++ b/doxygen/aliases @@ -243,7 +243,7 @@ ALIASES += ref_mdc_in_hdf5="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 H5Secnode() / H5Sdecode() Format Change" +ALIASES += ref_sencode_fmt_change="RFC H5Secnode() / H5Sdecode() Format Change" ALIASES += ref_vlen_strings="\Emph{Creating variable-length string datatypes}" ALIASES += ref_vol_doc="VOL documentation" diff --git a/doxygen/examples/intro_SWMR.html b/doxygen/examples/intro_SWMR.html index 7b7ece3e20f..f4cd586f5f8 100644 --- a/doxygen/examples/intro_SWMR.html +++ b/doxygen/examples/intro_SWMR.html @@ -4,10 +4,13 @@

Introduction to SWMR

The Single-Writer / Multiple-Reader (SWMR) feature enables multiple processes to read an HDF5 file while it is being written to (by a single process) without using locks or requiring communication between processes.

+

tutr-swmr1.png

All communication between processes must be performed via the HDF5 file. The HDF5 file under SWMR access must reside on a system that complies with POSIX write() semantics.

The basic engineering challenge for this to work was to ensure that the readers of an HDF5 file always see a coherent (though possibly not up to date) HDF5 file.

The issue is that when writing data there is information in the metadata cache in addition to the physical file on disk:

+

tutr-swmr2.png

However, the readers can only see the state contained in the physical file:

+

tutr-swmr3.png

The SWMR solution implements dependencies on when the metadata can be flushed to the file. This ensures that metadata cache flush operations occur in the proper order, so that there will never be internal file pointers in the physical file that point to invalid (unflushed) file addresses.

A beneficial side effect of using SWMR access is better fault tolerance. It is more difficult to corrupt a file when using SWMR.

Documentation

@@ -46,7 +49,8 @@

SWMR Writer:

Periodically flush data.

Example Code:

Create the file using the latest file format property:

-

fapl = H5Pcreate (H5P_FILE_ACCESS); +

+ fapl = H5Pcreate (H5P_FILE_ACCESS); status = H5Pset_libver_bounds (fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST); fid = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); [Create objects (files, datasets, ...). Close any attributes and named datatype objects. Groups and datasets may remain open before starting SWMR access to them.]

diff --git a/doxygen/examples/intro_VDS.html b/doxygen/examples/intro_VDS.html index 5f3e0336e4c..6e573b9b75c 100644 --- a/doxygen/examples/intro_VDS.html +++ b/doxygen/examples/intro_VDS.html @@ -5,11 +5,11 @@

The HDF5 Virtual Dataset (VDS) feature enables users to access data in a collection of HDF5 files as a single HDF5 dataset and to use the HDF5 APIs to work with that dataset.

For example, your data may be collected into four files:

-

+

tutrvds-multimgs.png

You can map the datasets in the four files into a single VDS that can be accessed just like any other dataset:

-

+

tutrvds-snglimg.png

The mapping between a VDS and the HDF5 source datasets is persistent and transparent to an application. If a source file is missing the fill value will be displayed.

See the Virtual (VDS) Documentation for complete details regarding the VDS feature.

@@ -42,6 +42,7 @@

Programming Examples Example 1 This example creates three HDF5 files, each with a one-dimensional dataset of 6 elements. The datasets in these files are the source datasets that are then used to create a 4 x 6 Virtual Dataset with a fill value of -1. The first three rows of the VDS are mapped to the data from the three source datasets as shown below:

+

tutrvds-ex.png

In this example the three source datasets are mapped to the VDS with this code:

src\_space = H5Screate\_simple (RANK1, dims, NULL);
 for (i = 0; i < 3; i++) {
@@ -67,4 +68,5 @@
 The h5dump utility can be used to view a VDS. The h5dump output for a VDS looks exactly like that for any other dataset. If h5dump cannot find a source dataset then the fill value will be displayed.

 
You can determine that a dataset is a VDS by looking at its properties with h5dump -p. It will display each source dataset mapping, beginning with Mapping 0. Below is an excerpt of the output of h5dump -p on the vds.h5 file created in Example 1.You can see that the entire source file a.h5 is mapped to the first row of the /VDS dataset:

 
+
tutrvds-map.png

 
diff --git a/doxygen/img/images_to_copy.dox b/doxygen/img/images_to_copy.dox
new file mode 100644
index 00000000000..cd4b8a50148
--- /dev/null
+++ b/doxygen/img/images_to_copy.dox
@@ -0,0 +1,11 @@
+/** \page HTML_IMGS Images for html files
+
+
+
+
+
+
+
+
+
+*/
diff --git a/src/H5Fmodule.h b/src/H5Fmodule.h
index f72d4463707..9192db4e18b 100644
--- a/src/H5Fmodule.h
+++ b/src/H5Fmodule.h
@@ -891,7 +891,7 @@
  * @see 
  * HDF5 File Image Operations
  * section for information on more advanced usage of the Memory file driver, and
- * @see 
+ * @see 
  * Modified Region Writes
  * section for information on how to set write operations so that only modified regions are written
  * to storage.