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Correct URLs in documentation (#4823)
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byrnHDF authored Sep 13, 2024
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2 changes: 1 addition & 1 deletion CITATION.cff
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Expand Up @@ -9,4 +9,4 @@ authors:
website: 'https://www.hdfgroup.org'
repository-code: 'https://github.com/HDFGroup/hdf5'
url: 'https://www.hdfgroup.org/HDF5/'
repository-artifact: 'https://support.hdfgroup.org/downloads/HDF5'
repository-artifact: 'https://support.hdfgroup.org/downloads/index.html'
30 changes: 14 additions & 16 deletions HDF5Examples/README.md
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Expand Up @@ -9,54 +9,52 @@ in science, engineering, and research communities worldwide.

The HDF Group is the developer, maintainer, and steward of HDF5 software. Find more
information about The HDF Group, the HDF5 Community, and other HDF5 software projects,
tools, and services at The HDF Group's website.

https://www.hdfgroup.org/
tools, and services at [The HDF Group's website](https://www.hdfgroup.org/).



HELP AND SUPPORT
----------------
Information regarding Help Desk and Support services is available at

https://hdfgroup.atlassian.net/servicedesk/customer/portals
https://help.hdfgroup.org



FORUM and NEWS
--------------
The following public forums are provided for public announcements and discussions
The [HDF Forum](https://forum.hdfgroup.org) is provided for public announcements and discussions
of interest to the general HDF5 Community.

- Homepage of the Forum
https://forum.hdfgroup.org

- News and Announcement
- News and Announcements
https://forum.hdfgroup.org/c/news-and-announcements-from-the-hdf-group

- HDF5 and HDF4 Topics
- HDF5 Topics
https://forum.hdfgroup.org/c/hdf5

These forums are provided as an open and public service for searching and reading.
Posting requires completing a simple registration and allows one to join in the
conversation. Please read the following instructions pertaining to the Forum's
use and configuration
https://forum.hdfgroup.org/t/quickstart-guide-welcome-to-the-new-hdf-forum
conversation. Please read the [instructions](https://forum.hdfgroup.org/t/quickstart-guide-welcome-to-the-new-hdf-forum
) pertaining to the Forum's use and configuration.


HDF5 SNAPSHOTS, PREVIOUS RELEASES AND SOURCE CODE
--------------------------------------------
Full Documentation and Programming Resources for this HDF5 can be found at

https://support.hdfgroup.org/documentation/hdf5/index.html
https://support.hdfgroup.org/documentation/index.html

Periodically development code snapshots are provided at the following URL:

https://github.com/HDFGroup/hdf5/releases
https://github.com/HDFGroup/hdf5/releases/tag/snapshot

Source packages for current and previous releases are located at:

https://support.hdfgroup.org/releases/hdf5/downloads/
hdf5 1.14 releases:
https://support.hdfgroup.org/releases/hdf5/v1_14/index.html

Archived releases:
https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/index.html

Development code is available at our Github location:

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2 changes: 1 addition & 1 deletion config/cmake/README.md.cmake.in
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Expand Up @@ -75,6 +75,6 @@ For more information see USING_CMake_Examples.txt in the install folder.
===========================================================================

Documentation for this release can be found at the following URL:
https://support.hdfgroup.org/hdf5/@HDF5_PACKAGE_NAME@-@HDF5_PACKAGE_VERSION@/documentation/doxygen/index.html
https://support.hdfgroup.org/releases/hdf5/@${H5_VERS_MAJOR}@_@${H5_VERS_MINOR}@/@${H5_VERS_MAJOR}@_@${H5_VERS_MINOR}@_@${H5_VERS_RELEASE}@/documentation/doxygen/index.html

Bugs should be reported to [email protected].
6 changes: 3 additions & 3 deletions doc/parallel-compression.md
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Expand Up @@ -340,9 +340,9 @@ hid_t file_id = H5Fcreate("file.h5", H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
[u5]: https://hdfgroup.github.io/hdf5/develop/group___d_c_p_l.html#ga85faefca58387bba409b65c470d7d851
[u6]: https://hdfgroup.github.io/hdf5/develop/group___d_c_p_l.html#ga4335bb45b35386daa837b4ff1b9cd4a4
[u7]: https://hdfgroup.github.io/hdf5/develop/group___d_c_p_l.html#ga6bd822266b31f86551a9a1d79601b6a2
[u8]: https://support.hdfgroup.org/documentation/hdf5/parallel-compression-improvements-in-hdf5-1-13-1
[u9]: https://support.hdfgroup.org/documentation/hdf5/chunking_in_hdf5.html
[u10]: https://support.hdfgroup.org/documentation/hdf5/technotes/TechNote-HDF5-ImprovingIOPerformanceCompressedDatasets.pdf
[u8]: https://www.hdfgroup.org/2022/03/04/parallel-compression-improvements-in-hdf5-1-13-1/
[u9]: https://support.hdfgroup.org/releases/hdf5/documentation/advanced_topics/chunking_in_hdf5.md
[u10]: https://support.hdfgroup.org/releases/hdf5/documentation/hdf5_topics/HDF5ImprovingIOPerformanceCompressedDatasets.pdf
[u11]: https://hdfgroup.github.io/hdf5/develop/group___f_a_p_l.html#gab99d5af749aeb3896fd9e3ceb273677a
[u12]: https://hdfgroup.github.io/hdf5/develop/group___f_c_p_l.html#ga167ff65f392ca3b7f1933b1cee1b9f70
[u13]: https://hdfgroup.github.io/hdf5/develop/group___f_c_p_l.html#gad012d7f3c2f1e1999eb1770aae3a4963
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10 changes: 5 additions & 5 deletions doxygen/aliases
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Expand Up @@ -258,13 +258,13 @@ ALIASES += sa_metadata_ops="\sa \li H5Pget_all_coll_metadata_ops() \li H5Pget_co

ALIASES += ref_cons_semantics="<a href=\"https://\RFCURL/RFC%20PHDF5%20Consistency%20Semantics%20MC%20120328.docx.pdf\">Enabling a Strict Consistency Semantics Model in Parallel HDF5</a>"
ALIASES += ref_file_image_ops="<a href=\"https://\RFCURL/HDF5FileImageOperations.pdf\">HDF5 File Image Operations</a>"
ALIASES += ref_filter_pipe="<a href=\"https://\DOCURL/HDF5+Data+Flow+Pipeline+for+H5Dread\">Data Flow Pipeline for H5Dread()</a>"
ALIASES += ref_filter_pipe="<a href=\"https://\DOCURL/advanced_topics/data_flow_pline_H5Dread.md\">Data Flow Pipeline for H5Dread()</a>"
ALIASES += ref_group_impls="<a href=\"https://\DOXURL/group___h5_g.html\">Group implementations in HDF5</a>"
ALIASES += ref_h5lib_relver="<a href=\"https://\ARCURL/TechNotes/Version.html\">HDF5 Library Release Version Numbers</a>"
ALIASES += ref_mdc_in_hdf5="<a href=\"https://\DOCURL/Metadata+Caching+in+HDF5\">Metadata Caching in HDF5</a>"
ALIASES += ref_mdc_logging="<a href=\"https://\DOCURL/H5F_START_MDC_LOGGING\">Metadata Cache Logging</a>"
ALIASES += ref_news_112="<a href=\"https://\DOCURL/release_specifics/new_features_1_12.html\">New Features in HDF5 Release 1.12</a>"
ALIASES += ref_h5ocopy="<a href=\"https://\DOCURL/Copying+Committed+Datatypes+with+H5Ocopy\">Copying Committed Datatypes with H5Ocopy()</a>"
ALIASES += ref_mdc_in_hdf5="<a href=\"https://\DOCURL/advanced_topics/FineTuningMetadataCache.md\">Metadata Caching in HDF5</a>"
ALIASES += ref_mdc_logging="<a href=\"https://\RFCURL/Design-MetadataCache-Logging-THG20140224-v4.pdf\">Metadata Cache Logging</a>"
ALIASES += ref_news_112="<a href=\"https://\DOCURL/release_specifics/new_features_1_12.md\">New Features in HDF5 Release 1.12</a>"
ALIASES += ref_h5ocopy="<a href=\"https://\DOCURL/advanced_topics/CopyingCommittedDatatypesWithH5Ocopy.pdf\">Copying Committed Datatypes with H5Ocopy()</a>"
ALIASES += ref_sencode_fmt_change="<a href=\"https://\RFCURL/H5Sencode_format.docx.pdf\">RFC H5Sencode() / H5Sdecode() Format Change</a>"
ALIASES += ref_vlen_strings="\Emph{Creating variable-length string datatypes}"
ALIASES += ref_vol_doc="VOL documentation"
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1 change: 0 additions & 1 deletion doxygen/dox/IntroHDF5.dox
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Expand Up @@ -617,7 +617,6 @@ on the <a href="http://hdfeos.org/">HDF-EOS Tools and Information Center</a> pag
\li \ref LBExamples
\li \ref ExAPI
\li <a href="https://\SRCURL/HDF5Examples">Examples in the Source Code</a>
\li <a href="https://\DOCURL/Other+Examples">Other Examples</a>

\section secHDF5ExamplesCompile How To Compile
For information on compiling in C, C++ and Fortran, see: \ref LBCompiling
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28 changes: 9 additions & 19 deletions doxygen/dox/LearnBasics3.dox
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Expand Up @@ -181,9 +181,9 @@ 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
<a href="https://\DOCURL/chunking_in_hdf5.html">Chunking in HDF5</a>
(See the documentation on <a href="https://\DOCURL/advanced_topics_list.html">Advanced Topics in HDF5</a>)
see \ref sec_plist in the HDF5 \ref UG.
<a href="https://\DOCURL/advanced_topics/chunking_in_hdf5.md">Chunking in HDF5</a>
(See the documentation on <a href="https://\DOCURL/advanced_topics_list.md">Advanced Topics in HDF5</a>)
\see \ref sec_plist in the HDF5 \ref UG.

<hr>
Previous Chapter \ref LBPropsList - Next Chapter \ref LBExtDset
Expand All @@ -201,7 +201,7 @@ 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, <a href="https://\DOCURL/chunking_in_hdf5.html">Chunking in HDF5</a>.)
be sure to see the advanced topic, <a href="https://\DOCURL/advanced_topics/chunking_in_hdf5.md">Chunking in HDF5</a>.)

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.
Expand Down Expand Up @@ -243,15 +243,15 @@ 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, <a href="https://\DOCURL/chunking_in_hdf5.html">Chunking in HDF5</a>.)
be sure to see the advanced topic, <a href="https://\DOCURL/advanced_topics/chunking_in_hdf5.md">Chunking in HDF5</a>.)

The following operations are required in order to create a compressed dataset:
\li Create a dataset creation property list.
\li Modify the dataset creation property list instance to enable chunking and to enable compression.
\li Create the dataset.
\li Close the dataset creation property list and dataset.

For more information on compression, see the FAQ question on <a href="https://\DOCURL/Using+Compression+in+HDF5">Using Compression in HDF5</a>.
For more information on compression, see the FAQ question on <a href="https://\DOCURL/hdf5_topics/UsingCompressionInHDF5.md">Using Compression in HDF5</a>.

\section secLBComDsetProg Programming Example

Expand Down Expand Up @@ -968,16 +968,15 @@ or on WINDOWS you may need to add the path to the bin folder to PATH.
\section secLBCompilingCMake Compiling an Application with CMake

\subsection subsecLBCompilingCMakeScripts CMake Scripts for Building Applications
Simple scripts are provided for building applications with different languages and options.
See <a href="https://\DOCURL/CMake+Scripts+for+Building+Applications">CMake Scripts for Building Applications</a>.
See <a href="https://\SRCURL/release_docs/USING_CMake_examples.txt">Using CMake to Build Applications</a> to build applications with different languages and options.

For a more complete script (and to help resolve issues) see the script provided with the HDF5 Examples project.

\subsection subsecLBCompilingCMakeExamples HDF5 Examples
The installed HDF5 can be verified by compiling the HDF5 Examples project, included with the CMake built HDF5 binaries
in the share folder or you can go to the <a href="https://\SRCURL/HDF5Examples">HDF5 Examples</a> in the HDF5 github repository.

Go into the share directory and follow the instructions in USING_CMake_examples.txt to build the examples.
Go into the share directory and follow the instructions in <a href="https://\SRCURL/release_docs/USING_CMake_examples.txt">Using CMake to Build Examples</a> to build the examples.

In general, users must first set the HDF5_ROOT environment variable to the installed location of the CMake
configuration files for HDF5. For example, on Windows the following path might be set:
Expand Down Expand Up @@ -1031,17 +1030,8 @@ For example, on Unix the log files will be in:
There are log files for the configure, test, and build.

<hr>
Previous Chapter \ref LBQuizAnswers - Next Chapter \ref LBTraining
Previous Chapter \ref LBQuizAnswers

Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics

@page LBTraining Training Videos

Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics

<a href="https://\DOCURL/Training+Videos">Training Videos</a>

<hr>
Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics

*/
2 changes: 1 addition & 1 deletion doxygen/dox/LearnHDFView.dox
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Expand Up @@ -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
<a href="https://\DOCURL/advanced_topics/chunking_in_hdf5.html">Chunking in HDF5</a> documentation.
<a href="https://\DOCURL/advanced_topics/chunking_in_hdf5.md">Chunking in HDF5</a> documentation.

Also see the HDF5 Tutorial topic on \ref secLBComDsetCreate.
<ul>
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4 changes: 2 additions & 2 deletions doxygen/dox/VOLConnGuide.dox
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Expand Up @@ -92,7 +92,7 @@ Public header Files you will need to be familiar with include:
</table>

Many VOL connectors are listed on The HDF Group's VOL plugin registration page, located at:
<a href="https://\DOCURL/registered_vol_connectors.html">Registered VOL Connectors</a>.
<a href="https://\DOCURL/registered_vol_connectors.md">Registered VOL Connectors</a>.
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

Expand Down Expand Up @@ -195,7 +195,7 @@ contact <a href="[email protected]">[email protected]</a> 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:
<a href="https://\DOCURL/registered_vol_connectors.html">Registered VOL Connectors</a>
<a href="https://\DOCURL/registered_vol_connectors.md">Registered VOL Connectors</a>

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
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6 changes: 3 additions & 3 deletions doxygen/hdf5doxy_layout.xml
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Expand Up @@ -5,12 +5,12 @@
<tab type="user" url="@ref GettingStarted" title="Getting started" />
<tab type="user" url="@ref UG" title="User Guide" />
<tab type="user" url="@ref RM" title="Reference Manual" />
<!-- <tab type="user" url="https://support.hdfgroup.org/documentation/hdf5/HDF5+Application+Developer%27s+Guide" title="Application Developer's Guide" />
<tab type="user" url="https://support.hdfgroup.org/documentation/hdf5/An_Overview_of_the_HDF5_Library_Architecture.v2.pdf" title="HDF5 Library Architecture Overview" /> -->
<!-- <tab type="user" url="https://support.hdfgroup.org/releases/hdf5/documentation/HDF5+Application+Developer%27s+Guide" title="Application Developer's Guide" />
<tab type="user" url="https://support.hdfgroup.org/releases/hdf5/documentation/An_Overview_of_the_HDF5_Library_Architecture.v2.pdf" title="HDF5 Library Architecture Overview" /> -->
<tab type="user" url="@ref Cookbook" title="Cookbook" />
<tab type="user" url="@ref TN" title="Technical Notes" />
<!-- <tab type="user" url="@ref VOL_Connector" title="HDF5 VOL Connector Author Guide" />
<tab type="user" url="https://support.hdfgroup.org/documentation/hdf5/HDF5+VOL+User%27s+Guide" title="HDF5 VOL User's Guide" /> -->
<tab type="user" url="https://support.hdfgroup.org/releases/hdf5/documentation/HDF5+VOL+User%27s+Guide" title="HDF5 VOL User's Guide" /> -->
<tab type="user" url="@ref RFC" title="RFCs" />
<tab type="user" url="@ref SPEC" title="Specifications" />
<tab type="user" url="@ref GLS" title="Glossary" />
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2 changes: 1 addition & 1 deletion hl/src/H5DOpublic.h
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Expand Up @@ -161,7 +161,7 @@ H5_HLDLL herr_t H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis, size_t e
* from one datatype to another, and the filter pipeline to write the chunk.
* Developers should have experience with these processes before
* using this function. Please see
* <a href="https://\DOCURL/Using+the+Direct+Chunk+Write+Function">
* <a href="https://\DOCURL/advanced_topics/UsingDirectChunkWrite.pdf">
* Using the Direct Chunk Write Function</a>
* for more information.
*
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4 changes: 2 additions & 2 deletions hl/src/H5DSpublic.h
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Expand Up @@ -147,7 +147,7 @@ H5_HLDLL herr_t H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx);
* dimension \p idx of dataset \p did. This deletes the entries in the
* #DIMENSION_LIST and #REFERENCE_LIST attributes,
* as defined in section 4.2 of
* <a href="https://support.hdfgroup.org/documentation/HDF5/HL/H5DS_Spec.pdf">
* <a href="https://support.hdfgroup.org/releases/hdf5/documentation/hdf5_topics/H5DS_Spec.pdf">
* HDF5 Dimension Scale Specification</a>.
*
* Fails if:
Expand Down Expand Up @@ -180,7 +180,7 @@ H5_HLDLL herr_t H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx);
* as defined above. Creates the CLASS attribute, set to the value
* "DIMENSION_SCALE" and an empty #REFERENCE_LIST attribute,
* as described in
* <a href="https://support.hdfgroup.org/documentation/HDF5/HL/H5DS_Spec.pdf">
* <a href="https://support.hdfgroup.org/releases/hdf5/documentation/hdf5_topics/H5DS_Spec.pdf">
* HDF5 Dimension Scale Specification</a>.
* (PDF, see section 4.2).
*
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2 changes: 1 addition & 1 deletion hl/src/H5LTpublic.h
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Expand Up @@ -1625,7 +1625,7 @@ H5_HLDLL htri_t H5LTpath_valid(hid_t loc_id, const char *path, hbool_t check_obj
* \note **Recommended Reading:**
* \note This function is part of the file image operations feature set.
* It is highly recommended to study the guide
* <a href="https://\DOCURL/HDF5+File+Image+Operations">
* <a href="https://\RFCURL/HDF5FileImageOperations.pdf">
* HDF5 File Image Operations</a> before using this feature set.\n
* See the “See Also” section below for links to other elements of
* HDF5 file image operations.
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2 changes: 1 addition & 1 deletion java/src/hdf/overview.html
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Expand Up @@ -91,6 +91,6 @@ <h3>
and the HDF5 library.

<h3>To Obtain</h3>
The JHI5 is included with the <a href="https://support.hdfgroup.org/downloads/HDF5/index.html">HDF5</a> library.
The JHI5 is included with the <a href="https://support.hdfgroup.org/downloads/index.html">HDF5</a> library.

</body>
2 changes: 1 addition & 1 deletion release_docs/INSTALL
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Expand Up @@ -49,7 +49,7 @@ CONTENTS
include the Szip library with the encoder enabled. These can be found
here:

https://support.hdfgroup.org/downloads/HDF5
https://support.hdfgroup.org/downloads/index.html

Please notice that if HDF5 configure cannot find a valid Szip library,
configure will not fail; in this case, the compression filter will
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4 changes: 2 additions & 2 deletions release_docs/INSTALL_Autotools.txt
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Expand Up @@ -334,7 +334,7 @@ III. Full installation instructions for source distributions
(or '--with-pthread=DIR') flag to the configure script.
For further information, see:

https://support.hdfgroup.org/documentation/HDF5/Questions+about+thread-safety+and+concurrent+access
https://support.hdfgroup.org/releases/hdf5/documentation/gen_topics/Questions+about+thread-safety+and+concurrent+access

The high-level, C++, Fortran and Java interfaces are not compatible
with the thread-safety option because the lock is not hoisted
Expand Down Expand Up @@ -492,7 +492,7 @@ IV. Using the Library
For information on using HDF5 see the documentation, tutorials and examples
found here:

https://support.hdfgroup.org/documentation/HDF5/index.html
https://support.hdfgroup.org/documentation/index.html

A summary of the features included in the built HDF5 installation can be found
in the libhdf5.settings file in the same directory as the static and/or
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2 changes: 1 addition & 1 deletion release_docs/INSTALL_parallel
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Expand Up @@ -90,7 +90,7 @@ nodes. They would probably work for other Cray systems but have
not been verified.

Obtain the HDF5 source code:
https://support.hdfgroup.org/downloads/HDF5
https://support.hdfgroup.org/downloads/index.html

The entire build process should be done on a MOM node in an interactive allocation and on a file system accessible by all compute nodes.
Request an interactive allocation with qsub:
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