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<a accesskey="h" href=""> UP </a>
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<h1 class="title">HDF5 back end</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
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<li><a href="#org296fc0b">1. HDF5 back end</a>
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<ul>
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<li><a href="#orgcbf5324">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org1362474">1.2. Template for HDF5 structures</a></li>
<li><a href="#org6fb743f">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org1e43f1f">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgcbd0458">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orgeb6cfbd">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#org97b0074">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org06de11a">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orgeb3710c">1.9. Helper functions</a></li>
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</ul>
</li>
</ul>
</div>
</div>
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<div id="outline-container-org296fc0b" class="outline-2">
<h2 id="org296fc0b"><span class="section-number-2">1</span> HDF5 back end</h2>
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<div class="outline-text-2" id="text-1">
</div>
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<div id="outline-container-orgcbf5324" class="outline-3">
<h3 id="orgcbf5324"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
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<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
<span style="color: #483d8b;">#define</span> $GROUP_NUM$_NAME <span style="color: #8b2252;">"$group_num$"</span>
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<span style="color: #483d8b;">#define</span> $GROUP_DSET$_NAME <span style="color: #8b2252;">"$group_dset$"</span>
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<span style="color: #483d8b;">#define</span> $GROUP_STR$_NAME <span style="color: #8b2252;">"$group_str$"</span>
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</pre>
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<div id="outline-container-org1362474" class="outline-3">
<h3 id="org1362474"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
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<div class="outline-text-3" id="text-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_hdf5_s</span> {
<span style="color: #228b22;">trexio_t</span> <span style="color: #a0522d;">parent</span> ;
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<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">file_id</span>;
hid_t $group$_group;
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} <span style="color: #228b22;">trexio_hdf5_t</span>;
</pre>
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<div id="outline-container-org6fb743f" class="outline-3">
<h3 id="org6fb743f"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
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<div class="outline-text-3" id="text-1-3">
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<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_inquire</span>(<span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span>* <span style="color: #a0522d;">file_name</span>)
{
/* <span style="color: #b22222;">H5Fis_hdf5 determines whether file is in HDF5 format </span>*/
<span style="color: #228b22;">htri_t</span> <span style="color: #a0522d;">rc</span> = H5Fis_hdf5(file_name);
<span style="color: #a020f0;">if</span> (rc &gt; 0 ) {
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS; //<span style="color: #b22222;">exists and HDF5</span>
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (rc == 0) {
<span style="color: #a020f0;">return</span> TREXIO_FILE_ERROR; //<span style="color: #b22222;">exists but not HDF5</span>
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">return</span> TREXIO_FAILURE; //<span style="color: #b22222;">does not exist or function fails</span>
}
}
</pre>
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<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_init</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>)
{
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
/* <span style="color: #b22222;">If file doesn't exist, create it </span>*/
<span style="color: #228b22;">int</span> <span style="color: #a0522d;">f_exists</span> = 0;
<span style="color: #a020f0;">struct</span> <span style="color: #228b22;">stat</span> <span style="color: #a0522d;">st</span>;
<span style="color: #a020f0;">if</span> (stat(file-&gt;file_name, &amp;st) == 0) f_exists = 1;
<span style="color: #a020f0;">if</span> (f_exists == 1) {
<span style="color: #a020f0;">switch</span> (file-&gt;mode) {
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'r'</span>:
// <span style="color: #b22222;">reading the existing file -&gt; open as RDONLY</span>
f-&gt;file_id = H5Fopen(file-&gt;file_name, H5F_ACC_RDONLY, H5P_DEFAULT);
<span style="color: #a020f0;">break</span>;
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'w'</span>:
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// <span style="color: #b22222;">writing the existing file -&gt; open as RDWRITE</span>
f-&gt;file_id = H5Fopen(file-&gt;file_name, H5F_ACC_RDWR, H5P_DEFAULT);
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<span style="color: #a020f0;">break</span>;
}
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">switch</span> (file-&gt;mode) {
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'r'</span>:
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// <span style="color: #b22222;">reading non-existing file -&gt; error</span>
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<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'w'</span>:
// <span style="color: #b22222;">writing non-existing file -&gt; create it</span>
f-&gt;file_id = H5Fcreate(file-&gt;file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">break</span>;
}
}
/* <span style="color: #b22222;">Create or open groups in the hdf5 file assuming that they exist if file exists </span>*/
<span style="color: #a020f0;">switch</span> (file-&gt;mode) {
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'r'</span>:
f-&gt;$group$_group = H5Gopen(f-&gt;file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">break</span>;
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'w'</span>:
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<span style="color: #a020f0;">if</span> (f_exists == 1) {
f-&gt;$group$_group = H5Gopen(f-&gt;file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
} <span style="color: #a020f0;">else</span> {
f-&gt;$group$_group = H5Gcreate(f-&gt;file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
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<span style="color: #a020f0;">break</span>;
}
<span style="color: #a020f0;">if</span> (f-&gt;$group$_group &lt;= 0L) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
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</pre>
</div>
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<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
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<span style="color: #0000ff;">trexio_hdf5_deinit</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>)
{
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
H5Gclose(f-&gt;$group$_group);
f-&gt;$group$_group = 0;
H5Fclose(f-&gt;file_id);
f-&gt;file_id = 0;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
</div>
</div>
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<div id="outline-container-org1e43f1f" class="outline-3">
<h3 id="org1e43f1f"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
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<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
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<span style="color: #0000ff;">trexio_hdf5_read_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, $group_num_dtype_double$* <span style="color: #a020f0;">const</span> num)
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{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #a020f0;">if</span> (num == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>*) file;
/* <span style="color: #b22222;">Quit if the dimensioning attribute is missing in the file </span>*/
<span style="color: #a020f0;">if</span> (H5Aexists(f-&gt;$group$_group, $GROUP_NUM$_NAME) == 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
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/* <span style="color: #b22222;">Read the $group_num$ attribute of $group$ group </span>*/
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">num_id</span> = H5Aopen(f-&gt;$group$_group, $GROUP_NUM$_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (num_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Aread(num_id, H5T_$GROUP_NUM_H5_DTYPE$, num);
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H5Aclose(num_id);
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<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
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<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
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<span style="color: #0000ff;">trexio_hdf5_write_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #a020f0;">const</span> $group_num_dtype_double$ num)
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{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
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/* <span style="color: #b22222;">Write the dimensioning variables </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype</span> = H5Tcopy(H5T_$GROUP_NUM_H5_DTYPE$);
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace</span> = H5Screate(H5S_SCALAR);
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">num_id</span> = H5Acreate(f-&gt;$group$_group, $GROUP_NUM$_NAME,
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dtype, dspace, H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (num_id &lt;= 0) {
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H5Sclose(dspace);
H5Tclose(dtype);
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<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Awrite(num_id, dtype, &amp;(num));
<span style="color: #a020f0;">if</span> (status &lt; 0) {
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H5Aclose(num_id);
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H5Sclose(dspace);
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H5Tclose(dtype);
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<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
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}
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H5Sclose(dspace);
H5Aclose(num_id);
H5Tclose(dtype);
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
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}
</pre>
</div>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_has_$group_num$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #228b22;">htri_t</span> <span style="color: #a0522d;">status</span> = H5Aexists(f-&gt;$group$_group, $GROUP_NUM$_NAME);
/* <span style="color: #b22222;">H5Aexists returns positive value if attribute exists, 0 if does not, negative if error </span>*/
<span style="color: #a020f0;">if</span> (status &gt; 0){
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (status == 0) {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
}
</pre>
</div>
</div>
</div>
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<div id="outline-container-orgcbd0458" class="outline-3">
<h3 id="orgcbd0458"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
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<div class="outline-text-3" id="text-1-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
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<span style="color: #0000ff;">trexio_hdf5_read_$group_dset$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, $group_dset_dtype$* <span style="color: #a020f0;">const</span> $group_dset$, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">rank</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint64_t</span>* <span style="color: #a0522d;">dims</span>)
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{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
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<span style="color: #a020f0;">if</span> ($group_dset$ == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>*) file;
// <span style="color: #b22222;">open the dataset to get its dimensions</span>
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<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dopen(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
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<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
// <span style="color: #b22222;">allocate space for the dimensions to be read</span>
<span style="color: #228b22;">hsize_t</span>* <span style="color: #a0522d;">ddims</span> = CALLOC( (<span style="color: #228b22;">int</span>) rank, hsize_t);
<span style="color: #a020f0;">if</span> (ddims == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
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// <span style="color: #b22222;">get the dataspace of the dataset</span>
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace_id</span> = H5Dget_space(dset_id);
// <span style="color: #b22222;">get the rank and dimensions of the dataset</span>
<span style="color: #228b22;">int</span> <span style="color: #a0522d;">rrank</span> = H5Sget_simple_extent_dims(dspace_id, ddims, <span style="color: #008b8b;">NULL</span>);
// <span style="color: #b22222;">check that dimensions are consistent</span>
<span style="color: #a020f0;">if</span> (rrank != (<span style="color: #228b22;">int</span>) rank) {
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FREE(ddims);
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H5Sclose(dspace_id);
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_3;
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}
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">i</span>=0; i&lt;rank; ++i){
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<span style="color: #a020f0;">if</span> (ddims[i] != dims[i]) {
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FREE(ddims);
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H5Sclose(dspace_id);
H5Dclose(dset_id);
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<span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_4;
}
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}
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FREE(ddims);
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H5Sclose(dspace_id);
H5Dclose(dset_id);
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/* <span style="color: #b22222;">High-level H5LT API. No need to deal with dataspaces and datatypes </span>*/
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<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTread_dataset(f-&gt;$group$_group,
$GROUP_DSET$_NAME,
H5T_$GROUP_DSET_H5_DTYPE$,
$group_dset$);
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<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
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<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
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<span style="color: #0000ff;">trexio_hdf5_write_$group_dset$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #a020f0;">const</span> $group_dset_dtype$* $group_dset$, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">rank</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint64_t</span>* <span style="color: #a0522d;">dims</span>)
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{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
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<span style="color: #a020f0;">if</span> ($group_dset$ == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
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<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
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<span style="color: #a020f0;">if</span> ( H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME) != 1 ) {
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTmake_dataset(f-&gt;$group$_group,
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$GROUP_DSET$_NAME,
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(<span style="color: #228b22;">int</span>) rank, (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span>*) dims,
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H5T_$GROUP_DSET_H5_DTYPE$,
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$group_dset$);
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<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
} <span style="color: #a020f0;">else</span> {
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<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dopen(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
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<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
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<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Dwrite(dset_id,
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H5T_$GROUP_DSET_H5_DTYPE$,
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H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$);
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H5Dclose(dset_id);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
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<span style="color: #0000ff;">trexio_hdf5_has_$group_dset$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>)
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{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
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<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME);
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/* <span style="color: #b22222;">H5LTfind_dataset returns 1 if dataset exists, 0 otherwise </span>*/
<span style="color: #a020f0;">if</span> (status == 1){
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (status == 0) {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
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}
</pre>
</div>
</div>
</div>
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<div id="outline-container-orgeb6cfbd" class="outline-3">
<h3 id="orgeb6cfbd"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
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<div class="outline-text-3" id="text-1-6">
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<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
due to the fact that the sparse data will be written in chunks of user-defined size.
</p>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_write_$group_dset$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">offset_file</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">size</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">size_max</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int32_t</span>* <span style="color: #a0522d;">index_sparse</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">double</span>* <span style="color: #a0522d;">value_sparse</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">index_dtype</span>;
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<span style="color: #228b22;">void</span>* <span style="color: #a0522d;">index_p</span> = <span style="color: #008b8b;">NULL</span>;
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<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">size_ranked</span> = (<span style="color: #228b22;">uint64_t</span>) size * $group_dset_rank$;
/* <span style="color: #b22222;">Determine the optimal type for storing indices depending on the size_max (usually mo_num or ao_num) </span>*/
<span style="color: #a020f0;">if</span> (size_max &lt; UINT8_MAX) {
<span style="color: #228b22;">uint8_t</span>* <span style="color: #a0522d;">index</span> = CALLOC(size_ranked, uint8_t);
<span style="color: #a020f0;">if</span> (index == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_ALLOCATION_FAILED;
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<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">i</span>=0; i&lt;size_ranked; ++i){
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index[i] = (<span style="color: #228b22;">uint8_t</span>) index_sparse[i];
}
index_p = index;
index_dtype = H5T_NATIVE_UINT8;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (size_max &lt; UINT16_MAX) {
<span style="color: #228b22;">uint16_t</span>* <span style="color: #a0522d;">index</span> = CALLOC(size_ranked, uint16_t);
<span style="color: #a020f0;">if</span> (index == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_ALLOCATION_FAILED;
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<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">i</span>=0; i&lt;size_ranked; ++i){
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index[i] = (<span style="color: #228b22;">uint16_t</span>) index_sparse[i];
}
index_p = index;
index_dtype = H5T_NATIVE_UINT16;
} <span style="color: #a020f0;">else</span> {
index_p = (<span style="color: #228b22;">int32_t</span>*) index_sparse;
index_dtype = H5T_NATIVE_INT32;
}
/* <span style="color: #b22222;">Store float values in double precision </span>*/
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">value_dtype</span> = H5T_NATIVE_DOUBLE;
/* <span style="color: #b22222;">Arrays of chunk dims that will be used for chunking the dataset </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">chunk_i_dims</span>[1] = {size_ranked};
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">chunk_v_dims</span>[1] = {size};
/* <span style="color: #b22222;">Indices and values are stored as 2 independent datasets in the HDF5 file </span>*/
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<span style="color: #228b22;">char</span> <span style="color: #a0522d;">dset_index_name</span>[256];
<span style="color: #228b22;">char</span> <span style="color: #a0522d;">dset_value_name</span>[256];
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/* <span style="color: #b22222;">Build the names of the datasets </span>*/
strncpy(dset_index_name, $GROUP_DSET$_NAME <span style="color: #8b2252;">"_indices"</span>, 256);
strncpy(dset_value_name, $GROUP_DSET$_NAME <span style="color: #8b2252;">"_values"</span>, 256);
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc_write</span> = TREXIO_FAILURE;
/* <span style="color: #b22222;">NOTE: chunk size is set upon creation of the HDF5 dataset and cannot be changed ! </span>*/
<span style="color: #a020f0;">if</span> ( H5LTfind_dataset(f-&gt;$group$_group, dset_index_name) != 1 ) {
/* <span style="color: #b22222;">If the file does not exist -&gt; create it and write </span>*/
/* <span style="color: #b22222;">Create chunked dataset with index_dtype datatype and write indices into it </span>*/
rc_write = trexio_hdf5_create_write_dset_sparse(f-&gt;$group$_group, dset_index_name, index_dtype, chunk_i_dims, index_p);
<span style="color: #a020f0;">if</span> (index_p != index_sparse) FREE(index_p);
<span style="color: #a020f0;">if</span> (rc_write != TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> rc_write;
/* <span style="color: #b22222;">Create chunked dataset with value_dtype datatype and write values into it </span>*/
rc_write = trexio_hdf5_create_write_dset_sparse(f-&gt;$group$_group, dset_value_name, value_dtype, chunk_v_dims, value_sparse);
<span style="color: #a020f0;">if</span> (rc_write != TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> rc_write;
} <span style="color: #a020f0;">else</span> {
/* <span style="color: #b22222;">If the file exists -&gt; open it and write </span>*/
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">offset_i</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) offset_file * $group_dset_rank$};
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">offset_v</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) offset_file};
/* <span style="color: #b22222;">Create chunked dataset with index_dtype datatype and write indices into it </span>*/
rc_write = trexio_hdf5_open_write_dset_sparse(f-&gt;$group$_group, dset_index_name, index_dtype, chunk_i_dims, offset_i, index_p);
<span style="color: #a020f0;">if</span> (index_p != index_sparse) FREE(index_p);
<span style="color: #a020f0;">if</span> (rc_write != TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> rc_write;
/* <span style="color: #b22222;">Create chunked dataset with value_dtype datatype and write values into it </span>*/
rc_write = trexio_hdf5_open_write_dset_sparse(f-&gt;$group$_group, dset_value_name, value_dtype, chunk_v_dims, offset_v, value_sparse);
<span style="color: #a020f0;">if</span> (rc_write != TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> rc_write;
}
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_read_$group_dset$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">offset_file</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">size</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int64_t</span> <span style="color: #a0522d;">size_max</span>,
<span style="color: #228b22;">int64_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">eof_read_size</span>,
<span style="color: #228b22;">int32_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">index_read</span>,
<span style="color: #228b22;">double</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">value_read</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #a020f0;">if</span> (eof_read_size == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_5;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>*) file;
/* <span style="color: #b22222;">Indices and values are stored as 2 independent datasets in the HDF5 file </span>*/
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<span style="color: #228b22;">char</span> <span style="color: #a0522d;">dset_index_name</span>[256];
<span style="color: #228b22;">char</span> <span style="color: #a0522d;">dset_value_name</span>[256];
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/* <span style="color: #b22222;">Build the names of the datasets </span>*/
strncpy(dset_index_name, $GROUP_DSET$_NAME <span style="color: #8b2252;">"_indices"</span>, 256);
strncpy(dset_value_name, $GROUP_DSET$_NAME <span style="color: #8b2252;">"_values"</span>, 256);
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">offset_i</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) offset_file * $group_dset_rank$};
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">count_i</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) size * $group_dset_rank$};
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">offset_v</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) offset_file};
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">count_v</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) size};
<span style="color: #228b22;">int</span> <span style="color: #a0522d;">is_index</span> = 1, <span style="color: #a0522d;">is_value</span> = 0;
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc_read</span>;
// <span style="color: #b22222;">attempt to read indices</span>
rc_read = trexio_hdf5_open_read_dset_sparse(f-&gt;$group$_group, dset_index_name, offset_i, count_i, <span style="color: #008b8b;">NULL</span>, is_index, index_read);
<span style="color: #a020f0;">if</span> (rc_read != TREXIO_SUCCESS &amp;&amp; rc_read != TREXIO_END) <span style="color: #a020f0;">return</span> rc_read;
// <span style="color: #b22222;">attempt to read values</span>
// <span style="color: #b22222;">when EOF is encountered - the count_v[0] is modified and contains the number of elements being read</span>
rc_read = trexio_hdf5_open_read_dset_sparse(f-&gt;$group$_group, dset_value_name, offset_v, count_v, eof_read_size, is_value, value_read);
<span style="color: #a020f0;">if</span> (rc_read != TREXIO_SUCCESS &amp;&amp; rc_read != TREXIO_END) <span style="color: #a020f0;">return</span> rc_read;
<span style="color: #a020f0;">return</span> rc_read;
}
</pre>
</div>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_read_$group_dset$_size</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #228b22;">int64_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">size_max</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dopen(f-&gt;$group$_group, $GROUP_DSET$_NAME <span style="color: #8b2252;">"_values"</span>, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">fspace_id</span> = H5Dget_space(dset_id);
<span style="color: #a020f0;">if</span> (fspace_id &lt; 0) {
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
// <span style="color: #b22222;">allocate space for the dimensions to be read</span>
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">ddims</span>[1] = {0};
// <span style="color: #b22222;">get the rank and dimensions of the dataset</span>
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H5Sget_simple_extent_dims(fspace_id, ddims, <span style="color: #008b8b;">NULL</span>);
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H5Dclose(dset_id);
H5Sclose(fspace_id);
*size_max = (<span style="color: #228b22;">int64_t</span>) ddims[0];
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_has_$group_dset$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME <span style="color: #8b2252;">"_values"</span>);
/* <span style="color: #b22222;">H5LTfind_dataset returns 1 if dataset exists, 0 otherwise </span>*/
<span style="color: #a020f0;">if</span> (status == 1){
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (status == 0) {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
}
</pre>
</div>
</div>
</div>
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<div id="outline-container-org97b0074" class="outline-3">
<h3 id="org97b0074"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
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<div class="outline-text-3" id="text-1-7">
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<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_read_$group_dset$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #228b22;">char</span>* <span style="color: #a020f0;">const</span> $group_dset$, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">rank</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint64_t</span>* <span style="color: #a0522d;">dims</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">max_str_len</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #a020f0;">if</span> ($group_dset$ == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span>;
// <span style="color: #b22222;">open the dataset to get its dimensions</span>
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dopen(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
// <span style="color: #b22222;">allocate space for the dimensions to be read</span>
<span style="color: #228b22;">hsize_t</span>* <span style="color: #a0522d;">ddims</span> = CALLOC( (<span style="color: #228b22;">int</span>) rank, hsize_t);
<span style="color: #a020f0;">if</span> (ddims == <span style="color: #008b8b;">NULL</span>) {
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_ALLOCATION_FAILED;
}
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<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace</span> = H5Dget_space(dset_id);
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<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) {
FREE(ddims);
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H5Dclose(dset_id);
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<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
// <span style="color: #b22222;">get the rank of the dataset in a file</span>
<span style="color: #228b22;">int</span> <span style="color: #a0522d;">rrank</span> = H5Sget_simple_extent_dims(dspace, ddims, <span style="color: #008b8b;">NULL</span>);
<span style="color: #a020f0;">if</span> (rrank != (<span style="color: #228b22;">int</span>) rank) {
FREE(ddims);
H5Dclose(dset_id);
H5Sclose(dspace);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_3;
}
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">int</span> <span style="color: #a0522d;">i</span>=0; i&lt;rrank; i++) {
<span style="color: #a020f0;">if</span> (ddims[i] != dims[i]) {
H5Dclose(dset_id);
H5Sclose(dspace);
FREE(ddims);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_4;
}
}
FREE(ddims);
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">memtype</span> = H5Tcopy (H5T_C_S1);
status = H5Tset_size(memtype, H5T_VARIABLE);
<span style="color: #a020f0;">if</span> (status &lt; 0 || memtype &lt;= 0) {
H5Dclose(dset_id);
H5Sclose(dspace);
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
<span style="color: #228b22;">char</span>** <span style="color: #a0522d;">rdata</span> = CALLOC(dims[0], <span style="color: #228b22;">char</span>*);
<span style="color: #a020f0;">if</span> (rdata == <span style="color: #008b8b;">NULL</span>) {
H5Dclose(dset_id);
H5Sclose(dspace);
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H5Tclose(memtype);
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<span style="color: #a020f0;">return</span> TREXIO_ALLOCATION_FAILED;
}
status = H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
<span style="color: #a020f0;">if</span> (status &lt; 0) {
FREE(rdata);
H5Dclose(dset_id);
H5Sclose(dspace);
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H5Tclose(memtype);
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<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
// <span style="color: #b22222;">copy contents of temporary rdata buffer into the group_dset otherwise they are lost</span>
// <span style="color: #b22222;">after calling H5Treclaim or H5Dvlen_reclaim functions</span>
strcpy($group_dset$, <span style="color: #8b2252;">""</span>);
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">i</span>=0; i&lt;dims[0]; i++) {
strncat($group_dset$, rdata[i], max_str_len);
strcat($group_dset$, TREXIO_DELIM);
}
// <span style="color: #b22222;">H5Dvlen_reclaim is deprecated and replaced by H5Treclaim in HDF5 v.1.12.0</span>
<span style="color: #483d8b;"> #if</span> (H5_VERS_MAJOR &lt;= 1 &amp;&amp; H5_VERS_MINOR &lt; 12)
status = H5Dvlen_reclaim(memtype, dspace, H5P_DEFAULT, rdata);
<span style="color: #483d8b;"> #else</span>
status = H5Treclaim(memtype, dspace, H5P_DEFAULT, rdata);
<span style="color: #483d8b;"> #endif</span>
<span style="color: #a020f0;">if</span> (status &lt; 0) {
FREE(rdata);
H5Dclose(dset_id);
H5Sclose(dspace);
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H5Tclose(memtype);
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<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
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FREE(rdata);
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H5Dclose(dset_id);
H5Sclose(dspace);
H5Tclose(memtype);
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_write_$group_dset$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span>** $group_dset$, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">rank</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint64_t</span>* <span style="color: #a0522d;">dims</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #a020f0;">if</span> ($group_dset$ == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span>;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span>;
/* <span style="color: #b22222;">we are going to write variable-length strings </span>*/
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">memtype</span> = H5Tcopy (H5T_C_S1);
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<span style="color: #a020f0;">if</span> (memtype &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
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status = H5Tset_size (memtype, H5T_VARIABLE);
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<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
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<span style="color: #a020f0;">if</span> ( H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME) != 1 ) {
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/* <span style="color: #b22222;">code to create dataset </span>*/
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<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">filetype</span> = H5Tcopy (H5T_FORTRAN_S1);
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<span style="color: #a020f0;">if</span> (filetype &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
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status = H5Tset_size (filetype, H5T_VARIABLE);
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<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
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<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace</span> = H5Screate_simple( (<span style="color: #228b22;">int</span>) rank, (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span>*) dims, <span style="color: #008b8b;">NULL</span>);
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<span style="color: #a020f0;">if</span> (dspace &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
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dset_id = H5Dcreate (f-&gt;$group$_group, $GROUP_DSET$_NAME, filetype, dspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
status = H5Dwrite (dset_id, memtype,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$);
H5Dclose (dset_id);
H5Sclose (dspace);
H5Tclose (filetype);
H5Tclose (memtype);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
} <span style="color: #a020f0;">else</span> {
dset_id = H5Dopen(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
/* <span style="color: #b22222;">code to write dataset </span>*/
status = H5Dwrite(dset_id, memtype,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$);
H5Dclose(dset_id);
H5Tclose(memtype);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_has_$group_dset$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME);
/* <span style="color: #b22222;">H5LTfind_dataset returns 1 if dataset exists, 0 otherwise </span>*/
<span style="color: #a020f0;">if</span> (status == 1){
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (status == 0) {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
}
</pre>
</div>
</div>
</div>
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<div id="outline-container-org06de11a" class="outline-3">
<h3 id="org06de11a"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string attribute</h3>
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<div class="outline-text-3" id="text-1-8">
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<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_read_$group_str$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #228b22;">char</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">str</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">max_str_len</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #a020f0;">if</span> (str == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>*) file;
/* <span style="color: #b22222;">Quit if the string attribute is missing in the file </span>*/
<span style="color: #a020f0;">if</span> (H5Aexists(f-&gt;$group$_group, $GROUP_STR$_NAME) == 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
/* <span style="color: #b22222;">Read the $group_str$ attribute of $group$ group </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">str_id</span> = H5Aopen(f-&gt;$group$_group, $GROUP_STR$_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (str_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">ftype_id</span> = H5Aget_type(str_id);
<span style="color: #a020f0;">if</span> (ftype_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">sdim</span> = H5Tget_size(ftype_id);
sdim++; /* <span style="color: #b22222;">Make room for null terminator </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">mem_id</span> = H5Tcopy(H5T_C_S1);
<span style="color: #a020f0;">if</span> (mem_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span>;
status = (max_str_len+1) &gt; sdim ? H5Tset_size(mem_id, sdim) : H5Tset_size(mem_id, max_str_len+1) ;
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
status = H5Aread(str_id, mem_id, str);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
H5Aclose(str_id);
H5Tclose(mem_id);
H5Tclose(ftype_id);
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_write_$group_str$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>, <span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span>* <span style="color: #a0522d;">str</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #a020f0;">if</span> (str == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
<span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">f</span> = (<span style="color: #228b22;">trexio_hdf5_t</span>*) file;
/* <span style="color: #b22222;">Setup the dataspace </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype_id</span> = H5Tcopy(H5T_C_S1);
<span style="color: #a020f0;">if</span> (dtype_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">str_attr_len</span> = strlen(str) + 1;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span>;
status = H5Tset_size(dtype_id, str_attr_len);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
status = H5Tset_strpad(dtype_id, H5T_STR_NULLTERM);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace_id</span> = H5Screate(H5S_SCALAR);
<span style="color: #a020f0;">if</span> (dspace_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
/* <span style="color: #b22222;">Create the $group_str$ attribute of $group$ group </span>*/
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">str_id</span> = H5Acreate(f-&gt;$group$_group, $GROUP_STR$_NAME, dtype_id, dspace_id,
H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (str_id &lt;= 0) {
H5Sclose(dspace_id);
H5Tclose(dtype_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
status = H5Awrite(str_id, dtype_id, str);
<span style="color: #a020f0;">if</span> (status &lt; 0) {
H5Aclose(str_id);
H5Sclose(dspace_id);
H5Tclose(dtype_id);
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
H5Aclose(str_id);
H5Sclose(dspace_id);
H5Tclose(dtype_id);
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_has_$group_str$</span> (<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>)
{
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #228b22;">htri_t</span> <span style="color: #a0522d;">status</span> = H5Aexists(f-&gt;$group$_group, $GROUP_STR$_NAME);
/* <span style="color: #b22222;">H5Aexists returns positive value if attribute exists, 0 if does not, negative if error </span>*/
<span style="color: #a020f0;">if</span> (status &gt; 0){
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (status == 0) {
<span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
} <span style="color: #a020f0;">else</span> {
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
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}
</pre>
</div>
</div>
</div>
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<div id="outline-container-orgeb3710c" class="outline-3">
<h3 id="orgeb3710c"><span class="section-number-3">1.9</span> Helper functions</h3>
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<div class="outline-text-3" id="text-1-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_create_write_dset_sparse</span> (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">group_id</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span>* <span style="color: #a0522d;">dset_name</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype_id</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span>* <span style="color: #a0522d;">chunk_dims</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">void</span>* <span style="color: #a0522d;">data_sparse</span>)
{
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int</span> <span style="color: #a0522d;">h5_rank</span> = 1;
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">maxdims</span>[1] = {H5S_UNLIMITED};
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace</span> = H5Screate_simple(h5_rank, chunk_dims, maxdims);
<span style="color: #a020f0;">if</span> (dspace &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">prop</span> = H5Pcreate(H5P_DATASET_CREATE);
<span style="color: #a020f0;">if</span> (prop &lt; 0) {
H5Sclose(dspace);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Pset_chunk(prop, h5_rank, chunk_dims);
<span style="color: #a020f0;">if</span> (status &lt; 0) {
H5Sclose(dspace);
H5Pclose(prop);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dcreate(group_id,
dset_name,
dtype_id,
dspace,
H5P_DEFAULT,
prop,
H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt; 0) {
H5Sclose(dspace);
H5Pclose(prop);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
status = H5Dwrite(dset_id,
dtype_id,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
data_sparse);
H5Sclose(dspace);
H5Pclose(prop);
H5Dclose(dset_id);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
<span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_open_write_dset_sparse</span> (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">group_id</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span>* <span style="color: #a0522d;">dset_name</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype_id</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span>* <span style="color: #a0522d;">chunk_dims</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span>* <span style="color: #a0522d;">offset_file</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">void</span>* <span style="color: #a0522d;">data_sparse</span>)
{
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int</span> <span style="color: #a0522d;">h5_rank</span> = 1;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dopen(group_id, dset_name, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">fspace</span> = H5Dget_space(dset_id);
<span style="color: #a020f0;">if</span> (fspace &lt; 0) {
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
// <span style="color: #b22222;">allocate space for the dimensions to be read</span>
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">ddims</span>[1] = {0};
// <span style="color: #b22222;">get the rank and dimensions of the dataset</span>
<span style="color: #228b22;">int</span> <span style="color: #a0522d;">rrank</span> = H5Sget_simple_extent_dims(fspace, ddims, <span style="color: #008b8b;">NULL</span>);
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<span style="color: #a020f0;">if</span> (rrank != h5_rank) {
H5Sclose(fspace);
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
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ddims[0] += chunk_dims[0];
// <span style="color: #b22222;">extend the dset size</span>
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Dset_extent(dset_id, ddims);
<span style="color: #a020f0;">if</span> (status &lt; 0) {
H5Sclose(fspace);
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
// <span style="color: #b22222;">close and reopen the file dataspace to take into account the extension</span>
H5Sclose(fspace);
fspace = H5Dget_space(dset_id);
<span style="color: #a020f0;">if</span> (fspace &lt; 0) {
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
// <span style="color: #b22222;">select hyperslab to be written using chunk_dims and offset values</span>
status = H5Sselect_hyperslab(fspace, H5S_SELECT_SET, offset_file, <span style="color: #008b8b;">NULL</span>, chunk_dims, <span style="color: #008b8b;">NULL</span>);
<span style="color: #a020f0;">if</span> (status &lt; 0) {
H5Sclose(fspace);
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
// <span style="color: #b22222;">create memory dataspace to write from</span>
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace</span> = H5Screate_simple(h5_rank, chunk_dims, <span style="color: #008b8b;">NULL</span>);
<span style="color: #a020f0;">if</span> (dspace &lt; 0) {
H5Sclose(fspace);
H5Sclose(dspace);
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
status = H5Dwrite(dset_id,
dtype_id,
dspace, fspace, H5P_DEFAULT,
data_sparse);
H5Dclose(dset_id);
H5Sclose(dspace);
H5Sclose(fspace);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
<span style="color: #228b22;">trexio_exit_code</span>
<span style="color: #0000ff;">trexio_hdf5_open_read_dset_sparse</span> (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">group_id</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span>* <span style="color: #a0522d;">dset_name</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span>* <span style="color: #a0522d;">offset_file</span>,
<span style="color: #228b22;">hsize_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">size_read</span>,
<span style="color: #228b22;">int64_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">eof_read_size</span>,
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int</span> <span style="color: #a0522d;">is_index</span>,
<span style="color: #228b22;">void</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">data_sparse</span>
)
{
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int</span> <span style="color: #a0522d;">h5_rank</span> = 1;
// <span style="color: #b22222;">get the dataset handle</span>
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dopen(group_id, dset_name, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
// <span style="color: #b22222;">get the dataspace of the dataset</span>
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">fspace_id</span> = H5Dget_space(dset_id);
<span style="color: #a020f0;">if</span> (fspace_id &lt; 0) {
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
/* <span style="color: #b22222;">get dims of the dset stored in the file to check whether reading with user-provided chunk size</span>
<span style="color: #b22222;"> will reach end of the dataset (i.e. EOF in TEXT back end)</span>
<span style="color: #b22222;"> </span>*/
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">ddims</span>[1] = {0};
<span style="color: #228b22;">int</span> <span style="color: #a0522d;">rrank</span> = H5Sget_simple_extent_dims(fspace_id, ddims, <span style="color: #008b8b;">NULL</span>);
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<span style="color: #a020f0;">if</span> (rrank != h5_rank) {
H5Sclose(fspace_id);
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
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<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">max_offset</span> = offset_file[0] + size_read[0];
<span style="color: #228b22;">int</span> <span style="color: #a0522d;">is_EOF</span> = 0;
// <span style="color: #b22222;">if max_offset exceed current dim of the dset =&gt; EOF</span>
<span style="color: #a020f0;">if</span> (max_offset &gt; ddims[0]) {
is_EOF = 1;
// <span style="color: #b22222;">lower the value of count to reduce the number of elements which will be read</span>
size_read[0] -= max_offset - ddims[0];
// <span style="color: #b22222;">modified the value of eof_read_size passed by address</span>
<span style="color: #a020f0;">if</span> (eof_read_size != <span style="color: #008b8b;">NULL</span>) *eof_read_size = size_read[0];
}
// <span style="color: #b22222;">special case when reading int indices</span>
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<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">size_ranked</span> = (<span style="color: #228b22;">uint64_t</span>) size_read[0];
<span style="color: #228b22;">void</span>* <span style="color: #a0522d;">index_p</span> = <span style="color: #008b8b;">NULL</span>;
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// <span style="color: #b22222;">read the datatype from the dataset and compare with the pre-defined values</span>
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype</span> = H5Dget_type(dset_id);
<span style="color: #a020f0;">if</span> (is_index == 1) {
<span style="color: #a020f0;">if</span> (H5Tequal(dtype, H5T_NATIVE_UINT8) &gt; 0) {
<span style="color: #228b22;">uint8_t</span>* <span style="color: #a0522d;">index</span> = CALLOC(size_ranked, uint8_t);
<span style="color: #a020f0;">if</span> (index == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_ALLOCATION_FAILED;
index_p = index;
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (H5Tequal(dtype, H5T_NATIVE_UINT16) &gt; 0) {
<span style="color: #228b22;">uint16_t</span>* <span style="color: #a0522d;">index</span> = CALLOC(size_ranked, uint16_t);
<span style="color: #a020f0;">if</span> (index == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_ALLOCATION_FAILED;
index_p = index;
} <span style="color: #a020f0;">else</span> {
index_p = data_sparse;
}
}
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, offset_file, <span style="color: #008b8b;">NULL</span>, size_read, <span style="color: #008b8b;">NULL</span>);
<span style="color: #a020f0;">if</span> (status &lt; 0) {
H5Sclose(fspace_id);
H5Dclose(dset_id);
<span style="color: #a020f0;">if</span> (index_p != data_sparse) FREE(index_p);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">memspace_id</span> = H5Screate_simple(h5_rank, size_read, <span style="color: #008b8b;">NULL</span>);
<span style="color: #a020f0;">if</span> (memspace_id &lt; 0) {
H5Sclose(fspace_id);
H5Dclose(dset_id);
<span style="color: #a020f0;">if</span> (index_p != data_sparse) FREE(index_p);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
<span style="color: #a020f0;">if</span> (is_index == 1) {
status = H5Dread(dset_id,
dtype,
memspace_id, fspace_id, H5P_DEFAULT,
index_p);
} <span style="color: #a020f0;">else</span> {
status = H5Dread(dset_id,
dtype,
memspace_id, fspace_id, H5P_DEFAULT,
data_sparse);
}
H5Sclose(fspace_id);
H5Sclose(memspace_id);
H5Dclose(dset_id);
<span style="color: #a020f0;">if</span> (status &lt; 0) {
<span style="color: #a020f0;">if</span> (index_p != data_sparse) FREE(index_p);
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
<span style="color: #a020f0;">if</span> (is_index == 1) {
<span style="color: #a020f0;">if</span> (H5Tequal(dtype, H5T_NATIVE_UINT8) &gt; 0) {
<span style="color: #228b22;">uint8_t</span>* <span style="color: #a0522d;">index</span> = (<span style="color: #228b22;">uint8_t</span>*) index_p;
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<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">i</span>=0; i&lt;size_ranked; ++i){
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((<span style="color: #228b22;">int32_t</span>*)data_sparse)[i] = (<span style="color: #228b22;">int32_t</span>) index[i];
}
FREE(index_p);
} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (H5Tequal(dtype, H5T_NATIVE_UINT16) &gt; 0) {
<span style="color: #228b22;">uint16_t</span>* <span style="color: #a0522d;">index</span> = (<span style="color: #228b22;">uint16_t</span>*) index_p;
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<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">i</span>=0; i&lt;size_ranked; ++i){
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((<span style="color: #228b22;">int32_t</span>*)data_sparse)[i] = (<span style="color: #228b22;">int32_t</span>) index[i];
}
FREE(index_p);
}
}
<span style="color: #a020f0;">if</span> (is_EOF == 1) <span style="color: #a020f0;">return</span> TREXIO_END;
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
}
</pre>
</div>
</div>
</div>
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</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
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<p class="date">Created: 2022-01-24 Mon 17:22</p>
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<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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