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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>
<li><a href="#org4c9efee">1. HDF5 back end</a>
<ul>
<li><a href="#orgeef4f7f">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org90403f5">1.2. Template for HDF5 structures</a></li>
<li><a href="#org5d61539">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org83f86df">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org9b88311">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orgb9ec75d">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org04255d5">1.7. Template for HDF5 has/read/write the string attribute</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org4c9efee" class="outline-2">
<h2 id="org4c9efee"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgeef4f7f" class="outline-3">
<h3 id="orgeef4f7f"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<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>
<span style="color: #483d8b;">#define</span> $GROUP_DSET$_NAME <span style="color: #8b2252;">"$group_dset$"</span>
<span style="color: #483d8b;">#define</span> $GROUP_STR$_NAME <span style="color: #8b2252;">"$group_str$"</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org90403f5" class="outline-3">
<h3 id="org90403f5"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<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> ;
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">file_id</span>;
hid_t $group$_group;
} <span style="color: #228b22;">trexio_hdf5_t</span>;
</pre>
</div>
</div>
</div>
<div id="outline-container-org5d61539" class="outline-3">
<h3 id="org5d61539"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div class="outline-text-3" id="text-1-3">
<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>:
// <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);
<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>:
// <span style="color: #b22222;">reading non-existing file -&gt; error</span>
<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>:
<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);
}
<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;
}
<span style="color: #228b22;">trexio_exit_code</span>
<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>
<div id="outline-container-org83f86df" class="outline-3">
<h3 id="org83f86df"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<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>
<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)
{
<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;
/* <span style="color: #b22222;">Read the $group_num$ attribute of $group$ group </span>*/
<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;
<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);
H5Aclose(num_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>
<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)
{
<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;
/* <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);
<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,
dtype, dspace, H5P_DEFAULT, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (num_id &lt;= 0) {
H5Sclose(dspace);
H5Tclose(dtype);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
}
<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) {
H5Aclose(num_id);
H5Sclose(dspace);
H5Tclose(dtype);
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
H5Sclose(dspace);
H5Aclose(num_id);
H5Tclose(dtype);
<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_$group_num$</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>
<div id="outline-container-org9b88311" class="outline-3">
<h3 id="org9b88311"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<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>
<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>)
{
<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: #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>) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
// <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) {
FREE(ddims);
H5Sclose(dspace_id);
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_3;
}
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">i</span>=0; i&lt;rank; ++i){
<span style="color: #a020f0;">if</span> (ddims[i] != dims[i]) {
FREE(ddims);
H5Sclose(dspace_id);
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_4;
}
}
FREE(ddims);
H5Sclose(dspace_id);
H5Dclose(dset_id);
/* <span style="color: #b22222;">High-level H5LT API. No need to deal with dataspaces and datatypes </span>*/
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTread_dataset(f-&gt;$group$_group,
$GROUP_DSET$_NAME,
H5T_$GROUP_DSET_H5_DTYPE$,
$group_dset$);
<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_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>)
{
<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: #a020f0;">if</span> ( H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME) != 1 ) {
<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,
$GROUP_DSET$_NAME,
(<span style="color: #228b22;">int</span>) rank, (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hsize_t</span>*) dims,
H5T_$GROUP_DSET_H5_DTYPE$,
$group_dset$);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
} <span style="color: #a020f0;">else</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: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Dwrite(dset_id,
H5T_$GROUP_DSET_H5_DTYPE$,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$);
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>
<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>
<div id="outline-container-orgb9ec75d" class="outline-3">
<h3 id="orgb9ec75d"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div class="outline-text-3" id="text-1-6">
<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;
}
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace</span> = H5Dget_space(dset_id);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) {
FREE(ddims);
H5Dclose(dset_id);
<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);
H5Tclose(memtype);
<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);
H5Tclose(memtype);
<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);
H5Tclose(memtype);
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
}
FREE(rdata);
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);
<span style="color: #a020f0;">if</span> (memtype &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
status = H5Tset_size (memtype, H5T_VARIABLE);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">if</span> ( H5LTfind_dataset(f-&gt;$group$_group, $GROUP_DSET$_NAME) != 1 ) {
/* <span style="color: #b22222;">code to create dataset </span>*/
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">filetype</span> = H5Tcopy (H5T_FORTRAN_S1);
<span style="color: #a020f0;">if</span> (filetype &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
status = H5Tset_size (filetype, H5T_VARIABLE);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<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>);
<span style="color: #a020f0;">if</span> (dspace &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
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>
<div id="outline-container-org04255d5" class="outline-3">
<h3 id="org04255d5"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the string attribute</h3>
<div class="outline-text-3" id="text-1-7">
<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);
<span style="color: #a020f0;">if</span> (sdim &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
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;
}
}
</pre>
</div>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-10-07 Thu 07:56</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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