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HTML
1804 lines
112 KiB
HTML
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</head>
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<body>
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<div id="org-div-home-and-up">
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<a accesskey="h" href=""> UP </a>
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<a accesskey="H" href="index.html"> HOME </a>
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</div><div id="content">
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<h1 class="title">HDF5 back end</h1>
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<div id="table-of-contents">
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<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
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<ul>
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<li><a href="#org49c4075">1. Template for HDF5 definitions</a></li>
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<li><a href="#org87fb328">2. Template for HDF5 structures</a></li>
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<li><a href="#org2f99c28">3. Template for HDF5 init/deinit</a></li>
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<li><a href="#orgfb9b95b">4. Template for HDF5 has/read/write a numerical attribute</a></li>
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<li><a href="#org9b7ef5b">5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
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<li><a href="#org0a9c2ae">6. Template for HDF5 has/read/write a dataset of sparse data</a></li>
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<li><a href="#orgb31c882">7. Template for HDF5 has/read/write a dataset of strings</a></li>
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<li><a href="#org7fea7f6">8. Template for HDF5 has/read/write a string attribute</a></li>
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<li><a href="#org20dc905">9. Template for HDF5 delete a group (UNSAFE mode)</a></li>
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<li><a href="#orged8ae62">10. Source code for the determinant part</a></li>
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<li><a href="#orgc376ec9">11. Helper functions</a></li>
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</ul>
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</div>
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</div>
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<div id="outline-container-org49c4075" class="outline-2">
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<h2 id="org49c4075"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
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<div class="outline-text-2" id="text-1">
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<div class="org-src-container">
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<pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
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<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>
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</div>
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</div>
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<div id="outline-container-org87fb328" class="outline-2">
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<h2 id="org87fb328"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
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<div class="outline-text-2" id="text-2">
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<p>
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Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
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corresponding types for all back ends can be safely casted to
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<code>trexio_t</code>. This is done by making the back-end structs start with
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<code>trexio_t parent</code> attribute:
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</p>
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<div class="org-src-container">
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<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> {
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<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>;
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hid_t $group$_group;
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} <span style="color: #228b22;">trexio_hdf5_t</span>;
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</pre>
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</div>
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</div>
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</div>
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<div id="outline-container-org2f99c28" class="outline-2">
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<h2 id="org2f99c28"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
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<div class="outline-text-2" id="text-3">
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<div class="org-src-container">
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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_inquire</span>(<span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span>* <span style="color: #a0522d;">file_name</span>)
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{
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/* <span style="color: #b22222;">H5Fis_hdf5 determines whether file is in HDF5 format </span>*/
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<span style="color: #228b22;">htri_t</span> <span style="color: #a0522d;">rc</span> = H5Fis_hdf5(file_name);
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<span style="color: #a020f0;">if</span> (rc > 0 ) {
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<span style="color: #a020f0;">return</span> TREXIO_SUCCESS; //<span style="color: #b22222;">exists and HDF5</span>
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} <span style="color: #a020f0;">else</span> <span style="color: #a020f0;">if</span> (rc == 0) {
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<span style="color: #a020f0;">return</span> TREXIO_FILE_ERROR; //<span style="color: #b22222;">exists but not HDF5</span>
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} <span style="color: #a020f0;">else</span> {
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<span style="color: #a020f0;">return</span> TREXIO_FAILURE; //<span style="color: #b22222;">does not exist or function fails</span>
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}
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}
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</pre>
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</div>
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<div class="org-src-container">
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<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->file_name, &st) == 0) f_exists = 1;
|
|
|
|
<span style="color: #a020f0;">if</span> (f_exists == 1) {
|
|
|
|
<span style="color: #a020f0;">switch</span> (file->mode) {
|
|
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'r'</span>:
|
|
// <span style="color: #b22222;">reading the existing file -> open as RDONLY</span>
|
|
f->file_id = H5Fopen(file->file_name, H5F_ACC_RDONLY, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">break</span>;
|
|
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'u'</span>:
|
|
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'w'</span>:
|
|
// <span style="color: #b22222;">writing the existing file -> open as RDWRITE</span>
|
|
f->file_id = H5Fopen(file->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->mode) {
|
|
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'r'</span>:
|
|
// <span style="color: #b22222;">reading non-existing file -> error</span>
|
|
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'u'</span>:
|
|
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'w'</span>:
|
|
// <span style="color: #b22222;">writing non-existing file -> create it</span>
|
|
f->file_id = H5Fcreate(file->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->mode) {
|
|
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'r'</span>:
|
|
<span style="color: #a020f0;">if</span> (H5Lexists(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT) > 0) f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (H5Lexists(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT) == 0) f->$group$_group = (<span style="color: #228b22;">hid_t</span>) 0;
|
|
<span style="color: #a020f0;">break</span>;
|
|
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'u'</span>:
|
|
<span style="color: #a020f0;">case</span> <span style="color: #8b2252;">'w'</span>:
|
|
<span style="color: #a020f0;">if</span> (f_exists == 1) {
|
|
<span style="color: #a020f0;">if</span> (H5Lexists(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT) > 0) f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (H5Lexists(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT) == 0) f->$group$_group = H5Gcreate(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
} <span style="color: #a020f0;">else</span> {
|
|
f->$group$_group = H5Gcreate(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
}
|
|
<span style="color: #a020f0;">break</span>;
|
|
}
|
|
<span style="color: #a020f0;">if</span> (f->$group$_group < (<span style="color: #228b22;">hid_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_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_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;
|
|
|
|
<span style="color: #a020f0;">if</span> (f->$group$_group != (<span style="color: #228b22;">hid_t</span>) 0) H5Gclose(f->$group$_group);
|
|
f->$group$_group = 0;
|
|
|
|
H5Fclose(f->file_id);
|
|
f->file_id = 0;
|
|
|
|
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
|
|
|
|
}
|
|
</pre>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orgfb9b95b" class="outline-2">
|
|
<h2 id="orgfb9b95b"><span class="section-number-2">4</span> Template for HDF5 has/read/write a numerical attribute</h2>
|
|
<div class="outline-text-2" id="text-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->$group$_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->$group$_group, $GROUP_NUM$_NAME, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (num_id <= 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 < 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;">Delete the attribute if it exists and if the file is open in UNSAFE mode </span>*/
|
|
<span style="color: #a020f0;">if</span> (trexio_hdf5_has_$group_num$(file) == TREXIO_SUCCESS && file->mode == <span style="color: #8b2252;">'u'</span>) {
|
|
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status_del</span> = H5Adelete(f->$group$_group, $GROUP_NUM$_NAME);
|
|
<span style="color: #a020f0;">if</span> (status_del < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
}
|
|
|
|
/* <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_$GROUP_NUM_H5_DTYPE$);
|
|
<span style="color: #a020f0;">if</span> (dtype_id <= 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;">dspace_id</span> = H5Screate(H5S_SCALAR);
|
|
<span style="color: #a020f0;">if</span> (dspace_id <= 0) {
|
|
H5Tclose(dtype_id);
|
|
<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;">num_id</span> = H5Acreate(f->$group$_group,
|
|
$GROUP_NUM$_NAME,
|
|
dtype_id, dspace_id,
|
|
H5P_DEFAULT, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (num_id <= 0) {
|
|
H5Sclose(dspace_id);
|
|
H5Tclose(dtype_id);
|
|
<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_id, &num);
|
|
|
|
H5Sclose(dspace_id);
|
|
H5Aclose(num_id);
|
|
H5Tclose(dtype_id);
|
|
<span style="color: #a020f0;">if</span> (status < 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_$group_num$</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: #a020f0;">if</span> (f->$group$_group == (<span style="color: #228b22;">hsize_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
|
|
|
|
<span style="color: #228b22;">htri_t</span> <span style="color: #a0522d;">status</span> = H5Aexists(f->$group$_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 > 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-org9b7ef5b" class="outline-2">
|
|
<h2 id="org9b7ef5b"><span class="section-number-2">5</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
|
|
<div class="outline-text-2" id="text-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->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (dset_id <= 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<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->$group$_group,
|
|
$GROUP_DSET$_NAME,
|
|
H5T_$GROUP_DSET_H5_DTYPE$,
|
|
$group_dset$);
|
|
<span style="color: #a020f0;">if</span> (status < 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: #b22222;"> Try to delete an existing dataset by unlinking it from the group (UNSAFE mode).</span>
|
|
<span style="color: #b22222;"> NOTE: In principle, HDF5 should see the deallocated (unused) file space and free it,</span>
|
|
<span style="color: #b22222;"> thus reducing the size of the HDF5 file. In practic, this is not always the case.</span>
|
|
|
|
<span style="color: #b22222;"> Consider using HDF5-native h5repack utility after deleting/overwriting big datasets.</span>
|
|
<span style="color: #b22222;"> </span>*/
|
|
<span style="color: #a020f0;">if</span> (H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) == 1 && file->mode == <span style="color: #8b2252;">'u'</span>) {
|
|
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status_del</span> = H5Ldelete(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (status_del < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
}
|
|
|
|
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace_id</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_id <= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
|
|
|
|
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dcreate (f->$group$_group,
|
|
$GROUP_DSET$_NAME,
|
|
H5T_$GROUP_DSET_H5_DTYPE$,
|
|
dspace_id,
|
|
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (dset_id <= 0) {
|
|
H5Sclose(dspace_id);
|
|
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
|
|
}
|
|
|
|
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Dwrite(dset_id,
|
|
H5T_$GROUP_DSET_H5_DTYPE$,
|
|
H5S_ALL,
|
|
dspace_id,
|
|
H5P_DEFAULT,
|
|
$group_dset$);
|
|
H5Dclose(dset_id);
|
|
H5Sclose(dspace_id);
|
|
<span style="color: #a020f0;">if</span> (status < 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: #a020f0;">if</span> (f->$group$_group == (<span style="color: #228b22;">hsize_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
|
|
|
|
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f->$group$_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-org0a9c2ae" class="outline-2">
|
|
<h2 id="org0a9c2ae"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
|
|
<div class="outline-text-2" id="text-6">
|
|
<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>;
|
|
<span style="color: #228b22;">void</span>* <span style="color: #a0522d;">index_p</span> = <span style="color: #008b8b;">NULL</span>;
|
|
<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 < 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;
|
|
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">i</span>=0; i<size_ranked; ++i){
|
|
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 < 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;
|
|
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">i</span>=0; i<size_ranked; ++i){
|
|
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>*/
|
|
<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];
|
|
/* <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->$group$_group, dset_index_name) != 1 ) {
|
|
/* <span style="color: #b22222;">If the file does not exist -> 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->$group$_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->$group$_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 -> 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->$group$_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->$group$_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>*/
|
|
<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];
|
|
/* <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->$group$_group, dset_index_name, $group_dset_rank$, offset_i, count_i, <span style="color: #008b8b;">NULL</span>, is_index, index_read);
|
|
<span style="color: #a020f0;">if</span> (rc_read != TREXIO_SUCCESS && 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->$group$_group, dset_value_name, 1, offset_v, count_v, eof_read_size, is_value, value_read);
|
|
<span style="color: #a020f0;">if</span> (rc_read != TREXIO_SUCCESS && 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;">if</span> (size_max == <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;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME <span style="color: #8b2252;">"_values"</span>, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (dset_id <= 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 < 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>
|
|
H5Sget_simple_extent_dims(fspace_id, ddims, <span style="color: #008b8b;">NULL</span>);
|
|
|
|
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: #a020f0;">if</span> (f->$group$_group == (<span style="color: #228b22;">hsize_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
|
|
|
|
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f->$group$_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>
|
|
|
|
<div id="outline-container-orgb31c882" class="outline-2">
|
|
<h2 id="orgb31c882"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of strings</h2>
|
|
<div class="outline-text-2" id="text-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_$group_dset$</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->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (dset_id <= 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 <= 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<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 < 0 || memtype <= 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 < 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<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 <= 1 && H5_VERS_MINOR < 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 < 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: #b22222;"> Try to delete an existing dataset by unlinking it from the group (UNSAFE mode).</span>
|
|
<span style="color: #b22222;"> NOTE: In principle, HDF5 should see the deallocated (unused) file space and free it,</span>
|
|
<span style="color: #b22222;"> thus reducing the size of the HDF5 file. In practic, this is not always the case.</span>
|
|
|
|
<span style="color: #b22222;"> Consider using HDF5-provided h5repack utility after deleting/overwriting big datasets.</span>
|
|
<span style="color: #b22222;"> </span>*/
|
|
<span style="color: #a020f0;">if</span> (H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) == 1 && file->mode == <span style="color: #8b2252;">'u'</span>) {
|
|
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status_del</span> = H5Ldelete(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (status_del < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
}
|
|
|
|
<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 <= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
|
|
|
|
status = H5Tset_size (memtype, H5T_VARIABLE);
|
|
<span style="color: #a020f0;">if</span> (status < 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 <= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
|
|
|
|
/* <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 <= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
|
|
|
|
status = H5Tset_size (filetype, H5T_VARIABLE);
|
|
<span style="color: #a020f0;">if</span> (status < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
|
|
dset_id = H5Dcreate (f->$group$_group, $GROUP_DSET$_NAME, filetype, dspace,
|
|
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (dset_id <= 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 < 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: #a020f0;">if</span> (f->$group$_group == (<span style="color: #228b22;">hsize_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
|
|
|
|
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f->$group$_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-org7fea7f6" class="outline-2">
|
|
<h2 id="org7fea7f6"><span class="section-number-2">8</span> Template for HDF5 has/read/write a string attribute</h2>
|
|
<div class="outline-text-2" id="text-8">
|
|
<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->$group$_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->$group$_group, $GROUP_STR$_NAME, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (str_id <= 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 <= 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 <= 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) > sdim ? H5Tset_size(mem_id, sdim) : H5Tset_size(mem_id, max_str_len+1) ;
|
|
<span style="color: #a020f0;">if</span> (status < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
|
|
status = H5Aread(str_id, mem_id, str);
|
|
<span style="color: #a020f0;">if</span> (status < 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;">Delete the attribute if it exists and if the file is open in UNSAFE mode </span>*/
|
|
<span style="color: #a020f0;">if</span> (trexio_hdf5_has_$group_str$(file) == TREXIO_SUCCESS && file->mode == <span style="color: #8b2252;">'u'</span>) {
|
|
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status_del</span> = H5Adelete(f->$group$_group, $GROUP_STR$_NAME);
|
|
<span style="color: #a020f0;">if</span> (status_del < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
}
|
|
|
|
/* <span style="color: #b22222;">Setup the datatype for variable length string </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 <= 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 < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
|
|
status = H5Tset_strpad(dtype_id, H5T_STR_NULLTERM);
|
|
<span style="color: #a020f0;">if</span> (status < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
|
|
/* <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;">dspace_id</span> = H5Screate(H5S_SCALAR);
|
|
<span style="color: #a020f0;">if</span> (dspace_id <= 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->$group$_group,
|
|
$GROUP_STR$_NAME,
|
|
dtype_id, dspace_id,
|
|
H5P_DEFAULT, H5P_DEFAULT);
|
|
|
|
<span style="color: #a020f0;">if</span> (str_id <= 0) {
|
|
H5Sclose(dspace_id);
|
|
H5Tclose(dtype_id);
|
|
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
|
|
}
|
|
|
|
status = H5Awrite(str_id, dtype_id, str);
|
|
|
|
H5Aclose(str_id);
|
|
H5Sclose(dspace_id);
|
|
H5Tclose(dtype_id);
|
|
|
|
<span style="color: #a020f0;">if</span> (status < 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_$group_str$</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: #a020f0;">if</span> (f->$group$_group == (<span style="color: #228b22;">hsize_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
|
|
|
|
<span style="color: #228b22;">htri_t</span> <span style="color: #a0522d;">status</span> = H5Aexists(f->$group$_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 > 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-org20dc905" class="outline-2">
|
|
<h2 id="org20dc905"><span class="section-number-2">9</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
|
|
<div class="outline-text-2" id="text-9">
|
|
<p>
|
|
<b><b>Note:</b></b> in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected
|
|
and the associated memory was not necessarily freed (see <a href="https://stackoverflow.com/questions/1124994/removing-data-from-a-hdf5-file">this StackOverflow discussion</a> for example).
|
|
Nevertheless, some space might remain occupied even after deleting the associated object in recent version.
|
|
To take the best use of the deleted file space, we recommend to write the deleted group within the same session
|
|
(i.e. before closing the TREXIO file).
|
|
</p>
|
|
|
|
<p>
|
|
In principle, one can use HDF5-provided <code>h5repack</code> binary, which copies all existing objects from one file into another.
|
|
Thus, any corrupted/lost file space will remain in the first file. The use of <code>h5repack</code> is highly encouraged.
|
|
</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_delete_$group$</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: #b22222;">delete the link to the existing group: this should free the associated space</span>
|
|
H5Gclose(f->$group$_group);
|
|
f->$group$_group = 0;
|
|
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Ldelete(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (status < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
|
|
// <span style="color: #b22222;">re-create the group (with the new link ?)</span>
|
|
f->$group$_group = H5Gcreate(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (f->$group$_group <= 0L) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
|
|
|
|
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
|
|
}
|
|
</pre>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
<div id="outline-container-orged8ae62" class="outline-2">
|
|
<h2 id="orged8ae62"><span class="section-number-2">10</span> Source code for the determinant part</h2>
|
|
<div class="outline-text-2" id="text-10">
|
|
<p>
|
|
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
|
|
Chunks are used to read/write the data to prevent memory overflow. Chunks have a given <code>int64_t dims[0]*dims[1]</code>.
|
|
Size specifies the number of data items (e.g. determinants) to process.
|
|
</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_read_determinant_list</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;">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: #228b22;">int64_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">eof_read_size</span>,
|
|
<span style="color: #228b22;">int64_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">list</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;">if</span> (list == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_6;
|
|
|
|
<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;">char</span> <span style="color: #a0522d;">dset_det_name</span>[256] = <span style="color: #8b2252;">"determinant_list"</span>;
|
|
|
|
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">offset</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) offset_file * dims[1]};
|
|
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">count</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) dims[0] * dims[1]};
|
|
|
|
/* <span style="color: #b22222;">Attempt to read determinants (if EOF -> eof_read_size is modified with the number of elements read and return code is TREXIO_END)</span>
|
|
<span style="color: #b22222;"> 0 argument below is requires to skip internal treatment specific to sparse indices (i.e. their de-compression).</span>*/
|
|
<span style="color: #a020f0;">return</span> trexio_hdf5_open_read_dset_sparse(f->determinant_group, dset_det_name, (<span style="color: #228b22;">uint32_t</span>) dims[1], offset, count, eof_read_size, 0, list);
|
|
}
|
|
|
|
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #0000ff;">trexio_hdf5_read_determinant_coefficient</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;">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: #228b22;">int64_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">eof_read_size</span>,
|
|
<span style="color: #228b22;">double</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">coeff</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;">if</span> (coeff == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_6;
|
|
|
|
<span style="color: #228b22;">char</span> <span style="color: #a0522d;">dset_coeff_name</span>[128];
|
|
memset(dset_coeff_name, 0, <span style="color: #a020f0;">sizeof</span>(dset_coeff_name));
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int32_t</span> <span style="color: #a0522d;">trexio_state</span> = file->state;
|
|
|
|
<span style="color: #a020f0;">if</span> (trexio_state != 0) {
|
|
sprintf(dset_coeff_name, <span style="color: #8b2252;">"determinant_coefficient_state_%"</span> PRId32, trexio_state);
|
|
} <span style="color: #a020f0;">else</span> {
|
|
strncpy(dset_coeff_name, <span style="color: #8b2252;">"determinant_coefficient"</span>, 24);
|
|
}
|
|
|
|
<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;">hsize_t</span> <span style="color: #a0522d;">offset</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) offset_file};
|
|
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">count</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) dims[0]};
|
|
|
|
/* <span style="color: #b22222;">Attempt to read determinants (if EOF -> eof_read_size is modified with the number of elements read and return code is TREXIO_END)</span>
|
|
<span style="color: #b22222;"> 0 argument below is requires to skip internal treatment specific to sparse indices (i.e. their de-compression).</span>*/
|
|
<span style="color: #a020f0;">return</span> trexio_hdf5_open_read_dset_sparse(f->determinant_group, dset_coeff_name, 1, offset, count, eof_read_size, 0, coeff);
|
|
}
|
|
</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_determinant_list</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;">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;">int64_t</span>* <span style="color: #a0522d;">list</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> (list == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_5;
|
|
|
|
<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;">det_dtype</span> = H5T_NATIVE_INT64;
|
|
<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">size_ranked</span> = dims[1]*dims[0];
|
|
|
|
/* <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_dims</span>[1] = {size_ranked};
|
|
|
|
/* <span style="color: #b22222;">Indices and values are stored as 2 independent datasets in the HDF5 file </span>*/
|
|
<span style="color: #228b22;">char</span> <span style="color: #a0522d;">dset_det_name</span>[256] = <span style="color: #8b2252;">"determinant_list"</span>;
|
|
|
|
<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->determinant_group, dset_det_name) != 1 ) {
|
|
/* <span style="color: #b22222;">If the file does not exist -> create it and write </span>*/
|
|
|
|
/* <span style="color: #b22222;">Create chunked dataset with det_dtype datatype and write indices into it </span>*/
|
|
rc_write = trexio_hdf5_create_write_dset_sparse(f->determinant_group, dset_det_name, det_dtype, chunk_dims, list);
|
|
<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 -> open it and write </span>*/
|
|
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">offset_data</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) offset_file * dims[1]};
|
|
|
|
/* <span style="color: #b22222;">Create chunked dataset with det_dtype datatype and write indices into it </span>*/
|
|
rc_write = trexio_hdf5_open_write_dset_sparse(f->determinant_group, dset_det_name, det_dtype, chunk_dims, offset_data, list);
|
|
<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;
|
|
}
|
|
|
|
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #0000ff;">trexio_hdf5_write_determinant_coefficient</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;">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;">double</span>* <span style="color: #a0522d;">coeff</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> (coeff == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_5;
|
|
|
|
<span style="color: #228b22;">char</span> <span style="color: #a0522d;">dset_coeff_name</span>[128];
|
|
memset(dset_coeff_name, 0, <span style="color: #a020f0;">sizeof</span>(dset_coeff_name));
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int32_t</span> <span style="color: #a0522d;">trexio_state</span> = file->state;
|
|
|
|
<span style="color: #a020f0;">if</span> (trexio_state != 0) {
|
|
sprintf(dset_coeff_name, <span style="color: #8b2252;">"determinant_coefficient_state_%"</span> PRId32, trexio_state);
|
|
} <span style="color: #a020f0;">else</span> {
|
|
strncpy(dset_coeff_name, <span style="color: #8b2252;">"determinant_coefficient"</span>, 24);
|
|
}
|
|
|
|
<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;">det_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_dims</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) dims[0]};
|
|
|
|
<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->determinant_group, dset_coeff_name) != 1 ) {
|
|
/* <span style="color: #b22222;">If the file does not exist -> create it and write </span>*/
|
|
|
|
/* <span style="color: #b22222;">Create chunked dataset with det_dtype datatype and write indices into it </span>*/
|
|
rc_write = trexio_hdf5_create_write_dset_sparse(f->determinant_group, dset_coeff_name, det_dtype, chunk_dims, coeff);
|
|
<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 -> open it and write </span>*/
|
|
<span style="color: #228b22;">hsize_t</span> <span style="color: #a0522d;">offset_data</span>[1] = {(<span style="color: #228b22;">hsize_t</span>) offset_file};
|
|
|
|
/* <span style="color: #b22222;">Create chunked dataset with det_dtype datatype and write indices into it </span>*/
|
|
rc_write = trexio_hdf5_open_write_dset_sparse(f->determinant_group, dset_coeff_name, det_dtype, chunk_dims, offset_data, coeff);
|
|
<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;
|
|
}
|
|
|
|
<span style="color: #228b22;">trexio_exit_code</span>
|
|
<span style="color: #0000ff;">trexio_hdf5_read_determinant_coefficient_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;">if</span> (size_max == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
|
|
|
|
<span style="color: #228b22;">char</span> <span style="color: #a0522d;">dset_coeff_name</span>[128];
|
|
memset(dset_coeff_name, 0, <span style="color: #a020f0;">sizeof</span>(dset_coeff_name));
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int32_t</span> <span style="color: #a0522d;">trexio_state</span> = file->state;
|
|
|
|
<span style="color: #a020f0;">if</span> (trexio_state != 0) {
|
|
sprintf(dset_coeff_name, <span style="color: #8b2252;">"determinant_coefficient_state_%"</span> PRId32, trexio_state);
|
|
} <span style="color: #a020f0;">else</span> {
|
|
strncpy(dset_coeff_name, <span style="color: #8b2252;">"determinant_coefficient"</span>, 24);
|
|
}
|
|
|
|
<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->determinant_group, dset_coeff_name, H5P_DEFAULT);
|
|
<span style="color: #a020f0;">if</span> (dset_id <= 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 < 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>
|
|
H5Sget_simple_extent_dims(fspace_id, ddims, <span style="color: #008b8b;">NULL</span>);
|
|
|
|
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_determinant_list</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: #a020f0;">if</span> (f->determinant_group == (<span style="color: #228b22;">hsize_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
|
|
|
|
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f->determinant_group, <span style="color: #8b2252;">"determinant_list"</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;
|
|
}
|
|
}
|
|
|
|
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #0000ff;">trexio_hdf5_has_determinant_coefficient</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: #a020f0;">if</span> (f->determinant_group == (<span style="color: #228b22;">hsize_t</span>) 0) <span style="color: #a020f0;">return</span> TREXIO_HAS_NOT;
|
|
|
|
<span style="color: #228b22;">char</span> <span style="color: #a0522d;">dset_coeff_name</span>[128];
|
|
memset(dset_coeff_name, 0, <span style="color: #a020f0;">sizeof</span>(dset_coeff_name));
|
|
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">int32_t</span> <span style="color: #a0522d;">trexio_state</span> = file->state;
|
|
|
|
<span style="color: #a020f0;">if</span> (trexio_state != 0) {
|
|
sprintf(dset_coeff_name, <span style="color: #8b2252;">"determinant_coefficient_state_%"</span> PRId32, trexio_state);
|
|
} <span style="color: #a020f0;">else</span> {
|
|
strncpy(dset_coeff_name, <span style="color: #8b2252;">"determinant_coefficient"</span>, 24);
|
|
}
|
|
|
|
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTfind_dataset(f->determinant_group, dset_coeff_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-orgc376ec9" class="outline-2">
|
|
<h2 id="orgc376ec9"><span class="section-number-2">11</span> Helper functions</h2>
|
|
<div class="outline-text-2" id="text-11">
|
|
<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 < 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 < 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 < 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 < 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 < 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 <= 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 < 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>);
|
|
<span style="color: #a020f0;">if</span> (rrank != h5_rank) {
|
|
H5Sclose(fspace);
|
|
H5Dclose(dset_id);
|
|
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
}
|
|
|
|
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 < 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 < 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 < 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 < 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 < 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;">uint32_t</span> <span style="color: #a0522d;">dset_rank</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: #a020f0;">if</span> (dset_rank == 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_3;
|
|
|
|
// <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 <= 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 < 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>);
|
|
<span style="color: #a020f0;">if</span> (rrank != h5_rank) {
|
|
H5Sclose(fspace_id);
|
|
H5Dclose(dset_id);
|
|
<span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
|
}
|
|
|
|
<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 => EOF</span>
|
|
<span style="color: #a020f0;">if</span> (max_offset > 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]/dset_rank;
|
|
}
|
|
|
|
// <span style="color: #b22222;">special case when reading int indices</span>
|
|
<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>;
|
|
// <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) > 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) > 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 < 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 < 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 < 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) > 0) {
|
|
<span style="color: #228b22;">uint8_t</span>* <span style="color: #a0522d;">index</span> = (<span style="color: #228b22;">uint8_t</span>*) index_p;
|
|
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">i</span>=0; i<size_ranked; ++i){
|
|
((<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) > 0) {
|
|
<span style="color: #228b22;">uint16_t</span>* <span style="color: #a0522d;">index</span> = (<span style="color: #228b22;">uint16_t</span>*) index_p;
|
|
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint64_t</span> <span style="color: #a0522d;">i</span>=0; i<size_ranked; ++i){
|
|
((<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>
|
|
</div>
|
|
<div id="postamble" class="status">
|
|
<p class="author">Author: TREX-CoE</p>
|
|
<p class="date">Created: 2022-06-03 Fri 08:39</p>
|
|
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
|
</div>
|
|
</body>
|
|
</html>
|