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<div class="textblock"><h1><a class="anchor" id="secFiles"></a>
Files</h1>
<h2><a class="anchor" id="CB_FreeSpace"></a>
Tracking Free Space in HDF5 Files</h2>
<dl class="section user"><dt>Problem</dt><dd>You sometimes delete objects in HDF5 files and don't have new content to use the free space, but would like to reuse it in the future.</dd></dl>
<dl class="section user"><dt>Solution</dt><dd>At file creation time, set the file space management strategy and persistence of free space tracking information via <a class="el" href="group___f_c_p_l.html#ga167ff65f392ca3b7f1933b1cee1b9f70" title="Sets the file space handling strategy and persisting free-space values for a file creation property l...">H5Pset_file_space_strategy()</a>.</dd></dl>
<dl class="section note"><dt>Note</dt><dd>This feature is only supported in HDF5 1.10.1+.</dd></dl>
<div class="fragment"><div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  {</div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  __label__ fail_fcpl, fail_fapl, fail_file;</div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  <a class="code" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a> fcpl, fapl, file;</div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  </div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  <span class="keywordflow">if</span> ((fcpl = <a class="code" href="group___p_l_c_r.html#gaf1b11da01d4d45d788c45f8bc5f0cbfa">H5Pcreate</a>(<a class="code" href="_h5_ppublic_8h.html#a206f334f1e6c973e1215a3148b45b977">H5P_FILE_CREATE</a>)) < 0) {</div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  ret_val = EXIT_FAILURE;</div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  <span class="keywordflow">goto</span> fail_fcpl;</div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  }</div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#if H5_VERSION_GE(1, 10, 1)</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  <span class="keywordflow">if</span> (<a class="code" href="group___f_c_p_l.html#ga167ff65f392ca3b7f1933b1cee1b9f70">H5Pset_file_space_strategy</a>(fcpl, <a class="code" href="_h5_fpublic_8h.html#a9cc492c4b5c936e48716a8dab3691bcca4eb2323fa7feed13452676d57cc27a87">H5F_FSPACE_STRATEGY_FSM_AGGR</a>, 1, 4096) < 0) {</div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor">#else</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#error HDF5 1.10.1+ required</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  ret_val = EXIT_FAILURE;</div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keywordflow">goto</span> fail_fapl;</div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  }</div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  </div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="keywordflow">if</span> ((fapl = <a class="code" href="group___p_l_c_r.html#gaf1b11da01d4d45d788c45f8bc5f0cbfa">H5Pcreate</a>(<a class="code" href="_h5_ppublic_8h.html#a60ec2d4334addfc0eda89614598ee38e">H5P_FILE_ACCESS</a>)) < 0) {</div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  ret_val = EXIT_FAILURE;</div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keywordflow">goto</span> fail_fapl;</div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  }</div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#if H5_VERSION_GE(1, 10, 1)</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordflow">if</span> (<a class="code" href="group___f_a_p_l.html#gacbe1724e7f70cd17ed687417a1d2a910">H5Pset_libver_bounds</a>(fapl, <a class="code" href="_h5_fpublic_8h.html#a2d963b599894f684571fbd4d5e8a96a2a33c6cdc401a3a32dbf63d74019fad4b3">H5F_LIBVER_V110</a>, <a class="code" href="_h5_fpublic_8h.html#a47d050173da48a2b85c730446f0771c0">H5F_LIBVER_LATEST</a>) < 0) {</div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#else</span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#error HDF5 1.10.x+ required</span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  ret_val = EXIT_FAILURE;</div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordflow">goto</span> fail_file;</div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  }</div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  </div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordflow">if</span> ((file = <a class="code" href="group___h5_f.html#gae64b51ee9ac0781bc4ccc599d98387f4">H5Fcreate</a>(<span class="stringliteral">"free_space.h5"</span>, <a class="code" href="_h5_fpublic_8h.html#a5a2d6726f9ad8d2bca8df2b817e5ad6a">H5F_ACC_TRUNC</a>, fcpl, fapl)) < 0) {</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  ret_val = EXIT_FAILURE;</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordflow">goto</span> fail_file;</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  }</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <a class="code" href="group___h5_f.html#gac55cd91d80822e4f8c2a7f04ea71b124">H5Fclose</a>(file);</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> fail_file:</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <a class="code" href="group___p_l_c_r.html#ga5dce61149211d3ef319452aa598887fb">H5Pclose</a>(fapl);</div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> fail_fapl:</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <a class="code" href="group___p_l_c_r.html#ga5dce61149211d3ef319452aa598887fb">H5Pclose</a>(fcpl);</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> fail_fcpl:;</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  }</div>
<div class="ttc" id="a_h5_fpublic_8h_html_a2d963b599894f684571fbd4d5e8a96a2a33c6cdc401a3a32dbf63d74019fad4b3"><div class="ttname"><a href="_h5_fpublic_8h.html#a2d963b599894f684571fbd4d5e8a96a2a33c6cdc401a3a32dbf63d74019fad4b3">H5F_LIBVER_V110</a></div><div class="ttdeci">@ H5F_LIBVER_V110</div><div class="ttdef"><b>Definition:</b> H5Fpublic.h:188</div></div>
<div class="ttc" id="a_h5_fpublic_8h_html_a47d050173da48a2b85c730446f0771c0"><div class="ttname"><a href="_h5_fpublic_8h.html#a47d050173da48a2b85c730446f0771c0">H5F_LIBVER_LATEST</a></div><div class="ttdeci">#define H5F_LIBVER_LATEST</div><div class="ttdef"><b>Definition:</b> H5Fpublic.h:195</div></div>
<div class="ttc" id="a_h5_fpublic_8h_html_a5a2d6726f9ad8d2bca8df2b817e5ad6a"><div class="ttname"><a href="_h5_fpublic_8h.html#a5a2d6726f9ad8d2bca8df2b817e5ad6a">H5F_ACC_TRUNC</a></div><div class="ttdeci">#define H5F_ACC_TRUNC</div><div class="ttdef"><b>Definition:</b> H5Fpublic.h:50</div></div>
<div class="ttc" id="a_h5_fpublic_8h_html_a9cc492c4b5c936e48716a8dab3691bcca4eb2323fa7feed13452676d57cc27a87"><div class="ttname"><a href="_h5_fpublic_8h.html#a9cc492c4b5c936e48716a8dab3691bcca4eb2323fa7feed13452676d57cc27a87">H5F_FSPACE_STRATEGY_FSM_AGGR</a></div><div class="ttdeci">@ H5F_FSPACE_STRATEGY_FSM_AGGR</div><div class="ttdef"><b>Definition:</b> H5Fpublic.h:202</div></div>
<div class="ttc" id="a_h5_ipublic_8h_html_a0045db7ff9c22ad35db6ae91662e1943"><div class="ttname"><a href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a></div><div class="ttdeci">int64_t hid_t</div><div class="ttdef"><b>Definition:</b> H5Ipublic.h:60</div></div>
<div class="ttc" id="a_h5_ppublic_8h_html_a206f334f1e6c973e1215a3148b45b977"><div class="ttname"><a href="_h5_ppublic_8h.html#a206f334f1e6c973e1215a3148b45b977">H5P_FILE_CREATE</a></div><div class="ttdeci">#define H5P_FILE_CREATE</div><div class="ttdef"><b>Definition:</b> H5Ppublic.h:51</div></div>
<div class="ttc" id="a_h5_ppublic_8h_html_a60ec2d4334addfc0eda89614598ee38e"><div class="ttname"><a href="_h5_ppublic_8h.html#a60ec2d4334addfc0eda89614598ee38e">H5P_FILE_ACCESS</a></div><div class="ttdeci">#define H5P_FILE_ACCESS</div><div class="ttdef"><b>Definition:</b> H5Ppublic.h:52</div></div>
<div class="ttc" id="agroup___f_a_p_l_html_gacbe1724e7f70cd17ed687417a1d2a910"><div class="ttname"><a href="group___f_a_p_l.html#gacbe1724e7f70cd17ed687417a1d2a910">H5Pset_libver_bounds</a></div><div class="ttdeci">herr_t H5Pset_libver_bounds(hid_t plist_id, H5F_libver_t low, H5F_libver_t high)</div><div class="ttdoc">Controls the range of library release versions used when creating objects in a file.</div></div>
<div class="ttc" id="agroup___f_c_p_l_html_ga167ff65f392ca3b7f1933b1cee1b9f70"><div class="ttname"><a href="group___f_c_p_l.html#ga167ff65f392ca3b7f1933b1cee1b9f70">H5Pset_file_space_strategy</a></div><div class="ttdeci">herr_t H5Pset_file_space_strategy(hid_t plist_id, H5F_fspace_strategy_t strategy, hbool_t persist, hsize_t threshold)</div><div class="ttdoc">Sets the file space handling strategy and persisting free-space values for a file creation property l...</div></div>
<div class="ttc" id="agroup___h5_f_html_gac55cd91d80822e4f8c2a7f04ea71b124"><div class="ttname"><a href="group___h5_f.html#gac55cd91d80822e4f8c2a7f04ea71b124">H5Fclose</a></div><div class="ttdeci">herr_t H5Fclose(hid_t file_id)</div><div class="ttdoc">Terminates access to an HDF5 file.</div></div>
<div class="ttc" id="agroup___h5_f_html_gae64b51ee9ac0781bc4ccc599d98387f4"><div class="ttname"><a href="group___h5_f.html#gae64b51ee9ac0781bc4ccc599d98387f4">H5Fcreate</a></div><div class="ttdeci">hid_t H5Fcreate(const char *filename, unsigned flags, hid_t fcpl_id, hid_t fapl_id)</div><div class="ttdoc">Creates an HDF5 file.</div></div>
<div class="ttc" id="agroup___p_l_c_r_html_ga5dce61149211d3ef319452aa598887fb"><div class="ttname"><a href="group___p_l_c_r.html#ga5dce61149211d3ef319452aa598887fb">H5Pclose</a></div><div class="ttdeci">herr_t H5Pclose(hid_t plist_id)</div><div class="ttdoc">Terminates access to a property list.</div></div>
<div class="ttc" id="agroup___p_l_c_r_html_gaf1b11da01d4d45d788c45f8bc5f0cbfa"><div class="ttname"><a href="group___p_l_c_r.html#gaf1b11da01d4d45d788c45f8bc5f0cbfa">H5Pcreate</a></div><div class="ttdeci">hid_t H5Pcreate(hid_t cls_id)</div><div class="ttdoc">Creates a new property list as an instance of a property list class.</div></div>
</div><!-- fragment --> <dl class="section user"><dt>Discussion</dt><dd>Free space tracking is supported only in HDF5 versions 1.10.x and higher. This has implications for the accessibility of your HDF5 files and should be considered carefully. If compatibility with previous versions of HDF5 must be maintained, space reclamation via <code>h5repack</code> might be an option.<br />
The file space strategy <a class="el" href="_h5_fpublic_8h.html#a9cc492c4b5c936e48716a8dab3691bcca4eb2323fa7feed13452676d57cc27a87">H5F_FSPACE_STRATEGY_FSM_AGGR</a> is not the only option that supports free-space tracking. <a class="el" href="_h5_fpublic_8h.html#a9cc492c4b5c936e48716a8dab3691bccacd625bd864903e71132c9098929f5a0a">H5F_FSPACE_STRATEGY_PAGE</a> is another option, which adds paged allocation and is used most effectively with page buffering.<br />
For an in-depth account of HDF5 file space management, paged-allocation, and page buffering, see the following documents: <ul>
<li><a href="https://docs.hdfgroup.org/hdf5/rfc/FileSpaceManagement.pdf">HDF5 File Space Management</a> </li>
<li><a href="https://docs.hdfgroup.org/hdf5/rfc/paged_aggregation.pdf">HDF5 File Space Management: Paged Aggregation</a> </li>
<li><a href="https://docs.hdfgroup.org/hdf5/rfc/RFC-Page_Buffering.pdf">Page Buffering</a></li>
</ul>
</dd></dl>
<dl class="section user"><dt>See Also</dt><dd>See <a class="el" href="_accessibility.html#CB_MaintainCompat">Maintaining Compatibility with other HDF5 Library Versions</a> for HDF5 compatibility implications.</dd></dl>
<h2><a class="anchor" id="CB_RemoveUnusedSpace"></a>
Removing Unused Space from HDF5 Files</h2>
<dl class="section user"><dt>Problem</dt><dd>Based on estimates or <code>h5stat</code> output you know that a large portion of an HDF5 file consists of free or unaccounted space, and you would like to remove it.</dd></dl>
<h2><a class="anchor" id="CB_UserBlock"></a>
Creating an HDF5 File User Block</h2>
<dl class="section user"><dt>Problem</dt><dd>You would like to include certain ancillary, non-HDF5 content in an HDF5 file such that it can be accessed without the HDF5 library.</dd></dl>
<dl class="section user"><dt>Solution</dt><dd>Use a file creation property list in which the user block size is set via <a class="el" href="group___f_c_p_l.html#ga403bd982a2976c932237b186ed1cff4d" title="Sets user block size.">H5Pset_userblock()</a>. In the example below, we create an 8 MiB user block. <div class="fragment"><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  {</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  __label__ fail_fcpl, fail_file;</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <a class="code" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a> fcpl, file;</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  </div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordflow">if</span> ((fcpl = <a class="code" href="group___p_l_c_r.html#gaf1b11da01d4d45d788c45f8bc5f0cbfa">H5Pcreate</a>(<a class="code" href="_h5_ppublic_8h.html#a206f334f1e6c973e1215a3148b45b977">H5P_FILE_CREATE</a>)) < 0) {</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  ret_val = EXIT_FAILURE;</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keywordflow">goto</span> fail_fcpl;</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  }</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keywordflow">if</span> (<a class="code" href="group___f_c_p_l.html#ga403bd982a2976c932237b186ed1cff4d">H5Pset_userblock</a>(fcpl, 8192 * 1024) < 0) {</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  ret_val = EXIT_FAILURE;</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keywordflow">goto</span> fail_file;</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  }</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordflow">if</span> ((file = <a class="code" href="group___h5_f.html#gae64b51ee9ac0781bc4ccc599d98387f4">H5Fcreate</a>(<span class="stringliteral">"userblock.h5"</span>, <a class="code" href="_h5_fpublic_8h.html#a5a2d6726f9ad8d2bca8df2b817e5ad6a">H5F_ACC_TRUNC</a>, fcpl, <a class="code" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>)) < 0) {</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  ret_val = EXIT_FAILURE;</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordflow">goto</span> fail_file;</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  }</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <a class="code" href="group___h5_f.html#gac55cd91d80822e4f8c2a7f04ea71b124">H5Fclose</a>(file);</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  </div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span> fail_file:</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <a class="code" href="group___p_l_c_r.html#ga5dce61149211d3ef319452aa598887fb">H5Pclose</a>(fcpl);</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> fail_fcpl:;</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  }</div>
<div class="ttc" id="a_h5_ppublic_8h_html_afa85e97bfbf9bf1c58e39263846c568f"><div class="ttname"><a href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a></div><div class="ttdeci">#define H5P_DEFAULT</div><div class="ttdef"><b>Definition:</b> H5Ppublic.h:102</div></div>
<div class="ttc" id="agroup___f_c_p_l_html_ga403bd982a2976c932237b186ed1cff4d"><div class="ttname"><a href="group___f_c_p_l.html#ga403bd982a2976c932237b186ed1cff4d">H5Pset_userblock</a></div><div class="ttdeci">herr_t H5Pset_userblock(hid_t plist_id, hsize_t size)</div><div class="ttdoc">Sets user block size.</div></div>
</div><!-- fragment --> </dd></dl>
<dl class="section user"><dt>Discussion</dt><dd>The user block begins at offset 0 and must be at least 512 bytes and a power of 2. The HDF5 library ignores any content between the beginning of the file and the end of the user block.<br />
You can add or strip a user block to/from an existing HDF5 file with the <code>h5jam</code>/<code>h5unjam</code> tool, respectively. </dd></dl>
<dl class="section warning"><dt>Warning</dt><dd>If you try to embed content into the user block for use by other applications, pay close attention to how they handle space beyond the last used byte in the user block or the user block in general. In the worst case, applications might try to truncate the rest of the file and destroy the HDF5 portion of the file.</dd></dl>
<dl class="section user"><dt>See Also</dt><dd>References to related recipes </dd></dl>
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