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<p class="MsoNormal"><span lang="EN-US">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks for getting back to me!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Unfortunately, we used Scilab’s pretty cool way of doing object orientation, so we have big nested tlist structures with multiple instances of various lists of filters and other structures, as in my example. Saving those
structures in some explicit manual way would be extremely complicated. Or is there some way of writing explicit HDF5 saving/loading schemes using overloading? That would be great! I am sure we could find the main culprits and do something explicit for them,
but as they can be located wherever in a big nested structure, it would be painful to do anything on the top level.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Another, related I guess, problem here is that the new file format uses about 15 times as much disk space as the old format (for a typical ill-behaved nested structure). That adds to the save/load time too I guess, but
is probably not the main source here.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I think I might have reported this earlier using Bugzilla, but I’m not sure. I’ll check and report it if not.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Arvid<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><b><span lang="EN-US" style="font-size:12.0pt;color:black">From:
</span></b><span lang="EN-US" style="font-size:12.0pt;color:black">users <users-bounces@lists.scilab.org> on behalf of "amonmayr@laas.fr" <amonmayr@laas.fr><br>
<b>Reply-To: </b>"antoine.monmayrant@laas.fr" <antoine.monmayrant@laas.fr>, Users mailing list for Scilab <users@lists.scilab.org><br>
<b>Date: </b>Monday, 15 October 2018 at 11:08<br>
<b>To: </b>"users@lists.scilab.org" <users@lists.scilab.org><br>
<b>Subject: </b>Re: [Scilab-users] HDF5 save is super slow<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal" style="margin-left:36.0pt">Hello,<br>
<br>
I tried your code in 5.5.1 and the last nightly-build of 6.0: I see a slowdown of around 175 between old save in 5.5.1 and new (and only) save in 6.0.<br>
It's really related to the data structure, because we use hdf5 read/write a lot here and did not experience significant slowdowns using 6.0.<br>
I think the overhead might come to the translation of your fairly complex variable (a long array of tlist) in the corresponding hdf5 structure.<br>
In the old save, this translation was not necessary.<br>
Maybe you could try to save your data in a different way.<br>
For example:<br>
3) you could save each element of "filters" in a separate file.<br>
2) you could bypass save and directly write your data in a hdf5 file by using h5open(), h5write() directly. It means you need to write your own load() for your custom file format. But this way, you can try to find the best way to layout your data in hdf5 format.<br>
3) in addition to 2) you could try to save each entry of your "filters" array as one dataset in a given hdf5 file.<br>
<br>
Did you search on bugzilla whether this bug was already submitted?<br>
Could you try to report it?<br>
<br>
<br>
Antoine<br>
<br>
Le 15/10/2018 à 10:11, Arvid Rosén a écrit :<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">/////////////////////////////////</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">N = 4;</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">n = 10000;</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">filters = list();</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">for i=1:n</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New""> G=syslin('c', rand(N,N), rand(N,1), rand(1,N), rand(1,1));</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New""> filters($+1) = G;</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">end</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">tic();</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">save('filters.dat', filters);</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">ts1 = toc();</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">tic();</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">save('filters.dat', 'filters');</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">ts2 = toc();</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">printf("old save %.2fs\n", ts1);</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">printf("new save %.2fs\n", ts2);</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">printf("slowdown %.1f\n", ts2/ts1);</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span lang="EN-US" style="font-family:"Courier New"">/////////////////////////////////</span><o:p></o:p></p>
</blockquote>
<p style="margin-left:36.0pt"><o:p> </o:p></p>
<pre style="margin-left:36.0pt">-- <o:p></o:p></pre>
<pre style="margin-left:36.0pt">+++++++++++++++++++++++++++++++++++++++++++++++++++++++<o:p></o:p></pre>
<pre style="margin-left:36.0pt"><o:p> </o:p></pre>
<pre style="margin-left:36.0pt"> Antoine Monmayrant LAAS - CNRS<o:p></o:p></pre>
<pre style="margin-left:36.0pt"> 7 avenue du Colonel Roche<o:p></o:p></pre>
<pre style="margin-left:36.0pt"> BP 54200<o:p></o:p></pre>
<pre style="margin-left:36.0pt"> 31031 TOULOUSE Cedex 4<o:p></o:p></pre>
<pre style="margin-left:36.0pt"> FRANCE<o:p></o:p></pre>
<pre style="margin-left:36.0pt"><o:p> </o:p></pre>
<pre style="margin-left:36.0pt"> Tel:+33 5 61 33 64 59<o:p></o:p></pre>
<pre style="margin-left:36.0pt"> <o:p></o:p></pre>
<pre style="margin-left:36.0pt"> email : <a href="mailto:antoine.monmayrant@laas.fr">antoine.monmayrant@laas.fr</a><o:p></o:p></pre>
<pre style="margin-left:36.0pt"> permanent email : <a href="mailto:antoine.monmayrant@polytechnique.org">antoine.monmayrant@polytechnique.org</a><o:p></o:p></pre>
<pre style="margin-left:36.0pt"><o:p> </o:p></pre>
<pre style="margin-left:36.0pt">+++++++++++++++++++++++++++++++++++++++++++++++++++++++<o:p></o:p></pre>
<pre style="margin-left:36.0pt"><o:p> </o:p></pre>
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