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<p>Hi Pramod,</p>
<p><br>
</p>
<p>I generally use the LD_LIBRARY_PATH variable as there is no need to use LD_PRELOAD. I would also check the PYTHONPATH variable too to ensure Python knows how to load HDF5 and this is probably what is causing your issue.
<br>
</p>
<p><br>
</p>
<p>Regards,</p>
<p>Wadud.<br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> darshan-users-bounces@lists.mcs.anl.gov <darshan-users-bounces@lists.mcs.anl.gov> on behalf of pramod kumbhar <pramod.s.kumbhar@gmail.com><br>
<b>Sent:</b> 09 April 2017 16:49:24<br>
<b>To:</b> darshan-users@lists.mcs.anl.gov<br>
<b>Subject:</b> Re: [Darshan-users] h5py python application error : Darshan failed to map symbol: H5get_libversion</font>
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<div dir="ltr"><font face="arial, helvetica, sans-serif">It seems like hdf5 library is not loaded into memory and hence dlsym() is failing ?</font>
<div><font face="arial, helvetica, sans-serif">I tried LD_PRELOAD-ing both darshan as well as hdf5 library and the above example is working fine.</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">darshan-parser --file-list show the hdf5 file and then I use <span style="color:rgb(0,0,0);white-space:nowrap">darshan-convert --file to get profile of specific hdf5 that I am interested in.</span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="color:rgb(0,0,0);white-space:nowrap"><br>
</span></font></div>
<div><font color="#000000" face="arial, helvetica, sans-serif"><span style="white-space:nowrap">But, while profiling actual application, I have another issue. In the profile of large application, </span></font><font face="arial, helvetica, sans-serif">darshan-parser
--file-list doesn't show the hdf5 created by application. What could be wrong?</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">The application is using scipy, numpy, Image etc. Initially I thought importing scipy modules somehow causing the issue but I am not able to reproduce it with small isolated test.</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">Could someone provide any hints? (note that the job_name.darshan log file is generated but pdf from </font><a href="http://darshan-job-summary.pl">darshan-job-summary.pl</a><font face="arial, helvetica, sans-serif"> says
"This Darshan log contains incomplete data which...").</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">Thanks in advance!</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">-Pramod</font></div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Apr 9, 2017 at 1:02 PM, pramod kumbhar <span dir="ltr">
<<a href="mailto:pramod.s.kumbhar@gmail.com" target="_blank">pramod.s.kumbhar@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">Hello All,
<div><br>
</div>
<div>I have used darshan for parallel c/c++ application without issue but trying to analyse python(3) application first time. This application uses h5py.</div>
<div><br>
</div>
<div>I compiled darshan with --enable-HDF5-pre-1.10 (or --enable-HDF5-post-1.10).</div>
<div><br>
</div>
<div>When I now run simple h5py test serially I get :</div>
<div><br>
</div>
<div>
<div>$ python3 test.py</div>
<div>Darshan failed to map symbol: H5get_libversion</div>
</div>
<div><br>
</div>
<div>If I don't enable hdf5 during configure then I see profiles being generated.</div>
<div>What am I missing here? Do I need parallel h5py application? Any hints will be helpful!</div>
<div><br>
</div>
<div>Regards,</div>
<div>Pramod</div>
<div><br>
</div>
<div>p.s. h5py test program</div>
<div><br>
</div>
<div>import h5py</div>
<div>a = [1,2,3,4,5]<br>
</div>
<div>h5f = h5py.File('data.h5', 'w')</div>
<div>h5f.create_dataset('dataset_1'<wbr>, data=a)</div>
<div>h5f.close()</div>
</div>
</blockquote>
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