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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US">Hi again Shane,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US">When I try to create the job summary report, the command gets stuck:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US">[wadud@WM-porlock ~]$ darshan-job-summary.pl pr1ebt05_bt.A.9.mpi_io_full_id2483888_11-29-65132-8929929721473377761_1.darshan
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US">Slowest unique file time: 0.001923<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US">Slowest shared file time: 0.130845<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US">Total bytes read and written by app (may be incorrect): 104858212<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US">Total absolute I/O time: 0.132768<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US">**NOTE: above shared and unique file times calculated using MPI-IO timers if MPI-IO interface used on a given file, POSIX timers
otherwise.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US">This has happened also on my laptop. When I run “top -H” I don’t see the process doing anything. Any help will be appreciated.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US">Wadud.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"> Shane Snyder [mailto:ssnyder@mcs.anl.gov]
<br>
<b>Sent:</b> 29 November 2016 20:50<br>
<b>To:</b> Wadud Miah <wadud.miah@nag.co.uk>; darshan-users@lists.mcs.anl.gov<br>
<b>Subject:</b> Re: [Darshan-users] Darshan trace file creation<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hi Wadud,<br>
<br>
I'm assuming this is a Fortran app, right?<br>
<br>
If so, I believe this is tied back to a known issue with Intel MPI's Fortran bindings. Long story short, these bindings are calling the PMPI variants of the MPI function calls directly which bypasses any profiling tool that wraps the MPI interface at the C
layer (e.g., Darshan). See this post for more details: <a href="https://software.intel.com/en-us/forums/intel-clusters-and-hpc-technology/topic/279445">
https://software.intel.com/en-us/forums/intel-clusters-and-hpc-technology/topic/279445</a><br>
<br>
I haven't personally confirmed this on Intel MPI 5.x versions (the post I reference above is regarding a 4.x version of Intel MPI), but I believe other users have reported the problem still exists.<br>
<br>
It should be possible to work around the issue by modifying Darshan to provide an additional interface for intercepting Fortran MPI calls natively at the Fortran layer, but we have not undertaken this development effort as of yet. Lacking that, I'm not sure
what, if any, other solutions there are, unfortunately.<br>
<br>
Thanks,<br>
--Shane<o:p></o:p></p>
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<p class="MsoNormal">On 11/28/2016 02:58 PM, Wadud Miah wrote:<o:p></o:p></p>
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<p style="background:white"><span style="font-family:"Calibri",sans-serif">Hello,
<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif">I built Darshan with Intel MPI 5.1.3 and gcc 4.3.4 with the following configure flags:<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p style="background:white"><code><span style="font-size:11.0pt">./configure --prefix=$HOME/darshan-3.1.2-impi --with-mem-align=8 --with-jobid-env=NONE --with-log-path-by-env=DARSHAN_LOGPATH</span></code><span style="font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif">which built fine. I set
</span><code><span style="font-size:10.0pt">DARSHAN_LOGPATH</span></code><span style="font-family:"Calibri",sans-serif"> to
</span><code><span style="font-size:10.0pt">darshan-trace-dir</span></code><span style="font-family:"Calibri",sans-serif"> and I created the directory
</span><code><span style="font-size:10.0pt">darshan-trace-dir</span></code><span style="font-family:"Calibri",sans-serif">. I then executed my MPI code which does I/O using:<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p style="background:white"><code><span style="font-size:11.0pt">mpirun -n 9 -env LD_PRELOAD /home/pr1ebt00/pr1ebt05/darshan-3.1.2-impi/lib/libdarshan.so ./bt.A.9.mpi_io_full</span></code><span style="font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif">in the same directory that has the
</span><code><span style="font-size:10.0pt">darshan-trace-dir</span></code><span style="font-family:"Calibri",sans-serif"> directory. However, I do not see any tracefile in the directory
</span><code><span style="font-size:10.0pt">darshan-trace-dir</span></code><span style="font-family:"Calibri",sans-serif"> and no error messages. Any help will be greatly appreciated.
<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif">Thanks in advance,
<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif">Wadud.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
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<p style="background:white"><span style="font-family:"Calibri",sans-serif">---------------------------------------<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif">Dr. Wadud Miah<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif">Computational Scientist<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif">Numerical Algorithms Group<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif">01865 518035<o:p></o:p></span></p>
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