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<div class="moz-cite-prefix">Thanks Bilel. Shane Snyder has been
debugging this too and was able to reproduce the petsc example on
a NERSC system. We'll work on getting a simpler reproducer in
our nightly tests and then put out a point release with a long
term fix. In the mean time that manual modification should be
safe.<br>
<br>
thanks!<br>
-Phil<br>
<br>
On 02/27/2018 11:36 AM, Bilel Hadri wrote:<br>
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<p class="MsoNormal"><span style="font-size:12.0pt">Hi Phil,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Awesome,
your workaround fixed the issue.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Regarding
the linker, we are under CLE6Up5, and SUSE12 SP3 on the
front end node, we are using xalt ( the wrapper to track
library usage at linking and execution does not conflict
with darshan), so the ld used is xalt wrapper and it works
perfectly with both version.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">which ld<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">/sw/xc40cle6/xalt/1.1.2/sles12.3_cce8.6.5/bin/ld<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">ld --version<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">GNU ld (GNU
Binutils) 2.26.0.20160224<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Copyright
(C) 2015 Free Software Foundation, Inc.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">This program
is free software; you may redistribute it under the terms of<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">the GNU
General Public License version 3 or (at your option) a later
version.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">This program
has absolutely no warranty.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">I really
appreciate your kind and prompt help.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Bilel <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span
style="font-size:10.5pt;color:black">-------<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span
style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:12.0pt;color:black">Bilel Hadri, PhD<o:p></o:p></span></p>
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<p class="MsoNormal"><span
style="font-size:12.0pt;color:black">Computational
Scientist<o:p></o:p></span></p>
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<p class="MsoNormal"><span
style="font-size:12.0pt;color:black">KAUST
Supercomputing Lab<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:12.0pt;color:black">From: </span></b><span
style="font-size:12.0pt;color:black">Phil Carns
<a class="moz-txt-link-rfc2396E" href="mailto:carns@mcs.anl.gov"><carns@mcs.anl.gov></a><br>
<b>Date: </b>Tuesday, February 27, 2018 at 6:18 PM<br>
<b>To: </b><a class="moz-txt-link-rfc2396E" href="mailto:bilel.hadri@kaust.edu.sa">"bilel.hadri@kaust.edu.sa"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:bilel.hadri@kaust.edu.sa"><bilel.hadri@kaust.edu.sa></a>,
<a class="moz-txt-link-rfc2396E" href="mailto:darshan-users@lists.mcs.anl.gov">"darshan-users@lists.mcs.anl.gov"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:darshan-users@lists.mcs.anl.gov"><darshan-users@lists.mcs.anl.gov></a><br>
<b>Subject: </b>Re: [Darshan-users] darshan3.1.5 issue on
Cray XC40 cle6.up05<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">On 02/27/2018 12:34 AM, Bilel Hadri
wrote:<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">Hi
Phil,
<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Sure,
test_scalapack.f90 call ScaLAPACK routines and uses inside
MPI library. The output of the failing ftn command with the
craype-verbose flag<o:p></o:p></p>
</blockquote>
<p><o:p> </o:p></p>
<p>Thanks Bilel. The petsc example helps too. This clarifies
that the trigger on Cray up05 is to compile a program that
doesn't directly use MPI symbols on its own but instead links
in another library that indirectly uses MPI symbols on its
behalf.<o:p></o:p></p>
<p>This isn't an unusual use case (scalapack and petsc have done
this forever), and the linker options in Darshan are set up to
handle it, but something has obviously changed in the linker
in this respect in this update.<o:p></o:p></p>
<p>We are still trying to work out how to reproduce this but it
may be a little bit. In the mean time would you be willing to
try something in your 3.1.5 install to help debug?
<o:p></o:p></p>
<p>Can you manually edit
/sw/xc40cle6/darshan/3.1.5/sles12.3_gcc7.2.0/share/ld-opts/darshan-base-ld-opts
and add this line to the top of the file, then try again to
compile your examples with 3.1.5 loaded?<o:p></o:p></p>
<p>--undefined=__wrap_MPI_Init<o:p></o:p></p>
<p>By my (admittedly slightly murky) interpretation of the link
order and the flags that we are setting, that shouldn't be
necessary, but it would be helpful to see what it does for
your example.<o:p></o:p></p>
<p>thanks,<o:p></o:p></p>
<p>-Phil<o:p></o:p></p>
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