<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
</head>
<body style="font-family: 'Segoe UI',Frutiger,'Frutiger Linotype','Dejavu Sans','Helvetica Neue',Arial,sans-serif; font-size: 14px;">
<div class="hiri-body-wrapper" contenteditable="true">
<div>Excellent, thanks for sharing the reproducer, Mahzad. We have confirmed the problem; we have a bug in the darshan-convert utility that should be easy to fix. Will report back with an update soon.<br>
<br>
thanks,<br>
-Phil<br>
</div>
</div>
<div class="hiri-extra" contenteditable="false">
<p>On 2019-01-21 21:18:51-05:00 Mahzad Khoshlessan wrote:</p>
<blockquote style="padding-left:10px; border-left:1px solid #ccc; margin:0">
<div>
<div dir="ltr">
<div class="gmail_default" style="font-family:times new roman,serif;font-size:small">
Hi Phil,</div>
<div class="gmail_default" style="font-family:times new roman,serif;font-size:small">
</div>
<div class="gmail_default" style="font-family:times new roman,serif;font-size:small">
Yes, <a target="_blank" href="http://darshan-job-summary.pl">darshan-job-summary.pl</a> and darshan-parser work fine.</div>
<div class="gmail_default" style="font-family:times new roman,serif;font-size:small">
Sure, I have attached my logfile.</div>
<div class="gmail_default" style="font-family:times new roman,serif;font-size:small">
</div>
<div class="gmail_default" style="font-family:times new roman,serif;font-size:small">
Thanks for the help.</div>
<div class="gmail_default" style="font-family:times new roman,serif;font-size:small">
<div class="gmail_chip gmail_drive_chip" style="width:396px;height:18px;max-height:18px;background-color:rgb(245,245,245);padding:5px;color:rgb(34,34,34);font-family:arial;font-style:normal;font-weight:bold;font-size:13px;border:1px solid rgb(221,221,221);line-height:1">
<a target="_blank" style="display:inline-block;max-width:366px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0;border:none" href="https://drive.google.com/file/d/1QfNXQ_l31FW38yGJxSEKXuZWgaUio-Py/view?usp=drive_web"><img style="vertical-align: bottom; border: none;" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <span dir="ltr" style="color:rgb(17,85,204);text-decoration:none;vertical-align:bottom">mkhoshle_python_id30468_1-21-57554-509712531345...</span></a><img style="opacity: 0.55; cursor: pointer; float: right; position: relative; top: -1px; display: none;" src="//ssl.gstatic.com/ui/v1/icons/common/x_8px.png"></div>
</div>
<div>
<div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div><br>
<font face="times new roman, serif">Mahzad Khoshlessan<br>
<br>
Research Associate<br>
Arizona State University<br>
Center for Biological Physics and Department of Physics</font></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Jan 18, 2019 at 7:55 AM Carns, Philip H. via Darshan-users <<a href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a>> wrote:</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="font-family:"Segoe UI",Frutiger,"Frutiger Linotype","Dejavu Sans","Helvetica Neue",Arial,sans-serif;font-size:14px">
<div class="gmail-m_-3094951750910174914hiri-body-wrapper">
<div>Hi Mahzad,<br>
<br>
Everything you are doing looks fine to me. It's possible that we have a bug that is being triggered in darshan-convert (this is a command line utility called within darshan-summary-per-file.sh to help split up the data). <br>
<br>
Are you able to run <a target="_blank" href="http://darshan-job-summary.pl">darshan-job-summary.pl</a> and/or darshan-parser on the log file?<br>
<br>
Can you share your log file for us to have a look at it and see if we can reproduce?<br>
<br>
thanks!<br>
-Phil<br>
</div>
</div>
<div class="gmail-m_-3094951750910174914hiri-extra">
<p>On 2019-01-15 19:54:20-05:00 Darshan-users wrote:</p>
<blockquote style="padding-left:10px;border-left:1px solid rgb(204,204,204);margin:0px">
<div>Hello all,
<div></div>
<div>I have a python code and I am using parallel hdf5 through h5py. </div>
<div>I compiled darshan with the following options:<br>
./configure --prefix=/home/mkhoshle/installs/darshan --with-mem- align=8 --with-log-path=/oasis/scratch/comet/mkhoshle/temp_project/darshan-logs --with-jobid-env=PBS_JOBID --enable-HDF5-post-1.10 CC=mpicc </div>
<div></div>
<div>I set the the environment variable LD_PRELOAD as:</div>
<div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures;color:rgb(193,101,28)">export</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(46,174,187)"> LD_PRELOAD=</span><span style="font-variant-ligatures:no-common-ligatures">/home/mkhoshle/installs/darshan/lib/libdarshan.so:/home/mkhoshle/hdf5/v1.10.1/lib/libhdf5.so</span></div>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">And I am using Darshan 3.1.5.</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
I can run my code with no error but when I run darshan-summary-per-file.sh I get the following error and I get no output.</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<div style="margin:0px;font-stretch:normal;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures">darshan-summary-per-file.sh /oasis/scratch/comet/mkhoshle/temp_project/darshan-logs/2019/1/15/mkhoshle_python_id10574_1-15-58292-3565400970146387705_1.darshan
/oasis/scratch/comet/mkhoshle/temp_project/darshan/58292</span></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures">Status: Generating summary for file 1 of 64: __init__.py</span></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures">=======================================================</span></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures">/home/mkhoshle/installs/darshan/bin/darshan-summary-per-file.sh: line 63: 27764 Segmentation fault darshan-convert --file $hash $1 $2/$file.darshan</span></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures">=======================================================</span></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"><span style="font-variant-ligatures:no-common-ligatures">darshan-summary-per-file.sh done. Results can be found in /oasis/scratch/comet/mkhoshle/temp_project/darshan/58292/*.pdf.</span></div>
<div style="margin:0px;font-stretch:normal;line-height:normal"></div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Am I doing anything wrong? </div>
<div style="margin:0px;font-stretch:normal;line-height:normal"></div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Thanks,</div>
</div>
</div>
</blockquote>
</div>
</div>
_______________________________________________<br>
Darshan-users mailing list<br>
<a target="_blank" href="mailto:Darshan-users@lists.mcs.anl.gov">Darshan-users@lists.mcs.anl.gov</a><br>
<a rel="noreferrer" target="_blank" href="https://lists.mcs.anl.gov/mailman/listinfo/darshan-users">https://lists.mcs.anl.gov/mailman/listinfo/darshan-users</a></blockquote>
</div>
</div>
</blockquote>
</div>
</body>
</html>