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Hi Mahzad,<br>
<br>
Thanks again for bringing this to our attention and providing us with info for reproducing the error.<br>
<br>
I was able to push a fix for this to Darshan's master branch just now that should resolve this problem and allow you to run darshan-convert and darshan-job-summary tools. I've tested on your log and things all appear to be working fine on my end.<br>
<br>
FYI, I also just released the latest version of Darshan (3.1.7), and this bug fix is the last we included in that particular release if you want to use something a bit more stable than master. You can download it here:
<a class="moz-txt-link-freetext" href="https://www.mcs.anl.gov/research/projects/darshan/download/">
https://www.mcs.anl.gov/research/projects/darshan/download/</a><br>
<br>
Thanks!<br>
--Shane<br>
<br>
<div class="moz-cite-prefix">On 1/22/19 9:54 AM, Carns, Philip H. via Darshan-users wrote:<br>
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<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>
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thanks,<br>
-Phil<br>
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<p>On 2019-01-21 21:18:51-05:00 Mahzad Khoshlessan wrote:</p>
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Hi Phil,</div>
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Yes, <a target="_blank" href="http://darshan-job-summary.pl" moz-do-not-send="true">
darshan-job-summary.pl</a> and darshan-parser work fine.</div>
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Sure, I have attached my logfile.</div>
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Thanks for the help.</div>
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bottom; border: none;" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png" moz-do-not-send="true"> <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;
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<div><br>
<font face="times new
roman, serif">Mahzad Khoshlessan<br>
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Research Associate<br>
Arizona State University<br>
Center for Biological Physics and Department of Physics</font></div>
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<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" moz-do-not-send="true">darshan-users@lists.mcs.anl.gov</a>> wrote:</div>
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<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" moz-do-not-send="true">
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>
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<p>On 2019-01-15 19:54:20-05:00 Darshan-users wrote:</p>
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<div>Hello all,
<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>I set the the environment variable LD_PRELOAD as:</div>
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<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>
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<span style="font-variant-ligatures:no-common-ligatures">And I am using Darshan 3.1.5.</span></div>
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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>
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<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"><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">Am I doing anything wrong? </div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Thanks,</div>
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