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<p>Hi Adam</p>
<p>Thanks for the quick answer !</p>
<p>I also do believe that it will be beneficial to use the one process read + broadcasting approach in the future</p>
<p>especially when using distributed file system lie lustre</p>
<p><br>
</p>
<p>Denis</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Reyes, Adam <adam.reyes@rochester.edu><br>
<b>Sent:</b> Wednesday, June 19, 2024 10:04:32 AM<br>
<b>To:</b> Bertini, Denis Dr.<br>
<b>Cc:</b> flash-users@flash.rochester.edu<br>
<b>Subject:</b> Re: [FLASH-USERS] FLASH initialisation hanging on Lustre filesystem</font>
<div> </div>
</div>
<div>Hi Denis,
<div><br>
</div>
<div>That’s great to hear that you were able to figure it out! </div>
<div><br>
</div>
<div>The files get read two times in calls originating from "source/physics/Eos/EosMain/Tabulated/eos_initTabulated.F90” with calls to “eos_tabBrowseTables” and “eos_tabReadTables”. The first is just to determine the size of arrays to allocate for the tables
and the second will actually fill them. If you follow the calls you will end up in the browse/read routines for each supported table type, “eos_tab[Read|Browse]Ionmix4Tables.F90 “ for the “.cn4” tables. </div>
<div><br>
</div>
<div>In principle these don’t need to be read by every single MPI process and instead could be read by one and broadcast to the rest<br id="lineBreakAtBeginningOfMessage">
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*********************************************<br>
Adam Reyes</div>
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<span><img alt="FLASH-pride-sml.png" src="cid:CE45460D-2261-4A69-865C-5CF7BEACF620"></span>
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*********************************************</div>
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<div><br>
<blockquote type="cite">
<div>On Jun 19, 2024, at 9:51 AM, Bertini, Denis Dr. <D.Bertini@gsi.de> wrote:</div>
<br class="Apple-interchange-newline">
<div>
<div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;">
<div style="margin-top: 0px; margin-bottom: 0px;">Dear Flash developper,</div>
<div style="margin-top: 0px; margin-bottom: 0px;">I finally found out why flash simulation are systematically hanging on our lustre filesystem when using AMD EPYC 7k compute node ( 128 physical cores ).</div>
<div style="margin-top: 0px; margin-bottom: 0px;"><br>
</div>
<p style="margin-top: 0px; margin-bottom: 0px;"></p>
<div>The problem lies in concurrent reading on lustre. </div>
<div><br>
</div>
<div>When FLASH start initialization, all processes needs to read the same input data files ( the .cn4 etc ) and need to allocate</div>
<div>in memory parameters , data arrays etc ...</div>
<div>The problem is that this reading is of course asynchronous ( as it should be with MPI ) but do not need in principle complex synchronization or distributed lock mechanism </div>
<div>which should be only relevant in the writing case.</div>
<div>In fact when too many processes from one client try to read concurently the same .cn4 input file all the processes will hang and the lustre directory get corrupted and not accessible anymore.</div>
<div><span style="font-size: 12pt;">Moving all the needed input files to the /tmp (strict posix ) on each node ( they are copied once per node )and adapting the </span><span style="font-size: 12pt;"> flash.par file to read from /tmp and NOT from /lustre</span></div>
<div> solved the issue. </div>
<div><span style="font-size: 12pt;">Using this approach, flash simulation jobs run now stable and can use all cores / node even on AMD EPYC 7k architecture.</span><br>
</div>
<div>Writing shows no problem since in this case there is no scaling issue ( collective MPI-IO is used )</div>
<div>FLASH I/O writing capability has been tested with a adapted/modified version of the official flash I/O benchmark</div>
<div>in order to be able to run with latest gfortran, MPI and HDF5 libraries.</div>
<div><br>
</div>
<div>For those interested the modified version can be freely downloaded here:</div>
<div><a href="https://git.gsi.de/d.bertini/pp-flash/-/tree/main/flash_io?ref_type=heads" class="OWAAutoLink">https://git.gsi.de/d.bertini/pp-flash/-/tree/main/flash_io?ref_type=heads</a><br>
</div>
<div><br>
</div>
<div>The FLASH I/O writing benchmarks is stable and shows good results on /lustre</div>
<br>
<p style="margin-top: 0px; margin-bottom: 0px;"></p>
<div style="margin-top: 0px; margin-bottom: 0px;">As this seems to be related to a lustre bug ( client or server side ? ) it would be nice to create a small MPI program that just read these .cn4 file to</div>
<div style="margin-top: 0px; margin-bottom: 0px;">reproduce this problem.</div>
<div style="margin-top: 0px; margin-bottom: 0px;">Could you tell me which routines in flash are reading the .cn4 file for initialisation ?</div>
<div style="margin-top: 0px; margin-bottom: 0px;"><br>
</div>
<div style="margin-top: 0px; margin-bottom: 0px;">Thanks in advance </div>
<div style="margin-top: 0px; margin-bottom: 0px;"><br>
</div>
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<div><span style="font-size: 9pt;">---------</span><span style="font-size: 9pt;"></span></div>
<div><span style="font-size: 9pt;">Denis Bertini</span></div>
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<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">flash-users
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<a href="mailto:flash-users@flash.rochester.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">flash-users@flash.rochester.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">For
list info, including unsubscribe:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<a href="https://flash.rochester.edu/mailman/listinfo/flash-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">https://flash.rochester.edu/mailman/listinfo/flash-users</a></div>
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