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<p>It does not happen with a uniform grid, this is also consistent with the fact that it does not happen at any
<br>
</p>
<p>of the blocks where there is no refinement boundary. <br>
<br>
</p>
<p>It actually seems to happen at the first refinement boundary, there is nothing else special about that location.</p>
<p>It happens right after the <span>initialization</span> is done. The code gets into the hydro solver, where it needs to fill some guard cells,</p>
<p>and during the guard-cell filling it crashes at the first refinement boundary it encounters. The guard cells are filled</p>
<p>appropriately at the other end of the block, ie the end not near the refinement boundary.
<br>
<br>
I fully agree with your assessment, it looks like an uninitialized value or a division by zero. The question is then,
<br>
</p>
<p>where this this come from? <br>
</p>
<p><br>
</p>
<p>Best,<br>
Haakon<br>
</p>
<p><br>
</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> 30 April 2024 11:08:44<br>
<b>To:</b> Haakon Andresen<br>
<b>Cc:</b> flash-users@flash.rochester.edu<br>
<b>Subject:</b> Re: [EXT] [FLASH-USERS] Code crash when moving to an AMD based machine</font>
<div> </div>
</div>
<div>That density looks like an uninitialized value or a divide by zero both of which could be handled differently depending on the compiler. If this is, as you say, is happening at an interior boundary it should just be doing prolongation/restriction of interior
data from another block.
<div><br>
</div>
<div>A couple of questions I have:</div>
<div>
<ul class="MailOutline">
<li>Does this happen only if you include a refinement jump, or also with a uniform refinement? </li><li>Does it happen during initialization or in the middle of a simulation after the evolution has begun?</li></ul>
<div>
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*********************************************<br>
Adam Reyes</div>
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/ him / his)</span><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); 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; text-decoration: none;">
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*********************************************</div>
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<blockquote type="cite">
<div>On Apr 30, 2024, at 10:36 AM, Haakon Andresen <haakon.andresen@astro.su.se> wrote:</div>
<br class="Apple-interchange-newline">
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<div style="margin-top: 0px; margin-bottom: 0px;">Hi,</div>
<div style="margin-top: 0px; margin-bottom: 0px;"><br>
</div>
<div style="margin-top: 0px; margin-bottom: 0px;">I can with<span class="Apple-converted-space"> </span><span>one caveat</span>: I am using a modified version of FLASH4. I suspect the error is coming from part of the code that</div>
<div style="margin-top: 0px; margin-bottom: 0px;">has not been modified, but I am not 100% certain at this point in time.</div>
<div style="margin-top: 0px; margin-bottom: 0px;"><br>
</div>
<div style="margin-top: 0px; margin-bottom: 0px;">I am using the Intel compilers on the machine where it works and cray (also tested gnu) on the machine where the code crashes.</div>
<div style="margin-top: 0px; margin-bottom: 0px;">After talking to a<span class="Apple-converted-space"> </span><span>colleague</span>, I have learned that the code compiled with Intel compilers runs on the<span class="Apple-converted-space"> </span><span>AMD
EPYC 7763 CPUs.<br>
However, the Intel compilers are not available on the machine I am using.<br>
<br>
Boundary conditions are "reflect" at the inner-boundary and "user" at the outer boundary<span class="Apple-converted-space"> </span><br>
(the user condition essentially specifies an outflow/inflow with some modifications for density/gpot/radiation...<br>
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;"><span><a target="_blank" class="c-link" data-stringify-link="https://github.com/snaphu-msu/BANG/blob/master/source/Simulation/SimulationMain/CoreCollapse/Grid_bcApplyToRegionSpecialized.F90" data-sk="tooltip_parent" href="https://urldefense.com/v3/__https://github.com/snaphu-msu/BANG/blob/master/source/Simulation/SimulationMain/CoreCollapse/Grid_bcApplyToRegionSpecialized.F90__;!!CGUSO5OYRnA7CQ!f__vTvYYlGfba4-Oyv1RWCg_LbkVjHUoZTCAXd4NtbxngsxkeIgCHlCBzEFCKAz8BdVnv1luHlZXGOTpliubyVybqJfDIgbq6eQ$" rel="noopener noreferrer">/Simulation/SimulationMain/CoreCollapse/Grid_bcApplyToRegionSpecialized.F90</a><span class="Apple-converted-space"> </span>if
it exists in the standard FLASH version).</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;"><span><br>
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;"><span>I have traced the issue back to negative density values in some guard cells near an refinement boundary, but far away from the outer grid boundary and</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;"><span>not close to the inner grid boundary.<span class="Apple-converted-space"> </span><br>
<br>
As for error messages, it is<span class="Apple-converted-space"> </span><br>
"<span>Error message is [EOS] rho < rhomin</span>"<span class="Apple-converted-space"> </span><br>
when using Cray and<span class="Apple-converted-space"> </span><br>
<br>
"</span></div>
<div> Newton-Raphson failed in subroutine eos_helmholtz<br>
(e and rho as input):<br>
<span class="Apple-converted-space"> </span><br>
too many iterations 50<br>
<span class="Apple-converted-space"> </span><br>
temp = NaN<br>
dens = -2.2471185595023190E+307<br>
pres = NaN<br>
<br>
</div>
"<br>
when using GNU. I am not sure these are informative for you since they could be specific to our version of
<p style="margin-top: 0px; margin-bottom: 0px;"></p>
<div style="margin-top: 0px; margin-bottom: 0px;"><span>FLASH. The root cause is the negative densities that somehow appear in the guard-cell fill.</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;"><span><br>
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;"><span>Thanks for your help.</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;"><span><br>
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;"><span>Best,<br>
Haakon<br>
</span></div>
</div>
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<font face="Calibri, sans-serif" style="font-size: 11pt;"><b>From:</b><span class="Apple-converted-space"> </span>Reyes, Adam <adam.reyes@rochester.edu><br>
<b>Sent:</b><span class="Apple-converted-space"> </span>30 April 2024 10:04:20<br>
<b>To:</b><span class="Apple-converted-space"> </span>Haakon Andresen<br>
<b>Cc:</b><span class="Apple-converted-space"> </span>flash-users@flash.rochester.edu<br>
<b>Subject:</b><span class="Apple-converted-space"> </span>Re: [FLASH-USERS] Code crash when moving to an AMD based machine</font>
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Hi Haakon,
<div><br>
</div>
<div>Could you share a bit more context about what you’re observing, maybe the exact error from FLASH and the boundary conditions that you’re using? Are you using the same compiler between the two machines?<br id="lineBreakAtBeginningOfMessage">
<div>
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*********************************************<br>
Adam Reyes</div>
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<span><span id="cid:EA5A7E59-94B9-4162-879C-B52E774AEA24"><FLASH.jpg></span></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;">
<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;">Code
Group Leader, Flash Center for </span><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;">Computational
Science</span><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;"> </span><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;"> </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;">
<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;">Research
Scientist, Dept. of Physics and </span><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;">Astronomy</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;">
<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;">University
of Rochester</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;">
<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;">River
Campus: Bausch and Lomb Hall, </span><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;">369</span><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;"> </span><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;"> </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;">
<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;">500
Wilson Blvd. PO Box 270171, </span><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;">Rochester,
NY 14627</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;">
<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;">Email</span><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;"> </span><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;">adam.reyes@rochester.edu</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;">
<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;">Web</span><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;"> </span><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;">https://flash.rochester.edu</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;">
<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;"> </span><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;">(he
/ him / his)</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;">
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<div>On Apr 29, 2024, at 4:02 PM, Haakon Andresen <haakon.andresen@astro.su.se> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;">Dear Flash users,</div>
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I am currently testing FLASH on a machine with AMD CPUs, specifically<span class="Apple-converted-space"> </span><span>AMD EPYC 7763</span>. Previously, I have only used the code on Intel based architecture. I have encountered a bug, which I believe is related
to guard-cell fills, but I have not found the root cause yet.<span class="Apple-converted-space"> </span><br>
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<div style="margin-top: 0px; margin-bottom: 0px;">I am doing core-collapse simulations with paramesh, the code initializes and writes the first checkpoint file, but then crashes in hydro-solver. The crash occurs during a call to the subroutine that is responsible
for filling guard cells. My debugging has lead me all the way into the paramesh routines. The error, guard cells being filled with bad values, happens at a refinement boundary. The test is done in 1D.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;">The puzzling part is that the code, with the exact same setup, runs just fine on a different machine (an intel machine). I am wondering if anyone have seen similar behavior in the past. I am not sure that the
root cause is in paramesh, but if anyone have experience anything similar I would love to hear about it, maybe it will help me identify the issue. </div>
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<div style="margin-top: 0px; margin-bottom: 0px;">Best,<br>
Haakon Andresen<br>
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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;">_______________________________________________</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;">
<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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">https://flash.rochester.edu/mailman/listinfo/flash-users</a></div>
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