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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am searching for representative input cases for GROMACS for performance evaluation.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The selection criteria is centered on (priority order):<o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:38.25pt;text-indent:-.25in;mso-list:l2 level1 lfo2">
<![if !supportLists]><span style="mso-list:Ignore">1.<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>inputs that are good representatives for the GROMACS user community<o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:38.25pt;text-indent:-.25in;mso-list:l2 level1 lfo2">
<![if !supportLists]><span style="mso-list:Ignore">2.<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>desirable to run in a single node (approx. 96 ARM cores / CPU-only) in no more than 1 hour<o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:38.25pt;text-indent:-.25in;mso-list:l2 level1 lfo2">
<![if !supportLists]><span style="mso-list:Ignore">3.<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>makes good use of the memory system and exploits well the SIMD units (NEON and possibly SVE)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Currently I have in mind 2 inputs cases:<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l1 level1 lfo3"><![if !supportLists]><span style="mso-list:Ignore">1.<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>The “<b>ion channel”</b> that belongs to the Unified European Applications Benchmark Suite (UEABS). This input seems to be a good representative for the industry of proteins and polymer simulation (<a href="https://hpc.nih.gov/apps/gromacs/">https://hpc.nih.gov/apps/gromacs/</a>).
<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l1 level1 lfo3"><![if !supportLists]><span style="mso-list:Ignore">2.<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>The “<b>nonbonded-benchmark</b>” which is integrated inside GROMACS. The benchmark would allow analyzing different problem sizes and internal kernels (https://manual.gromacs.org/documentation/current/onlinehelp/gmx-nonbonded-benchmark.html).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I would appreciate some guidance or feedback about these two inputs cases and suggestions for considering. Are there good representatives of what the community normally use when they run GROMACS? Are there special parameters (such as time
steps or problem size, etc.) to take into account for finally saying that the simulations are good examples of normal GROMACS executions?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;color:#666666">Best regards | Mit freundlichen Grüßen</span></b><span style="font-size:10.0pt;color:#666666"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;color:#666666"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;color:#666666">Guido Giuntoli</span></b><b><span style="font-size:10.0pt;color:#1F497D"><o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;color:#666666">Software Solution Architect for Advance Computing<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;color:#666666"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;color:#666666"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span style="color:#1F497D"><img border="0" width="70" height="71" id="Picture_x0020_1" src="cid:image002.png@01D6F8C0.793BCDA0" alt="HW_POS_RBG_Vertical-300ppi"><b><o:p></o:p></b></span></p>
<p class="MsoNormal">HUAWEI TECHNOLOGIES Duesseldorf GmbH<br>
Hansaallee 205, 40549 Dusseldorf, Germany, <a href="http://www.huawei.com/"><b><span style="color:blue">www.huawei.com</span></b></a><br>
Registered Office: Düsseldorf, Register Court Düsseldorf, HRB 56063, <br>
Managing Director: Li Peng, Li Jian, Shi Yanli<b><span style="font-size:8.0pt;font-family:"Arial",sans-serif;color:gray"><o:p></o:p></span></b></p>
<p class="MsoNormal"><span lang="DE">Sitz der Gesellschaft: Düsseldorf, Amtsgericht Düsseldorf, HRB 56063,
<br>
Geschäftsführer: Li Peng, Li Jian, Shi Yanli<o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-GB" style="font-size:9.0pt">-----------------------------------------------------------------------------------------------</span></b><span style="color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:9.0pt">This e-mail and its attachments contain confidential information from HUAWEI, which is intended only for the person or entity whose address is listed above. Any use of the information contained herein in
any way (including, but not limited to, total or partial disclosure, reproduction, or dissemination) by persons other than the intended recipient(s) is prohibited. If you receive this e-mail in error, please notify the sender by phone or email immediately
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<p class="MsoNormal"><o:p> </o:p></p>
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