<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Dear Tyler,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>We also got a quad for testing, but we got better performance from it (quad 2.5GHz, <FONT class="Apple-style-span" size="4"><SPAN class="Apple-style-span" style="font-size: 14px;">GROMACS 3.3, </SPAN></FONT><FONT class="Apple-style-span" size="4"><SPAN class="Apple-style-span" style="font-size: 14px;">MPI 7.0.6, </SPAN></FONT><FONT class="Apple-style-span" size="4"><SPAN class="Apple-style-span" style="font-size: 14px;">FFTW 3.0.1 compiled with </SPAN></FONT><FONT class="Apple-style-span" size="4"><SPAN class="Apple-style-span" style="font-size: 14px;">GCC powerpc-apple-darwin8-gcc-4.0.0 on </SPAN></FONT><FONT class="Apple-style-span" size="4"><SPAN class="Apple-style-span" style="font-size: 14px;">OS X.4.4) 30.9ns/day.</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" size="4"><SPAN class="Apple-style-span" style="font-size: 14px;"><BR class="khtml-block-placeholder"></SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" size="4"><SPAN class="Apple-style-span" style="font-size: 14px;">Best Itamar.</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" size="4"><SPAN class="Apple-style-span" style="font-size: 14px;"><BR class="khtml-block-placeholder"></SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" size="4"><SPAN class="Apple-style-span" style="font-size: 14px;">p.s. I did not see any 2.GHz G5.</SPAN></FONT></DIV><DIV><FONT class="Apple-style-span" size="4"><SPAN class="Apple-style-span" style="font-size: 14px;"><BR></SPAN></FONT><DIV><DIV>On Feb 11, 2006, at 12:51 AM, Tyler Luchko wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hello everybody,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Has anyone had any experience running GROMACS on a PowerMac Quad machine? We have purchased one as a test but have seen very poor performance when running the benchmarks.<SPAN class="Apple-converted-space"> </SPAN>For example, I have compared the results of the d.villin benchmark from the web with that on my dual 2.7 GHz PowerMac and our quad 2.5 GHz PowerMac:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2.5 GHz G5 (gromacs.org, v-3.2.1):<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>15309 ps/day</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2.7 GHz G5 (my dual 2.7,compiled w/ gcc-3.3, v-3.3):<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>15451 ps/day</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2.7 GHz G5 (my dual 2.7,precompiled, v-3.3):<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>13492 ps/day</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2.5 GHz G5 (my quad 2.5,compiled w/ gcc-3.3, v-3.3):<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> 7516 ps/day</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2.5 GHz G5 (my quad 2.5,precompiled, v-3.3):<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN> 6475 ps/day</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2.5 GHz G5 x 4 (my quad 2.5,compiled w/ gcc-3.3, v-3.3):28800 ps/day</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">As you can see the Quad is not doing well with the GROMACS code.<SPAN class="Apple-converted-space"> </SPAN>I have tried the benchmark tool XBench and my own very simple C code but have not reproduced these problems.<SPAN class="Apple-converted-space"> </SPAN>Any insights or suggestion would be greatly appreciated.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thank you,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Tyler</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>________________________________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(_<SPAN class="Apple-converted-space"> </SPAN>Tyler Luchko <SPAN class="Apple-converted-space"> </SPAN>Ph.D. Candidate<SPAN class="Apple-converted-space"> </SPAN>_)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>_) <SPAN class="Apple-converted-space"> </SPAN>Department of Physics<SPAN class="Apple-converted-space"> </SPAN>University of Alberta <SPAN class="Apple-converted-space"> </SPAN>(_</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(_<SPAN class="Apple-converted-space"> </SPAN>Edmonton, Alberta, Canada <SPAN class="Apple-converted-space"> </SPAN>_)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>_) <SPAN class="Apple-converted-space"> </SPAN>780-492-1063 <SPAN class="Apple-converted-space"> </SPAN><A href="mailto:tluchko@ualberta.ca">tluchko@ualberta.ca</A> <SPAN class="Apple-converted-space"> </SPAN>(_</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(________________________________________________________________)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use thewww interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">===========================================</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Itamar Kass</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| The Alexander Silberman</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Institute of Life Sciences</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Department of Biological Chemistry</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| The Hebrew University, Givat-Ram</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Jerusalem, 91904, Israel</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Tel: +972-(0)2-6585194</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Fax: +972-(0)2-6584329</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Email: <A href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">| Homepage: <A href="http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html">http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">============================================</DIV><BR class="Apple-interchange-newline"></SPAN></SPAN> </DIV><BR></DIV></BODY></HTML>