<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font><div><div><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">On Jun 29, 2008, at 4:07 PM, Michael Wilde wrote:</span></font></div><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br class="Apple-interchange-newline"></span></font><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">Ben,</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">On 6/29/08 2:19 PM, Ben Clifford wrote:</span></font></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">On Sun, 29 Jun 2008, Michael Wilde wrote:</span></font></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">The app that accelerated this discussion is CHARMM for molecular dynamics. CHARMM on BGP with the parameters needed in the use case in question has a long runtime on 1 CPU (24-36 hours), and seems to peak in performance using MPI at 32 CPUS. Runs >6 hours are also not runnable today on the Argonne BGP without a reservation. So the most effective way to use the BGP for some specific CHARMM runs needed by Benoit Roux's group is to run large numbers of multi-hour 32-rank MPI jobs.</span></font></div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">OK.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">This seems like an interesting application.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">I can spend some time working on this in the next few weeks, as long as you provide me with the following:</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> </span></font></span><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">i) someone who knows how the charmm applications work (eg from Benoit's group)</span></font></div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">Wei Jiang from Benoit's group spent several hours with me Friday explaining how they run CHARMM.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">The approach uses scripts that Yuqing Deng, who recently left the group, developed.</span></font><span class="Apple-converted-space"><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"> </span></font></span><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">These are on the Argonne "KBT" cluster. You should get on the Argonne accounts web and request access to that cluster, kbt.mcs.anl.gov.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">One there, you can run perl scripts that generate either shell scripts or pbs jobs to do a CHARMM run. It was fairly complex, and I need to transcribe some notes on this.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="2"><span class="Apple-style-span" style="font-size: 10px;">Benoit was going to try to locate slides and/or docs from a talk that Yuqing gave before he left, on how to run his tools.</span></font></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; "><b>Ray Loy of the ALCF team is working on compiling a non-MPI CHARMM runnable under ZeptoOS on the BGP, and he also wanted to try HTC mode.</b></div></blockquote><div><br class="webkit-block-placeholder"></div><b>Note that a non-MPI CHARMM job on BG would be not super fast, and MPI capability would be desirable.</b></div><div><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;">Nika's latest workflows running CHARMM are also a good reference point.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;">Wei can provide info on how to do a sample run from Yuquing's scripts.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"><br></span></font></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"> </span></font></span><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;">ii) someone who knows how MPI works on the BG/P (maybe Kamil?)</span></font></div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;">MPI on BGP under ZeptoOS is still several weeks away from friendly-user testing capability. Kamil and Kaz (and Pete Beckman) are the Argonne ZeptoOS team. Kaz is working on ZeptoOS MPI and just reached hello-world about a week ago.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 11px;">- Mike</span></font></div> </blockquote></div><br></body></html>