1.0UCT HPChttps://ucthpc.uct.ac.zaAndrew Lewishttps://ucthpc.uct.ac.za/index.php/author/andrew-lewis/rich600338<blockquote class="wp-embedded-content" data-secret="5Xr83sQBVd"><a href="https://ucthpc.uct.ac.za/index.php/2012/08/21/molecular-visualization/">Molecular visualization</a></blockquote><iframe sandbox="allow-scripts" security="restricted" src="https://ucthpc.uct.ac.za/index.php/2012/08/21/molecular-visualization/embed/#?secret=5Xr83sQBVd" width="600" height="338" title="“Molecular visualization” — UCT HPC" data-secret="5Xr83sQBVd" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" class="wp-embedded-content"></iframe><script type="text/javascript"> /*! This file is auto-generated */ !function(c,d){"use strict";var e=!1,o=!1;if(d.querySelector)if(c.addEventListener)e=!0;if(c.wp=c.wp||{},c.wp.receiveEmbedMessage);else if(c.wp.receiveEmbedMessage=function(e){var t=e.data;if(!t);else if(!(t.secret||t.message||t.value));else if(/[^a-zA-Z0-9]/.test(t.secret));else{for(var r,s,a,i=d.querySelectorAll('iframe[data-secret="'+t.secret+'"]'),n=d.querySelectorAll('blockquote[data-secret="'+t.secret+'"]'),o=new RegExp("^https?:$","i"),l=0;l<n.length;l++)n[l].style.display="none";for(l=0;l<i.length;l++)if(r=i[l],e.source!==r.contentWindow);else{if(r.removeAttribute("style"),"height"===t.message){if(1e3<(s=parseInt(t.value,10)))s=1e3;else if(~~s<200)s=200;r.height=s}if("link"===t.message)if(s=d.createElement("a"),a=d.createElement("a"),s.href=r.getAttribute("src"),a.href=t.value,!o.test(a.protocol));else if(a.host===s.host)if(d.activeElement===r)c.top.location.href=t.value}}},e)c.addEventListener("message",c.wp.receiveEmbedMessage,!1),d.addEventListener("DOMContentLoaded",t,!1),c.addEventListener("load",t,!1);function t(){if(o);else{o=!0;for(var e,t,r,s=-1!==navigator.appVersion.indexOf("MSIE 10"),a=!!navigator.userAgent.match(/Trident.*rv:11\./),i=d.querySelectorAll("iframe.wp-embedded-content"),n=0;n<i.length;n++){if(!(r=(t=i[n]).getAttribute("data-secret")))r=Math.random().toString(36).substr(2,10),t.src+="#?secret="+r,t.setAttribute("data-secret",r);if(s||a)(e=t.cloneNode(!0)).removeAttribute("security"),t.parentNode.replaceChild(e,t);t.contentWindow.postMessage({message:"ready",secret:r},"*")}}}}(window,document); </script> Why is molecular visualization cool?  Take a look at this animation from WEHI:  One of the molecular visualization tools we support is NAMD.  We recently updated our version from 2.7 to 2.9 and compiled it to run with OpenMPI rather than NAMD's own multi processor controler, CHARM.  This makes resource requesting and job submission much easier.  Below is the native NAMD method of addressing multiple cores in a distributed architecture:#PBS -N NAMD-CHARMRUN#PBS -l nodes=node1:ppn=4+node2:ppn=4+node3:ppn=4+node4:ppn=4+node5:ppn=4charmrun namd2 +p20 ++remote-shell ssh ++nodelist machine.file test.namd > charmout.txtNow instead of using the above cumbersome method the standard mpirun executable can be called:#PBS -N NAMD=MPIRUN#PBS -l nodes=5:ppn=4:series200mpirun -hostfile $PBS_NODEFILE namd2 test.namd > mpiout.txtThis also functions much better with PBStorque as it's designed to work hand in glove with OpenMPI.  In the 2nd example you'll note that it's no longer necessary to tell mpirun or namd how many processors are required, it works that out from the job requirements, 5 nodes x 4 cores = 20 cores total.Below is the method we used to compile NAMD with OpenMPI support:Unpack NAMD and matching Charm++ source code and enter directory:  tar xzf NAMD_2.9_Source.tar.gz  cd NAMD_2.9_Source  tar xf charm-6.4.0.tar  cd charm-6.4.0Build and test the Charm++/Converse library (MPI version):  env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production  cd mpi-linux-x86_64/tests/charm++/megatest  make pgm  mpirun -n 4 ./pgm    (run as any other MPI program on your cluster)  cd ../../../../..Download and install TCL and FFTW libraries:  (cd to NAMD_2.9_Source if you're not already there)  wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz  tar xzf fftw-linux-x86_64.tar.gz  mv linux-x86_64 fftw  wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz  wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz  tar xzf tcl8.5.9-linux-x86_64.tar.gz  tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz  mv tcl8.5.9-linux-x86_64 tcl  mv tcl8.5.9-linux-x86_64-threaded tcl-threadedSet up build directory and compile:  MPI version: ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64  cd Linux-x86_64-g++  makeQuick tests using one and two processes (network version):  (this is a 66-atom simulation so don't expect any speedup)  ./namd2  ./namd2 src/alanin  ./charmrun ++local +p2 ./namd2  ./charmrun ++local +p2 ./namd2 src/alanin  (for MPI version, run namd2 binary as any other MPI executable)Longer test using four processes:  wget http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz  tar xzf apoa1.tar.gz  ./charmrun ++local +p4 ./namd2 apoa1/apoa1.namd  (FFT optimization will take a several seconds during the first run.)