<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>I've noticed a problem when running simulations using PME with the CVS version of gromacs. I can run simulations with 1,2,3, and 4 processors, but when I try to run on 8 or 16 processors things aren't working correctly. Gromacs seems to start correctly, but hangs before the output line for step 0 is printed. Mpich prints out the following error: "Timeout in establishing connection to remote process: 0". Strangely the logfile for nodes 0-3 end with:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Iniitalizing LINear Constraint Solver</DIV><DIV>....</DIV><DIV>..</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>While nodes 4-7 end with:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Started mdrun on node X DATE</DIV><DIV>Grid: ...</DIV><DIV>Configuring non-bonded kernels</DIV><DIV>Testing AMD 3DNow support... not present</DIV><DIV>Testing ia32 SSE support... present</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>So it appears that some of the nodes aren't initializing properly. This is run on a cluster of dual xeons running ROCKS. I should mention that all of these jobs run fine with 3.2.1, although the performance is obviously quite poor for more than two processors.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Justin</DIV><DIV><P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: 14.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">--------------------------</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Justin MacCallum<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">PhD Student</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Departement of Biological Sciences</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">University of Calgary</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: 14.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">email: <A href="mailto:jlmaccal@ucalgary.ca">jlmaccal@ucalgary.ca</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">web: moose.bio.ucalgary.ca</FONT></P> </DIV><BR></BODY></HTML>