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Hi,<br><br>I guess you are not aware that you are using 128 cores and you ask for 32 cores to do PME.<br>Using -npme 64 will probably result in a much higher performance, but you should check<br>the information printed at the end of the log file. If you PME load is really around 0.5, the real<br>PME load ratio (not the guess like grompp and mdrun print) can be found at the end of the log file,<br>you should decrease your PME load by increasing the cut-off and the grid spacing by the same amount.<br>This will provide higher performance.<br><br>I don't know what happens with tpbconv. The crash is surely not caused by something that happened<br>in your simulation.<br>You could try to use the -time option of tpbconv to select one of the last frames.<br><br>But in Gromacs 4 you should no longer use tpbconv.<br>You can use checkpoint files.<br>Simply make a tpr file with the complete runtime (you can use tpbconv -until or -nsteps without -f and -e),<br>and run mdrun with the options -cpi to read a checkpoint and -maxh to finish after a certain number of hours.<br><br>Berk<br><br><hr id="stopSpelling">From: regafan@hotmail.com<br>To: gmx-users@gromacs.org<br>Date: Thu, 5 Mar 2009 15:21:08 +0000<br>Subject: [gmx-users] problem extending simulation 64 proc<br><br>
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<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">Hello,</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">I have a problem in extending a MD simulation in Gromacs.</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">When I use 32 processors for the calculation, everything goes OK. The simulation finishes well and I can extend it with tpbconv.</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">However, I would like to increase the number of processors used up to 64. </font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">Using the same options for mdrun as I have used for 32 proc except for the number of processors:</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">srun<span style=""> </span>-n 64 /gpfs/apps/GROMACS/4.0.2/bin/mdrun -v -deffnm equilibrado9 -dlb auto</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">I get this error:</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">-------------------------------------------------------</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">Program mdrun, VERSION 4.0.2</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">Source code file: domdec_setup.c, line: 132</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Courier New" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">Fatal error:</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">Could not find an appropriate number of separate PME nodes. i.e. >= 0.474960*#nodes (58) and <= #nodes/2 (64) and reasonable performance wise (grid_x=384, grid_y=162).</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">Use the -npme option of mdrun or change the number of processors or the PME grid dimensions, see the manual for details.</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">When I changed to </font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">srun<span style=""> </span>-n 64 /gpfs/apps/GROMACS/4.0.2/bin/mdrun -v -deffnm equilibrado9 -dlb auto –npme 32</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Courier New" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">the calculation finished correctly. However, when I try to extend this simulation with tpbconv:</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><font color="#000000" face="Times New Roman" size="3">/<font face="Courier New">gpfs/apps/GROMACS/4.0.4/bin/tpbconv -s equilibrado9.tpr -f equilibrado9.trr -e equilibrado9.edr -n index.ndx -o equilibrado10.tpr -extend 1600</font></font></p>
<p class="EC_MsoNormal" style=""><font color="#000000" face="Times New Roman" size="3"> </font></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">The process dies, I don´t know why:</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">READING COORDS, VELS AND BOX FROM TRAJECTORY equilibrado9.trr...</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Courier New" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">Opened equilibrado9.edr as single precision energy file</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">trn version: GMX_trn_file (single precision)</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Courier New">Read<span style=""> </span>trr frame<span style=""> </span>452: step 2652000 time 5304.000Killed</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">When I used gmxcheck I have not found anything strange. I have also tried with the version 4.0.4 of Gromacs to do tpbconv, but the error is the same. This occurred in several calculations, always using 64 processors and -npme 32, so it is not a punctual error, something must be happening in the calculation but I don´t know what.</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">Does anybody has any idea?</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font size="3"><font color="#000000"><font face="Times New Roman">Thank you very much for your help in advance,</font></font></font></span></p>
<p class="EC_MsoNormal" style=""><span style="" lang="EN-GB"><font color="#000000" face="Times New Roman" size="3"> </font></span></p>
<p class="EC_MsoNormal" style=""><font color="#000000" face="Times New Roman" size="3">Rebeca Garcia</font></p>
<p class="EC_MsoNormal" style=""><font color="#000000" face="Times New Roman" size="3">Parc Cientific of Barcelona</font></p>
<p class="EC_MsoNormal" style=""><font color="#000000" face="Times New Roman" size="3">regafan@hotmail.com</font></p><br><hr>Nuevo Windows Live, un mundo lleno de posibilidades <a href="http://www.microsoft.com/windows/windowslive/default.aspx">Descúbrelo.</a><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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