<br><br><div class="gmail_quote">On Wed, May 4, 2011 at 4:46 AM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br><br><span>On 04/05/11, <b>Igor Leontyev </b> <<a href="mailto:ileontyev@ucdavis.edu" target="_blank">ileontyev@ucdavis.edu</a>> wrote:</span><blockquote style="border-left:1px solid rgb(0, 0, 255);padding-left:13px;margin-left:0pt" type="cite">
<div>To make partial charges be adjustable according to acting field I have introduced modifications to gromacs 4.0.7. The serial (single thread) version seems to be ready and I want to implement parallelization (with particle decomposition). In my current implementation:<br>
- values of mdatoms->chargeA for local atoms are updated in "do_md" at the begininig of each timestep;<br>- 'MPI_Sendrecv' + 'gmx_wait' are used in "do_force" (right after the call "move_cgcm") to distribute the new charges over parallel nodes.<br>
After this the array mdatoms->chargeA have updated values on all nodes. But some problem arises later in "gmx_pme_do" (modification free routine) hanging up execution and even PC.</div></blockquote><br></div>
Standard procedure is to use a debugger to see which memory access from where is problematic. I'm not aware of a free parallel debugger, however. Bisecting with printf() calls can work...</blockquote><div><br></div><div>
As free parallel debuggers you can use:</div><div>- gdb/xterm trick. See section Debugging: <a href="http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer's_Guide">http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer's_Guide</a> </div>
<div>- Eclipse/PTP: <a href="http://www.eclipse.org/ptp/">http://www.eclipse.org/ptp/</a></div><div><br></div><div>Roland</div><div><br></div><div><br></div></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>
865-241-1537, ORNL PO BOX 2008 MS6309<br>