<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">Hi Francesco and Mark,</span><div style="font-family:arial,sans-serif;font-size:13px">Thanks for your precious advice. Now this time I didn't insert any code but use the .mdp options instead. I used the following steps: first set the environment variable GMX_NB_GENERIC=1, run the GROMACS, and run again with the same input but GMX_NB_GENERIC unset. Next, compare two force.xvg generated from two traj.trr using g_traj. However, I still found the results different from each other.. My gcc version is 4.6.3(almost the newest), my fftw version is 3.3.3(double precision, and GROMACS is also build in double-precision) and I use the argument --reprod to make sure the calculation of PME is reproducible. </div>
<div style="font-family:arial,sans-serif;font-size:13px">My running command for GROMACS is</div><div style="font-family:arial,sans-serif;font-size:13px">mpirun -np 2 mdrun_mpi -s test.tpr -v -reprod</div><div style="font-family:arial,sans-serif;font-size:13px">
I tried to attach my test tpr and mdp file in this email but my attempt was not approved by administrator because the email would be oversized..</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">
-Mark</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sat, Jun 8, 2013 at 7:25 AM, francesco oteri <span dir="ltr"><<a href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">In my case the excuse was that the system administrator never updated the compiler. <div>So I after a couple of days I installed the new compiler.</div>
<div>In any case, I noticed that the problem disappeared using the "Debug" version so I guess </div>
<div>it is something related either to the optimized kernel or the optimization strategy used by the compiler. </div><span class="HOEnZb"><font color="#888888"><div><br></div><div><br></div><div>Francesco</div></font></span></div>
<div class="HOEnZb"><div class="h5"><div class="gmail_extra">
<br><br><div class="gmail_quote">2013/6/8 Mark Abraham <span dir="ltr"><<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote"><div>On Sat, Jun 8, 2013 at 12:59 PM, francesco oteri <span dir="ltr"><<a href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">H Mark,<div>I had a similar problem recently and, eventually, I figured out the cause was the compiler version.</div>
<div>I was using gcc4.1 and my problem got solved using a more recent version. Actually, this issue </div>
<div>in the website is clearly stated. So, which compiler are you using?</div><div>Could you report an example of inconsistency?</div></div></blockquote><div><br></div></div><div>That warning has been there many years, but AFAIK nobody ever identified the real problem (if it exists). Nevertheless, there is no excuse for using both GROMACS and such an old compiler! :-)</div>
<span><font color="#888888">
<div><br></div><div>Mark</div></font></span><div><div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><br></div><div>Francesco </div>
</div><div class="gmail_extra">
<div><div>
<br><br><div class="gmail_quote">2013/6/8 Mark Abraham <span dir="ltr"><<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Sat, Jun 8, 2013 at 1:44 AM, Mark Tianwu Zang <span dir="ltr"><<a href="mailto:zangtw@gmail.com" target="_blank">zangtw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear all,<div>I have inserted only a few lines after update() in md.c to monitor how forces change after every step. My codes are very simple, just like:</div>
<div> </div><div>for i=0 to md->nalloc</div>
<div><div> fprintf f[i][0], f[i][1], f[i][2]</div></div></div></blockquote><div><br></div><div>That seems like the hard way to do it, with nstfout available in the .mdp file. </div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div><div>However, I found the results of my output become quite different after exporting GMX_NB_GENERIC=1, which means the forces calculated by generic kernel and interaction-specific kernel are not the same. I am a little confused now.. It this phenomena quite normal or I ignored something important?</div>
</div></div></blockquote><div><br></div><div>AFAIK the generic kernel should serve as a reference for the interaction-specific kernels. If not, there might a problem to fix. Hard to say without context.</div><div><br>
</div><div>Mark</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>
<div>Thanks a lot!</div><span><font color="#888888"><div>-Mark</div><div><br></div></font></span></div><div><br></div></div><span><font color="#888888">
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