<br><br><div class="gmail_quote">On Mon, Jul 5, 2010 at 5:59 PM, <span dir="ltr"><<a href="mailto:hess@sbc.su.se">hess@sbc.su.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi,<br>
<br>
Which Gromacs version is this?<br></blockquote><div> Head from two weeks ago (commit: 0541796)</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
And this is not with GBSA?<br></blockquote><div>no GBSA. PME.</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I assume this is in parallel?<br></blockquote><div>yes </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
In all 4.0 versions there is a bug in the graph code,<br>
but I have never seen that being triggered.<br></blockquote><div>you mean GCC 4 or GROMACS 4? </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
You probably wouldn't know if 4.1.3 does better?<br></blockquote><div>no. Only tested those two GCC versions.</div><div><br></div><div>BTW: Are MDP files supposed to be upward compatible? Because the default for nstcalcenergy is -1 in grompp. Thus if one has an old mdp file without the nstcalcenergy option one gets a different tpr file with grompp from HEAD than grompp 4.0.7. Should we set nstcalcenergy to 1 if it is missing or print a NOTICE if is it is missing and we set it to -1?</div>
<div><br></div><div>(We noticed this while looking at the origin of the large energy fractionation. The (short-term) fluctuation are increased with nstcalcenergy -1 (it is using 10) but much smaller than the increase caused by GCC 4.1 - which are longer term fluctuations)</div>
<div><br></div><div>Roland </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Berk<br>
<div><div></div><div class="h5"><br>
> Hi,<br>
><br>
> we have a simulation in our group (Xiaohu's system) which shows much<br>
> larger<br>
> energy fluctuations (on a ~10ns time-scale) if compiled with 4.1.2.<br>
> These fluctuation are large enough for the system to explode infrequently.<br>
> The system behaves as expected (without the large fluctuations/explosions)<br>
> when compiled with 4.4.4.<br>
><br>
> Roland<br>
><br>
> On Thu, Jun 24, 2010 at 11:05 AM, Berk Hess <<a href="mailto:hess@cbr.su.se">hess@cbr.su.se</a>> wrote:<br>
><br>
>> Hi,<br>
>><br>
>> We just found out a that a bug that frequently showed up and we thought<br>
>> might be due to a bug in gcc 4.1<br>
>> was actually a bug in the GB sse2 (not sse3) code that only got<br>
>> triggered with gcc 4.1 with -O2 or -O3.<br>
>><br>
>> So my question is now:<br>
>> Do you know of any issues with gcc 4.1.x on non-GB simulations?<br>
>><br>
>> Thanks,<br>
>><br>
>> Berk<br>
>><br>
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>><br>
><br>
><br>
><br>
> --<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <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>