Hi,<div><br></div><div>it is always possible that your simulation is isn't well equilibrated and different rouding errors make it crash with one binary/hardware but not with another. See also <a href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a>. You should first make sure that this isn't the case by taking a well equilibrated structure from your working hardware as a starting structure for the Ivy-Bridge run and see whether you still observe the crash.</div>
<div><br></div><div>If you want to see whether it is really a problem with the binary on Ivy-Bridge, you should write out the energy on all steps (nstenergy=1) and compare the energy between the working and the non-working simulation (gmxcheck). If the energy disagrees already for the first 40 steps it is likely a problem (later differences are expected because of the chaotic nature of MD). You should also write a bit more about how you installed Gromacs (including the full cmake/configure command line).</div>
<div><br></div><div>Roland</div><div><br><div class="gmail_quote">On Fri, May 25, 2012 at 8:44 AM, 石子枫 <span dir="ltr"><<a href="mailto:lv-wenping@live.cn" target="_blank">lv-wenping@live.cn</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Dear，every one!<br>
<br>
We found some problems of run gmx4.5.5 in parallel on the E3-1230 V2 CPU (<span></span>Ivy Bridge).<br>
<span lang="en"><span>T</span><span>he</span>
<span>compilers we used were </span>ifort and icc (<span>Version 12.0.3</span><span>).</span></span><br>
It only if the value of the option "-nt" > 2, the mdrun program crashed after hundreds MD steps.<br>
And we also noticed that the same .tpr file could successfully run on both the i7-2600 and AMD platforms.<br>
<br>
The typically error outputs are attached below. Thanks for any responses and suggestions.<br>
<br>
Wade Lv<br>
<br>
<br>
Error Outputs:<br>
==================================================<br>
step 222: Water molecule starting at atom 3633 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
<br>
step 222: Water molecule starting at atom 3882 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>
<br>
-------------------------------------------------------<br>
Program mdrun, VERSION 4.5.5<br>
Source code file: pme.c, line: 538<br>
<br>
Fatal error:<br>
1 particles communicated to PME node 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.<br>
This usually means that your system is not well equilibrated.<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
=====================================================<br>
<br>
<div><u></u><br>
<u></u></div>
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</blockquote></div><br><br clear="all"><div><br></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>
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