[gmx-users] Problems of gmx4.5.5 on the E3-1230 V2 CPU (Ivy Bridge)

[Roland Schulz]

Hi,

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
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. 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.

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).

Roland

On Fri, May 25, 2012 at 8:44 AM, 石子枫 <lv-wenping at live.cn> wrote:

>  Dear，every one!
>
> We found some problems of run gmx4.5.5 in parallel on the E3-1230 V2 CPU (Ivy
> Bridge).
> The compilers we used were ifort and icc (Version 12.0.3).
> It only if the value of the option "-nt" > 2, the mdrun program crashed
> after hundreds MD steps.
> And we also noticed that the same .tpr file could successfully run on both
> the i7-2600 and AMD platforms.
>
> The typically error outputs are attached below. Thanks for any responses
> and suggestions.
>
> Wade Lv
>
>
> Error Outputs:
> ==================================================
> step 222: Water molecule starting at atom 3633 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> step 222: Water molecule starting at atom 3882 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.5
> Source code file: pme.c, line: 538
>
> Fatal error:
> 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.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> =====================================================
>
> **
> **
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120526/bf45e62b/attachment.html>