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 <[email protected]> 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
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