Hello,
Perhaps you submitted it to a queue and you ran out of wall-time? Do
the tests pass? (in both serial and parallel) Maybe your files are
getting too large and amber can no longer handle it? You are printing
out very frequently... It's unlikely that anyone will try and
reproduce your error since it doesn't occur until the 283,000th step
or so.
Perhaps try reducing output frequency (ntwx=1000, ntpr=1000) and see
if that helps at all? (How large are your files?)
Good luck!
Jason
On Tue, Mar 23, 2010 at 2:02 AM, aneesh cna <aneeshcna.gmail.com> wrote:
> Dear amber users,
>
> I am doing SGMD (self guided molecular dynamics) with
> Amber 9.0 version. But the simulation get terminated with some error as
> shown below after 6ns run.
>
> ******************************************************************************************
> MPI Application rank 11 exited before MPI_Finalize() with status 1
> forrtl: error (78): process killed (SIGTERM)
> Image PC Routine Line
> Source
> libpthread.so.0 0000003CE890C4F0 Unknown Unknown Unknown
> libmpi.so.1 0000002A956EBDDD Unknown Unknown Unknown
> libmpi.so.1 0000002A956D7165 Unknown Unknown Unknown
> libmpi.so.1 0000002A957437DA Unknown Unknown Unknown
> libmpi.so.1 0000002A95733C88 Unknown Unknown Unknown
> libmpi.so.1 0000002A95749F20 Unknown Unknown Unknown
> sander.MPI 00000000004ED9AF Unknown Unknown Unknown
> sander.MPI 00000000004BD5D4 Unknown Unknown Unknown
> sander.MPI 00000000004B2FAD Unknown Unknown Unknown
> sander.MPI 0000000000404DA2 Unknown Unknown Unknown
> libc.so.6 0000003CE821C3FB Unknown Unknown Unknown
> sander.MPI 0000000000404CEA Unknown Unknown Unknown
> forrtl: error (78): process killed (SIGTERM)
> **********************************************************************************************
>
> Here is input for SGMD.........
>
>
> ********************************************************
> &cntrl
> imin = 0, ntx = 7, irest = 1,
> ntpr = 100, ntwx = 500, ntwe = 0,
> ntc = 2, ntf = 2,iwrap = 0,
> nstlim = 1000000, dt =0.002,
> tempi=274.0, temp0 = 274.0, ntt =1, tautp =1.0,
> ntb = 1, ntp = 0,cut =12.0,
> isgld =1, tsgavg =0.2, tempsg =1.0,
> isgsta =8701, isgend =8826 ( atom numbers of protein)
> &end
> **********************************************************
>
>
> and at the end of the run the output file look like as
> shown.................
>
> ***************************************************************************************************
> NSTEP = 233800 TIME(PS) = 6767.600 TEMP(K) = 289.61 PRESS =
> 0.0
> Etot = -11218.2624 EKtot = 7343.7475 EPtot =
> -18562.0099
> BOND = 2779.1812 ANGLE = 3562.7218 DIHED =
> 4418.6891
> 1-4 NB = 1301.6957 1-4 EEL = 26368.3968 VDWAALS =
> -4423.1948
> EELEC = -52569.4997 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.1366E-04
> SGFT= 0.8172 TEMPSGI= 1.0000 K
> ------------------------------------------------------------------------------
>
>
> NSTEP = 233900 TIME(PS) = 6767.800 TEMP(K) = 284.05 PRESS =
> 0.0
> Etot = -11117.5166 EKtot = 7202.8946 EPtot =
> -18320.4112
> BOND = 2829.0841 ANGLE = 3809.7204 DIHED =
> 4370.6374
> 1-4 NB = 1333.1363 1-4 EEL = 26341.0330 VDWAALS =
> -4377.1936
> EELEC = -52626.8286 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.5218E-04
> SGFT= 0.6368 TEMPSGI= 1.0000 K
> ------------------------------------------------------------------------------
> *************************************************************************************************************
>
> what could be the reason for this early termination? Waiting for your
> valuable reply....
>
>
>
> Thanks in advance
>
> Sincerely
> Aneesh
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Mar 23 2010 - 10:30:04 PDT
