Hi Jason,
Okay. Here is my input file and I used to be able to submit this job on a
nonlocal computer cluster and it was fine running there.
production
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0= 1.0, ntp = 1,
taup = 2.0,scee = 1.0,scnb = 1.0,
ig = 712,
cut = 8, ntr = 0,
ntc = 2, ntf = 2,
tempi = 323.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 100000, dt = 0.002,
ntpr = 10000, ntwx = 1000, ntwr = 1000
/
&ewald vdwmeth=0 /
/
END
Best,
Mo
On Thu, Oct 13, 2011 at 3:40 PM, Jason Swails <jason.swails.gmail.com>wrote:
> What is line 5 of your MDIN file? (or rather print your whole mdin file
> here).
>
> There's an unsupported namelist variable you're trying to use.
>
> HTH,
> Jason
>
> On Thu, Oct 13, 2011 at 3:27 PM, Mo Chen <mc842.cornell.edu> wrote:
>
> > Dear Amber users/developers,
> > I have run into some problems when I used pmemd and pmemd.MPI to run a
> > simulation. And the error messages are as below. May I ask how I could
> > solve
> > this problem? Thank you very much!
> >
> > chen.sugar9:~/celf-lbox/celf-bglc$ ./test
> > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> unit
> > 5, file /home/chen/celf-lbox/celf-bglc/celfbglc_prod_3.in, line 5,
> > position
> > 17
> > Image PC Routine Line
> > Source
> > libintlc.so.5 00007F38E335AF7A Unknown Unknown
> Unknown
> > libintlc.so.5 00007F38E3359AF5 Unknown Unknown
> Unknown
> > libifcore.so.5 00007F38E429C1F2 Unknown Unknown
> Unknown
> > libifcore.so.5 00007F38E42115FB Unknown Unknown
> Unknown
> > libifcore.so.5 00007F38E4210D0E Unknown Unknown
> Unknown
> > libifcore.so.5 00007F38E4252E52 Unknown Unknown
> Unknown
> > pmemd 00000000005A84B2 Unknown Unknown
> Unknown
> > pmemd 00000000004ED11E Unknown Unknown
> Unknown
> > pmemd 00000000004EC109 Unknown Unknown
> Unknown
> > pmemd 0000000000402E2C Unknown Unknown
> Unknown
> > libc.so.6 00007F38E2FD5EFF Unknown Unknown
> Unknown
> > pmemd 0000000000402D29 Unknown Unknown
> Unknown
> > chen.sugar9:~/celf-lbox/celf-bglc$ ./test
> > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> unit
> > 5, file /home/chen/celf-lbox/celf-bglc/celfbglc_prod_3.in, line 5,
> > position
> > 17
> > Image PC Routine Line
> > Source
> > libintlc.so.5 00007F596B17BF7A Unknown Unknown
> Unknown
> > libintlc.so.5 00007F596B17AAF5 Unknown Unknown
> Unknown
> > libifcore.so.5 00007F596C0BD1F2 Unknown Unknown
> Unknown
> > libifcore.so.5 00007F596C0325FB Unknown Unknown
> Unknown
> > libifcore.so.5 00007F596C031D0E Unknown Unknown
> Unknown
> > libifcore.so.5 00007F596C073E52 Unknown Unknown
> Unknown
> > pmemd.MPI 000000000062278F Unknown Unknown
> Unknown
> > pmemd.MPI 000000000050EF19 Unknown Unknown
> Unknown
> > pmemd.MPI 0000000000508B99 Unknown Unknown
> Unknown
> > pmemd.MPI 000000000042031C Unknown Unknown
> Unknown
> > libc.so.6 00007F596ADF6EFF Unknown Unknown
> Unknown
> > pmemd.MPI 0000000000420219 Unknown Unknown
> Unknown
> >
> --------------------------------------------------------------------------
> > mpirun has exited due to process rank 0 with PID 23582 on
> > node sugar9 exiting without calling "finalize". This may
> > have caused other processes in the application to be
> > terminated by signals sent by mpirun (as reported here).
> >
> --------------------------------------------------------------------------
> >
> >
> >
> > Best,
> > Mo Chen
> > Graduate Student
> > 120 Stocking Hall
> > Cornell University
> > Ithaca, NY 14850
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Oct 13 2011 - 13:00:05 PDT
