Hello George,
Just to confirm this is a sander.MPI issue, perhaps you can try running the
above input file with pmemd? It recognizes all of the options except
restraintmask, which has to be recast as a group format input. The below
input file will have exactly the same result, but will run with either
sander.MPI or pmemd. (Even if it does turn out that only sander.MPI has an
issue with it, you can still use pmemd).
heat 3ogn-3og
&cntrl
imin=0,irest=0,ntx=1,
nstlim=25000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=1,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0, ig=-1,
tempi=0.0, temp0=300.0,
ntr=1,
nmropt=1
/
&wt TYPE='TEMP0', istep1=0, istep2=25000,
value1=0.1, value2=300.0, /
&wt TYPE='END' /
Restraints
2.0
RES 1 138
END
END
Does it work with mpirun -np 12 pmemd.MPI ?
Good luck!
Jason
On Sun, Dec 12, 2010 at 11:10 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Apologies. Fingers are sometimes quicker than the mind.
>
> The installed compilers is gcc44.
>
> Just in case this helps in the diagnostics.
>
> Setting -np to 8 works.
>
> pmemd.MPI with -np 12 also works.
>
> Cheers
>
> George
>
>
> On Dec 12, 2010, at 3:46 PM, George Tzotzos wrote:
>
> > Many thanks for the prompt reply.
> >
> > I'm using OSX 10.6.5 (2 x 2.93 GHz 6-Core Intel Xeon)
> >
> > The MPI is mpich2 and the compiler gcc installed from MacPorts
> >
> > The output file is attached.
> >
> > Many thanks
> >
> > George<heat.out>
> >
> >
> >
> >
> > On Dec 12, 2010, at 3:32 PM, case wrote:
> >
> >> On Sun, Dec 12, 2010, George Tzotzos wrote:
> >>>
> >>> In the previous message mpirun -np was set to 12.
> >>> Setting -np to 4 does not produce the same error. sander.MPI works.
> >>
> >> Can you tell us what version of MPI you are using, and which compilers
> and OS?
> >> Also, what was in the output file? (That is, did the failure occur
> right
> >> away?)
> >>
> >> Second, could you try the simulation without the &rst namelist? That
> facility
> >> doesn't get used with minimization, and is not often used, so there
> might be a
> >> bug lurking related to that.
> >>
> >> ...thanks...dac
> >>
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Dec 12 2010 - 10:00:04 PST
