Hi George,
Firstly it is NOT advisable to run sander.MPI with the number of processors
not being a power of 2. Sander uses a different way of collating the forces
when there is a non-power of 2 cpus and thus the efficiency is often a LOT
lower. You may find that using 8 cores is actually faster than 12. What I
suspect is happening is that there is a bug in the code used when the number
of MPI processes is not a power of 2. PMEMD is unaffected by this because it
uses point to point communications.
The non-power of 2 code in sander is probably very rarely tested so it is
possible there is a bug in there.
Can you let me know the exact version of AMBER you are running along with
what bugfixes have been applied.
All the best
Ross
> -----Original Message-----
> From: George Tzotzos [mailto:gtzotzos.me.com]
> Sent: Sunday, December 12, 2010 8:10 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] error on running sander.MPI
>
> 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
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 12 2010 - 10:30:04 PST
