can you send me directly (not to all of amber) the
other files needed, such as the prmto pand inpcrd? then
I can try to run it.
On 5/24/07, Jason K <jmk9jmk.gmail.com> wrote:
>
>
> Hello,
> I have attached the exact input files; the oREMD2.bash is the script that
> is actually submitted.
> The parallel sander excecutable actually appears in the $AMBERHOME/exe /
> directory as sander_mpi
>
> Of course, I did simplify for command for clarity, if there is something
> evidently wrong I would really appreciate if you could point it out.
>
> Many thanks,
>
> Jason
>
>
> On 5/22/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> >
> > I'm puzzled- can you send me the actual input files? there could be some
> > typo etc when you
> > write what you think you are running- for example, is it really
> > sander_mpi or is
> > it sander.MPI ?
> > carlos
> >
> > On 5/21/07, Jason K <jmk9jmk.gmail.com> wrote:
> > >
> > >
> > > Dear AMBER,
> > >
> > > I have been trying to run a replica exchange simulation on our
> > > departmental cluster (on which parallel jobs can be run on up to 12
> > > four-processor nodes). The command that I use is - essentially - the
> > > following
> > >
> > > mpirun -np 8 -machinefile {machine file} $AMBERHOME/exe/sander_mpi -ng
> > > 2 -groupfile groupfile
> > >
> > > the groupfile being the one exemplified in the test cases (I have
> > > checked that it does not contain any errors)
> > >
> > > Nevertheless, when I submit the job I get error messages similar to
> > > these:
> > >
> > >
> > > Error: specified more groups ( 2 ) than the number of
> > > processors (
> > > 1 ) !
> > > p0_2936: p4_error: : 1
> > >
> > > [0] MPI Abort by user Aborting program !
> > > [0] Aborting program!
> > >
> > >
> > > Can anyone suggest what may be the cause of this behaviour? Is this a
> > > message generated by sander, or is it a failure with either MPI or the
> > > queueing system?
> > >
> > > I can attach the actual files containing the standard output / error
> > > as well as the input files if that can be any help.
> > >
> > > All help will be greatly appreciated.
> > >
> > > Jason
> > >
> > >
> > >
> >
> >
> > --
> > ===================================================================
> > Carlos L. Simmerling, Ph.D.
> > Associate Professor Phone: (631) 632-1336
> > Center for Structural Biology Fax: (631) 632-1555
> > CMM Bldg, Room G80
> > Stony Brook University E-mail: carlos.simmerling.gmail.com
> > Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> > ===================================================================
>
>
>
>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
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Received on Sun May 27 2007 - 06:07:26 PDT
