Okay - so I think maybe I'm missing something in the Amber14 install? Going
through the tutorials I still can't get TI to work (with pmemd or sander).
I keep getting the same "number of processors must be >1" error (even
though -np >1) when I get to the point of trying to run the groupfile. At
first when I thought it was working with sander that was because I
referenced the old Amber12 sander still on my computer which does run.
When I update the path to the Amber14 it won't run. Ideas?? Thanks so much
for helping!
On Fri, Sep 4, 2015 at 11:17 AM, <hannes.loeffler.stfc.ac.uk> wrote:
> For pmemd you have to generate only one prmtop containing both states.
> But then you run the simulation just like a straight MD run. You would
> have to be more specific as to what exactly is failing.
>
> I understand that this can be very confusing and I am certainly also open
> to any hints where the tutorial fails to explain properly.
>
> ________________________________________
> From: Timothy Christopher Schutt [tschutt.mymail.mines.edu]
> Sent: 04 September 2015 18:10
> To: AMBER Mailing List
> Subject: Re: [AMBER] Trouble running Thermodynamic Integration in Amber14
> with pmemd.
>
> Thank you for the replies! I can get it to work with Sander however still
> failing with pmemd. I have been going through the tutorials and am still
> confused for now but I'll keep trying, Thanks for the help!
>
> -Tim
>
> On Fri, Sep 4, 2015 at 12:38 AM, <hannes.loeffler.stfc.ac.uk> wrote:
>
> > You may also want to look into tutorial A9 to see how to run TI with
> > sander and pmemd but also to learn about the different ways of setup.
> The
> > programs are quite different in this. See
> > http://ambermd.org/tutorials/advanced/tutorial9/
> >
> > ________________________________________
> > From: Timothy Christopher Schutt [tschutt.mymail.mines.edu]
> > Sent: 03 September 2015 23:04
> > To: amber.ambermd.org
> > Subject: [AMBER] Trouble running Thermodynamic Integration in Amber14
> > with pmemd.
> >
> > Hello all,
> >
> > I could really use some help. I've recently installed Amber14 and have
> > been trying to get TI to run on my machine but I keep getting an error
> > before it even tries to execute the simulation.
> >
> > Primary job terminated normally, but 1 process returned
> > a non-zero exit code.. Per user-direction, the job has been aborted.
> > -------------------------------------------------------
> > setup_groups: MPI size is not a multiple of -ng
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >
> > even though I'm calling for:
> >
> > ~/Amber14/amber14/bin/mpirun -np 2 ~/Amber14/amber14/bin/pmemd.MPI -ng 2
> > -groupfile TI.groupfile
> >
> > I've attempted all sorts of different values for -np as well as tried
> > redoing the make install for mpi with no change in result. What am I
> doing
> > wrong? Thanks in advance for any help!
> >
> > -Tim
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> >
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> >
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Received on Mon Sep 07 2015 - 10:00:03 PDT
