AMBER Archive (2008)

Subject: Re: AMBER: Problem In Paralklel Amber

From: Ranga Swamy (balimidiswamy_at_yahoo.co.in)
Date: Mon Sep 29 2008 - 00:23:57 CDT

Hi,
   Thanks for your reply. Following are the details

Script :

lamboot

LAUNCH="mpirun -machinefile hostfile -np 4 /home/amber10/bin/sander.MPI -O -i lysribo-min-8.in -o lysribo-min-8.out -p lysribosolion.prmtop -c lysribo-min-7.rst -ref lysribo-min-7.rst -r lysribo-min-8.rst -x lysribo-min-8.mdcrd -v lysribo-min-8.mdvel -e lysribo-min-8.mden -inf lysribo-min-8.mdinfo "

${LAUNCH}
exit
------------------------------------------------------------------------------------------------------------------------
machinefile :

headnode
headnode
oscarnode1
oscarnode1

...............................................................................................................................

I am using Amber10 package. When I submit the job with -np 4, it spawns only 1 process on headnode. And no second process on headnode, and nothing on oscarnode1.

Thanks in advance....

B.Ranga Swamy,
Project Engineer,
C-DAC, Pune.
Mobile : 09881133489
Land Office : 020-25694121
Office Mail Id : rangab_at_cdac.in
Personal Mail Id : balimidiswamy_at_yahoo.co.in

--- On Fri, 26/9/08, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:

> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> Subject: Re: AMBER: Problem In Paralklel Amber
> To: amber_at_scripps.edu
> Date: Friday, 26 September, 2008, 5:22 PM
> please tell us exactly what you are doing- what is your job
> script,
> machinefile, which sander version, how you set your
> configure script,
> etc.
> there is simply no way to help with the minimal information
> you have given.
>
>
> On Fri, Sep 26, 2008 at 7:10 AM, Ranga Swamy
> <balimidiswamy_at_yahoo.co.in> wrote:
> > Hi,
> >
> > I am running amber using Lam-MPI.
> > I've created hostfile with four entries. And
> trying with -np 4. It is a linux cluster built with Oscar
> suit. But job is running only on one where the job submitted
> and only with one process. It is is not spawning the
> processes onto other nodes.
> >
> > Please help me if anybody knows the solution
> >
> > Thanks & Regards
> > ----------------------------------------
> > B.Ranga Swamy,
> > Project Engineer,
> > C-DAC, Pune.
> > Mobile : 09881133489
> > Land Office : 020-25694121
> > Office Mail Id : rangab_at_cdac.in
> > Personal Mail Id : balimidiswamy_at_yahoo.co.in
> >
> >
> > Add more friends to your messenger and enjoy! Go
> to http://in.messenger.yahoo.com/invite/
> >
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