AMBER Archive (2008)

Subject: RE: AMBER: Problem In Paralklel Amber

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Sep 29 2008 - 09:35:50 CDT

Hi Ranga,

Lam comes with a series of test files, have you run these to make sure 'simple' mpi programs work? I would suggest you try to debug things this way first rather than trying it with a sander run which is just going to confuse things. You can also try things like:

mpirun -np 4 ls

and see if it spawns 4 copies of ls and thus gives you 4 directory listings. If you only see 1 copy then this suggests that there is something wrong with your mpi installation. Where did you get this copy of lam? Is it the one that comes with Linux in some cases or the version shipped with AMBER?

You should also check that your path is setup correctly. I.e. try:

which lamboot

and see what path you get - is it what you expect. Then try

which mpirun

and see what you get - is it the mpirun for this version of lam or is it running some other mpirun that is lying around? Often this can be the problem when multiple different mpi installations are on the same machine.

There may also be ways to run lamboot and mpirun in debug mode so it writes data lots of data to the terminal about what it is doing. Try man lamboot and man mpirun.

Good luck,
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Ranga Swamy
> Sent: Sunday, September 28, 2008 10:24 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Problem In Paralklel Amber
>
> 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/
> > >
> > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" (in
> > the *body* of the email)
> > > to majordomo_at_scripps.edu
> > >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" (in the
> > *body* of the email)
> > to majordomo_at_scripps.edu
>
>
> Unlimited freedom, unlimited storage. Get it now, on
> http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu