well ! first of all...thank you so much for your
interest karl..
my $MPICH_HOME/share/machines.LINUX file looks like
this..
# Change this file to contain the machines that you
want to use
# to run MPI jobs on. The format is one host name per
line, with either
# hostname
# or
# hostname:n
# where n is the number of processors in an SMP. The
hostname should
# be the same as the result from the command
"hostname"
node0
node1
node2
node3
node4
node5
node6
node7
i would like you to note that the path of this file is
not the same as you mentioned...you mentioned it as
$MPICH_HOME/util/machines/machines.LINUX and i have it
at $MPICH_HOME/share/machines.LINUX..does this make a
difference??
second thing....i dont think ssh could be at fault
coz, i was running my parallel jobs in amber7 on the
same cluster using ssh..moreover, i had not configured
rsh at all for my cluster..so, i dont think ssh could
make a difference..
thanks for your help karl..
regards,
--- "Karl N. Kirschner" <kkirschn.hamilton.edu> wrote:
> Hi again,
> So, two suggestions. 1 - I you have to have the
> list of nodes that
> you want to use in the
> $MPICH_HOME/util/machines/machines.LINUX. This
> is the only way that mpich knows which nodes to send
> jobs to. Read the
> README in that directory for format. 2- if that
> doesn't help maybe try
> to configure mpich with rsh instead of ssh, again
> making it
> passwordless. If that works then you know it is an
> issue of ssh and can
> debug that. Hope that helps.
>
> Cheers,
> Karl
>
> On Thu, 2004-06-24 at 18:06, spookie wrote:
> > well ! i have mpich1.2.5.2 compiled for icc8 (as
> reqd
> > by amber8) on my server in /usr/local/mpich and
> this
> > directory is also crossmounted along with the
> > installation of amber, on to the rest of the
> nodes..my
> > MPICH_HOME is also appropriately set..(i mean, to
> > /usr/local/mpich). I've also configured ssh
> without a
> > password, both for root and any other users on the
> > cluster.. i've tried running jobs both as root and
> the
> > user.. no luck whatsoever !! :( i've written a
> file by
> > name mach in my benchmarks directory which
> contains
> > the hostnames of the nodes i plan to run the job
> > on...!! is the filename specific or is it left to
> the
> > user's choice?? (i think it isn't specific...is
> it?)
> >
> > thanx for your help..
> > regards..
> >
> > --- "Karl N. Kirschner" <kkirschn.hamilton.edu>
> wrote:
> > > You have to have a program that will distribute
> the
> > > jobs on the node,
> > > such as mpich. If you are using mpich then you
> have
> > > to specify in the
> > > machine.Linux file the nodes you would like to
> use
> > > in your cluster.
> > > Depending on the program you choose you also
> have to
> > > open an appropriate
> > > passwordless "door" to the machines, such as
> > > passwordless ssh. Hope
> > > this helps.
> > >
> > > Karl
> > >
> > > On Thu, 2004-06-24 at 00:50, spookie wrote:
> > > > dear all,
> > > > i have a sixteen node p4 1.5GHz linux
> cluster
> > > > running RHL 9 on them. i have installed amber8
> > > > recently on my server and have cross mounted
> it on
> > > to
> > > > all other nodes. i could successfully compile
> > > amber8
> > > > in parallel mode after facing some problems
> with
> > > > shared libraries of the icc and ifort
> > > compilers..:)
> > > > but now, when i am trying to run the
> benchmarks
> > > given
> > > > with the amber package, the job fails to run
> on
> > > the
> > > > nodes specified. it doesnot even throw any
> errors.
> > > a
> > > > temporary file with the process id of the job
> is
> > > > created, in which, when i try to run the job
> on 2
> > > > processors, it lists the server's hostname
> twice,
> > > > instead of taking up the hostnames i've
> specified
> > > in
> > > > my machinefile..where could the problem be
> > > !?...any
> > > > help would be greatly appreciated...
> > > >
> > > > thanks in anticipation...
> > > > regards..
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> >
>
___________________________________________________________ALL-NEW
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> > > express yourself http://uk.messenger.yahoo.com
> > > >
> > >
> >
>
-----------------------------------------------------------------------
> > > > The AMBER Mail Reflector
> > > > To post, send mail to amber.scripps.edu
> > > > To unsubscribe, send "unsubscribe amber" to
> > > majordomo.scripps.edu
> > > --
> > > ---------------------------------
> > > Karl Nicholas Kirschner, Ph.D.
> > > Assistant Professor of Chemistry
> > > Hamilton College, NY 1323
> > > ---------------------------------
> > >
> > >
> >
> >
> >
> >
> >
> >
>
___________________________________________________________ALL-NEW
> Yahoo! Messenger - sooooo many all-new ways to
> express yourself http://uk.messenger.yahoo.com
> --
> ---------------------------------
> Karl Nicholas Kirschner, Ph.D.
> Assistant Professor of Chemistry
> Hamilton College, NY 1323
> ---------------------------------
>
>
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Received on Fri Jun 25 2004 - 16:53:01 PDT
