o thank you so much karl...i just wanna make some
clarifications...i have been using the same version of
mpich for my amber7 also...but i have recompiled it
with icc8 in a new location...i mean, my $MPICH_HOME
is different for amber7 and amber8..i shall give a try
with the ip addresses too...as u said...
thanx again karl..
regards,
--- "Karl N. Kirschner" <kkirschn.hamilton.edu> wrote:
> Your machine.LINUX file looks okay, as long as the
> name of the nodes
> (node0, node1, etc) are how you named the nodes in
> your hosts file. You
> might try to specifically put the ip addresses
> instead of the node
> name. I didn't know you had amber7 running on the
> cluster - if this is
> the case and you are running the same mpich with
> amber7, then the
> problem is in the compiling of amber8. I am running
> out of
> suggestions...I will think some more and if I come
> up with something I
> will let you know.
> Karl
>
> On Fri, 2004-06-25 at 09:42, spookie wrote:
> > 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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> > > > >
> > > >
> > >
> >
>
-----------------------------------------------------------------------
> > > > > > The AMBER Mail Reflector
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> to
> > > > > majordomo.scripps.edu
> > > > > --
> > > > > ---------------------------------
> > > > > Karl Nicholas Kirschner, Ph.D.
> > > > > Assistant Professor of Chemistry
> > > > > Hamilton College, NY 1323
> > > > > ---------------------------------
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> >
>
___________________________________________________________ALL-NEW
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> > > --
> > > ---------------------------------
> > > Karl Nicholas Kirschner, Ph.D.
> > > Assistant Professor of Chemistry
> > > Hamilton College, NY 1323
> > > ---------------------------------
> > >
> > >
> >
> >
> >
> >
> >
> >
>
___________________________________________________________ALL-NEW
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>
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> --
> ---------------------------------
> Karl Nicholas Kirschner, Ph.D.
> Assistant Professor of Chemistry
> Hamilton College, NY 1323
> ---------------------------------
>
>
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Received on Fri Jun 25 2004 - 19:53:01 PDT
