AMBER Archive (2009)

Subject: Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade

From: Dmitri Nilov (nilovdm_at_gmail.com)
Date: Thu Nov 05 2009 - 08:38:32 CST

On Thu, Nov 5, 2009 at 5:12 PM, Jason Swails <jason.swails_at_gmail.com> wrote:

> Hello,
>
> mpirun is NOT used during installation. mpif90 and mpicc are used during
> installation as the compiler wrappers to invoke the desired compilers and
> link to the proper mpi libraries in a 'blackbox' sort of way. mpirun is
> only used during MPI execution in amber. You should make sure that your
> environment is set up to use the mvapich that you want. Try typing "which
> mpif90" to see exactly which mpi installation you're using. You can use
> mpi-selector to choose an mpi installation, and this should automatically
> set up your environment to use that MPI.
>
> Your email sounds like it does not allow users to run mpirun interactively
> (i.e. typing it on the command-line) and it is only available to run when
> submitted to the queue (though i may be wrong). Have you been trying to
> run
> interactively or submitting to the queue? Your system administrators
> should
> be able to help you get your environment set up correctly to build amber.
>
> Good luck!
> Jason
>
> On Thu, Nov 5, 2009 at 8:39 AM, Dmitri Nilov <nilovdm_at_gmail.com> wrote:
>
> > 'which mpirun' gives /usr/bin only.
> > System administrator have given some
> > explanations:
> > /usr/bin/mpirun is a script to queue the task. All mpirun/mpiexec/etc
> > scripts are forbidden for regular users for simple 'fool protection' of
> > head node. Direct task run is forbidden.
> > Just before task execution it gets special group priveleges and since
> > this moment it can execute mpirun from mpi-selector pointed location.
> >
> > So now the question is: how mpirun is used during amber installation?
> >
> > Thanks!
> > Dmitri Nilov,
> > Lomonosov Moscow State University
> >
> > On Wed, Nov 4, 2009 at 2:13 AM, Ross Walker <ross_at_rosswalker.co.uk>
> wrote:
> >
> > > Hi Dmitri,
> > >
> > > > And one thing more.
> > > > mpif90 is in /usr/lib/mvapich-intel-x86_64/bin/ on cluster. There is
> > > > also
> > > > mpirun in this folder but its execution is forbidden. That was made
> for
> > > > running mpirun only from /usr/bin/. So could it make some problem?
> > >
> > > Yes this is almost certainly your problem. If the mpirun being used to
> > > execute the code is not the same mpirun as the mpi installation used to
> > > build the code you will get very strange and unpredictable behavior. Is
> > > there a mpiexec in the mvapich bin directory that you can execute? You
> > may
> > > need to use this instead. Or ask your admin to give you execute
> > permission
> > > on the mvapich mpirun.
> > >
> > > Right now if you execute 'which mpirun' which one do you get? If it is
> > the
> > > /usr/bin one and not the mvapich one then this is where your problem
> > lies.
> > >
> > > Good luck,
> > > Ross
> > >
> > > /\
> > > \/
> > > |\oss Walker
> > >
> > > | Assistant Research Professor |
> > > | San Diego Supercomputer Center |
> > > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > > | http://www.rosswalker.co.uk | PGP Key available on request |
> > >
> > > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> > not
> > > be read every day, and should not be used for urgent or sensitive
> issues.
> > >
> > >
> > >
> > >
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>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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