AMBER Archive (2009)

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

From: Jason Swails (jason.swails_at_gmail.com)
Date: Thu Nov 05 2009 - 08:12:39 CST

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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