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 - 07:39:59 CST

'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 |
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