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 - 08:55:16 CST

Hello, mpif90, mpicc and mpirun are all in desired folder
/usr/lib/mvapich-intel-x86_64/bin/.

User run task by typing in command line "mpirun -np 32 -maxtime 1000 -queue
regular sander.MPI -sander_options". This is instruction for /usr/bin/mpirun
script that just add task to queue. When processors are available this task
is run by genuine mpirun.

I'm not shure that problem is related with this "sophisticated" procedure
because it works before upgrades..

Thanks,
Dmitri Nilov
Lomonosov Moscow State University
On Thu, Nov 5, 2009 at 5:38 PM, Dmitri Nilov <nilovdm_at_gmail.com> wrote:

>
>
> 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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>
>
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