[GE users] Running MPICH jobs

Goncalo Borges goncalo at lip.pt
Tue May 2 10:22:35 BST 2006


Hi Duong,
The fact that your job is permantly waiting could be due to different 
things, most of them probably related to configuration issues.
Therefore I suggest to do the following thing:

- when your job is in waiting state, please do a "qstat -j". This will 
give you some message explaining why it is not running. 
Alternatively, you can also use SGE GUI qmon tool. Choose the 
job panel -> pending jobs panel -> explain button 
to know why is your job not running.

Cheers
Goncalo  




On Tue, 2 May 2006, Duong Ta wrote:

> Dear Reuti,
> 
> Previously I used $round-robin in my PE. Just now I changed to $fill_up
> following what you have suggested. For allocation_rule=$fill_up, when I
> submit a MPI job requiring 4 slots, all 4 "fake" slots in one machine is
> used, the other machine remains untouched. However, when I try to request
> more than 4 slots, the job just keeps waiting (status = qw).
> 
> One more thing, occasionally I've got this error when running MPI jobs over
> SGE (I suspect this might be related to the above problem):
> 
> error: commlib error: access denied (client IP resolved to host name "".
> This is not identical to clients host name "")
> error: executing task of job 198 failed: failed sending task to execd at viz002:
> can't find connection
> p0_14351:  p4_error: Child process exited while making connection to remote
> process on viz002: 0
> p0_14351: (3.828125) net_send: could not write to fd=4, errno = 32
> 
> Should there be anything wrong with my cluster configuration?
> 
> Thank you in advance.
> 
> Best regards,
> Duong
> 
> 
> On 5/2/06, Reuti <reuti at staff.uni-marburg.de> wrote:
> > 
> > Hi,
> > 
> > Am 02.05.2006 um 09:45 schrieb Duong Ta:
> > 
> > > Dear Rayson,
> > >
> > > After I changed the slots attribute, the output of qstat -f is as
> > > follows:
> > >
> > > queuename                      qtype used/tot. load_avg
> > > arch          states
> > > ----------------------------------------------------------------------
> > > ------
> > > all.q at viz001.ihpc.a-star.edu.s BIP   0/4       1.03     lx24-amd64
> > > ----------------------------------------------------------------------
> > > ------
> > > all.q at viz002.ihpc.a-star.edu.s BIP   0/4       1.00     lx24-amd64
> > >
> > > Then I am able to run over SGE a tightly-integrated MPI job that
> > > requires 4 slots, plus a few more batch jobs at the same time. That
> > > means the trick worked, i.e., the system now has 8 "fake" slots,
> > > however, I could not run MPI jobs requiring more than 4 slots
> > > (which is the number of "real" slots in the system). Any advice?
> > 
> > which allocation_rule did you specify in your PE definition? For your
> > application it should be $round_robin or $fill_up.
> > 
> > -- Reuti
> > 
> > 
> > >
> > > Thank you very much.
> > >
> > > Best regards,
> > > Duong
> > >
> > >
> > > On 5/2/06, Rayson Ho <rayrayson at gmail.com> wrote: You can change
> > > the "slots" attribute, something like:
> > > http://gridengine.sunsource.net/servlets/ReadMsg?
> > > list=users&msgNo=13087
> > >
> > > Rayson
> > >
> > >
> > >
> > > On 5/1/06, Duong Ta <duongtnb at gmail.com> wrote:
> > > > Dear,
> > > >
> > > > I'd like to run a MPICH job over tight-integration with SGE that
> > > needs to
> > > > start 7 processes (1 master, 6 slaves) in total. However, my
> > > cluster only
> > > > has 4 slots (2 dual-core execution hosts). Is there any trick to
> > > force SGE
> > > > to start more than one MPI processes on a slot?
> > > >
> > > > Best regards,
> > > > Duong
> > > >
> > >
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> 

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