[GE users] Running MPICH jobs

Duong Ta duongtnb at gmail.com
Tue May 2 10:30:58 BST 2006


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Dear Goncalo,

Yes, I did a qstat -j, and the reason was: Jobs can not run because
available slots combined under PE are not in range of job 199.

A qstat -f gave (the job requires 6 slots):

queuename                      qtype used/tot. load_avg arch          states
----------------------------------------------------------------------------
all.q at viz001.ihpc.a-star.edu.s BIP   0/4       0.00     lx24-amd64
----------------------------------------------------------------------------
all.q at viz002.ihpc.a-star.edu.s BIP   0/4       0.01     lx24-amd64

############################################################################
 - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS
############################################################################
    199 0.55500 cpi        griduser     qw    05/02/2006 16:54:05     6

Best regards,
Duong

On 5/2/06, Goncalo Borges <goncalo at lip.pt> wrote:
>
>
> 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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