[Beowulf] the solution for qdel fail.....

Fred L Youhanaie fly at anydata.co.uk
Thu Jan 6 19:36:40 EST 2005


Hi,

Since you are using PBS you may want to consider mpiexec, 
http://www.osc.edu/~pw/mpiexec/, it is basically a replacement for 
mpirun, but with tight integration with PBS, so once you issue qdel for 
a job it will kill all the subtasks on the remote nodes. It will also do 
a better resource accounting, e.g. total cpu used by all nodes, and will 
eliminate the need for ssh/rsh :)

Even if you are not using mpi, you can spawn multiple instances of a 
program with the '--comm=none' option.

Cheers
f.


William Scullin wrote:
> Howdy,
> 
> 	The --gm-kill is specific to clusters using myrinet and mostly is there
> to ensure that slave processes using myrinet's mpi hang up when the
> master process is done running. The number after the --gm-kill is the
> timeout in seconds.
> 
> 	I am not sure which version, type, or member of the PBS family you are
> using. If you are using PBS Pro (also probably true for torque and Open
> PBS), you should be able to place two scripts in
> /var/spool/PBS/mom_priv/ called prologue and epilogue on every compute
> node. They must be owned by root and be executable / readable / writable
> only by root. The prologue script will run before every job and the
> epilogue script will run after every job. In the epilogue and prologue
> scripts we use, we clean the nodes of all lingering user processes and
> do some basic checking of node health.
> 
> 	Even if an epilogue script misses a process – or a user a user launches
> a process outside of the queuing system – the prologue will still catch
> it before the next job starts to run.
> 
> 	Best,
> 	William
>  
> On Thu, 2005-01-06 at 14:33, Jerry Xu wrote:
> 
>>Hey, Huang:
>>
>>  I found one solution that works for me, maybe you can try it and see
>>whether it works for you.
>>
>>in your pbs script, try to add this "kill -gm 5" syntax between the
>>processor number and your program
>>
>>like this 
>>
>>mpirun -machinefile $PBS_NODEFILE -np $NPROCS --gm-kill 5 myprogram
>>
>>it works for me.
>>
>>Jerry.
>>
>>/**********************************************************
>>Hi,
>>
>>We have a new system set up. The vendor set up the PBS for us. For
>>administration reasons, we created a new queue "dque" (set to default)
>>using the "qmgr" command:
>>
>>create queue dque queue_type=e
>>s q dqueue enabled=true, started=true
>>
>>I was able to submit jobs using the "qsub" command to queue "dque".
>>However, when I use "qdel" to kill a job, the job disappears from the
>>job list shown by "qstat -a", but the executable is still running on
>>the compute nodes. Every time I have to login the corresponding the
>>compute node and kill the running job.
>>
>>I am wondering if I missed something in setting up the queue so that I
>>am unable to kill the job completely using "qdel".
>>
>>Thanks.


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