[GE users] OpenMPI job on stay on one node

sgexav xaviercouvelard at gmail.com
Mon Sep 7 11:53:30 BST 2009


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Hi, i still have the same problem
12 job on 8 core.......
while polist is OK
/opt/gridengine/default/spool/compute-0-3/active_jobs/35.1/pe_hostfile
compute-0-3
compute-0-3
compute-0-3
compute-0-3
compute-0-3
compute-0-3
compute-0-3
compute-0-3
compute-0-1
compute-0-1
compute-0-1
compute-0-1

**** compute-0-3
  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  
COMMAND           
10857 xavier    25   0  228m  61m 5092 R 100.1  0.4   0:29.90 
roms             
10853 xavier    25   0  228m  52m 5068 R 99.8  0.3   0:29.39 
roms              
10860 xavier    25   0  228m  61m 5036 R 99.8  0.4   0:29.48 
roms              
10855 xavier    25   0  228m  61m 5144 R 99.1  0.4   0:29.83 
roms              
10863 xavier    25   0  228m  61m 5036 R 56.2  0.4   0:17.37 
roms              
10856 xavier    25   0  228m  61m 5108 R 54.2  0.4   0:16.75 
roms              
10859 xavier    25   0  228m  61m 5044 R 51.2  0.4   0:15.60 
roms              
10862 xavier    25   0  228m  61m 5032 R 50.5  0.4   0:15.62 
roms              
10861 xavier    25   0  228m  61m 5036 R 49.5  0.4   0:15.53 
roms              
10854 xavier    25   0  228m  61m 5108 R 48.9  0.4   0:15.45 
roms              
10858 xavier    25   0  228m  61m 5076 R 45.2  0.4   0:14.07 
roms              
10864 xavier    25   0  228m  49m 4896 R 43.6  0.3   0:13.97 
roms            

nothing on compute-0-1.

Xav

reuti a écrit :
> Hi,
>
> Am 07.09.2009 um 12:04 schrieb sgexav:
>
>   
>> Hi,
>> I am running a parallel code with openmpi.
>> the code needs 12 proc and nodes have 8.
>>
>> With the classicam mpirun -np 12 ........; it works prefectly
>>
>> But with SGE the 12 process stay on one node.
>>
>> qsub script.sh
>> Here is may submission script,
>>  #!/bin/sh
>> #
>> # job name
>> #$ -N ROMS_TEST
>> #
>> # Use current working directory
>> #$ -cwd
>> #
>> # Join stdout and stderr
>> #$ -j y
>>
>> # define queue
>> #$ -q all.q
>>
>> #$ -pe mpi 12
>>
>> # Run job through bash shell
>> #$ -S /bin/bash
>> #
>> echo "Got $NSLOTS processors."
>> echo "Machines:"
>> cat $TMPDIR/machines
>>
>> export PATH=/opt/openmpi-1.3.3/bin/:$PATH
>> export
>> LD_LIBRARY_PATH=/opt/openmpi-1.3.3/lib:/opt/intel/Compiler/11.1/046/ 
>> lib/intel64:$LD_LIBRARY_PATH
>> #export OMPI_MCA_pls_rsh_agent=rsh
>>
>> mpirun -np $NSLOTS  -hostfile $TMPDIR/machines ./roms roms.in
>>     
>
> a) you compiled Open MPI with SGE support?
>
> b) what does your PE look like - you followed the Howto for SGE on  
> the Open MPI site (http://www.open-mpi.org/faq/?category=running#run- 
> n1ge-or-sge)?
>
> -- Reuti
>
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