Hi,
Am 04.09.2014 um 14:43 schrieb Donato Pera:
> using this script :
>
> #!/bin/bash
> #$ -S /bin/bash
> #$ -pe orte 64
> #$ -cwd
> #$ -o ./file.out
> #$ -e ./file.err
>
> export LD_LIBRARY_PATH=/home/SWcbbc/openmpi-1.6.5/lib:$LD_LIBRARY_PATH
> export OMP_NUM_THREADS=1
>
> CPMD_PATH=/home/tanzi/myroot/X86_66intel-mpi/
> PP_PATH=/home/tanzi
> /home/SWcbbc/openmpi-1.6.5/bin/mpirun ${CPMD_PATH}cpmd.x input
> ${PP_PATH}/PP/ > out
Is this text below in out, file.out or file.err - any hint in the other files?
-- Reuti
>
> The program run for about 2 minutes and after I get this error
>
> WARNING: A process refused to die!
>
> Host: compute-2-2.local
> PID: 24897
>
> This process may still be running and/or consuming resources.
>
> --------------------------------------------------------------------------
> [compute-2-2.local:24889] 25 more processes have sent help message
> help-odls-default.txt / odls-default:could-not-kill
> [compute-2-2.local:24889] Set MCA parameter "orte_base_help_aggregate"
> to 0 to see all help / error messages
> [compute-2-2.local:24889] 27 more processes have sent help message
> help-odls-default.txt / odls-default:could-not-kill
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 0 with PID 24896 on
> node compute-2-2.local exiting improperly. There are two reasons this
> could occur:
>
> 1. this process did not call "init" before exiting, but others in
> the job did. This can cause a job to hang indefinitely while it waits
> for all processes to call "init". By rule, if one process calls "init",
> then ALL processes must call "init" prior to termination.
>
> 2. this process called "init", but exited without calling "finalize".
> By rule, all processes that call "init" MUST call "finalize" prior to
> exiting or it will be considered an "abnormal termination"
>
> This may have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
> [compute-2-2.local:24889] 1 more process has sent help message
> help-odls-default.txt / odls-default:could-not-kill
>
>
> Thanks and Regards Donato
>
>
>
>
> On 03/09/2014 13:19, Reuti wrote:
>> Am 03.09.2014 um 13:11 schrieb Donato Pera:
>>
>>> I get
>>>
>>> ompi_info | grep grid
>>> MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.6.5)
>> Good.
>>
>>
>>> and using this script
>>>
>>> #!/bin/bash
>>> #$ -S /bin/bash
>>> #$ -pe orte 64
>>> #$ -cwd
>>> #$ -o ./file.out
>>> #$ -e ./file.err
>>>
>>> export LD_LIBRARY_PATH=/home/SWcbbc/openmpi-1.6.5/lib:$LD_LIBRARY_PATH
>>> export OMP_NUM_THREADS=1
>>>
>>> CPMD_PATH=/home/tanzi/myroot/X86_66intel-mpi/
>>> PP_PATH=/home/tanzi
>>> /home/SWcbbc/openmpi-1.6.5/bin/mpirun -mca btl openib -np 64
>>> -machinefile $TMPDIR/machines ${CPMD_PATH}cpmd.x input ${PP_PATH}/PP/
>> In the PE "orte" is no "start_proc_args" defined which could generate the
>> machinefile. Please try to start the application with:
>>
>> /home/SWcbbc/openmpi-1.6.5/bin/mpirun -mca btl openib ${CPMD_PATH}cpmd.x
>> input ${PP_PATH}/PP/
>>
>> -- Reuti
>>
>>
>>>> out
>>>
>>> I get this error
>>>
>>> Open RTE was unable to open the hostfile:
>>> /tmp/21213.1.debug.q/machines
>>> Check to make sure the path and filename are correct.
>>> --------------------------------------------------------------------------
>>> [compute-2-6.local:22452] [[5218,0],0] ORTE_ERROR_LOG: Not found in file
>>> base/rmaps_base_support_fns.c at line 207
>>> [compute-2-6.local:22452] [[5218,0],0] ORTE_ERROR_LOG: Not found in file
>>> rmaps_rr.c at line 82
>>> [compute-2-6.local:22452] [[5218,0],0] ORTE_ERROR_LOG: Not found in file
>>> base/rmaps_base_map_job.c at line 88
>>> [compute-2-6.local:22452] [[5218,0],0] ORTE_ERROR_LOG: Not found in file
>>> base/plm_base_launch_support.c at line 105
>>> [compute-2-6.local:22452] [[5218,0],0] ORTE_ERROR_LOG: Not found in file
>>> plm_rsh_module.c at line 1173
>>>
>>>
>>>
>>>
>>>
>>> Instead using this script
>>>
>>>
>>> #!/bin/bash
>>> #$ -S /bin/bash
>>> #$ -pe orte 64
>>> #$ -cwd
>>> #$ -o ./file.out
>>> #$ -e ./file.err
>>>
>>> export LD_LIBRARY_PATH=/home/SWcbbc/openmpi-1.6.5/lib:$LD_LIBRARY_PATH
>>> export OMP_NUM_THREADS=1
>>>
>>> CPMD_PATH=/home/tanzi/myroot/X86_66intel-mpi/
>>> PP_PATH=/home/tanzi
>>> /home/SWcbbc/openmpi-1.6.5/bin/mpirun -mca btl openib -np 64
>>> $TMPDIR/machines ${CPMD_PATH}cpmd.x input ${PP_PATH}/PP/ > out
>>>
>>>
>>> I get
>>> Executable: /tmp/21214.1.debug.q/machines
>>> Node: compute-2-0.local
>>>
>>> while attempting to start process rank 0.
>>> --------------------------------------------------------------------------
>>>
>>> can you help me
>>>
>>>
>>> Thanks and Regards Donato
>>>
>>>
>>>
>>>
>>> On 03/09/2014 12:28, Reuti wrote:
>>>> ompi_info | grep grid
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>>
>
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