Just to help separate out the issues, you might try running the hello_c program
in the OMPI examples directory - this will verify whether the problem is in the
mpirun command or in your program
On Sep 4, 2014, at 6:26 AM, Donato Pera <donato.p...@dm.univaq.it> wrote:
> Hi,
>
> the text was on the file.err file in the file.out file I get only the name
> of the node where the program run.
>
> Thanks Donato.
>
>
> On 04/09/2014 15:14, Reuti wrote:
>> 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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