[gridengine users] export of environment variables from start_proc_args

[Reuti]

Am 05.07.2012 um 16:06 schrieb SLIM H.A.:

> Hmmm. If OMP_NUM_THREADS is not set in the job script then the startup_method will be effective and the executed program has the variable set to $NSLOTS.
> However if the job script does set OMP_NUM_THREADS its value is not overwritten.

Did you define it as readonly in your starter_method?

Normally you can redefine them in the jobscript without any problems.

-- Reuti


> Any ideas why this is?
> 
> Thanks
> 
> Henk
> 
>> -----Original Message-----
>> From: SLIM H.A.
>> Sent: 05 July 2012 14:48
>> To: 'Reuti'
>> Cc: users at gridengine.org
>> Subject: RE: [gridengine users] export of environment variables from
>> start_proc_args
>> 
>>> $1 will be the jobscript to be started
>>> $2 first command_argument (if any) you supplied at the end of `qsub`, i.e.
>> $1
>>> inside the script
>>> $3 second command_argument (if any) you supplied at the end of `qsub`,
>>> i.e. $2 inside the script
>> 
>> I suspected this but when I ran a trial job before, it  failed and  I got this
>> error message:
>> 
>> Unknown colorls variable 'rs'
>> 
>> Googling  this gives various causes of this error and suggest a connection
>> with using tcsh (the job script is C shell) . Including a line
>> 
>> unset  LS_COLORS
>> 
>> before
>> 
>> exec "$@"
>> 
>> fixes this.
>> 
>> Regards
>> 
>> Henk
>> 
>> 
>>> -----Original Message-----
>>> From: Reuti [mailto:reuti at staff.uni-marburg.de]
>>> Sent: 05 July 2012 13:07
>>> To: SLIM H.A.
>>> Cc: users at gridengine.org
>>> Subject: Re: [gridengine users] export of environment variables from
>>> start_proc_args
>>> 
>>> Am 05.07.2012 um 13:53 schrieb SLIM H.A.:
>>> 
>>>> Thanks Reuti,
>>>> 
>>>>> You could provide a startup_method for the queue(s) in question:
>>>>> 
>>>>> #!/bin/sh
>>>>> export OMP_NUM_THREADS=$NSLOTS
>>>>> exec "$@"
>>>> 
>>>> "@$" would expand to the startup_method arguments but these are
>>> absent? The documentation about the starter_method is not clear to me,
>>> are the "job arguments" the command_args to command in qsub?
>>> 
>>> $1 will be the jobscript to be started
>>> $2 first command_argument (if any) you supplied at the end of `qsub`, i.e.
>> $1
>>> inside the script
>>> $3 second command_argument (if any) you supplied at the end of `qsub`,
>>> i.e. $2 inside the script
>>> ...
>>> 
>>> -- Reuti
>>> 
>>> 
>>>> Thanks
>>>> 
>>>> Henk
>>>> 
>>>>> -----Original Message-----
>>>>> From: Reuti [mailto:reuti at staff.uni-marburg.de]
>>>>> Sent: 04 July 2012 15:37
>>>>> To: SLIM H.A.
>>>>> Cc: users at gridengine.org
>>>>> Subject: Re: [gridengine users] export of environment variables from
>>>>> start_proc_args
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> Am 04.07.2012 um 14:57 schrieb SLIM H.A.:
>>>>> 
>>>>>> I want to constrain the number of OpenMP threads in a job from
>> within
>>>>> GridEngine. The user should set this to $NSLOTS in the job script but can
>>> this
>>>>> be enforced by including this in a PE start script?
>>>>>> 
>>>>>> I set a start_proc_args script "startopenmp.sh" with argument
>> $pe_slots
>>> in
>>>>> an openmp PE and the script contains the line
>>>>>> 
>>>>>> export OMP_NUM_THREADS=$1
>>>>> 
>>>>> The start_proc_args is an independent script started before the actual
>>> job.
>>>>> Nothing is inherited to the executed jobscript.
>>>>> 
>>>>> You could provide a startup_method for the queue(s) in question:
>>>>> 
>>>>> #!/bin/sh
>>>>> export OMP_NUM_THREADS=$NSLOTS
>>>>> exec "$@"
>>>>> 
>>>>> Thsi will also work without requesting a PE, as $NSLOTS will then
>>> evaluate
>>>>> to 1.
>>>>> 
>>>>> The problem with -v is, that it's evaluated at submission time, but not
>>>>> during execution.
>>>>> 
>>>>> -- Reuti
>>>>> 
>>>>> 
>>>>>> and then run a simple test job that prints the environment.
>>>>> OMP_NUM_THREADS has not been set. Is there a way to achieve this
>>>>> otherwise?
>>>>>> 
>>>>>> Thanks
>>>>>> 
>>>>>> Henk
>>>>>> 
>>>>>> _______________________________________________
>>>>>> users mailing list
>>>>>> users at gridengine.org
>>>>>> https://gridengine.org/mailman/listinfo/users
>>>> 
>>>> 
> 
>