[gridengine users] export of environment variables from start_proc_args
SLIM H.A.
h.a.slim at durham.ac.uk
Thu Jul 5 15:48:01 UTC 2012
Conclusion must be that there is no way the gridengine administrator can use starter methods to override a setting like
OMP_NUM_THREADS=3
by the user in the job script.
In the case of OpenMP jobs using the #$ -v and #$ -V prefix would be superfluous as gridengine will start only one process. So the jsv method appears the only way?
Thanks
Henk
> -----Original Message-----
> From: wish.dumain at gmail.com [mailto:wish.dumain at gmail.com] On
> Behalf Of William Hay
> Sent: 05 July 2012 15:46
> To: SLIM H.A.
> Cc: Reuti; users at gridengine.org
> Subject: Re: [gridengine users] export of environment variables from
> start_proc_args
>
> On 5 July 2012 15:26, SLIM H.A. <h.a.slim at durham.ac.uk> wrote:
> > I want to redefine the env in the starter_method to capture any erroneous
> setting in the job script. But I realize that it works the other way round?
> Anything set in the starter_method can be redefined in the job script?
> Depends what you mean
> If you script looks something like this
> #!/bin/bash
> #$ -v OMP_NUM_THREADS=2
>
> OMP_NUM_THREADS=3
>
>
> Then the first setting gets overridden by whatever you do in
> starter_method but the second doesn't
> because it is changed during the execution of the job.
>
> >
> >> -----Original Message-----
> >> From: Reuti [mailto:reuti at staff.uni-marburg.de]
> >> Sent: 05 July 2012 15:10
> >> 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 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
> >> >>>>
> >> >>>>
> >> >
> >> >
> >
> >
> > _______________________________________________
> > users mailing list
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> > https://gridengine.org/mailman/listinfo/users
> >
> >
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