[GE users] mpich sge and exporting env vars

Reuti reuti at staff.uni-marburg.de
Wed Jun 14 14:29:10 BST 2006


Am 14.06.2006 um 14:57 schrieb michael bane:

> To clarify I execute 'qsub this.sh' where this.sh is something like
>
>         #! /bin/bash
>         #$ -pe mpich 2
>         #$ -l s_rt=1:00:00,h_rt=1:20:00
>         #$ -V
>         export M3DATA=${HOME}/models-3/data/TESTING/par
>         NPROCS=2; BASE=...;EXEC=...
>         mpirun -batch -np $NPROCS -machinefile $TMPDIR/machines
>         $BASE/$EXEC

I would recommend to use -np $NSLOTS to get the actual slots granted  
by SGE. The $BASE/$EXEC should expand in place already, so the -V  
shouldn't be necessary at all, as you are not interested in the  
environment variable of the interactive login while submitting the job.

To send these variables to the nodes, you can try (with Tigth  
Integration):

export RCMD_PREFIX="M3DATA=${HOME}/models-3/data/TESTING/par myvar2=a  
myvar3=b"
mpirun ...

-- Reuti


> but $EXEC when running doesn't know the value of M3DATA (and there's
> about a hundred more such env vars in the real script)
>
> Ta, Michael
>
> On Wed, 2006-06-14 at 12:48 +0000, Gruhn Daniel J Contractor AF/A9IT
> wrote:
>> Michael,
>>
>> If your script executes qsub to queue out your job, then #$ -V  
>> will have no
>> effect.  This only works for a script that is actually submitted  
>> by qsub to
>> the grid.
>>
>> Dan
>>
>> //SIGNED//
>> Daniel J.Gruhn, CTR (Group W Inc.)
>> HQ USAF/A9IT
>> Studies & Analyses, Assesments and Lessons Learned
>>
>> -----Original Message-----
>> From: michael bane [mailto:michael.bane at manchester.ac.uk]
>> Sent: Wednesday, June 14, 2006 8:26 AM
>> To: users at gridengine.sunsource.net
>> Subject: RE: [GE users] mpich sge and exporting env vars
>>
>> The cluster is down at the moment so cannot check this, but I've  
>> had #$ -V
>> at the top of my qsub script. Is this the correct place or does it  
>> have to
>> be placed once the env vars have been set in the script?
>>
>> I was wondering if it's anything to do with mpich1...
>>
>> More once the cluster is back
>> Ta, Michael
>>
>> On Wed, 2006-06-14 at 07:18 -0500, McCalla, Mac wrote:
>>> Hi,
>>>
>>> You can also try qsub option -V if you want to ship the entire
>>> environment variable set to the job, Or if there is a standard
>>> environment used by all jobs you can wrap the start of the compute
>>> nodes Sgeexecd in it.
>>>
>>> HTH,
>>>
>>> Mac Mccalla
>>>
>>> -----Original Message-----
>>> From: Gerd Marquardt [mailto:marquardt at rrzn.uni-hannover.de]
>>> Sent: Wednesday, June 14, 2006 6:07 AM
>>> To: users at gridengine.sunsource.net
>>> Subject: Re: [GE users] mpich sge and exporting env vars
>>>
>>> michael bane wrote:
>>>> I'm new to SGE but not a stranger to mpich. I've had a look in the
>>>> archives and elsewhere but cannot find a solution to my problem but
>>>> hope somebody here can point me in the right direction.
>>>>
>>>> We have a Linux cluster running SGE and with mpich1 available. I
>>>> have a code that makes heavy use of environment variables. However,
>>>> when I try and run this under SGE using mpich it falls over since
>>>> the running
>>>
>>>> executable claims to have no knowledge of the environment variables
>>>> even thought they are set in the qsub script.
>>>>
>>>> Thanks in advance,
>>>>
>>> Try the qsub-Option:
>>>    -v  variable[=value]
>>>
>>> --
>>>  Gerd Marquardt
>>>
>>>
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>> --
>> Michael Bane
>> Centre for Atmospheric Science
>> University of Manchester, U.K.
>>
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> -- 
> Michael Bane
> Centre for Atmospheric Science
> University of Manchester, U.K.
>
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