[GE users] PVM tight integration

Reuti reuti at staff.uni-marburg.de
Wed Apr 12 12:59:43 BST 2006


Am 12.04.2006 um 13:49 schrieb davide cittaro:

> On 4/12/06, Reuti <reuti at staff.uni-marburg.de> wrote:
>
>> Yes. Maybe you could echo the set $PATH in startpvm.sh, which might
>> give a clue where it's coming from. - Reuti
>>
>
> Before exporting with TMPDIR =
> /opt/n1ge6/bin/lx26-amd64:/usr/local/bin:/usr/bin:/bin:/opt/bin:/ 
> usr/x86_64-pc-linux-gnu/gcc-bin/3.4.3:/opt/blackdown-jdk-1.4.2.03/ 
> bin:/opt/blackdown-jdk-1.4.2.03/jre/bin:/opt/sci-biology/bin
>
>
> After =  /tmp/39720.1.bofh.q:/opt/n1ge6/bin/lx26-amd64:/usr/local/ 
> bin:/usr/bin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/3.4.3:/ 
> opt/blackdown-jdk-1.4.2.03/bin:/opt/blackdown-jdk-1.4.2.03/jre/bin:/ 
> opt/sci-biology/bin
>
> You said that GE automatically sets PATH adding TMPDIR to it... is
> this somehow configurable in queue or cluster configuration?

No, this is a hardcoded PATH in SGE. But can you check your /etc/ 
profile (or personal one) and so on... The things like sci-biology  
must come from a custom setting. Maybe you can adjust this to extend  
the PATH, and not replacing it completely.

> Also, I see (and it is clearly explained) that export PVM_TMP=$TMPDIR
> has to be set into all batch scripts. I can do this and well remember,
> but is there a way to *add* this automatically when a job has
> launched? I'm not sure that all users will always add that to their
> scripts, especially new users that *come after the manual*...

It should be possible to source this information in any of the login  
files like /etc/profile or ~/.bash_profile, ~/.profile... as at this  
time the $TMPDIR is already set. It won't work to specify it as a SGE  
request, as $TMPDIR is only known at runtime of the job.

-- Reuti


> d
>
>
> --
> dawe
> http://dawe.ilbello.com
> ---
> "Prediction is very difficult, especially if it's about the future." -
> Niels Bohr
>
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