[GE users] SGE unable to find my binary program

Reuti reuti at staff.uni-marburg.de
Thu Mar 23 07:44:11 GMT 2006


Hi,

Am 23.03.2006 um 07:31 schrieb laikwong:

> Hi,
>
> I am trying to place a binary program on my cluster so that users  
> can submit them as jobs to SGE.
>
> However I have a problem getting sge to find the path to the binary  
> program as well as the path to the shared library needed by the  
> binary program.
>
> I am using ROCKS as my cluster management software, it comes pre- 
> installed with SGE.
>
> The environment variables that I have setup are as follows.
>
> $PATH =
> /share/apps/bin:/opt/gridengine/bin/lx26-x86:/usr/kerberos/bin:/usr/ 
> java/jdk1.5.0_05/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:
> /opt/chromium/bin/Linux:/opt/ganglia/bin:/opt/lam/gnu/bin:/usr/ 
> share/pvm3/lib:/usr/share/pvm3/lib/LINUX:/usr/share/pvm3/bin/LINUX:/ 
> opt/rocks/bin:/opt/rocks/sbin:/home/trumper/bin
>
> $LD_LIBRARY_PATH =
> /share/apps/bin:/opt/gridengine/lib/lx26-x86
> I have placed the binary program and the shared library into /share/ 
> apps/bin which has been specified in both $PATH and $LD_LIBRARY_PATH.
>
> ROCKS has a native command called cluster-fork which allows you to  
> fork commands onto all nodes easily.
>

SGE will not use the defined $PATH/$LD_LIBRARY_PATH by default.  
Please try using the -V switch to give the environment to the job, i.e.:

qsub -b y -V -i myinput oc

HTH - Reuti


>
> I am able to do as follows:
> cluster-fork oc myinput
>
> And I am able to tell that my nodes are actually running my binary  
> program with the specified input. So far so good as my nodes are  
> able to pickup the path to the binary program and the shared library.
>
> However when I try to do this:
> qsub -b y -i myinput oc
> Sun grid engine successfully submits my job, however, it later  
> returns me "oc: Command not found." through stderr.
>
> Any ideas why Sun Grid Engine is unable to pickup my binary program?
>
> Thanks,
>
> Daniel
>
>

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