[GE users] How to find SGE default PATH

Kamlesh Singh kamleshsinghus at gmail.com
Sat Mar 12 00:09:23 GMT 2005


Hi...
I also have the similar problem, where PATH is not setup on the
execution Host. How do you recreate the PATH on the execution Host.
I can not pass it with -v PATH as value of $PATH (Application
Tree)would be different on different type of Host.
I tried to pass the prolog variable but some how Job starter does not
recreate the PATH as it run in a new shell b'se of #!/bin/csh
How do you recreate the ENV in the Job script. we use "modules" but
the alias do not get setup in the execution server ENV.

qsub -v PROLOG="/home/kamsingh/tmp/GRID/jobs_starter" -q all.q at host171
-cwd env.csh

Please help.
Thanks
Regards



On Fri, 11 Mar 2005 15:34:33 -0800 (PST), Ron Chen
<ron_chen_123 at yahoo.com> wrote:
> Yes, SGE by default adds
> <job-tmp- dir>:/usr/local/bin:/usr/ucb:/bin:/usr/bin
> to
> the PATH.
> 
> But you can also submit blast.sh, and may be it's
> easier?
> 
> -Ron
> 
> --- Chunyan Wang <wangch at cpsc.ucalgary.ca> wrote:
> > Thanks,
> > My problem is:
> > On my sge master host A, I want to submit a job to
> > run on an execution
> > host B, C, D, or E. I have a job script called
> >
> > sge-job.sh, and I use "qsub sge-job.sh" to submit
> > this job. In sge-job.sh file, It calls another
> > script blast.sh which is the script to run a Blast
> > job on the host whatever SGE selects. On execution
> > host, I have a blast.sh for the Blast job.
> > Therefore, I want to find the default PATH for
> > putting the blash.sh in each execution host. So when
> > SGE select host C to run sge-job.sh, then will
> > automaticlly execute the blast.sh on host C without
> > specify the full path of blast.sh in sge-job.sh
> > file. and SGE will find it where is the blast.sh on
> > host C and run it. This job will be run as
> > "apachebody" which doesn't have a shell on these
> > host B, C, D, and E. so I can not define the path in
> > .cshrc file.
> >
> > Thanks,
> >
> > joyce
> >
> >
> >
> > Rayson Ho wrote:
> >
> > >>I don't want to specified the full path for
> > sge-job.sh
> > >>file, So what is the default PATH for SGE to find
> > this file. Because I
> > >>want find the location for these job files without
> > specifying the full
> > >>PATH of the job file.
> > >>
> > >>
> > >
> > >How about qsub `which sge-job.sh`
> > >
> > >If the location is in the search path ($PATH), then
> > `which sge-job.sh` will
> > >print the abs path.
> > >
> > >Rayson
> > >
> > >
> > >
> > >
> > >
> > >>I hope my explaination is clear. Anyone can tell
> > me this.
> > >>By the way, I found
> >
> >>/tmp/266.1.cbr.q:/usr/local/bin:/usr/ucb:/bin:/usr/bin.
> > Is this the PATH?
> > >>
> > >>Thanks alot,
> > >>
> > >>Joyce
> > >>
> > >>
> > >>
> >
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