[GE users] newbie problem ... help needed

legol18 legol18 at gmail.com
Fri Feb 5 08:22:43 GMT 2010


I tried, it gives the same error
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Warning: untrusted X11 forwarding setup failed: xauth key data not generated
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/home/rajat/oldb/popl/lxpeff/pp: line 9: ifort: command not found
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So, what happens if instead of steps 3 & 4, you log out and then run the job script directly via ssh as I described before?

Daniel


On 02/04/10 06:38, Rajat. wrote:

    Well, the way I am running my job is as follows::
    (I am a newbie with this cluster stuff so i`ll let u know about the entire process, please bear it with me )

    1.) I remote log to the cluster via ssh from my laptop
    2.) Then cd to my destination directory where my program is, over there I create this file job file.
    3.) Once its done, I open up qmon via terminal ($ qmon&)
    4.) Over there I submit my job.

    It`s then that I am getting all those errors

    By the way, I forgot mentioning that it`s a linux cluster.

    Regards,


> What happens if you run your job script on one of the remote nodes via 
> ssh (i.e. ssh host1 /path/to/script.sh) ?  I assume the problem is that 
> you're setting your path after you log in to include where ifort lives.  
> By default Grid Engine does not transfer your shell's environment along 
> with your job.  The PATH for the job is therefore whatever you get when 
> you log in by default.  (There's another subtler problem that could also 
> be the culprit, but let's try the more obvious one first.)  To get the 
> job to inherit your environment, try using either -V or -v PATH when you 
> submit the job.
> 
> Daniel
> 
> On 02/04/10 04:52, legol18 wrote:
> > Hi,
> >
> > I just started using the grid engine on my cluster.
> > I use "g77","ifort" or "icc" for compiling my programs and they are already installed on the cluster.
> >
> > I am creating the job script inside which I am compiling the program and executing it ::
> >
> > JOB FILE :
> > ____________________________________________
> >
> > # /bin/csh
> >
> > cd /home/rajat/oldb/popl/lxpeff
> > # compile the fortran code then execute it with the ./ option
> > g77 test.f90 -o test
> > ./test
> > ____________________________________________
> >
> > Now, as mentioned, I have ifort installed on my cluster still the process gets terminated with the following error
> >
> > ERROR :
> > _____________________________________________
> >
> > opt/gridengine/default/spool/compute-0-0/job_scripts/53: line 9: ifort: command not found
> > /opt/gridengine/default/spool/compute-0-0/job_scripts/53: line 10: ./test: No such file or directory
> > _____________________________________________
> >
> > On the other hand if I try running a previously complied executable (which I compile normally on the terminal), it works fine.
> >
> > Am I missing something?
> >
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> >
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