[GE users] path in qsub

Patrice Seyed apseyed at bu.edu
Thu Jun 3 18:03:56 BST 2004


Without modifying the source code is there a mechanism within sge to append
PATH or export variables in general in the qsub environment? I was looking
into setting it up in prologue but not the best idea.

The $PATH during a running job is set to:
/tmp/736.1.compute-9-9.q:/usr/local/bin:/usr/ucb:/bin:/usr/bin:

for example and does not include any of the environment variables set in
/etc/profile.d/*.sh || *.csh.

Any ideas appreciated.

-Patrice

-----Original Message-----
From: Ron Chen [mailto:ron_chen_123 at yahoo.com] 
Sent: Wednesday, May 26, 2004 12:53 AM
To: SGE users
Subject: RE: [GE users] path in qsub

exec_job.c is in source/daemons/execd/, just download
the latest SGE 5.3 tarball (sge-V53p6_TAG-src.tar.gz):

http://gridengine.sunsource.net/servlets/ProjectDownloadList

I don't know much about the login shell thing, may be
someone else on the list can help?

 -Ron

--- Patrice Seyed <apseyed at bu.edu> wrote:
> Hi Ron,
> 
> Unix start mode I have set to "unix behavior".
> Without looking at the docs
> I'll assume a shell interpreter line in the script
> would override any
> default; either way the profile.d file I am
> referring to (which append to
> PATH) was written for .sh and .csh.
> 
> I am unable to find the exec_job.c file, where would
> it be located?
> Basically I have executables in /apps/genetics/bin
> and I want this to be
> appended to the default PATH as /usr/local/bin is.
> Hopefully this gives a
> better description of what I'm trying to do.
> 
> -Patrice
> 
> -----Original Message-----
> From: Ron Chen [mailto:ron_chen_123 at yahoo.com] 
> Sent: Tuesday, May 25, 2004 9:04 PM
> To: users at gridengine.sunsource.net
> Subject: Re: [GE users] path in qsub
> 
> - "/etc/profile.d not sourced" may be related to
> your
> shell start mode.
> 
> - "/tmp/1066.1.compute-1-15.q" is set by execd, see 
> sge_get_tmpdir() in tmpdir.c, and it is called in
> sge_exec_job() in exec_job.c:
> 
> add_or_replace_env(environmentList, "PATH", buffer)
> 
> I haven't tried that myself, but if you replace the
> line above that with:
> 
>
sprintf(buffer,"/usr/local/bin:/usr/ucb:/bin:/usr/bin:");
> 
> I'd assume it will work.
> 
>  -Ron
> 
> --- Patrice Seyed <apseyed at bu.edu> wrote:
> > In qsubing a script that outputs PATH I
> > see that the following are
> > included:
> >
>
/tmp/1066.1.compute-1-15.q:/usr/local/bin:/usr/ucb:/bin:/usr/bin:
> > and that the file in /etc/profile.d are not
> sourced
> > through the qsub
> > "session".
> > I would definitely want to avoid having to append
> to
> > the PATH on the user
> > level. Thanks in advance.
> > 
> > Regards,
> >  
> > Patrice Seyed
> > Linux System Administrator - SIG
> > RHCE, SCSA
> > Boston University School of Medicine
> > 
> > 
> > 
> >
>
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