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 "Please set the environment variable SGE_ROOT."

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courtnea.rainey Posted - May 03 2010 : 12:42:20 AM
Hello,

Whenever I try to submit a job on the cluster, I get the following error:

"Unable to initialize environment because of error: Please set the environment variable SGE_ROOT."

Does anyone know how I can fix this?

-Courtnea
5   L A T E S T    R E P L I E S    (Newest First)
petty Posted - Oct 06 2010 : 11:02:59 AM
Wait are you getting this error on the head node, or on the compute nodes when you submit a job?

The variable shouldn't be set on the compute nodes or the interactive nodes, so please remove that from your submission scripts (infact you can remove the other one also, since thats not necessary anymore).

and you should be returning that path when you echo the variable, because that is what the variable is supposed to be.

What exactly are you doing thats throwing the error?
rkozink Posted - Oct 06 2010 : 10:45:17 AM
I've tried logging out and back in twice and I'm still receiving the error. I also added the line:
source ./etc/profile.d/BIAC_vars.sh

right above the line that says:
source /etc/biac_sge.sh

It's still returning the same error message. When I type echo $SGE_ROOT, I get "/opt/gridengine" as the path.
petty Posted - Oct 06 2010 : 09:45:24 AM
can you log-out, then back in?

All the environmental variables are set via a script when you log in ... if its somehow gotten unset that will fix it.

Alternatively you could source the script thats sets those ENVs: ". /etc/profile.d/BIAC_vars.sh" (note the period as the first character)

Do either of those then: echo $SGE_ROOT ... which should return a valid path
rkozink Posted - Oct 06 2010 : 08:44:40 AM
I am receiving the same error:

Unable to initialize environment because of error: Please set the environment variable SGE_ROOT.
Exiting.

I am not running on the interactive node.
petty Posted - May 03 2010 : 2:56:16 PM
hey courtnea ... i think you are trying to submit jobs through the interactive nodes. the interact/compute nodes are missing this ENV for a very specific reason.

you can only submit through the head node for now.

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