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 "Please set the environment variable SGE_ROOT."		  New Topic  Reply to Topic
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courtnea.rainey
Starting Member

USA
1 Posts
Posted - May 03 2010 :  12:42:20 AM  Show Profile  Reply with Quote
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

petty
BIAC Staff

USA
453 Posts
Posted - May 03 2010 :  2:56:16 PM  Show Profile  Reply with Quote
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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rkozink
Junior Member

31 Posts
Posted - Oct 06 2010 :  08:44:40 AM  Show Profile  Reply with Quote
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.
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petty
BIAC Staff

USA
453 Posts
Posted - Oct 06 2010 :  09:45:24 AM  Show Profile  Reply with Quote
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
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rkozink
Junior Member

31 Posts
Posted - Oct 06 2010 :  10:45:17 AM  Show Profile  Reply with Quote
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.
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petty
BIAC Staff

USA
453 Posts
Posted - Oct 06 2010 :  11:02:59 AM  Show Profile  Reply with Quote
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?
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