[GE users] SGE noobie

pollinger harald.pollinger at sun.com
Tue Jun 2 16:21:42 BST 2009

biostat wrote:
> Hmmm. When I echoed $TMPDIR, i got this: 
> /var/folders/WF/WFbNEBgSHa8jWCIrXBrvnE+++yU/-Tmp-/

Looks a bit odd, but it should point to a local directory. You could set 
it simply to "/tmp" to be sure it's a valid and working local directory.

> Then, after the echo I tried qconf -mhgrp @allhosts, and it worked
> fine. No more error. Is it possible the echo somehow initialized the
> variable?

Hmm.. no. At least it should not.

> As for the other commands, apparently my $ARCH variable is not
> defined.

Did you source the $SGE_ROOT/$SGE_CELL/common/settings.sh (or .csh) 
before you use a SGE command? Even for the "-help" output?

If the installation succeeded, the file should be there. If not, please 
re-run the QMaster installation.

> qmaster: sge% $SGE_ROOT/bin/$ARCH/sge_qmaster -help | head -1 ARCH:
> Undefined variable. qmaster: sge% echo $ARCH ARCH: Undefined
> variable. qmaster: sge% source /SGE6/default/common/settings.csh 
> qmaster: sge% echo $ARCH ARCH: Undefined variable.
> To make things even stranger, exec3, the computer that was originally
> throwing the null object error, just started working again -- exec4
> is still throwing that error though. I've been messing around with
> things alot recently, trying to get everything working, but I haven't
> touched exec3 in days. I don't understand why it would start working
> again all of a sudden.
> Essentially, here are the somewhat convoluted order of events so far:
>  *Exec3 started throwing a "NULL object pointer passed to function
> "spool_flatfile_read_object"" error. *Exec4, in the middle of a run,
> starting throwing the same error. *My qmaster threw a "error getting
> temporary file name: File name too long" error when trying to run
> 'qconf -mhgrp @allhosts'. *Exec3 spontaneously started working again
> (by which I mean the qmaster stopped seeing its state as "currently
> unavailable", and I was able to send it jobs directly via 'qsub -l
> 'hostname=exec3'') even though I havent touched that computer in
> days. *I echoed $TMPDIR and the temp file name error on the qmaster
> disappeared. *Exec4 is still listed as "currently unavailable, and
> the $ARCH variable is undefined.

This looks like some environment changes. Be it NFS, be it some hardware 
issue, or something else.


> Thanks again for the help *
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Sun Microsystems GmbH         Harald Pollinger
Dr.-Leo-Ritter-Str. 7         Sun Grid Engine Engineering
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