[GE users] initialize environment failure

valentin valentin.ruano at gmail.com
Fri Mar 6 14:32:30 GMT 2009


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Hi,
at the end it turns out that it only affects submission with -sync y, at least I have not been able to reproduce the error without the sync, perhaps I did something else wrong. In fact now I could work around the problem by creating a small script that calls qsub and then waits until the job is finished; polls qstat -j jobnum until a non-zero return code.

Now, sticking to the -sync y cases:
the error is immediate and it does not give any job id to do a qstat -j upon; no new jobs of any kind appear in the qstat's output (neither regular current job listing nor -s z)

$ cat > dummy.sh <<EOF
ls /
EOF
$ qsub -sync y ./dummy.sh

Unable to initialize environment because of error: range_list containes no elements
Exiting.
$ echo $?
1

I can confirm that the error message above goes to the std.err. as one would expect anyway. Nothing goes to "messages" files in the spool directory for the qmaster nor any other executing node; last messages (tail) refer to unrelated old events.

regards, V.


On Fri, Mar 6, 2009 at 2:53 PM, reuti <reuti at staff.uni-marburg.de<mailto:reuti at staff.uni-marburg.de>> wrote:
Hi,

Am 05.03.2009 um 14:53 schrieb valentin:

> comes out immediately in the terminal right after executing qsub's
> command line, thus it should be in the qsub process' standard error.
>
> On Thu, Mar 5, 2009 at 2:36 PM, reuti <reuti at staff.uni-marburg.de<mailto:reuti at staff.uni-marburg.de>>
> wrote:
> Hi,
>
> Am 05.03.2009 um 13:54 schrieb valentin:
>
> > everything was going fine with the 6.2u1 queue I recently installed
> > but all in a sudden I cannot submit successfully any more jobs.
> > Regardless of the commands in the script and error appears  saying:
> >
> > Unable to initialize environment because of error: range_list
> > containes no elements
> > Exiting.
>
> is this the error on the command line or in one of the messages files
> of the qmaster or the node where it was supposed to be scheduled to?
>
> -- Reuti
>
>
> > I'm using  qsub -sync y in order to wait for the job to complete.
> > If I do a regular sync free submition, it gets sent to the queue
> > but it is in fact never executed; no <name>.[oe]ID files are
> produced.
> >

are you getting any message with:

$ qstat -j <jobid>

of the waiting jobs why it's not scheduled? I assume they are stuck
in state qw then. Is there any other entry in $SGE_ROOT/default/
common/qmaster/messages?

-- Reuti


> > I tried to google the error message but I had no luck, does any
> > body know what would be the problem or has encountered it before?
> >
> > thanks in advance.
> >
> > V.
>
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