Job stuck in the queue problem

At this point I'd do the following:

(1) As root, run the sorta-under-documented command "qconf -tsm" on your head node. That will cause a one-time scheduler profiling run to be dumped to a text file called "schedd_runlog" in your $SGE_ROOT/ $SGE_CELL/common/ directory. It may explain why your job is stuck in "qw" despite having available queue instances.

(2) Double check the qmaster/messages and qmaster/shedd/messages for any odd error states

(3) Does the command "qrsh hostname" even work?

(4) Check /tmp on the compute nodes, as the execd daemon will log there in panic situations when it can't get to its spooldir

Does this cluster share a $SGE_ROOT over NFS?

This does not seem like a network timeout or firewall/routing issue as you'd clearly see SGE alarm states in your qstat output showing that nodes are unreachable. Each node regularly reports its load data and SGE will notice when these are not coming in.

Regards,
Chris

On May 22, 2006, at 3:13 PM, Mark_Johnson@xxxxxxxxxxx wrote:

The job I have submitted is the simple.sh script. Below is qstat - j 43,
and qstat -f (part of it....as I have 250 nodes)

[urs1@medusa ~]$ qstat -j 43
job_number: 43
exec_file: job_scripts/43
submission_time: Mon May 22 15:09:53 2006
owner: urs1
uid: 500
group: urs1
gid: 500
sge_o_home: /home/urs1
sge_o_log_name: urs1
sge_o_path:
/opt/gridengine/bin/lx26-x86:/usr/kerberos/bin:/usr/java/jdk1.5.0
_05/bin:/opt/intel/itc60/bin:/opt/intel/ita60/bin:/opt/intel/fc/9.0/ bin:/opt/intel/idb/9.0/bin:/opt/intel/cc/9.0/bin:/usr/local/bin:/ bin:/usr/bin:/usr/X11R6/bin:/opt/mpich/intel/bin:/opt/chromium/bin/ Linux:/opt/ganglia/bin:/opt/lam/gnu/bin:/usr/share/pvm3/lib:/usr/ share/pvm3/lib/LINUX:/usr/share/pvm3/bin/LINUX:/opt/rocks/bin:/opt/ rocks/sbin:/home/urs1/bin
sge_o_shell: /bin/bash
sge_o_workdir: /home/urs1
sge_o_host: medusa
account: sge
mail_list: urs1@xxxxxxxxxxxxxxxxxxxxx
notify: FALSE
job_name: simple.sh
jobshare: 0
shell_list: /bin/sh
env_list:
script_file: simple.sh
scheduling info: queue instance "all.q@xxxxxxxxxxxxxxxxxxx"
dropped because it is temporarily not available
queue instance "all.q@xxxxxxxxxxxxxxxxxxx"
dropped because it is temporarily not available
queue instance "all.q@xxxxxxxxxxxxxxxxxxx"
dropped because it is full

[urs1@medusa ~]$

all.q@xxxxxxxxxxxxxxxxxx BIP 0/1 0.53 lx26-x86
---------------------------------------------------------------------- ------
all.q@xxxxxxxxxxxxxxxxxx BIP 0/1 0.68 lx26-x86
---------------------------------------------------------------------- ------
all.q@xxxxxxxxxxxxxxxxxx BIP 0/1 0.59 lx26-x86
---------------------------------------------------------------------- ------
all.q@xxxxxxxxxxxxxxxxxx BIP 0/1 0.70 lx26-x86
---------------------------------------------------------------------- ------
all.q@xxxxxxxxxxxxxxxxxx BIP 0/1 0.64 lx26-x86
---------------------------------------------------------------------- ------
all.q@xxxxxxxxxxxxxxxxxx BIP 0/1 0.66 lx26-x86
---------------------------------------------------------------------- ------
all.q@xxxxxxxxxxxxxxxxxx BIP 0/1 0.77 lx26-x86
---------------------------------------------------------------------- ------
all.q@xxxxxxxxxxxxxxxxxx BIP 0/1 0.64 lx26-x86

###################################################################### ######
- PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS
###################################################################### ######
43 0.55500 simple.sh urs1 qw 05/22/2006 15:09:53 1
[urs1@medusa ~]$





Chris Dagdigian
<dag@xxxxxxxxxxxx
To
users@xxxxxxxxxxxxxxxxxxxxxxxx
05/22/2006 03:04 cc
PM
Subject
Re: [GE users] SGE jobs in "qw"
Please respond to state
users@gridengine.
sunsource.net









Hi Mark,

Send us the output of "qstat -f" and also "qstat -j <jobID>" using a
jobID of a job that is pending in state 'qw'

The usual causes are:

• - sge is down cluster wide, resulting in no free execution hosts (if
  your qstat -f shows 'au' in the state column then this is the cause)
• - sge queues have all been knocked into a persistent error (E) state
  (will show up in "qstat -f")
• - most other causes will be revealed in the scheduler_info line of
  "qstat -j <jobID>" output

Judging by the output below I would not be surprised to see your
"qstat -f' output full of "au" states which means alarm/unreachable.
You need to restart SGE on any node showing 'au' in the state column.

Regards,
Chris


On May 22, 2006, at 2:50 PM, Mark_Johnson@xxxxxxxxxxx wrote:

I have built a Rocks 4.1 Cluster, and am trying to resolve a
problem with
the SGE.

I can submit jobs to the queue, but once sibmitted they just sit
thre in
the "qw" state. I have received good help from the Rocks
community, but am
still unable to get the jobs to start. Below are a few lines from the
/opt/gridengine/default/spool/qmaster/message. It looks like the
qmaster
cannot contact the "execd" on the nodes and timesout ?

Any thoughts or ideas are appreciated..

ps...dumb it down for me as I have a Windows Handicap...

Mark,

05/22/2006 10:39:06|qmaster|medusa|I|execd on compute-0-179.local
registered
05/22/2006 10:39:06|qmaster|medusa|I|execd on compute-0-178.local
registered
05/22/2006 10:39:07|qmaster|medusa|I|execd on compute-0-180.local
registered
05/22/2006 10:40:11|qmaster|medusa|E|got max. unheard timeout for
target
"execd" on host "compute-0-157.local", can't delivering job "42"
05/22/2006 10:40:11|qmaster|medusa|W|rescheduling job 42.1
05/22/2006 10:40:11|qmaster|medusa|E|failed delivering job 42.1
05/22/2006 10:40:26|qmaster|medusa|E|got max. unheard timeout for
target
"execd" on host "compute-0-156.local", can't delivering job "42"
05/22/2006 10:40:26|qmaster|medusa|W|rescheduling job 42.1
05/22/2006 10:40:26|qmaster|medusa|E|failed delivering job 42.1
05/22/2006 10:40:32|qmaster|medusa|I|urs1 has deleted job 42
[urs1@medusa qmaster]$

Etc

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