[torqueusers] jobs stuck in queue until I force execution with qrun

Gustavo Correa gus at ldeo.columbia.edu
Thu Feb 16 13:55:29 MST 2012


Hi Christina

This is just a vague thought, not sure if in the right direction.

I am a bit confused about the domain being admin.default.domain
Is this the sever name in $TORQUE/server_name on the head node?
Is it something else, perhaps the head node FQDN Internet address?

How about this line in the compute nodes'  $TORQUE/mom_priv/config file:
$pbsserver .....
What is the server name that appears there?

These items were a source of confusion for me long ago. 
I don't even remember anymore
what was the mistake and how it was fixed, but maybe there is something here.

Also, is there any hint of the problem in the $TORQUE/mom_logs files in the compute nodes?
How about the /var/log/messages on the compute nodes, any smoking gun there?

Can the compute nodes resolve the Torque server name [easy way via /etc/hosts]?
Can the Torque server resolve the compute nodes' names [ say in /etc/hosts]?
Is there a firewall between the server and the compute nodes?

Maybe the Torque Admin Guide, Ch. 1 [overview/installation/configuration] 
and Ch 11 [troubleshooting] can help:

http://www.adaptivecomputing.com/resources/docs/

I hope this helps,
Gus Correa

On Feb 16, 2012, at 3:10 PM, Christina Salls wrote:

> Hi all,
> 
>          My situation has improved but I am still not there.  I can submit a job successfully, but it will stay in the queue until I force execution with qrun. 
> 
> eg.
> 
> -bash-4.1$ qsub ./example_submit_script_1
> 22.admin.default.domain
> -bash-4.1$ qstat -a
> 
> admin.default.domain: 
>                                                                          Req'd  Req'd   Elap
> Job ID               Username Queue    Jobname          SessID NDS   TSK Memory Time  S Time
> -------------------- -------- -------- ---------------- ------ ----- --- ------ ----- - -----
> 22.admin.default     salls    batch    ExampleJob          --      1   1    --  00:01 Q   -- 
> 
> .[root at wings ~]# qrun 22
> [root at wings ~]# qstat -a
> 
> admin.default.domain: 
>                                                                          Req'd  Req'd   Elap
> Job ID               Username Queue    Jobname          SessID NDS   TSK Memory Time  S Time
> -------------------- -------- -------- ---------------- ------ ----- --- ------ ----- - -----
> 22.admin.default     salls    batch    ExampleJob        30429     1   1    --  00:01 R   -- 
> 
> [root at wings ~]# qstat -a
> 
> admin.default.domain: 
>                                                                          Req'd  Req'd   Elap
> Job ID               Username Queue    Jobname          SessID NDS   TSK Memory Time  S Time
> -------------------- -------- -------- ---------------- ------ ----- --- ------ ----- - -----
> 22.admin.default     salls    batch    ExampleJob        30429     1   1    --  00:01 C 00:00
> [root at wings ~]# 
> 
> 
> This is what tracejob output looks like:
> 
> [root at wings ~]# tracejob 22
> /var/spool/torque/mom_logs/20120216: No such file or directory
> /var/spool/torque/sched_logs/20120216: No matching job records located
> 
> Job: 22.admin.default.domain
> 
> 02/16/2012 13:46:51  S    enqueuing into batch, state 1 hop 1
> 02/16/2012 13:46:51  S    Job Queued at request of salls at admin.default.domain, owner = salls at admin.default.domain,
>                           job name = ExampleJob, queue = batch
> 02/16/2012 13:46:51  A    queue=batch
> 02/16/2012 13:53:53  S    Job Run at request of root at admin.default.domain
> 02/16/2012 13:53:53  S    Not sending email: User does not want mail of this type.
> 02/16/2012 13:53:53  A    user=salls group=man jobname=ExampleJob queue=batch ctime=1329421611 qtime=1329421611
>                           etime=1329421611 start=1329422033 owner=salls at admin.default.domain
>                           exec_host=n001.default.domain/0 Resource_List.neednodes=1 Resource_List.nodect=1
>                           Resource_List.nodes=1 Resource_List.walltime=00:01:00 
> 02/16/2012 13:54:03  S    Not sending email: User does not want mail of this type.
> 02/16/2012 13:54:03  S    Exit_status=0 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb
>                           resources_used.walltime=00:00:10
> 02/16/2012 13:54:03  A    user=salls group=man jobname=ExampleJob queue=batch ctime=1329421611 qtime=1329421611
>                           etime=1329421611 start=1329422033 owner=salls at admin.default.domain
>                           exec_host=n001.default.domain/0 Resource_List.neednodes=1 Resource_List.nodect=1
>                           Resource_List.nodes=1 Resource_List.walltime=00:01:00 session=30429 end=1329422043
>                           Exit_status=0 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb
>                           resources_used.walltime=00:00:10
> 
> 
> This is what the output files look like:
> 
> -bash-4.1$ more ExampleJob.o22
> Thu Feb 16 13:53:53 CST 2012
> Thu Feb 16 13:54:03 CST 2012
> -bash-4.1$ more ExampleJob.e22
> -bash-4.1$ 
> 
> This is my basic server config:
> 
> [root at wings ~]# qmgr
> Max open servers: 10239
> Qmgr: print server
> #
> # Create queues and set their attributes.
> #
> #
> # Create and define queue batch
> #
> create queue batch
> set queue batch queue_type = Execution
> set queue batch resources_default.nodes = 1
> set queue batch resources_default.walltime = 01:00:00
> set queue batch enabled = True
> set queue batch started = True
> #
> # Set server attributes.
> #
> set server scheduling = True
> set server acl_hosts = admin.default.domain
> set server acl_hosts += wings.glerl.noaa.gov
> set server managers = root at wings.glerl.noaa.gov
> set server managers += salls at wings.glerl.noaa.gov
> set server operators = root at wings.glerl.noaa.gov
> set server operators += salls at wings.glerl.noaa.gov
> set server default_queue = batch
> set server log_events = 511
> set server mail_from = adm
> set server scheduler_iteration = 600
> set server node_check_rate = 150
> set server tcp_timeout = 6
> set server mom_job_sync = True
> set server keep_completed = 300
> set server next_job_number = 23
> 
> Processes running on server:
> 
> root     32086     1  0 13:23 ?        00:00:00 /usr/local/sbin/pbs_server -d /var/spool/torque -H admin.default.domain
> root     32173     1  0 13:23 ?        00:00:00 /usr/local/sbin/pbs_sched -d /var/spool/torque
> 
> 
> My sched_config file looks like this.  I left the default values as is.
> 
> [root at wings sched_priv]# more sched_config
> 
> 
> # This is the config file for the scheduling policy
> # FORMAT:  option: value prime_option
> #	option 		- the name of what we are changing defined in config.h
> #	value  		- can be boolean/string/numeric depending on the option
> #	prime_option	- can be prime/non_prime/all ONLY FOR SOME OPTIONS
> 
> # Round Robin - 
> #	run a job from each queue before running second job from the
> #	first queue.
> 
> round_robin: False	all
> 
> 
> # By Queue - 
> #	run jobs by queues.
> #       If it is not set, the scheduler will look at all the jobs on
> #       on the server as one large queue, and ignore the queues set
> #       by the administrator
> #	PRIME OPTION
> 
> by_queue: True		prime
> by_queue: True		non_prime
> 
> 
> # Strict Fifo - 
> #	run jobs in strict fifo order.  If one job can not run
> #	move onto the next queue and do not run any more jobs
> #	out of that queue even if some jobs in the queue could
> #	be run.
> #	If it is not set, it could very easily starve the large
> #	resource using jobs.
> #	PRIME OPTION
> 
> strict_fifo: false	ALL
> 
> #
> # fair_share - schedule jobs based on usage and share values
> #	PRIME OPTION
> #
> fair_share: false	ALL
> 
> # Help Starving Jobs - 
> #	Jobs which have been waiting a long time will
> #	be considered starving.  Once a job is considered
> #	starving, the scheduler will not run any jobs 
> #	until it can run all of the starving jobs.  
> #	PRIME OPTION
> 
> help_starving_jobs	true	ALL
> 
> #
> # sort_queues - sort queues by the priority attribute
> #	PRIME OPTION
> #
> sort_queues	true	ALL
> 
> #
> # load_balancing - load balance between timesharing nodes
> #	PRIME OPTION
> #
> load_balancing: false	ALL
> 
> # sort_by:
> # key:
> # 	to sort the jobs on one key, specify it by sort_by
> #	If multiple sorts are necessary, set sory_by to multi_sort
> # 	specify the keys in order of sorting
> 
> # if round_robin or by_queue is set, the jobs will be sorted in their
> # respective queues.  If not the entire server will be sorted.
> 
> # different sorts - defined in globals.c
> # no_sort shortest_job_first longest_job_first smallest_memory_first 
> # largest_memory_first high_priority_first low_priority_first multi_sort
> # fair_share large_walltime_first short_walltime_first
> #
> #	PRIME OPTION
> sort_by: shortest_job_first	ALL
> 
> # filter out prolific debug messages
> # 256 are DEBUG2 messages 
> #	NO PRIME OPTION
> log_filter: 256
> 
> # all queues starting with this value are dedicated time queues
> # i.e. dedtime or dedicatedtime would be dedtime queues
> #	NO PRIME OPTION
> dedicated_prefix: ded
> 
> # ignored queues
> # you can specify up to 16 queues to be ignored by the scheduler
> #ignore_queue: queue_name
> 
> # this defines how long before a job is considered starving.  If a job has 
> # been queued for this long, it will be considered starving
> #	NO PRIME OPTION
> max_starve: 24:00:00
> 
> # The following three config values are meaningless with fair share turned off
> 
> # half_life - the half life of usage for fair share
> #	NO PRIME OPTION
> half_life: 24:00:00
> 
> # unknown_shares - the number of shares for the "unknown" group
> #	NO PRIME OPTION
> unknown_shares: 10
> 
> # sync_time - the amount of time between syncing the usage information to disk
> #	NO PRIME OPTION
> sync_time: 1:00:00
> 
> 
> Any idea what I need to do?
> 
> Thanks,
> 
>       Christina
> 
> 
> -- 
> Christina A. Salls
> GLERL Computer Group
> help.glerl at noaa.gov
> Help Desk x2127
> Christina.Salls at noaa.gov
> Voice Mail 734-741-2446 
> 
> 
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