[torqueusers] jobs stuck in queue until I force execution with qrun
Gustavo Correa
gus at ldeo.columbia.edu
Thu Feb 16 14:05:30 MST 2012
PS - For some diagnostic, you could also try '$TORQUE/bin/pbsnodes' on the server,
and '$TORQUE/sbin/momctl -d 3' on the compute nodes.
Gus Correa
On Feb 16, 2012, at 3:55 PM, Gustavo Correa wrote:
> 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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>
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