Lei -

It looks like you have two worker nodes, but both are currently listed as 
non-idle, yet have low load.  My guess is that something has gone wrong with 
the SGE configuration causing jobs to simply wait in the queue.  If you look at 
the contents of qconf and qstat on the admin page, does it look like there are 
jobs backed up and/or worker nodes processing the queue?  Depending on how 
comfortable you are working with SGE, it might be easiest to just click 
"restart" for SGE in the admin panel and see if everything goes back to normal.

-Dannon


On Nov 8, 2012, at 12:43 PM, Lei Yan <leiyan2...@gmail.com> wrote:

> Dear Dannon,
> 
> My name is Lei Yan, and I am a systems administrator at UTHSC.
> I installed a Cloud Galaxy on the Amazon EC2 about two months ago, and most 
> functions work well at that time.
> http://galaxycloud.genenetwork.org/
> But from the day before yesterday, jobs were hung up always. In my opinion, I 
> didn’t find any reasons, because all look correct from Galaxy Admin page (see 
> attachments please).
> Would you please help us to check it? I can give you the administrator 
> password if you need.
> Thanks so much.
> 
> 
> Lei Yan
> leiyan2...@gmail.com
> UTHSC
> 
> 
> 
> On Wed, Nov 7, 2012 at 4:07 PM, Larry Reiter <lrei...@uthsc.edu> wrote:
> Dannon,
> 
> Maybe you can, but not through me.  I'm just a lowly user and biologist.  You 
> would have to contact the guy who did the installation and runs the server: 
> Lei Yan (leiyan2...@gmail.com)
> 
> I would think he would be receptive to some help, so you should mail him.
> 
> LTR
> 
> On 11/7/12 4:05 PM, Dannon Baker wrote:
>> Main will complete the jobs eventually, though obviously that's not 
>> particularly useful in the context of your class today.  How is your cloud 
>> instance set up?  Cloud or local instances should be the best and most 
>> reliable option for teaching with and I'd definitely like to figure out why 
>> yours failed.
>> 
>> -Dannon
>> 
>> 
>> On Nov 7, 2012, at 3:57 PM, Larry Reiter 
>> <lrei...@uthsc.edu>
>>  wrote:
>> 
>> 
>>> Dannon,
>>> 
>>> Thanks for getting back to me.  Both the local cloud install and the main 
>>> server are frozen.  Well, not exactly frozen.  I can still rename or delete 
>>> jobs, etc.  I can even switch histories and such, but I can't get it to run 
>>> even simple jobs - like taking a demo file and running Fastq Groomer.  I 
>>> realize the load is high today on the main server, but we were able to get 
>>> jobs to run right up until we tried to MAP using Bowtie for Illumina.  At 
>>> that point, all members of the class - and me - could not go any further 
>>> (i.e. jobs are grey and never start to run).  Class ended almost three 
>>> hours ago.
>>> 
>>> Does this help?
>>> 
>>> LTR
>>> 
>>> On 11/7/12 2:52 PM, Dannon Baker wrote:
>>> 
>>>> Can you describe more about what is broken with your cloud install? 
>>>> 
>>>> Regarding main - the server has been under heavy load today and, while it 
>>>> shouldn't remain frozen, might be slow to dispatch and, depending on the 
>>>> type, execute) jobs.
>>>> 
>>>> -Dannon
>>>> 
>>>> On Nov 7, 2012, at 1:12 PM, Larry Reiter 
>>>> 
>>>> <lrei...@uthsc.edu>
>>>> 
>>>>  wrote:
>>>> 
>>>> 
>>>> 
>>>>> Tried to teach a class today on ChipSeq analysis, but the local Cloud 
>>>>> install is broken and then the Penn server froze on us.  Is there 
>>>>> something I should know?
>>>>> 
>>>>> LTR
>>>>> 
>>>>> -- 
>>>>> Lawrence T. Reiter, Ph.D.
>>>>> Associate Professor, Department of Neurology
>>>>> 855 Monroe Ave., Link 415
>>>>> Memphis, TN 38163
>>>>> 
>>>>> 
>>>>> 901-448-2635
>>>>>  (Office)
>>>>> 
>>>>> 901-448-7440
>>>>>  (FAX)
>>>>> 
>>>>> 901-448-7443
>>>>>  (Lab)
>>>>> e-mail: 
>>>>> 
>>>>> lrei...@uthsc.edu
>>>>> 
>>>>> 
>>>>> 
>>>>> Reiter Faculty Page
>>>>> Reiter Citation Index
>>>>> Tooth Study
>>>>> ___________________________________________________________
>>>>> The Galaxy User list should be used for the discussion of
>>>>> Galaxy analysis and other features on the public server
>>>>> at 
>>>>> usegalaxy.org
>>>>> .  Please keep all replies on the list by
>>>>> using "reply all" in your mail client.  For discussion of
>>>>> local Galaxy instances and the Galaxy source code, please
>>>>> use the Galaxy Development list:
>>>>> 
>>>>>  
>>>>> 
>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>>> 
>>>>> 
>>>>> 
>>>>> To manage your subscriptions to this and other Galaxy lists,
>>>>> please use the interface at:
>>>>> 
>>>>>  
>>>>> 
>>>>> http://lists.bx.psu.edu/
>>> -- 
>>> Lawrence T. Reiter, Ph.D.
>>> Associate Professor, Department of Neurology
>>> 855 Monroe Ave., Link 415
>>> Memphis, TN 38163
>>> 
>>> 
>>> 901-448-2635
>>>  (Office)
>>> 
>>> 901-448-7440
>>>  (FAX)
>>> 
>>> 901-448-7443
>>>  (Lab)
>>> e-mail: 
>>> lrei...@uthsc.edu
>>> 
>>> 
>>> Reiter Faculty Page
>>> Reiter Citation Index
>>> Tooth Study
>>> 
> 
> 
> -- 
> Lawrence T. Reiter, Ph.D.
> Associate Professor, Department of Neurology
> 855 Monroe Ave., Link 415
> Memphis, TN 38163
> 
> 901-448-2635 (Office)
> 901-448-7440 (FAX)
> 901-448-7443 (Lab)
> e-mail: lrei...@uthsc.edu
> 
> Reiter Faculty Page
> Reiter Citation Index
> Tooth Study
> 
> <2012-11-07 13-35-01.png><2012-11-07 13-36-16.png>


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